title: H2 production Timepoint 5 Slide 1

status: Public on Oct 28 2008

city: Bielefeld

first: Anh Vu

last: Nguyen

state: NRW

address: G2-154, CEBITEC, Universitaetsstr. 27

department: Cell and Molecular Biology

institute: Bielefeld University

description: Three hybridizations for the three replicates were performed on the same day.

hyb_protocol: After rehydration, UV cross linking and 1 hour prehybridisation (in 5x SSC, 0.1% SDS, 0.1 mg/ml BSA and 25% formaldehyde at 42 degree Celsius), the slide was washed twice with 0.1x SSC then water and spun dry. Labeled targets were pooled together and dried by vacuum centrifugation. The targets were resuspended in 60 microliters of Dig Easy Hyb solution (Roche) and hybridized to the slide in a Tecan 4800 HS hydridisation station at 42 degree for 2 hours.

scan_protocol: Following the washes, slides were dried by centrifugation (3 min, 185×g, 20 °C) and scanned with a pixel size of 10 μm using the ScanArray 4000 microarray scanner (Perkin-Elmer, Boston, MA, USA).

data_processing: Median signal and median local background intensities were obtained for each spot of the microarray images using the ImaGene 6.0 software for spot detection, image segmentation and signal quantification (Biodiscovery Inc., Los Angeles, CA, USA). The logarithm to the bases 2 of the ratio of intensities was calculated for each spot using the formula Mi=log2 (Ri/Gi). Ri=Ich1i−Bgch1i and Gi=Ich2i−Bgch2i, where Ich1i or Ich2i is the intensity of a spot in channel 1 or channel 2 and Bgch1i or Bgch2i is the background intensity of a spot in channel 1 or channel 2, respectively. Global Lowess normalization was applied. Genes significantly up- or down-regulated were identified by t-statistics. Genes were regarded as differentially expressed if P≤0.05, M-values ≥ 1.0 or ≤ −1.0.

organism: Chlamydomonas reinhardtii

source_name: CC124 - Peak H2 Sample_3 Cy3

label_protocol: Channel 1 was labeled using 5 micrograms of total RNA from Sample 3 following the Chipshot Indirect Labeling System (Promega) protocol.

extract_protocol: Twenty milliliters of culture were collected from the bioreactor through the gas tight septum with a syringe and centrifuged at 3000 x g for 2 minutes. The resulting pellet was immediately resuspended in 500 microliters of RNA Lysis Buffer (SV Total RNA Isolation System-Promega) and processed following the manufacturer's protocol.

tag: CC124 55h after S deprivation at peak H2 production-Sample 3 labeled with Cy3 dye

source_name: CC124 - Control Cy5

label_protocol: Channel 2 was labeled using 5 micrograms of total RNA from the Control following the Chipshot Indirect Labeling System (Promega) protocol.

extract_protocol: One hundred milliliters of Control culture were collected from a 400 ml culture by centrifugation at 3000 x g for 2 minutes. The resulting pellet was resuspended in 2000 microliters of RNA Lysis Buffer (SV Total RNA Isolation System-Promega) and processed following the manufacturer's protocol.

tag: CC124 in normal TAP medium -Control labeled with Cy5 dye


title: GBS_COH1_CDM_rep3

status: Public on Oct 29 2008

type: RNA

city: Shreveport

first: Daniel

middle: Wilson

last: Shelver

state: LA

address: 1501 Kings Highway

department: Microbiology and Immunology

country: USA

institute: LSU Health Sciences Center in Shreveport

description:
Biological replicate 3 of 3.
Scanned microarray images were analyzed using GeneChip Operating Software (GCOS) 1.4 (Affymetrix).

hyb_protocol: A hybridization cocktail containing 3.9 ug labelled cDNA was hybridized to the arrays. Hybridization was performed for 16 hours with a rotation of 60 rpm at a temperature of 45oC in a GeneChip Hybridization Oven 640 (Affymetrix). Arrays were washed and stained with a streptavidin-phycoerythrin conjugate using predefined protocols with a GeneChip Fluidics Station 450 (protocol ProkGE-WS2_450).

scan_protocol: Arrays were scanned with a GeneChip Scanner 300 7G (Affymetrix).

data_processing: Expression signals were calculated using the MAS5 statistical algorithm with the Affymetrix GCOS software version 1.4. Signal values were globally scaled to an intensity value of 500.

label: biotin

molecule: total RNA

organism: Streptococcus agalactiae

source_name: Streptococcus agalactiae COH1, grown in chemically defined medium

label_protocol: cDNA was synthesized from 10 ug of total RNA using Superscript II reverse transcriptase (Invitrogen). Carryover RNA was degraded with 1 N NaOH followed by 1 N HCl. cDNA was purified and concentrated using a MinElute PCR Purification kit (Qiagen). Samples were fragmented with DNase I (Promega; Madison, WI) and biotin end-labelled with GeneChip DNA Labeling Reagent (Affymetrix).

growth_protocol: Group B Streptococcus (GBS) strains were cultured in chemically defined medium (CDM) with 400ug/ml Met to an O.D.600 = 0.3.

extract_protocol: 50 ml of cells (O.D.600 = 0.3) were harvested by centrifugation. GBS cells were then placed in a 950 ul suspension of QBio lysing matrix B, 50mM sodium acetate pH 4.0, 0.5% SDS, and 25% acidic phenol (Amresco; Solon, OH).  Cells were mechanically disrupted with the lysing matrix using a FastPrep® 120 device (MP Biomedicals; Solon, OH) with a speed setting of 5 and pulse length of 22 s.  The mixture was separated by centrifugation for 10 minutes.  RNA was precipitated by adding sodium acetate (pH 5.2) to a final concentration of 0.3M and adding 2 volumes of 100% ethanol.  One ml of Trizol reagent (Sigma-Aldrich) was added and incubated at room temperature for 5 min.  200 ul of chloroform was added, shaken vigorously, and allowed to remain at room temperature for 2 minutes. The mixture was centrifuged for ten minutes, the aqueous phase was recovered and RNA was precipitated with an equal volume of 100% isopropanol.  The pellet was air-dried and resuspended in 50 ul DEPC-treated water.  Residual DNA was removed using DNaseI (Promega) and subsequent clean-up with a RNEasy mini spin column (Qiagen).

tag: Strain COH1, wild-type clinical isolate.


title: Btk knock out DT40 reconstituted with human BTK , FCS batch 1; B41-13 1 S6

status: Public on Oct 27 2008

city: Huddinge

first: Hossain

last: Nawaz

state: Stockholm

address: Hälsovägen 7

department: LABMED

country: Sweden

institute: Karolinska Institutet

description: Gene expression data from chicken B41-13 cell line grown for 6 hours in fetal calf serum batch 1 after stimulation with IgM

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Genechip Scanner 30007G.

data_processing: RMA

organism: Gallus gallus

source_name: B46-5 cells grown for 2 hours after stimulation with IgM

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

growth_protocol: DT40 and B7.10 cells were cultivated in three different fetal calf serum batches, while B41-13 and B46-5 were grown in a single serum batch. Both unstimulated and stimulated cells were grown in the same way, starting in 1 ml serum-free medium for 15 min at 37°C with 5% CO2.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit (Qiagen, Valencia, CA, USA).

treatment_protocol: All the cell lines were stimulated with IgM (M4)

tag: Genotype

value: Btk KO DT40 reconstituted with human BTK


title: Btk knock out DT40 reconstituted with kinase inactive human BTK , FCS batch 1; B46-5 1 S2

description: Gene expression data from chicken B46-5 cell line grown for 2 hours in fetal calf serum batch 1 after stimulation with IgM

value: Btk KO DT40 reconstituted with kinase inactive human BTK


title: Btk knock out DT40 reconstituted with human BTK , FCS batch 1; B41-13 1 C24

description: Gene expression data from chicken B41-13 cell line grown for 24 hours in fetal calf serum batch 1 without any stimulation

source_name: B41-13 cells grown for 24 hours without stimulation


title: Btk knock out DT40 reconstituted with kinase inactive human BTK , FCS batch 1; B46-5 1 C6

description: Gene expression data from chicken B46-5 cell line grown for 6 hours in fetal calf serum batch 1 without any stimulation

source_name: B46-5 cells grown for 6 hours without stimulation


title: Btk knock out DT40 reconstituted with kinase inactive human BTK , FCS batch 1; B46-5 1 S6

description: Gene expression data from chicken B46.5 cell line grown for 6 hours in fetal calf serum batch 1 after stimulation with IgM


title: Rice moderate drought Rice03

city: Golm

first: Karin

last: Koehl

state: Brandenburg

address: Am Muehlenberg 1

country: Germany

institute: Max-Planck-Institut of Molecular Plant Physiology

description: no further description

hyb_protocol: Prehybridization was done following the manufactures instructions: blocking of slide for 20 min at 42°C with Block Solution (2X SSC, 0.05% SDS, 0.25% NaBH4) followed by washing of slide with 1X SSC, 0.2X SSC and rinsing with Nanopure water. For hybridization labelled DNA was dissolved in 130µl hybridization buffer (0.1 % SDS, 25 % Formamide, 5x SSC, 10 mg/ml BSA, 40 mM Na3PO4 (pH 6.8)) and applied to the pre-warmed slide in the hybridization station Hybarray12 (Perkin Elmer, Wellesley, MA, USA). The Initial hybridization temperature was 45°C. The hybridization temperature was stepwise reduced every hour by 1K to reach final hybridization temperature of 41°C. After 10-12 hours of hybridization at 41°C, slides were washed with 2X SSC, 0.2% SDS at 42°C, 2X SSC and 0.2X SSC (all 4 cycles with 20s flow and 40s hold) and very shortly in Nanopure water, all at room temperature. Slides were dried in a centrifuge.

scan_protocol: Microarrays were scanned with a FLA-8000 laser scanner (Fuji, Tokyo, Japan) at maximum intensity. Software version was FLA-8000 V 1.12.

data_processing: The software GeneSpotter 2.4.3 (Microdiscovery, Berlin, Germany) was used to fit the grid position of the spots and to calculate spot intensities. Spots for which intensity was affected by dust or dirt were flagged manually (user tag column = 1). Background correction was done based on the expression signal of 218 spots representing a hygromycin resistance gene that is not in the genome of the investigated cultivars. Any spot with an expression below the mean plus threefold standard deviation of the intensity of the hygromycin gene spots of the respective array and dye was labelled as below background (tag column = 1). Normalization was performed using the R package limma (R 2.3.1, limma version 2.7.3; (Smyth, 2005)). The methods Robustspline for within array normalization and Quantile for between array normalization were applied.

label: Alexa Fluor 532

molecule: polyA RNA

organism: Oryza sativa

source_name: rice leaf;Nipponbare;control

label_protocol: For labeling 1 mg cDNA (in 15 µl buffer (10 mM Tris, pH 8.5)) were mixed with 5 µl of the fluorescent dye (Alexa Fluor 532 and 647 (Qiagen, Hilden, Germany)) and incubated for 30 - 45 min at 85 °C in the dark, followed by adding of 5 µl Stop Solution and an incubation for 10 min at room temperature.)

growth_protocol: Seeds were pre-germinated in tab water at 28°C for ten days. Then, plantlets were transferred in 10 cm diameter pots filled with 540 g sand mixed with 8 g of Lewatit HD 50 (Lanxess, Langenfeld, Germany), an ion-exchange resin loaded with nutrient ions and 0.4 g Fetrilon Combi (Compo, Münster, Germany). Pots were transferred to a climate chamber with 12 h day length at 600 µE m-2 s-1; temperature was 26°C in the light and 22°C at night, with a relative humidity of 75% in the light and 70% at night. Pots were positioned in polypropylene boxes filled with water to the level of the substrate surface. Pot surfaces were covered with black, pinpricked polythene film (Aquafol, Reinmann, Emsdetten, Germany) to prevent growth of algae. Forty-five days after sowing, plants were harvested five hours after the beginning of the light period. Samples for expression profiling were harvested from the middle section of the blades of fully expanded green leaves and immediately frozen in liquid nitrogen.

