title: CD8+ miR-181a mutant - mAdbID:88059

city: Bethesda

first: Nicholas

last: Restifo

state: MD

address: CRC Room 3-5762

institute: NCI

description: mAdb experiment ID: 88059

hyb_protocol: Hybridization Protocol (human) Other: The hybridization was carried out at 65°C for 16–18 hrs.

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.15;; 4.46 Temperature: 27.49

data_processing:
BRB Data Processing Protocol
Calculation Method: Statistical analysis was based on the BRB array software (http//:linus.nci.nih.gov/BRB-ArrayTools.html) by comparing classes using two way ANOVA in mouse experiments to identify genes differentially expressed in different experiment conditions. After background correction, collated data were filtered with 200 intensity cut off in both channels or override if one channel is below than 200. All flagged spots and spot with diameter less than 20um were eliminated. Data was normalized by median over the entire array. Log2 intensity ratios (test sample vs common reference sample) were used for class comparison. Out put ratio data with define p value cut off were exported for Cluster and Treeview analysis. Genes with missing values and expression change less than 2 fold between the compared phenotype were further eliminated during cluster analysis and visualized by Treeview program.

source_name: human control

label_protocol:
Cy3 Labeling Protocol (human)
Other: cDNA targets were labeled with Cy3 through reverse transcription reaction.

extract_protocol:
Trizol Extraction Protocol
Other: Cells were lysed with TRIzol reagent (Invitrogen, Carlsbad, CA) and total RNA was isolated according to the manufacturers instructions. RNA integrity was assessed by the presence of 28S and 18S bands by Agilent Bioanalyzer and spectrophotometry with A260/A280 ratios > 2.0.

value: blood

value: PBMC

source_name: CD8+ miR-181a mutant

label_protocol:
Cy5 Labeling Protocol (human)
Other: cDNA targets were labeled with Cy5 through reverse transcription reaction.

treatment_protocol:
Treatment type: small molecule
Agent: MDH1- MiR-181amut -1-PGK-GFP
In-vivo treatment: CD8 cells from PBL were positively selected using microbeads and magnetic columns according to manufacture’s instructions (Miltenyi Biotec Inc.) Six million HEK-293T cells were placed in 10 cm poly-L-Lysine coated dishes (BD Biosciences) with 10% FCS DMEM. One day later, the HEK-293T monolayer was cotransfected with the plasmid MDH1- MiR-181amut -1-PGK-GFP and the helper plasmid VSVG. Lipofectamine 2000 (Invitrogen Corp.) was used for transfection according to manufacture’s instructions. Briefly, 9 ug of retroviral vector plus 6.3 ug of VSVG were added to 1.5 ml of OPTI-MEM. In a separate tube, 60 ul of Lipofectamine 2000 were added to 1.5 ml of OPTI-MEM. These two solutions were combined, incubated for 20 minutes at room temperature, and added dropwise to HEK-293T cells cultured in 10 ml of DMEM plus 10% FCS (without antibiotics). The following day, the supernatant was replaced with fresh medium and incubated at 37C overnight. Retroviral supernatant was then collected from the transfected HEK-293T and used for T cell transduction.

value: CD8+ lymphocytes


title: CD4+ ctrl - mAdbID:88054

status: Public on Oct 01 2008

type: RNA

country: USA

description: mAdb experiment ID: 88054

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.15;; 4.37 Temperature: 26.82

molecule: total RNA

organism: Homo sapiens

tag: Tissue

tag: Cell type

source_name: CD4+ ctrl

treatment_protocol:
Treatment type: small molecule
Agent: MDH1-PGK-GFP-2.0
In-vivo treatment: CD4 cells from PBL were positively selected using microbeads and magnetic columns according to manufacture’s instructions (Miltenyi Biotec Inc.) Six million HEK-293T cells were placed in 10 cm poly-L-Lysine coated dishes (BD Biosciences) with 10% FCS DMEM. One day later, the HEK-293T monolayer was cotransfected with the plasmid MDH1-PGK-GFP-2.0 and the helper plasmid VSVG. Lipofectamine 2000 (Invitrogen Corp.) was used for transfection according to manufacture’s instructions. Briefly, 9 ug of retroviral vector plus 6.3 ug of VSVG were added to 1.5 ml of OPTI-MEM. In a separate tube, 60 ul of Lipofectamine 2000 were added to 1.5 ml of OPTI-MEM. These two solutions were combined, incubated for 20 minutes at room temperature, and added dropwise to HEK-293T cells cultured in 10 ml of DMEM plus 10% FCS (without antibiotics). The following day, the supernatant was replaced with fresh medium and incubated at 37C overnight. Retroviral supernatant was then collected from the transfected HEK-293T and used for T cell transduction.