extract_protocol:
PolyA+-RNA was extracted with magnetic beads (Dynabeads oligo (dT)25, Dynal, Oslo, Norway) following the manual instruction. In brief, 100mg leaf material was homogenized for 1.5 min at 28 Hz in a ball mill (Retsch) and 1.5 ml Lysis buffer (100 mM Tris, 500 mM LiCl, 10 mM EDTA, 1 % LiDS, 5 mM DTT, pH 8) was added. The solution was mixed and centrifugated at 4°C for 10min at 14000 rpm. 125µl beads were washed twice with 200µl Lysis buffer and were added to the supernatant. After gentle mixing for 5 min beads were washed twice with 1 ml washing buffer A (10 mM Tris, 150 mM LiCl, 1 mM EDTA, 0.1 % LiDS, 0.05% Tween, pH 8), beads were transferred to a new reaction vial and beads were washed twice with washing buffer B (10 mM Tris, 150 mM LiCl, 1 mM EDTA, 0.05% Tween, pH 8). PolyA+-RNA was extracted two times with 10 µl 10 mM Tris pH 7.5 heating 2 min to 95oC. For DNase treatment 20 µl RNA, 4 µl 5x Superscript III Puffer, 0.5 µl RNaseOUT (40 U, Invitrogen), 1 µl DNase (Roche) were incubated for 15 min at room temperature. After adding 1 µl 110 mM EDTA reaction was stopped by incubating for 10 min at 70°C.
mRNA from four plants originating from the same experiment, condition and cultivar was pooled. cDNA was synthesized using SuperScript III (Invitrogen, Carlsbad, CA, USA) and purified by precipitation, using Bioline Sure Clean (Bioline, Luckenwalde, Germany).

treatment_protocol: see growth protocol

tag: Cultivar

value: Nipponbare (IRGC accession 12731); Age:45 d; Tissue:middle section of the blades of fully expanded green leaves from 4 - 5 plants

label: Alexa Fluor  647

source_name: rice leaf;Nipponbare;drought

growth_protocol:
Seeds were pre-germinated in tab water at 28°C for ten days. Then, plantlets were transferred in 10 cm diameter pots filled with 540 g sand mixed with 8 g of Lewatit HD 50 (Lanxess, Langenfeld, Germany), an ion-exchange resin loaded with nutrient ions and 0.4 g Fetrilon Combi (Compo, Münster, Germany). Pots were transferred to a climate chamber with 12 h day length at 600 µE m-2 s-1; temperature was 26°C in the light and 22°C at night, with a relative humidity of 75% in the light and 70% at night. Pots were positioned in polypropylene boxes filled with water to the level of the substrate surface. Pot surfaces were covered with black, pinpricked polythene film (Aquafol, Reinmann, Emsdetten, Germany) to prevent growth of algae. Twenty-six days after sowing, water was removed from half of the boxes and plants were left to dry for four days, until the soil water content had reached the permanent wilting point (PWP) for 50% of the plants. Thereafter, the soil water content was kept constant to the fixed PWP value over a period of 14 days by weighing each pot at the end of the light period and adding the amount of water lost during the last 24 h.
After a total of 19 days of drought stress, plants were harvested five hours after the beginning of the light period. Samples for expression profiling were harvested from the middle section of the blades of fully expanded green leaves and immediately frozen in liquid nitrogen.


title: Btk knock out DT40 reconstituted with kinase inactive human BTK , FCS batch 1; B46-5 1 C24

source_name: B46-5 cells grown for 24 hours without stimulation


title: Btk knock out DT40, FCS batch 2; B7.10 2 S6

description: Gene expression data from chicken B7.10 cell line grown for 6 hours in fetal calf serum batch 6 after stimulation with IgM

source_name: B7.10 cells grown for 6 hours after stimulation with IgM

value: Btk KO DT40 without endogenous Btk


title: H2 production Timepoint 5 Slide 2

data_processing: Median signal and median local background intensities were obtained for each spot of the microarray images using the ImaGene 6.0 software for spot detection, image segmentation and signal quantification (Biodiscovery Inc., Los Angeles, CA, USA). The logarithm to the bases 2 of the ratio of intensities was calculated for each spot using the formula Mi=log2 (Gi/Ri). Ri=Ich1i−Bgch1i and Gi=Ich2i−Bgch2i, where Ich1i or Ich2i is the intensity of a spot in channel 1 or channel 2 and Bgch1i or Bgch2i is the background intensity of a spot in channel 1 or channel 2, respectively. Global Lowess normalization was applied. Genes significantly up- or down-regulated were identified by t-statistics. Genes were regarded as differentially expressed if P≤0.05, M-values ≥ 1.0 or ≤ −1.0.

source_name: CC124 - Control Cy3

label_protocol: Channel 1 was labeled using 5 micrograms of total RNA from the Control following the Chipshot Indirect Labeling System (Promega) protocol.

extract_protocol: One hundred milliliters of Control culture were collected from a 400 ml culture by centrifugation at 3000 x g for 2 minutes. The resulting pellet was immediately resuspended in 2000 microliters of RNA Lysis Buffer (SV Total RNA Isolation System-Promega) and processed following the manufacturer's protocol.

tag: CC124 in normal TAP medium -Control labeled with Cy3 dye

source_name: CC124 - Peak H2 Sample_2 Cy5

label_protocol: Channel 2 was labeled using 5 micrograms of total RNA from Sample 2 following the Chipshot Indirect Labeling System (Promega) protocol.

extract_protocol: Twenty milliliters of culture were collected from the bioreactor through the gas tight septum with a syringe and centrifuge at 3000 x g for 2 minutes. The resulting pellet was immediately resuspended in 500 microliters of RNA Lysis Buffer (SV Total RNA Isolation System-Promega) and processed following the manufacturer's protocol.

tag: CC124 55h after S deprivation at peak H2 production-Sample 2 labeled with Cy5 dye


title: Functionally-regressed Late luteal phase CL, biological rep 3

city: Beaverton

first: Randy

middle: Lloyd

last: Bogan

state: OR

address: 505 NW 185th Ave

department: Reproductive Sciences

institute: Oregon National Primate Research Center

description: Gene expression data from CL that are undergoing functional regression. Luteolysis (CL death) is subdivided into two steps: 1) a decrease in progesterone secretion (functional regression), and 2) apoptosis and structural remodeling of luteal tissue (structural regression). This stage corresponds to CL in the first stage of luteolysis (functional regression). They have, or are about to, quit producing progesterone, but the tissue has not yet started to degenerate.

hyb_protocol: Labeled target is fragmented at 95C in the presence of high magnesium concentration.  The fragmented material is combined with biotinylated hybridization control oligomer and biotinylated control cRNAs for BioB, BioC, BioD and CreX (Affymetrix) in hybridization buffer.  Ten micrograms of target is hybridized for 16 hours at 45C to the GeneChip Rhesus Macaque Genome array (Affymetrix), followed by washing, staining with streptavidin-phycoerythrin (Molecular Probes), signal amplification with biotinylated anti-streptavidin antibody (Vector Labs), and a final staining step on the Fluidics Station 450 (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 with the 7G upgrade (Affymetrix) and GCOS version 1.4.0 software (Affymetrix), yielding cell fluorescence intensity (.CEL files).  Image inspection was performed manually immediately following each scan.

data_processing: The processed image files (.CEL) were normalized across arrays using the robust multichip average (RMA) algorithm and log-transformed (base 2).After normalization, GeneSifter (VizX Labs) microarray expression analysis software was used to analyze the resultant data.

label: Biotin

organism: Macaca mulatta

source_name: Corpus luteum collected between days 14-16 after the midcycle LH surge from animal with serum concentrations of progesterone <0.5 ng/ml at time of CL collection

label_protocol: Messenger RNA is amplified and labeled from 2 micrograms of total RNA in two steps according to the standard Affymetrix one-cycle cDNA protocol (Expression Analysis Technical Manual Rev.4). In the first step, mRNA is converted to double-stranded cDNA using Superscript Reverse Transcriptase (Invitrogen) and an oligo-dT primer linked to a T7 RNA polymerase binding site sequence (Affymetrix).  In the second step, amplified and labeled cRNA (the target) is produced in an in vitro transcription reaction using T7 RNA polymerase and biotin-UTP (Affymetrix). Following removal of free nucleotides, target yield is measured by UV260 absorbance.

extract_protocol: Trizol (Invitrogen) extraction of total RNA was performed according to the manufacturer's instructions, and total RNA obtained by Trizol extraction was further purified using RNeasy spin columns (Qiagen) following manufacturer instructions.

treatment_protocol: Blood samples were collected daily by saphenous venipuncture starting six days after onset of menses. Serum was separated and samples were assayed daily for estradiol concentrations. Following the midcycle estradiol surge, the first day of low serum estradiol (< 100pg/ml) corresponds with the day after the LH surge (LH surge = day 0). On the appropriate day following the midcycle LH surge, the CL was collected during aseptic midline laparotomy, immediately flash frozen in liquid nitrogen, and stored at -80°C until total RNA was extracted.

tag: Gender:female, Tissue

value: Corpus luteum, reproductive state:normal menstrual cyclicity


title: Functionally-regressed Late luteal phase CL, biological rep 2


title: Btk knock out DT40 reconstituted with human BTK , FCS batch 1; B41-13 1 S2

description: Gene expression data from chicken B41-13 cell line grown for 2 hours in fetal calf serum batch 1 after stimulation with IgM

source_name: B41-13 cells grown for 2 hours after stimulation with IgM


title: Btk knock out DT40, FCS batch 3; B7.10 3 S6

description: Gene expression data from chicken B7.10 cell line grown for 6 hours in fetal calf serum batch 3 without any stimulation


title: Functionally-regressed Late luteal phase CL, biological rep 4


title: Functional Late luteal phase CL, biological rep 4

source_name: Corpus luteum collected between days 14-16 after the midcycle LH surge from animal with serum concentrations of progesterone >1.5 ng/ml at time of CL collection


title: Functionally-regressed Late luteal phase CL, biological rep 1


title: Btk knock out DT40, FCS batch 1; B7.10 1 S2

description: Gene expression data from chicken B7.10 cell line grown for 2 hours in fetal calf serum batch 1 after stimulation with IgM

source_name: B7.10 cells grown for 2 hours after stimulation with IgM


title: H2 production Timepoint 5 Slide 3

source_name: CC124 - Control - Cy3

extract_protocol: One hundred milliliters of Control culture were collected from 400 ml culture by centrifugation at 3000 x g for 2 minutes. The resulting pellet was immediately resuspended in 2000 microliters of RNA Lysis Buffer (SV Total RNA Isolation System-Promega) and processed following the manufacturer's protocol.

source_name: CC124 - Peak H2 Sample_1 Cy5

label_protocol: Channel 2 was labeled using 5 micrograms of total RNA from Sample 1 following the Chipshot Indirect Labeling System (Promega) protocol.

tag: CC124 55h after S deprivation at peak H2 production-Sample 1 labeled with Cy5 dye


title: Functional Late luteal phase CL, biological rep 3


title: Btk knock out DT40 reconstituted with human BTK , FCS batch 1; B41-13 1 C6

description: Gene expression data from chicken B41-13 cell line grown for 6 hours in fetal calf serum batch 1 without any stimulation

source_name: B41-13 cells grown for 6 hours without stimulation


title: Functional Late luteal phase CL, biological rep 1


title: Wild type DT40, FCS batch 1; DT40 1 S2

description: Gene expression data from chicken DT40 cell line grown for 2 hours in fetal calf serum batch 1 after stimulation with IgM

source_name: DT40 cells grown for 2 hours after stimulation with IgM

value: Parental DT40 with endogenous Btk


title: Mid-late luteal phase CL (baseline), biological rep 3

description: Gene expression data from CL that are still functional (i.e. producing progesterone) but are just prior to the time when CL regression (luteolysis) is initiated, i.e. this is a transitionary period from a functional CL to a regressing CL

source_name: Corpus luteum collected between days 10-12 after the midcycle LH surge


title: Btk knock out DT40, FCS batch 1; B7.10 1 C24

description: Gene expression data from Btk KO chicken DT40 cell line grown for 24 hours in fetal calf serum batch 1 without any stimulation

source_name: B7.10 cells grown for 24 hours without stimulation


title: Wild type DT40, FCS batch 2; DT40 2 C24

description: Gene expression data from chicken DT40 cell line grown for 24 hours in fetal calf serum batch 2 without any stimulation

source_name: DT40 cells grown for 24 hours without stimulation


title: Functional Late luteal phase CL, biological rep 2


title: Wild type DT40, FCS batch 3; DT40 3 S6

description: Gene expression data from chicken DT40 cell line grown for 6 hours in fetal calf serum batch 3 after stimulation with IgM

source_name: DT40 cells grown for 6 hours after stimulation with IgM


title: Mid-late luteal phase CL (baseline), biological rep 1


title: Wild type DT40, FCS batch 3; DT40 3 C6

description: Gene expression data from chicken DT40 cell line grown for 6 hours in fetal calf serum batch 3 without any stimulation

source_name: DT40 cells grown for 6 hours without stimulation


title: Btk knock out DT40, FCS batch 3; B7.10 3 C24

description: Gene expression data from Btk KO chicken DT40 cell line grown for 24 hours in fetal calf serum batch 3 without any stimulation


title: Btk knock out DT40, FCS batch 3; B7.10 3 C6

description: Gene expression data from Btk KO chicken DT40 cell line grown for 6 hours in fetal calf serum batch 3 without any stimulation

source_name: B7.10 cells grown for 6 hours without stimulation


title: Btk knock out DT40, FCS batch 2; B7.10 2 C6

description: Gene expression data from Btk KO chicken DT40 cell line grown for 6 hours in fetal calf serum batch 2 without any stimulation


title: Btk knock out DT40, FCS batch 1; B7.10 1 S6

description: Gene expression data from chicken B7.10 cell line grown for 6 hours in fetal calf serum batch 1 after stimulation with IgM

source_name: B7.10 cells grown for 6 hours after stimulation with IgM


title: Btk knock out DT40, FCS batch 2; B7.10 2 C24

description: Gene expression data from Btk KO chicken DT40 cell line grown for 24 hours in fetal calf serum batch 2 without any stimulation


title: Wild type DT40, FCS batch 1; DT40 1 S6

description: Gene expression data from chicken DT40 cell line grown for 6 hours in fetal calf serum batch 1 after stimulation with IgM


title: Mid-late luteal phase CL (baseline), biological rep 2


title: Mid-late luteal phase CL (baseline), biological rep 4


title: Btk knock out DT40, FCS batch 1; B7.10 1 C6

description: Gene expression data from Btk KO chicken DT40 cell line grown for 6 hours in fetal calf serum batch 1 without any stimulation


title: Wild type DT40, FCS batch 1; DT40 1 C24

description: Gene expression data from chicken DT40 cell line grown for 24 hours in fetal calf serum batch 1 without any stimulation


title: Wild type DT40, FCS batch 1; DT40 1 C6

description: Gene expression data from chicken DT40 cell line grown for 6 hours in fetal calf serum batch 1 without any stimulation


title: Wild type DT40, FCS batch 2; DT40 2 S6

description: Gene expression data from chicken DT40 cell line grown for 6 hours in fetal calf serum batch 2 after stimulation with IgM


title: Wild type DT40, FCS batch 3; DT40 3 C24

description: Gene expression data from chicken DT40 cell line grown for 24 hours in fetal calf serum batch 3 without any stimulation


title: Wild type DT40, FCS batch 2; DT40 2 C6

description: Gene expression data from chicken DT40 cell line grown for 6 hours in fetal calf serum batch 2 without any stimulation


title: eosinophil treated with 9-cis RA

status: Public on Oct 25 2008

city: Akita

first: Shigeharu

last: Ueki

department: Department of Clinical and Laboratory Medicine

country: Japan

institute: Akita University School of Medicine

description: no additional information

hyb_protocol: Competitive hybridization of Cy3-labeled and Cy5-labeled sample cDNA on the microarray was carried out according to Brown and Yanofsky[Proc Natl Acad Sci U S A. 2000;97:12170-12175] with chamber systems (Agilent Technologies, Palo Alto, CA).

scan_protocol: Slides were scanned five times with five different power ranges using ScanArray 5000 (PerkinElmer, Boston, MA).

data_processing: The data was converted from tif image data to signal using ImaGene software (BioDiscovery, El Segundo, CA) for further statistical analysis. Five file data of each four spot data corresponding each gene were merged to establish the single representative data for each gene (Patent pending: PCT/JP03/06677). The Cy3 (all-trans retinoic acid) /Cy5 (control) ratio of each mRNA signal was calculated for further analysis. The global Lowess normalization method was also applied before ratio calculation.

organism: Homo sapiens

source_name: vehicle control

label_protocol: Total RNA (1 microg) was transcribed and amplified to produce amplified sample RNA (aRNA) using the MessageAmp aRNA kit according to the manufacturer’s instructions. Next, an external control RNA mixture (LD, GP, and RL) was added to both the sample and reference aRNA (9 microg each). These mixed sample and reference aRNA were labeled using SuperScript II kit (Invitrogen, Carlsbad, CA) with random hexamer (TaKaRa, Kyoto, Japan) with Cy3-dUTP and Cy5-dUTP (PerkinElmer, Boston, MA), respectively.

extract_protocol: Total RNA was isolated using Isogen (Nippon Gene, Tokyo, Japan) as per the manufacturer’s instructions. RNA was repurified with phenol-chloroform extraction and ethanol precipitation.

treatment_protocol: Purified eosinophils were resuspended at 0.5 × 106 cells/ml in RPMI 1640 medium (Gibco, Grand Island, NY) with 10% FCS, and incubated with vehicle in 1% human serum albumin-coated plates, at 37 °C in humidified air with 5% CO2 for 4 hrs. For each cell culture condition, the total RNA from three donors was pooled, enabling us to acquire adequate amounts of RNA for microarray analysis.

tag: Purified human peripheral blood eosinophils treated with vehicle for 4 hrs

source_name: 9-cis RA treated

treatment_protocol: Purified eosinophils were resuspended at 0.5 × 106 cells/ml in RPMI 1640 medium (Gibco, Grand Island, NY) with 10% FCS, and incubated with 10-6M 9-cis RA in 1% human serum albumin-coated plates, at 37 °C in humidified air with 5% CO2 for 4 hrs. For each cell culture condition, the total RNA from three donors was pooled, enabling us to acquire adequate amounts of RNA for microarray analysis.

tag: Purified human peripheral blood eosinophils treated with 10-6 M of 9-cis RA for 4 hrs


title: TG1306_WT3_vs._TG1306_Dil3

city: Chicago

first: Andrea

middle: A.

last: Domenighetti

state: IL

address: 345 East Superior St

institute: Northwestern University & Rehabilitation Institute of Chicago

description: In the present study, microarray slides were produced at the DNA Array Facility (DAF) in Lausanne – Switzerland - by 32-pin robotic printing (http://www.unil.ch/dafl). PCR amplified cDNA clones were arrayed at high density in 1.5 M betaine, 3xSSC on NexterionTM glass Slide AL (Schott Nexterion, Mainz, Germany). The specific clone set printed onto the slides was the NIA 15K mouse embryonic clone set (National Institute of Aging, NIH - USA- http://lgsun.grc.nia.nih.gov/cDNA/15k.html), to which an additional 1563 custom clone set was added (GAL file: GPL4371). For post-experimental normalization of data, each microarray slide also possessed a subset of control spots including spikes, ‘housekeeping’ genes, blocking controls and negative controls.

hyb_protocol: For each slide, a hybridization mixture was prepared (volume 30 ul) containing 0.6 ug/ul poly-A (Sigma), 0.6 ug/ul yeast tRNA (Sigma), 0.6 ug/ul mouse Cot1 DNA (Invitrogen) and two purified Cy5- and Cy3-labeled cDNA samples to be compared. After heating (98 Celsius), the entire hybridization mixture was pipetted on the microarray slide and a 60x25 mm cover-slip was placed over the marked array region. The hybridization mixture was allowed to move by capillary action across the surface of the array. The slide was then placed horizontally in hybridization chambers (Corning), sealed and placed at the bottom of a 64 Celsius water bath where they incubated overnight in the dark.

scan_protocol: Following incubation, the array slides were removed from chambers, rinsed in SSC 20x, SDS 10% and Triton 10% solutions of different concentration and spun dry in a plate centrifuge. The microarray slides were placed in slide mailers and kept in a dark, desiccated environment prior to scanning. Each slide was imaged by an Agilent Technologies laser scanner which acquired two gray-scaled 16-bit single image TIFF files corresponding to the Cy5 and Cy3 fluorescence emission channels (argon laser operating at 635 nm and 532 nm excitation wavelengths respectively). The gray-scaled images were ‘pseudo colored’ (red intensities for Cy5, green intensities for Cy3) and merged to give one single picture for dual color (red/green) differential microarray analysis. The GenePix Pro 6.0 software (Molecular Devices, Sunnyvale, USA) extracted foreground and background intensities for individual spots on a microarray image, producing a matrix containing Cy5 (red) and Cy3 (green) intensities for each spot on the microarray.

data_processing: Raw data were normalized by print tip lowess normalization (Yang et al., Nucleic Acids Res. 2002,30(4):e15). Significantly changing genes (p≤ 0.05) were identified by t-test

organism: Mus musculus

source_name: Ventricles from 60 week old TG1306 'wild-type' mouse (WT3)

label_protocol: A total of 25 ug total RNA per dye labeling reaction was used for each ‘sample versus sample’ comparison, giving a total of 50 ug total RNA per array (2 labeling reactions per array). RNA was reverse transcribed (RT) into cDNA using oligo(dT) 21-mer (Invitrogen) to avoid transcription of non-messenger RNA populations. Several control spikes were added to the RT reactions, including SpotReport Alien and Arabidopsis Spikes (Stratagene). During each RT reaction, Cy3- or Cy5-labelled dCTP (Amersham) were incorporated into the cDNA population. After reverse transcription, the RNA template was hydrolyzed and each Cy-labeled cDNA was purified using the Qiagen’s MiniElute PCR Purification kit.

growth_protocol:
No special growth protocol.
Wild-type littermates are selected following genotyping (PCR).
For further information:
Domenighetti AA, Wang Q, Egger M, Richards SM, Pedrazzini T, Delbridge LM. Angiotensin II-mediated phenotypic cardiomyocyte remodeling leads to age-dependent cardiac dysfunction and failure. Hypertension. 2005 Aug;46(2):426-32. [PMID: 15998712]

extract_protocol: Total RNA was purified from heart tissue by Trizol reagent (Invitrogen), according to manufacturer’s protocol. The first step involved homogenizing ventricular mouse tissue samples using a Polytron Homogenizer (Kinematica AG) in a buffer containing Trizol (1 ml/50 mg of cardiac tissue). Total RNA was precipitated in isopropanol, washed in 80% ethanol, re-suspended in sterile RNase-free water and allowed to dissolve overnight at 4 Celsius. Samples were subsequently analyzed by spectrophotometry using a Nanodrop ND-100 UV-Vis Spectrophotometer (Nanodrop Technologies), where measurements of 220-750 nm absorbance were recorded. From these measurements, concentration (A260 nm) and quality (A260/A280) of each RNA sample was estimated. As a further check of RNA quality and quantity, each RNA sample was electrophoresed using a microfluidic Bioanalyzer 2100 (Agilent Technologies). Results were visualized for expression of and integrity of 21S and 18S rRNA bands.

treatment_protocol: No special treatment

tag: Strain

value: wild-type (-/-)

tag: Gender

value: male

tag: Age

value: ~60 weeks

tag: Tissue

value: right and left ventricles and septum

tag: Cardiac weight index

source_name: Ventricles from 60 week old TG1306 mouse with dilated heart (Dil3)

growth_protocol:
No special growth protocol.
Transgenic littermates are selected following genotyping (PCR). Hypertrophic or dilated hearts are selected according to genotype, chamber morphology, cardiac weight index and expression of hypertrophic markers.
For further information:
Domenighetti AA, Wang Q, Egger M, Richards SM, Pedrazzini T, Delbridge LM. Angiotensin II-mediated phenotypic cardiomyocyte remodeling leads to age-dependent cardiac dysfunction and failure. Hypertension. 2005 Aug;46(2):426-32. [PMID: 15998712]
And:
Croquelois A, Domenighetti AA, Nemir M, Lepore M, Rosenblatt-Velin N, Radtke F, Pedrazzini T. Control of the adaptive response of the heart to stress via the Notch1 receptor pathway. J Exp Med, accepted.

value: transgenic heterozygote (+/-)


title: eosinophil treated with ATRA

description: no additional information

source_name: ATRA treated

treatment_protocol: Purified eosinophils were resuspended at 0.5 × 106 cells/ml in RPMI 1640 medium (Gibco, Grand Island, NY) with 10% FCS, and incubated with 10-6M ATRA in 1% human serum albumin-coated plates, at 37 °C in humidified air with 5% CO2 for 4 hrs. For each cell culture condition, the total RNA from three donors was pooled, enabling us to acquire adequate amounts of RNA for microarray analysis.

tag: Purified human peripheral blood eosinophils treated with 10-6 M of ATRA for 4 hrs


title: TG1306_Hyp4_vs._TG1306_Dil4

source_name: Ventricles from 60 week old TG1306 hypertrophic mouse (Hyp4)

source_name: Ventricles from a 60 week old TG1306 mouse with dilated heart (Dil4)


title: TG1306_WT4_vs._TG1306_Hyp4

source_name: Ventricles from 60 week old TG1306 'wild-type' mouse (WT4)


title: TG1306_Dil3_vs._TG1306_Hyp3

source_name: Ventricles from a 60 week old TG1306 mouse with dilated heart (Dil3)

source_name: Ventricles from 60 week old TG1306 hypertrophic mouse (Hyp3)


title: TG1306_Hyp3_vs._TG1306_WT3


title: TG1306_Hyp2_vs._TG1306_WT2

source_name: Ventricles from 60 week old TG1306 hypertrophic mouse (Hyp2)

source_name: Ventricles from 60 week old TG1306 'wild-type' mouse (WT2)


title: TG1306_Hyp2_vs._TG1306_Dil2

source_name: Ventricles from a 60 week old TG1306 mouse with dilated heart (Dil2)


title: Xylem Pole Pericycle Cells at T6, biological rep1

status: Public on Oct 24 2008

city: Tuebingen

first: Ive

last: De Smet

address: Auf der Morgenstelle 3

institute: University of Tübingen - Center for Plant Molecular Biology

description: Gene expression data from xylem pole pericycle cells from 72-HAG-old Arabidopsis roots grown on NPA and 6h NAA

hyb_protocol: Following fragmentation, cRNA was hybridized on GeneChip Arabidopsis ATH1 Genome Array.  Treatments were done according to the protocol on the Duke Microarray Facility web site

scan_protocol: GeneChips were scanned using the Axon GenePix 4000B scanner (Molecular Devices)

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0)

organism: Arabidopsis thaliana

source_name: Arabidopsis roots at 72 HAG on NPA + 6h NAA

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

growth_protocol: Seedlings were grown on MS supplemented with 10 microM NPA (as described by Himanen et al., 2002) on top of nylon mesh. The seedlings were grown in 16h/8h day/night conditions at 22 C. At 72 HAG the seedlings were transfered to 10 microM NAA for 6h.

extract_protocol: Total RNA was isolated from frozen material using the Qiagen RNeasy kit (Valencia, California, United States) according to the manufacturer's instructions

treatment_protocol: Roots were treated according to Birnbaum et al (2002, 2005) to isolate xylem pole pericycle cells, which were frozen in RLT buffer

value: J0121 (for more information, please see the Dept. of Plant Sciences website of GAL4-GFP expressino patterns at the University of Cambridge)

tag: Age seedlings

value: 78 HAG


title: TG1306_WT1_vs._TG1306_Dil1

source_name: Ventricles from 60 week old TG1306 'wild-type' mouse (WT1)

source_name: Ventricles from 60 week old TG1306 mouse with dilated heart (Dil1)


title: Arabidopsis_5mM_SA_2h

status: Public on Oct 23 2008

city: Kaga-gun, Okayama

first: Yoshihiro

last: Narusaka

address: 7549-1, Kibityuo-town Yoshikawa

institute: Research Institute for Biological Sciences

description: Gene expression treated with 5 mM SA after 2 h

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software.

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log2 of processed Red signal/processed Green signal. Gene Spring software ver.6 was used.

source_name: Untreated plant (control)

label_protocol: A Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies Inc., Palo Alto, CA) was used to generate fluorescent complimentary RNA (cRNA).Five hundred nanograms of total RNA from plants were used to synthesize the cDNA using MMLV-RT and T7 promoter primers (Agilent Technologies Inc.). This cDNA was used as a template to synthesize cRNA. cRNA was synthesized using T7 RNA polymerase (Agilent Technologies Inc.), which simultaneously incorporates cyanine 3 (Cy3, for control samples) or cyanine 5 (Cy5, for treated samples) CTP (PerkinElmer/NEN Life Sciences, Tokyo, Japan). Labeled cRNA samples were purified in RNeasy mini spin columns (Qiagen, Kanagawa, Japan) to remove unincorporated dye-labeled nucleotides. Five hundred nanograms of Cy3-labeled cRNAs were mixed with the same amount of Cy5-labeled cRNA.

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

tag: Ecotype

value: Columbia, Age:28 days, Sample:whole plant (except for root)

source_name: Treatment with 5 mM SA for 2 h


title: TG1306_Dil4_vs._TG1306_WT4

source_name: Ventricles from 60 week old TG1306 mouse with dilated heart (Dil4)


title: Arabidopsis_5mM_SA_5h

description: Gene expression treated with 5 mM SA after 5 h

source_name: Treatment with 5 mM SA for 5 h


title: TG1306_Dil1_vs._TG1306_Hyp1

source_name: Ventricles from a 60 week old TG1306 mouse with dilated heart (Dil1)

source_name: Ventricles from 60 week old TG1306 hypertrophic mouse (Hyp1)


title: SIBA over-expression CA32F3 vs vector control

description: Gene expression of SIBA over-expression plant

source_name: vector control plant

value: 28 days, Sample:whole plant (except for root)

source_name: SIBA over-expression CA32F3 plant


title: Xylem Pole Pericycle Cells at T2, biological rep2

description: Gene expression data from xylem pole pericycle cells from 72-HAG-old Arabidopsis roots grown on NPA and 2h NAA

source_name: Arabidopsis roots at 72 HAG on NPA + 2h NAA

growth_protocol: Seedlings were grown on MS supplemented with 10 microM NPA (as described by Himanen et al., 2002) on top of nylon mesh. The seedlings were grown in 16h/8h day/night conditions at 22 C. At 72 HAG the seedlings were transfered to 10 microM NAA for 2h.

value: 74 HAG


title: TG1306_WT1_vs._TG1306_Hyp1


title: Arabidopsis_5mM_SA_10h

description: Gene expression treated with 5 mM SA after 10 h

source_name: Treatment with 5 mM SA for 10 h


title: Xylem Pole Pericycle Cells at T6, biological rep2


title: Xylem Pole Pericycle Cells at T2, biological rep1


title: ALL_ resistant_9+IR

city: Birmingham

first: Carmel

middle: M

last: McConville

state: UK

address: Vincent Drive

department: School of Cancer Sciences

country: United Kingdom

institute: University of Birmingham

description:
116_8h
Aliquots of 2 x 106 cells per time point were irradiated with 5 Gy IR (cobalt Co60)

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Data for all arrays was normalised in the GeneSpring GX 7.3.1 analysis package to the 50th percentile of total expression value data for each individual chip, and to the median for each gene across arrays (default parameters).

source_name: ALL, resistant, irradiated

label_protocol: Standard Affymetrix protocol

growth_protocol: Mononuclear cells were isolated from bone marrow aspirate using Ficoll-Paque (Amersham Biosciences, Piscataway, NJ), and cells were cultured in RPMI 1640. Only samples with more than 90% of blast cells were used for analysis.

extract_protocol: Standard Affymetrix protocol

treatment_protocol: Cells were irradiated and maintained in culture for 8 hours, or maintained for 8 h without irradiation.

tag: B-precursor ALL tumour

tag: resistant to IR-induced DNA damage

tag: female


title: Arabidopsis_5mM_SA_24h

description: Gene expression treated with 5 mM SA after 24 h

source_name: Treatment with 5 mM SA for 24 h


title: ALL_ resistant_11+IR

description:
122_8h
Aliquots of 2 x 106 cells per time point were irradiated with 5 Gy IR (cobalt Co60)


title: ALL_ resistant_10+IR

description:
119_8h
Aliquots of 2 x 106 cells per time point were irradiated with 5 Gy IR (cobalt Co60)

tag: male


title: ALL_ resistant_7+IR

description:
106_8h
Aliquots of 2 x 106 cells per time point were irradiated with 5 Gy IR (cobalt Co60)


title: SIBA over-expression CA32F4 vs vector control

source_name: SIBA over-expression CA32F4 plant


title: ALL_ resistant_8+IR

description:
109_8h
Aliquots of 2 x 106 cells per time point were irradiated with 5 Gy IR (cobalt Co60)


title: Xylem Pole Pericycle Cells at T0, biological rep1

description: Gene expression data from xylem pole pericycle cells from 72-HAG-old Arabidopsis roots grown on NPA

source_name: Arabidopsis roots at 72 HAG on NPA

growth_protocol: Seedlings were grown on MS supplemented with 10 microM NPA (as described by Himanen et al., 2002) on top of nylon mesh. The seedlings were grown in 16h/8h day/night conditions at 22 C

tag: Genotype

value: 72 HAG


title: ALL_ resistant_10-IR

source_name: ALL, resistant, no irradiation


title: Xylem Pole Pericycle Cells at T0, biological rep2


title: ALL_ resistant_3+IR

description:
85_8h
Aliquots of 2 x 106 cells per time point were irradiated with 5 Gy IR (cobalt Co60)


title: ALL_ resistant_5+IR

description:
99_8h
Aliquots of 2 x 106 cells per time point were irradiated with 5 Gy IR (cobalt Co60)


title: ALL_ resistant_6+IR

description:
104_8h
Aliquots of 2 x 106 cells per time point were irradiated with 5 Gy IR (cobalt Co60)


title: ALL_ resistant_1+IR

description:
82_8h
Aliquots of 2 x 106 cells per time point were irradiated with 5 Gy IR (cobalt Co60)


title: ALL_ resistant_4+IR

description:
93_8h
Aliquots of 2 x 106 cells per time point were irradiated with 5 Gy IR (cobalt Co60)


title: ALL_ resistant_9-IR


title: ALL_ resistant_4-IR


title: ALL_ resistant_8-IR


title: ALL_responsive_11+IR

description:
115_8h
Aliquots of 2 x 106 cells per time point were irradiated with 5 Gy IR (cobalt Co60)

source_name: ALL, responsive, irradiated

tag: responsive to IR-induced DNA damage


title: ALL_ resistant_2-IR


title: ALL_ resistant_6-IR


title: ALL_ resistant_3-IR


title: ALL_ resistant_7-IR


title: ALL_ resistant_1-IR


title: Mersacidin4_samples13793G_chip018

city: Bonn

first: Peter

last: Sass

address: Sigmund-Freud-Straße 25

department: Institute for Microbiology (IMMIP)

institute: University of Bonn

description: no additional information provided

hyb_protocol: Microarray-based transcriptional profiling by competitive hybridization of fluorescence-labeled cDNA was performed using the custom PCR product full-genome chip sciTracer (Scienion, Berlin, Germany). Each experiment was performed 4 times including a dye swap resulting in four chips per competitive comparison to increase reproducibility. Only strain SA137/93G incubated with 0.2 x MIC of mersacidin was reproduced in duplicate. All hybridizations were done with equal amounts of cDNA probes displaying similar picomoles of incorporated dye. Fluorescence-labeled cDNA probes were mixed in hybridization buffer (Scienion) in a total volume of 55 µl and denatured at 95°C for 2 min and subsequently applied to the microarray slide followed by incubation at 42°C for 72 hours under humidified conditions according to the manufacturer’s instructions. Hybridized microarrays were washed at room temperature in SSC buffer with decreasing salt concentrations (1 x SSC / 0.3% SDS for 5 min, 0.2 x SSC for 5 min, 0.06 x SSC for 30s).

scan_protocol: The intensity of fluorescence of the microarray was scanned with a GenePix 4000B scanner (Axon Instruments/Distribution by Biozyme Scientific GmbH, Hessisch Oldendorf, Germany). TIFF images were captured and analysed with GenePixPro4.1 software (Axon Instruments). The actual signal intensity was calculated by substracting the mean value of the local background intensity from the mean value of the signal intensity of the individual spot.

data_processing: The data sets were then normalized by using Acuity 3.1 software (Axon Instruments) and by applying the LOWESS algorithm. Significant changes of gene expression were determined by implementing SAM (significance analysis of microarrays; http://www-stat.stanford.edu/~tibs/SAM/; (Tusher, V. G., R. Tibshirani, and G. Chu. 2001. Significance analysis of microarrays applied to the ionizing radiation response. Proc.Natl.Acad.Sci.U.S.A 98:5116-5121.)) using the one class response and a false discovery rate of < 1% with a medium number of falsely called significant genes of <1.

organism: Staphylococcus aureus

source_name: Staphylococcus aureus 137/93G

label_protocol: Fluorescence-labeled single-stranded cDNA was obtained by reverse transcription of total RNA. To this end, aliquots of total RNA preparations from three different cultures of the respective experiment were pooled to a total amount of 9 µg (3 µg each) and transcribed into cDNA using 100 units (U) of BioScript reverse transcriptase (Bioline, Luckenwalde, Germany) following the manufacturer’s instructions. For direct cDNA labeling, the total reaction volume of 40 µl contained 75 µg/ml pd(N)6 random hexamers (GE Healthcare - Amersham, NJ, USA), 0.1 mM CyDye3- or CyDye5-dCTPs (GE Healthcare - Amersham) aside from 0.2 mM dCTP, 0.5 mM dATP, 0.5 mM dTTP, 0.5 mM dGTP and 25 U/ml RNase-OUT (Invitrogen, Karlsruhe, Germany). RNA was degraded by alkaline hydrolysis at 65°C and fluorescence-labeled cDNA was purified using the MinElute PCR purification kit (Qiagen). cDNA synthesis and CyDye3 / CyDye5 incorporation was verified using the Nanodrop spectrophotometer (Nanodrop Technologies).

extract_protocol: Exponential-phase cultures of 10 ml for total RNA preparations were grown as aforementioned and stabilized by incubation with two volumes of prewarmed RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany) for 5 min at 37°C. The culture was subsequently harvested by centrifugation and the pellets were shock-frozen in fluid nitrogen and kept at -70°C. The cells were lysed in the presence of 400 µg/ml lysostaphin (Genmedics, Reutlingen, Germany) and total RNA was extracted using the PrestoSpin R bug kit including DNase I treatment (Molzym, Bremen, Germany) following the manufacturer’s instructions. Quality and quantity of total RNA were confirmed by agarose gel electrophoresis and measured using the Nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, USA).

treatment_protocol: S. aureus cultures for RNA preparations were diluted 200-fold from overnight cultures and grown to exponential phase until they reached an OD600 of 0.5 in BHI broth. Then, mersacidin was added as indicated, and the cultures were further grown to an OD600 of 1.0 for RNA preparations (~ 30 min) or longer to assess growth behavior. CaCl2 was supplemented to all mersacidin containing cultures to a final concentration of 1 mM, since Ca2+-ions enhance the bactericidal effect of mersacidin.

tag: Methicillin-resistant S. aureus (MRSA) SA137/93A, isolated from a tracheal secretion and displays heterogeneous intermediate vancomycin resistance (hVISA strain, MIC

value: 8 mg/L in BHI). Subculturing in presence of 6 mg/L vancomycin generated a mutant with homogeneous intermediate vancomycin resistance, that showed an MIC value of 16 mg/L in BHI and was designated SA137/93G.

tag: Source

value: Reipert, A., K. Ehlert, T. Kast, and G. Bierbaum. 2003. Morphological and genetic differences in two isogenic Staphylococcus aureus strains with decreased susceptibilities to vancomycin. Antimicrob.Agents Chemother. 47:568-576.

treatment_protocol: S. aureus cultures for RNA preparations were diluted 200-fold from overnight cultures and grown to exponential phase until they reached an OD600 of 1.0 (~ 30 min). CaCl2 was supplemented to all mersacidin containing cultures to a final concentration of 1 mM, since Ca2+-ions enhance the bactericidal effect of mersacidin.


title: ALL_responsive_10+IR

description:
114_8h
Aliquots of 2 x 106 cells per time point were irradiated with 5 Gy IR (cobalt Co60)


title: Mersacidin4_samples13793G_chip017

description: no additional information provided

treatment_protocol: S. aureus cultures for RNA preparations were diluted 200-fold from fresh BHI broth overnight cultures and further incubated until they reached an OD600 ~ 1.0. CaCl2 was supplemented to all cultures to a final concentration of 1 mM since Ca2+-ions enhance the bactericidal effect of mersacidin.


title: ALL_responsive_9+IR

description:
110_8h
Aliquots of 2 x 106 cells per time point were irradiated with 5 Gy IR (cobalt Co60)


title: ALL_responsive_4+IR

description:
89_8h
Aliquots of 2 x 106 cells per time point were irradiated with 5 Gy IR (cobalt Co60)


title: ALL_responsive_5+IR

description:
91_8h
Aliquots of 2 x 106 cells per time point were irradiated with 5 Gy IR (cobalt Co60)


title: ALL_responsive_6+IR

description:
92_8h
Aliquots of 2 x 106 cells per time point were irradiated with 5 Gy IR (cobalt Co60)


title: ALL_responsive_7+IR

description:
98_8h
Aliquots of 2 x 106 cells per time point were irradiated with 5 Gy IR (cobalt Co60)


title: ALL_responsive_2+IR

description:
86_8h
Aliquots of 2 x 106 cells per time point were irradiated with 5 Gy IR (cobalt Co60)


title: ALL_ resistant_2+IR

description:
83_8h
Aliquots of 2 x 106 cells per time point were irradiated with 5 Gy IR (cobalt Co60)


title: ALL_ resistant_5-IR


title: ALL_responsive_1+IR

description:
33_8h
Aliquots of 2 x 106 cells per time point were irradiated with 5 Gy IR (cobalt Co60)


title: Mm_fasting liver_72h-3

city: Amsterdam

first: Milka

last: Sokolovic

address: Meibergdreef 15

department: Medical Biochemistry

country: Netherlands

institute: AMC

description: Gene-expression profiling, pathway analysis, and immunohistochemistry were carried out on mouse liver after 0, 12, 24, and 72 hours of fasting to look at the liver's adaptive response to fasting.

hyb_protocol: Hybridization protocol that acompanies the Agilent's 60-mer Mouse Development (22K) Oligo Microarray G4120A was strictly followed

scan_protocol: Agilent’s dual-laser microarray slide scanner was used. The data were retrieved with Agilent’s Feature Extraction software 6.1.1.

data_processing: Value column represents Log(REDsignal/GREENsignal) per feature. Processed signals from Agilent feature extraction file were used.

source_name: 72h fasted liver, 5-6

label_protocol: 20 μg mRNA, pooled from 2 livers (1&2), was reverse transcribed with Cy3-labelled dCTP (Perkin Elmer, Boston, USA), using the Agilent Fluorescent Direct Label Kit.

extract_protocol: Total liver RNA was extracted from frozen tissue with TRIzol (Invitrogen), followed by RNeasy (Qiagen) column purification. The quality of RNA was assessed with the RNA 6000 Nano LabChip® Kit in an Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, USA).

treatment_protocol: Mice were housed at 20-22°C, 50-60% humidity, a 12 hours light/dark cycle, and food and water ad libitum. At 6 weeks of age, mice were fasted by removing chow for up to 72 hours before sacrifice (n = 6 per group). The animals were kept in metabolic cages to prevent the consumption of beddings and were kept warm with an infrared lamp starting at 24h. All animals were sacrificed between 9:00 and 10:00 a.m. by cervical dislocation. The liver was removed quickly, weighed, snap-frozen in liquid N2, and stored at -80°C.

tag: Male FVB mice, at 6 weeks of age, 72h fasted

source_name: fed liver, 1-6

label_protocol: Cy5-labeled cDNA produced from RNA pooled from 6 fed animals served as the common reference across all arrays.

tag: Male FVB mice, at 6 weeks of age, fed


title: ALL_ resistant_11-IR


title: Mm_fasting liver_72h-2

source_name: 72h fasted liver, 3-4


title: Mm_fasting liver_72h-1

source_name: 72h fasted liver, 1-2


title: ALL_responsive_3+IR

description:
88_8h
Aliquots of 2 x 106 cells per time point were irradiated with 5 Gy IR (cobalt Co60)


title: ALL_responsive_9-IR

source_name: ALL, responsive, no irradiation


title: ALL_responsive_8+IR

description:
101_8h
Aliquots of 2 x 106 cells per time point were irradiated with 5 Gy IR (cobalt Co60)


title: Mm_fasting liver_24h-2

source_name: 24h fasted liver, 3-4

tag: Male FVB mice, at 6 weeks of age, 24h fasted


title: ALL_responsive_8-IR


title: ALL_responsive_10-IR


title: ALL_responsive_7-IR


title: ALL_responsive_6-IR


title: Mm_fasting liver_24h-1

source_name: 24h fasted liver, 1-2


title: Mm_fasting liver_12h-2

data_processing:
Value column represents Log(REDsignal/GREENsignal) per feature. Processed signals
from Agilent feature extraction file were used.

source_name: 12h fasted liver, 3-4

label_protocol: 20 μg mRNA, pooled from 2 livers, was reverse transcribed with Cy3-labelled dCTP (Perkin Elmer, Boston, USA), using the Agilent Fluorescent Direct Label Kit.

tag: Male FVB mice, at 6 weeks of age, 12h fasted


title: Mm_fasting liver_0h-2

source_name: fed liver, 3-4


title: Mm_fasting liver_0h-3

source_name: fed liver, 5-6


title: Mm_fasting liver_0h-1

source_name: fed liver, 1-2


title: ALL_responsive_5-IR


title: ALL_responsive_11-IR


title: Mm_fasting liver_12h-1

source_name: 12h fasted liver, 1-2


title: ALL_responsive_4-IR


title: ALL_responsive_3-IR


title: Mm_fasting liver_24h-3

source_name: 24h fasted liver, 5-6


title: ALL_responsive_1-IR


title: Mm_fasting liver_12h-3

source_name: 12h fasted liver, 5-6


title: ALL_responsive_2-IR


title: 20650

status: Public on Oct 22 2008

type: genomic

city: Nijmegen

first: Joris

middle: Andre

last: Veltman

address: Geert Grooteplein 10

department: Human Genetics

institute: Radboud University Nijmegen Medical Centre

description: Genotyping data from patients with deficit schizophrenia

data_processing: We identified genome-wide CNV using the Copy Number Analyzer for Affymetrix GeneChip (CNAG2.0) software, which uses a Hidden Markov Model (HMM) algorithm to calculate copy numbers.

molecule: genomic DNA

source_name: blood

extract_protocol: Salt-extraction from blood, no extra purification

tag: Gender

value: Male


title: 20615

value: Female


title: 20635


title: 11116


title: 20645


title: 20418


title: 31100


title: 20501


title: 20500


title: 20424


title: 20502


title: 20704


title: 20401


title: 20638


title: 20353


title: 20526


title: 20607


title: 20478


title: 11303


title: 20603


title: 20480


title: 20084


title: 20232


title: 20654


title: 20643


title: NK cells_Skin_II

city: Dallas

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

description: NK cells sorted as CD45+ CD3- Nkp46+ NK11+ from skin tissue

hyb_protocol: Labeled cRNA (1.5µg) were hybridized overnight to Illumina Mouse WG6 V1.1 BeadChip array, washed, blocked, and stained following manufacturer's protocols.

scan_protocol: BeadChip arrays were scanned on an Illumina BeadStation 500 following manufacturer's specifications.  BeadStudio V2 software was used to generate signal intensity values from scans, subtract background, and scale each microarray to the median average intensity for all samples.

data_processing: The data were analyzed using BeadStudio version 1.5.1.3 using the average chip normalization method

source_name: Mouse NK cells sorted from skin

label_protocol: Biotyilated cRNA were generated using Illumina TotalPrep-96 RNA Amplification Kit following manufacturer specifications

extract_protocol: RNeasy Micro Kit

tag: Age

value: 12 weeks

tag: Strain for C57BL/6


title: NK cells_Skin_I


title: NK cells_Intestine_II

description: NK cells sorted as CD45+ CD3- Nkp46+ NK11+ from gut lamina propria  tissue

source_name: Mouse NK cells sorted from intestine (LPL)


title: Staphylococcus aureus_magnolol_replicate3

city: Changchun

first: Xuming

last: Deng

address: Xi'an Street 5333#

country: China

institute: College of Animal Science and Veterinary Medicine, Jilin University

description: magnolol treatment

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Affymetrix GeneChip Opererating Software (GCOS) version 1.0

source_name: Staphylococcus aureus_magnolol

label_protocol: Conversion to cDNA and labeling was performed as described in Beenken et al., Journal of Bacteriology, 2004 July, 186(14):4665-4684

growth_protocol: (i) S. aureus strain ATCC25923 was grown overnight at 200 rpm in a rotary shaker at 37°C in 10 ml of MHB II, (ii) after 12 hours, the culture were inoculated to an initial OD600 of 0.05 in 100 ml of MHB II in 250-ml Erlenmeyer flasks, the bacteria were grown at 37°C at 200 rpm to an OD600 of 0.3. (iii) 500 µl of a 12800 µg /ml magnolol stock solution, prepared in dimethyl sulfoxide (DMSO), was added to the cultures, giving a certain concentration and incubation time, and the final concentration of DMSO was 1% (vol/vol).

extract_protocol: Total bacterial RNA was isolated as described by Beenken et al., 2004 July, 186(14):4665-4684

treatment_protocol: magnolol

tag: Standard strain ATCC25923


title: NK cells_Intestine_I


title: 20634


title: 11212


title: Staphylococcus aureus_magnolol_replicate2

description: magnolol treatment


title: Staphylococcus aureus_magnolol_replicate1

description: magnolol treatment


title: NK cells_Spleen_I

description: NK cells sorted as CD45+ CD3- Nkp46+ NK11+ from spleen tissue;

source_name: Mouse NK cells sorted from spleen


title: 20417


title: 20618


title: Staphylococcus aureus_control_replicate3

description: Control

source_name: Staphylococcus aureus_control

growth_protocol: (i) S. aureus strain ATCC25923 was grown overnight at 200 rpm in a rotary shaker at 37°C in 10 ml of MHB II, (ii) after 12 hours, the culture were inoculated to an initial OD600 of 0.05 in 100 ml of MHB II in 250-ml Erlenmeyer flasks, the bacteria were grown at 37°C at 200 rpm to an OD600 of 0.3. (iii) 1% (vol/vol) dimethyl sulfoxide (DMSO) was added to the culture, the bacterial suspensions were further incubated for a certain time at 37°C

treatment_protocol: Dimethyl sulfoxide (DMSO, 1% (vol/vol))


title: 20633


title: 20080


title: Staphylococcus aureus_control_replicate2

description: Control


title: 20421


title: NK cells_Spleen_II

description: NK cells sorted as CD45+ CD3- Nkp46+ NK11+ from spleen tissue


title: Staphylococcus aureus_sodium houttuyfonate_replicate3

description: sodium houttuyfonate treatment

growth_protocol: (i) S. aureus strain ATCC25923 was grown overnight at 200 rpm in a rotary shaker at 37°C in 10 ml of MHB II, (ii) after 12 hours, the culture were inoculated to an initial OD600 of 0.05 in 100 ml of MHB II in 250-ml Erlenmeyer flasks, the bacteria were grown at 37°C at 200 rpm to an OD600 of 0.3. (iii) 500 µl of a 12800 µg /ml sodium houttuyfonate stock solution, prepared in dimethyl sulfoxide (DMSO), was added to the cultures, giving a certain concentration and incubation time, and the final concentration of DMSO was 1% (vol/vol).

treatment_protocol: sodium houttuyfonate


title: Staphylococcus aureus_sodium houttuyfonate_replicate2

description: sodium houttuyfonate treatment


title: 20530


title: 20347


title: 20404


title: Origins from Luca's method vs G1-DNA

type: other

city: Paris

first: Jean-Charles

last: Cadoret

address: 15 rue Hélène Brion

country: France

institute: CNRS-IJM

description: Origins from Luca's method vs G1-DNA

hyb_protocol: Fragmentation of cRNA: cRNA are fragmented by Fragmentation Kit (AMBION) according to the manufacturer's instruction. Hybridisation of DNA microarrays: Hybridisation of Agilent's Human ENCODE ChIP-on-chip microarrays was mainly done according to manufacturer's instruction. The Cy5- and Cy3-labelled cRNA was mixed so that an equal quantity is hybridised on the array. The final volume was adjusted to 150 µl with RNase/DNase free H2O then 20µg of tRNA and polyt(T)+RNA were added. Hybridisation and wash of the slides were performed according to the manufacturer's instruction.(http://www.chem.agilent.com/).

scan_protocol: Microarrays were scanned with a GenePix 4000B scanner (Axon instruments) under the control of GenePix Pro 4.1 software (axon instruments). The photomultiplier voltage gain was always set at 900 for the red channel and 800 for the green channel.

data_processing: Feature extraction was done with Feature Extraction 9.1 software (Agilent technologies). Analysis was performed with Agilent Chip Analytics 1.3 software without normalization and the peak detection was carried out with the following criteria: 1) Maximum distance (in bp) for two probes to be considered as neighbours = 500; 2) A probe is considered “bound” if P(X bar) <10-5 and either central probe of the peak has P(X) < 10-5 and at last one neighbouring probe has P(X) <10-4, or at least 2 of the neighbours has P(X) < 10-4.

molecule: other

source_name: Origins from Luca's method

label_protocol:
Labelling of cRNA:
The aminoallyl-modified UTPs incorporated in the RNA were coupled with mono-reactive Cy3 or Cy5 dyes (Amersham Biosciences). To this end, one vial of mono-reactive dyes (40000 pmol) was dissolved in 12µl of DMSO (Sigma) and divided into 4µl aliquots. Purified RNAs were concentred into a 5µl volume and 11µl of 0.1 M pH=8.7 sodium bicarbonate was added. Then, the aliquot of mono-reactive dye was added to the sample for a 90 minutes coupling reaction at room temperature in the dark. The coupled reaction was applied to Microcon YM30 columns (Milipore) and washed five times with 400µl RNase and DNase free H2O according to manufacturer instructions. Thereafter, labelled RNA was collected and concentrated to 50µl. 1µl was used to calculate the degree of labelling and the quantity of produced RNA with the Microarray-Nanodrop program.

growth_protocol: HeLa S3 cells were cultured with the recommended ATCC complete growth medium: Ham’s F12K medium with L-Glutamine at 2mM, 1.5g.L-1 sodium bicarbonate, and 10% of fetal bovine serum in a humidified 5% CO2 atmosphere at 37°C.

extract_protocol:
Isolation of origins:
    EMBO Rep. 2007 Aug;8(8):770-7.
    High-throughput mapping of origins of replication in human cells.
    Lucas I, Palakodeti A, Jiang Y, Young DJ, Jiang N, Fernald AA, Le Beau MM.
Amplification of SNS:
 This approach is an adaptation of the TLAD amplification described by Liu   et al (2003). Firstly, we tailed a poly-dT at the 3’-end of SNS with Terminal Transferase (New England Biolabs) as described by Liu et al. After, second strand synthesis and incorporation of the T7 promoter sequence was carried out as follows: the tailing reaction product (20 l) was mixed with 1 μl of 0.15 μM T7-A18B primer
(5'-GCATTAGCGGCCGCGAAATTAATACGACTCACTATAGGGAG (A)18 [B], where B refers to C, G or T), 2.7 μL of 10X NEB-2 buffer and 1 μL 10 mM dNTPs (NEB). Samples were incubated at 94°C for 2 minutes, ramped down at -1 C°/sec to 25°C, held while T4 DNA polymerase (NEB) was added at a final concentration of 0.22 U/μl, and completed with H2O at 27µl. The sample was incubated at 37°C during 30 minutes and the reaction was stopped by the addition of 5 μl 0.5 M EDTA pH 8.0. Samples were purified with the MinElute Reaction Cleanup Kit (Qiagen), increasing the elution volume to 20 μl. Finally, an in vitro transcription was performed with the MegaScript Kit (Ambion) on concentrated 8µl sample according to instructions described in the Liu et al paper. The only modification was the NTP pool which was optimized for a good labelling of our RNA (‘t Hoen et al, 2003). 2µl of a 100mM mix of ATP, CTP and GTP, 2µl aminoallyl-UTP (Fermentas) 50mM, 1µl UTP 100mM were added. The product was purified with Rneasy Minikit (Qiagen) and RNA was quantified by Nanodrop and analysed by BioAnalyser with Lab-on-a-chip total RNA nano biosizing assay (Agilent Technologies).

tag: Origins from Luca's method from HeLa S3 human cells

source_name: G1 DNA

extract_protocol:
G1-DNA are extracted like this previous protocol by flow cytometry:
    Prioleau, M. N., Gendron, M. C., and Hyrien, O. (2003). Replication of the chicken beta-globin locus: early-firing origins at the 5' HS4 insulator and the rho- and betaA-globin genes show opposite epigenetic modifications. Mol Cell Biol 23, 3536-3549.
Amplification of SNS:
This approach is an adaptation of the TLAD amplification described by Liu et al (2003). Firstly, we tailed a poly-dT at the 3’-end of SNS with Terminal Transferase (New England Biolabs) as described by Liu et al. After, second strand synthesis and incorporation of the T7 promoter sequence was carried out as follows: the tailing reaction product (20 l) was mixed with 1 μl of 0.15 μM T7-A18B primer
(5'-GCATTAGCGGCCGCGAAATTAATACGACTCACTATAGGGAG (A)18 [B], where B refers to C, G or T), 2.7 μL of 10X NEB-2 buffer and 1 μL 10 mM dNTPs (NEB). Samples were incubated at 94°C for 2 minutes, ramped down at -1 C°/sec to 25°C, held while T4 DNA polymerase (NEB) was added at a final concentration of 0.22 U/μl, and completed with H2O at 27µl. The sample was incubated at 37°C during 30 minutes and the reaction was stopped by the addition of 5 μl 0.5 M EDTA pH 8.0. Samples were purified with the MinElute Reaction Cleanup Kit (Qiagen), increasing the elution volume to 20 μl. Finally, an in vitro transcription was performed with the MegaScript Kit (Ambion) on concentrated 8µl sample according to instructions described in the Liu et al paper. The only modification was the NTP pool which was optimized for a good labelling of our RNA (‘t Hoen et al, 2003). 2µl of a 100mM mix of ATP, CTP and GTP, 2µl aminoallyl-UTP (Fermentas) 50mM, 1µl UTP 100mM were added. The product was purified with Rneasy Minikit (Qiagen) and RNA was quantified by Nanodrop and analysed by BioAnalyser with Lab-on-a-chip total RNA nano biosizing assay (Agilent Technologies).

tag: DNA from G1 phase


title: 20405


title: gDNA/gDNA

description: gDNA/gDNA

source_name: HeLa S3 gDNA

extract_protocol:
Isolation of DNA:
Isolation of DNA by DNAzol reagent (invitrogen) following the manufacturer's instruction. After that, gDNA was sonicated to size up 500bp-800bp.
Amplification of sonicated gDNA:
This approach is an adaptation of the TLAD amplification described by Liu et al (2003). Firstly, we tailed a poly-dT at the 3’-end of SNS with Terminal Transferase (New England Biolabs) as described by Liu et al. After, second strand synthesis and incorporation of the T7 promoter sequence was carried out as follows: the tailing reaction product (20 l) was mixed with 1 μl of 0.15 μM T7-A18B primer
(5'-GCATTAGCGGCCGCGAAATTAATACGACTCACTATAGGGAG (A)18 [B], where B refers to C, G or T), 2.7 μL of 10X NEB-2 buffer and 1 μL 10 mM dNTPs (NEB). Samples were incubated at 94°C for 2 minutes, ramped down at -1 C°/sec to 25°C, held while T4 DNA polymerase (NEB) was added at a final concentration of 0.22 U/μl, and completed with H2O at 27µl. The sample was incubated at 37°C during 30 minutes and the reaction was stopped by the addition of 5 μl 0.5 M EDTA pH 8.0. Samples were purified with the MinElute Reaction Cleanup Kit (Qiagen), increasing the elution volume to 20 μl. Finally, an in vitro transcription was performed with the MegaScript Kit (Ambion) on concentrated 8µl sample according to instructions described in the Liu et al paper. The only modification was the NTP pool which was optimized for a good labelling of our RNA (‘t Hoen et al, 2003). 2µl of a 100mM mix of ATP, CTP and GTP, 2µl aminoallyl-UTP (Fermentas) 50mM, 1µl UTP 100mM were added. The product was purified with Rneasy Minikit (Qiagen) and RNA was quantified by Nanodrop and analysed by BioAnalyser with Lab-on-a-chip total RNA nano biosizing assay (Agilent Technologies).

tag: genomic DNA from HeLa S3


title: 20484


title: Staphylococcus aureus_sodium houttuyfonate_replicate1

description: sodium houttuyfonate treatment


title: 20351


title: 20402


title: SNS2/gDNA

type: mixed

source_name: HeLa S3 short nascent strands

extract_protocol:
Isolation of SNS:
Nascent strands were prepared as described previously (Prioleau et al, 2003), 1.5-2 kb SS DNA was selected after sucrose gradient separation. The quality of each preparation was tested by real-time quantitative PCR with primer pairs located in and around the Lamin B2 replicator (Giacca et al, 1994) and the c-myc origin (Malott and Leffak, 1999) shown in Table S1.
Amplification of SNS:
This approach is an adaptation of the TLAD amplification described by Liu et al (2003). Firstly, we tailed a poly-dT at the 3’-end of SNS with Terminal Transferase (New England Biolabs) as described by Liu et al. After, second strand synthesis and incorporation of the T7 promoter sequence was carried out as follows: the tailing reaction product (20 l) was mixed with 1 μl of 0.15 μM T7-A18B primer
(5'-GCATTAGCGGCCGCGAAATTAATACGACTCACTATAGGGAG (A)18 [B], where B refers to C, G or T), 2.7 μL of 10X NEB-2 buffer and 1 μL 10 mM dNTPs (NEB). Samples were incubated at 94°C for 2 minutes, ramped down at -1 C°/sec to 25°C, held while T4 DNA polymerase (NEB) was added at a final concentration of 0.22 U/μl, and completed with H2O at 27µl. The sample was incubated at 37°C during 30 minutes and the reaction was stopped by the addition of 5 μl 0.5 M EDTA pH 8.0. Samples were purified with the MinElute Reaction Cleanup Kit (Qiagen), increasing the elution volume to 20 μl. Finally, an in vitro transcription was performed with the MegaScript Kit (Ambion) on concentrated 8µl sample according to instructions described in the Liu et al paper. The only modification was the NTP pool which was optimized for a good labelling of our RNA (‘t Hoen et al, 2003). 2µl of a 100mM mix of ATP, CTP and GTP, 2µl aminoallyl-UTP (Fermentas) 50mM, 1µl UTP 100mM were added. The product was purified with Rneasy Minikit (Qiagen) and RNA was quantified by Nanodrop and analysed by BioAnalyser with Lab-on-a-chip total RNA nano biosizing assay (Agilent Technologies).

tag: HeLa S3 nascent strands

tag: HeLa S3 gDNA


title: 20406


title: 20602


title: 11361


title: 20085

value: XXY


title: tumor sample TME947

status: Public on Oct 21 2008

first: Esther

last: Lips

address: Plesmanlaan 121

department: Molecular Pathology

institute: NKI-AVL

description:
Expanded descriptions of Channel 1 'Characteristics':
TEM: transanal endoscopic microsurgical resection. TME: total mesorectal excision
AA: pure adenomas(in paper A/A), AC: adenoma fraction from cases with a carcinoma focus(in paper A/C), CA: tumor fractions consisting of a mixture of adenoma and carcinoma tissue(in paper AC/C), CC: carcinomas without lymph node metastasis(in paper C/C), CC(N): carcinomas with lymph node metastasis(in paper C/C(N+)).
The stages (T1N0) represent the TNM classification of colorectal tumors (International Union Against Cancer (UICC)).

hyb_protocol: Preheated hybridization buffer (25% formamide, 5× SSC, 0.1% SDS) was added and arrays were hybridised overnight 42°C to human 35K oligo microarrays

scan_protocol: Scanned on an Agilent G2565BA scanner.

data_processing: Images were quantified using Genepix 5.1 Software. The Limma (linear models for microarray data) package of Bioconductor (http://www.bioconductor.org) was used for importing the data, normalizing the arrays and identifying differentially expressed genes. Control spots and spots with more than 10% saturation, a diameter smaller than 60 μm or signal intensity less than 20 counts above background were excluded from the analysis. Data were corrected for local background (method normexp) and normalized within arrays by print-tip loess normalization and between arrays by quantile normalization.

source_name: tumor sample

label_protocol: Two ug of total RNA was amplified and labeled using Ambion's Amino Allyl MessageAmp™ aRNA kit and protocol (Ambion Inc., Austin, TX). For each microarray experiment, 2.0-μg aliquots of aRNA were labeled with Cy5 (Amersham Biosciences, Buckinghamshire, UK). The labeled aRNAs were mixed with equal amounts of Cy3-labeled reference aRNA. To the mixture of labeled reference and sample RNA, 20 μg human COT-1 DNA (Invitrogen, Carlsbad, CA), 8 μg yeast tRNA (Invitrogen) and 20 μg polyadenylic acid (Sigma-Aldrich, St. Louis, MO) were added.

tag: Rectal tumor tissue

tag: TME treated

tag: Group

value: AA

tag: Stage

source_name: Reference material consisting of pooled RNAs isolated from five colorectal cancer cell lines (HCT116, LS411N, SW480, HCT15, Caco2) and five normal rectum samples.

tag: reference


title: 20531


title: tumor sample TME739

value: CC


title: tumor sample TME890

value: AC


title: tumor sample TME772


title: tumor sample TME884


title: tumor sample TME715

value: CC(N)


title: 20229


title: tumor sample TME896


title: tumor sample TME674


title: tumor sample TME747


title: tumor sample TME658


title: SNS1/gDNA


title: tumor sample TME625


title: tumor sample TME607


title: tumor sample TME623


title: tumor sample TME598


title: tumor sample TME593


title: tumor sample TME603


title: tumor sample TME650

value: CA


title: tumor sample TME523


title: tumor sample TME382


title: tumor sample TME535


title: tumor sample TME420


title: tumor sample TME498


title: tumor sample TME365


title: 10078


title: tumor sample TME321


title: 11288


title: tumor sample TME385


title: tumor sample TME338


title: tumor sample TME30


title: 20372


title: tumor sample TME271


title: tumor sample TME247


title: tumor sample TME310


title: 11356


title: tumor sample TME209


title: tumor sample TME161


title: tumor sample TME1344


title: 11335


title: 11083


title: tumor sample TME1249


title: tumor sample TME1208


title: 11289


title: 11081


title: tumor sample 614

tag: TEM treated


title: tumor sample 609


title: tumor sample TME1203


title: tumor sample TME1183


title: tumor sample TME122


title: tumor sample TME277


title: tumor sample 613


title: tumor sample 618


title: tumor sample 569


title: tumor sample 617


title: tumor sample 571


title: tumor sample 575


title: 11082


title: tumor sample TME1124


title: tumor sample 572


title: tumor sample 608


title: tumor sample 621


title: tumor sample 565


title: tumor sample 544


title: tumor sample 567


title: tumor sample 542


title: tumor sample 539


title: tumor sample 568


title: tumor sample 547


title: tumor sample 534


title: tumor sample 543


title: tumor sample 536


title: tumor sample 528


title: tumor sample 511


title: tumor sample 220


title: tumor sample 221


title: tumor sample 515


title: tumor sample 209


title: tumor sample 204


title: tumor sample 514


title: tumor sample 205


title: tumor sample 206


title: tumor sample 217


title: tumor sample 219


title: tumor sample 510


title: tumor sample 215


title: tumor sample 525


title: tumor sample 203


title: tumor sample 160


title: infected wt Susceptibility T18 Col0

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17406.gif
Disease State: infected
Genotype: wt

hyb_protocol: not provided

scan_protocol: not provided

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)

source_name: Common Reference

label_protocol: not provided

extract_protocol: not provided

tag: Common Reference

source_name: col-0 T18

tag: col-0 T18


title: uninfected jar1 slide9

description:
Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26422.gif
Disease State: uninfected
Genotype: jar1

source_name: common reference

tag: common reference

source_name: uninfected jar-1 leaves exp II

tag: uninfected jar-1 leaves exp II


title: tumor sample 533


title: uninfected npr1 slide2

description:
Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26404.gif
Disease State: uninfected
Genotype: npr1

source_name: uninfected npr-1 leaves exp I

tag: uninfected npr-1 leaves exp I


title: infected wt slide10

description:
Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26424.gif
Disease State: infected
Genotype: wt

source_name: Col-0 infected leaves 18 hrs post infection exp II


title: uninfected wt slide1

description:
Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26402.gif
Disease State: uninfected
Genotype: wt

source_name: uninfected Col-0 leaves exp I

tag: uninfected Col-0 leaves exp I


title: uninfected jar1 slide3

description:
Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26407.gif
Disease State: uninfected
Genotype: jar1

source_name: uninfected jar-1 leaves exp I

tag: uninfected jar-1 leaves exp I


title: infected npr1 slide11

description:
Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26425.gif
Disease State: infected
Genotype: npr1

source_name: npr-1 infected leaves 18 hrs post infection exp II


title: infected jar1 Susceptibility T18 jar1

description:
Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17407.gif
Disease State: infected
Genotype: jar1

source_name: jar 1-T18

tag: jar 1-T18


title: infected wt slide4

description:
Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26409.gif
Disease State: infected
Genotype: wt

source_name: Col-0 infected leaves 18 hrs post infection exp I


title: infected jar1 slide12

description:
Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26426.gif
Disease State: infected
Genotype: jar1

source_name: jar-1 infected leaves 18 hrs post infection exp II


title: infected npr1 slide5

description:
Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26412.gif
Disease State: infected
Genotype: npr1

source_name: npr-1 infected leaves 18 hrs post infection exp I


title: uninfected npr1 Susceptibility T0 npr-1

description:
Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17460.gif
Disease State: uninfected
Genotype: npr1


title: uninfected wt slide7

description:
Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26418.gif
Disease State: uninfected
Genotype: wt

source_name: uninfected Col-0 leaves exp II

tag: uninfected Col-0 leaves exp II


title: uninfected npr1 slide8

description:
Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26421.gif
Disease State: uninfected
Genotype: npr1

source_name: uninfected npr-1 leaves exp II

tag: uninfected npr-1 leaves exp II


title: infected jar1 slide6

description:
Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26415.gif
Disease State: infected
Genotype: jar1

source_name: jar-1 infected leaves 18 hrs post infection exp I


title: infected jar1 Susceptibility T18 jar1 duplicate

description:
Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18323.gif
Disease State: infected
Genotype: jar1


title: infected npr1 Susceptibility T18 npr1 duplicate

description:
Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18324.gif
Disease State: infected
Genotype: npr1


title: T47D_MTVL_H1.2sh _+Dox_Repl_B

status: Public on Oct 20 2008

city: barcelona

first: BELEN

last: MINANA

state: barcelona

address: dr aiguader 88

department: GENE REGULATION, STEM CELLS AND CANCER

country: Spain

institute: Center for genomic regulation

description: Mean foreground and background intensities were extracted from the red (Cy5) and green (Cy3) channels for every spot on the microarray. The background intensities are used to correct the foreground intensities for local variation on the array surface, resulting in corrected red and green intensities.

hyb_protocol: Slides were pre-hybridized in prewarmed 5X SCC, 0.1% SDS and 0.1% BSA at 42ºC for 45 min, rinsed under milliQ water and spun dry using a centrifuge for 5 min at 1500 rpm. Labeled samples were redissolved in 42ºC prewarmed 12 microliter of Hybridization buffer A (50% formamide, 6X SSC, 0.5% SDS and 5X Denhardt’s applied to a glass coverslip, covered with the spotted glass slide. Arrays were incubated in a corning hybridization chamber for 18 hr at 42ºC in a humid environment (In Slide Out oven, Boeckel). Arrays were washed at room temperature using an orbital shaker for 10 min with a high stringency wash buffer (0.1X SSC, 0.1% SDS), twice for 10 min with a low stringency wash buffer (0.1X SSC), rinsed for 5 min in milliQ water and spun dry for 5 min at 1500 rpm using a centrifuge.

scan_protocol: Fluorescent images were obtained using the G2565BA Microarray Scanner System (Agilent) with 100% laser power and 100% PMT settings and 16-bit TIFF images, one for each channel, were quantified using GenePix Pro 6.0 microarray analysis software (Molecular Devices, www.moleculardevices.com).

data_processing:
Raw data were processed using LIMMA, a microarray statistical analysis package of Bioconductor (http://www.bioconductor.org, Dudoit et al. 2003) that runs in the R programming environment (Gentleman et al. 2004, Wettenhall et al. 2004). Gene intensities were locally background subtracted using Normexp, taking mean of channel intensities and the median of background intensities. Spots with intensities smaller than two times the local background in both dye filter channels (Cy3 or Cy5), as well as control spots, were excluded from normalization and are left blank.
Expression ratios were calculated as R/G, where R and G are the red and green color intensities, respectively. Ratios were transformed to logarithm base 2. Locally weighted linear regression (Lowess) analysis was used as a normalization method. We applied a local Lowess to each print-tip group or subgrid to correct any systematic spatial variation on the array, between spotting needles or variability on slide surface, by adjusting the mean of the Log2Ratio values in each subgrid to zero. We adjust the variance across all subgrids with a scaling factor for normalization, applying a smoothing factor f=0.2 to each subgrid in order to homogenize the variance of the log2Ratio within each print-tip. Normalized Log2Ratios across all arrays were scaled so that every array has the same median intensity and same absolute standard deviation, in order to give the same weight to every gene on the array.
After normalization, replicated spots of the same gene were average.

source_name: T47D-MTVL human breast cancer cell line, H1.2 sh, Dox treated

label_protocol:
Linear T7-oligodT mediated mRNA amplification (described by Van Gelder et al. 1990 and Eberwine et al. 1992)
3 microgram of the in vitro amplified aRNA samples were reverse transcribed with 4 microliter 5X first strand buffer, 2 microliter 0.1 M DTT, 0.4 microliter low dT-dNTP mix (25 mM dA, dC, dG, 10 mM dT), 1.5 microliter Superscript II (Invitrogen) and 2 microliter 25 mM Cy3-dUTP or Cy5-dUTP (Amersham). The reaction was incubated at 42ºC for 2 hr, chilled on ice and quick spun to bring down condensation. To stop the reaction 1 microliter 1 M NaOH/20 mM EDTA, was added followed by 80 microliter MilliQ-H20 and 10 microliter 3M NaOAc pH 5. Labeled samples were purified with Quiaquick PCR purification columns (Qiagen) and eluted twice with 50 microliter EB (10 mM Tris pH 8.5). Labeling efficiency was calculated by quantification with Nanodrop, obtaining between 50-80 pmol/microliter of Cy3 or Cy5 labeled probes. Labeled samples for the same array were combined, 1 microliter 1 microgram/microliter Human Cot DNA (Invitrogen) was added, and the labeled mix was desiccated by Speed-Vac centrifugation.

growth_protocol: These cell lines were grown in RPMI 1640 medium, supplemented with 10% FBS, 2mM L-glutamine, 100 U/ml penicillin, and 100µg/ml streptomycin. Doxicycline (Sigma) was added at 2.5 µg/ml when indicated.

extract_protocol:
RNeasy mini kit (QUIAGEN, cat.no. 74104)
Quality assesment of Total RNA samples were analyzed using the Agilent Bioanalyzer 2100 and the RNA 6000 LabChip Kit (Agilent) with the Eukaryote Total RNA Nano Assay.

treatment_protocol: Along a 6-day treatment with Dox, cells were passaged at day 3. Serum-containing media was replaced with serum-free media at day 4 for growth arrest.

tag: H1.2 (and control) knock-down cell lines were established from T47D-MTVL cells

value: Human breast cancer cell line T47D modified to contain one stably integrated copy of Luciferase reporter gene driven by the Mouse Mammary Tumor Virus promoter, named T47D-MTVL (Truss, M., J. Bartsch, A. Schelbert, R. J. Hache, and M. Beato. 1995).

tag: Initially, a cell line expressing the Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) was generated. Then, this cell line was infected with viruses for expression of the different H1 variants shRNAs (pLVTHM). The inducible knocked-down cell lines were sorted in a FACSvantageSE (Becton Dickinson) for RedFP-positive and GFP-positive fluorescence after 3 days of Dox treatment. Then cells were amplified in the absence of Dox until an experiment was performed. Plasmids for the lentivirus vector-mediated drug-inducible RNA interference system (pLVTHM, ptTR-KRAB-Red, pCMC-R8.91 and pMD.G) were provided by D. Trono (University of Geneva) (Wiznerowicz M & Trono D (2003) Conditional suppression of cellular genes

value: lentivirus vector-mediated drug-inducible RNA interference. J Virol 77:8957-8961).

source_name: Universal human reference RNA Stratagene® (cat.no.740000)

tag: pool of ten different tumor cell lines from different human tissues Stratagene® (cat.no.740000)


title: T47D_MTVL_H1.2sh _-Dox_Repl_D

source_name: T47D-MTVL human breast cancer cell line, H1.2 sh, Dox untreated


title: T47D_MTVL_H1.2sh _+Dox_Repl_D


title: T47D_MTVL_H1.2sh _+Dox_Repl_A


title: T47D_MTVL_H1.2sh _-Dox_Repl_C


title: T47D_MTVL_H1.2sh _+Dox_Repl_C


title: T47D_MTVL_H1.2sh _-Dox_Repl_A


title: B67 Epo-HBP

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39965.gif
Disease State: B67

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 1.3; Parameter Image Origin = 1160, 9480; Software: type: feature extraction; Performer: Minnie,,Sarwal Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-04-01; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 630; Parameter Laser on time = 86289; Parameter Laser Power = 1.48; Parameter Scan Time = 10:20:15; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.18; Performer: Minnie,,Sarwal Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-04-01; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 710; Parameter Scan Power = 100; Parameter Laser on time = 451397; Parameter Laser Power = 2.19; Parameter Scan Time = 10:20:15; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.18; Performer: Minnie,,Sarwal

source_name: aRNA by SH on 3/27/03 from cell lines

tag: aRNA by SH on 3/27/03 from cell lines

source_name: B67 Epo-HBP

tag: B67 Epo-HBP


title: T47D_MTVL_H1.2sh _-Dox_Repl_B


title: infected wt Susceptibility T18 Col0 duplicate

description:
Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18328.gif
Disease State: infected
Genotype: wt

source_name: Common Reference

source_name: col-0 T18


title: uninfected jar1 Susceptibility T0 jar1 duplicate

description:
Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18327.gif
Disease State: uninfected
Genotype: jar1

source_name: jar-1 T0

tag: jar-1 T0


title: B9 Epo-Ctrl

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39971.gif
Disease State: control

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 1.3; Parameter Image Origin = 1240, 9600; Software: type: feature extraction; Performer: Minnie,,Sarwal Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-04-01; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 630; Parameter Laser on time = 86407; Parameter Laser Power = 1.44; Parameter Scan Time = 12:18:08; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.81; Performer: Minnie,,Sarwal Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-04-01; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 740; Parameter Scan Power = 100; Parameter Laser on time = 451516; Parameter Laser Power = 2.34; Parameter Scan Time = 12:18:08; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.81; Performer: Minnie,,Sarwal

source_name: B9 Epo-Ctrl

tag: B9 Epo-Ctrl


title: T47D_MTVL_controlsh_+Dox_Repl_D

source_name: T47D-MTVL human breast cancer cell line, control sh, Dox treated


title: uninfected jar1 Susceptibility T0 jar1 bis

description:
Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18329.gif
Disease State: uninfected
Genotype: jar1

tag: Common Reference


title: infected npr1 Arabidopsis susceptibility npr-1 duplicate

description:
Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26878.gif
Disease State: infected
Genotype: npr1

source_name: common reference

source_name: npr-1 infected leaves 18 hrs post infection exp IV


title: B92 Epo-HBP2

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41767.gif
Disease State: B92

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 1.3; Parameter Image Origin = 1240, 9240; Software: type: feature extraction; Performer: Minnie,,Sarwal Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-06-03; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 650; Parameter Laser on time = 101510; Parameter Laser Power = 1.38; Parameter Scan Time = 10:01:39; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.26; Performer: Minnie,,Sarwal Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-06-03; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 690; Parameter Scan Power = 100; Parameter Laser on time = 466619; Parameter Laser Power = 1.98; Parameter Scan Time = 10:01:39; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.26; Performer: Minnie,,Sarwal

source_name: B92 Epo-HBP2

tag: B92 Epo-HBP2


title: uninfected wt Susceptibility T0 Col0 duplicate

description:
Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18325.gif
Disease State: uninfected
Genotype: wt

source_name: Col-0 T0

tag: Col-0 T0