value: CD4+ lymphocytes


title: CD8+ miR-181a - mAdbID:88057

description: mAdb experiment ID: 88057

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.18;; 4.19 Temperature: 29.32

source_name: CD8+ miR-181a

treatment_protocol:
Treatment type: small molecule
Agent: MDH1-miR-181a-1-PGK-GFP
In-vivo treatment: CD8 cells from PBL were positively selected using microbeads and magnetic columns according to manufacture’s instructions (Miltenyi Biotec Inc.) Six million HEK-293T cells were placed in 10 cm poly-L-Lysine coated dishes (BD Biosciences) with 10% FCS DMEM. One day later, the HEK-293T monolayer was cotransfected with the plasmid MDH1-miR-181a-1-PGK-GFP and the helper plasmid VSVG. Lipofectamine 2000 (Invitrogen Corp.) was used for transfection according to manufacture’s instructions. Briefly, 9 ug of retroviral vector plus 6.3 ug of VSVG were added to 1.5 ml of OPTI-MEM. In a separate tube, 60 ul of Lipofectamine 2000 were added to 1.5 ml of OPTI-MEM. These two solutions were combined, incubated for 20 minutes at room temperature, and added dropwise to HEK-293T cells cultured in 10 ml of DMEM plus 10% FCS (without antibiotics). The following day, the supernatant was replaced with fresh medium and incubated at 37C overnight. Retroviral supernatant was then collected from the transfected HEK-293T and used for T cell transduction.


title: CD8+ ctrl - mAdbID:88055

description: mAdb experiment ID: 88055

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.16;; 4.31 Temperature: 28.01

source_name: CD8+ ctrl

treatment_protocol:
Treatment type: small molecule
Agent: MDH1-PGK-GFP-2.0
In-vivo treatment: CD8 cells from PBL were positively selected using microbeads and magnetic columns according to manufacture’s instructions (Miltenyi Biotec Inc.) Six million HEK-293T cells were placed in 10 cm poly-L-Lysine coated dishes (BD Biosciences) with 10% FCS DMEM. One day later, the HEK-293T monolayer was cotransfected with the plasmid MDH1-PGK-GFP-2.0 and the helper plasmid VSVG. Lipofectamine 2000 (Invitrogen Corp.) was used for transfection according to manufacture’s instructions. Briefly, 9 ug of retroviral vector plus 6.3 ug of VSVG were added to 1.5 ml of OPTI-MEM. In a separate tube, 60 ul of Lipofectamine 2000 were added to 1.5 ml of OPTI-MEM. These two solutions were combined, incubated for 20 minutes at room temperature, and added dropwise to HEK-293T cells cultured in 10 ml of DMEM plus 10% FCS (without antibiotics). The following day, the supernatant was replaced with fresh medium and incubated at 37C overnight. Retroviral supernatant was then collected from the transfected HEK-293T and used for T cell transduction.


title: Pituitary 6hour(P2/S2);biological replicate

city: Santa Monica

first: Adrian

last: Anghel

state: CA

address: 2825 Santa Monica Blvd. Suite 200

department: Medicine

institute: University of California, Los Angeles (UCLA)

description: DNA microarrays were made at the SCCPRR Gene Array Facility (Department of Pharmacology, University of Washington) using the Programs for Genomic Applications (PGA) mouse 70mer oligo library generated at Massachusetts General Hospital (Boston, MA). The mRNAs to be compared are labeled with two different fluorescent cyanine dyes (Cy 3 or Cy5) using an indirect labeling method. Amino allyl-dUTP is incorporated during reverse transcription and then post-coupled with a NHS-esther mono-reactive cyanine dye. This indirect labeling method allows us to avoid one common form of false positive resulting from the fact that the reverse transcriptase enzyme differentially utilizes the Cy5 and Cy3 dyes. The two labeled cDNA samples are then combined and hybridized on a single microarray slide overnight using a standard formamide-based RNA hybridization protocol (see Protocols toggle on website). The following morning the slide is washed, dried, and scanned using the Axon 4000a scanner. The GenePix® software on the Axon 4000a scanner, after simultaneous laser scanning dual excitation/emission capturing the Cy5 and Cy3 channels, creates a merged 16-bit TIFF image, finds the spots, performs a background subtraction/signal to noise analysis, and then generates a .gpr file containing a variety of parameters concerning each individual spot.

hyb_protocol: For hybridizations, we used the dye-swap design for technical replicates in which duplicate microarrays were performed per RNA sample but the Cy dyes were "swapped", that is, one of the duplicates contained control (placebo) and morphine-treated samples labeled with Cy3 and Cy5, respectively (called polarity P+), and the other contained control and treatment samples that were reversely labeled with Cy5 and Cy3, respectively (called polarity P-). The differentially expressed genes (DEG) were determined based on each gene's average differential expression of the dye-swap pair (P+ and P-). The arrays were prehybridized in 40 microliter of 5X SSC with 0.1% SDS and 1% BSA at 42°C for 30 min. The prehybridization solution was removed, and arrays were hybridized for 16 h at 42Â°C in 5X SSC buffer containing Cy3/Cy5 labeled targets, 25% formamide, 0.1% SDS, 1 microgram Cot-1 DNA, and 1 microgram poly A RNA.

scan_protocol: After washing in molecular biology-grade water for 5 times, followed by one wash in isopropanol, hybridized microarrays were scanned for Cy3 and Cy5-labelled probes using a GenePix 4100A confocal scanner (Axon Instruments, Union City, CA) at 532 and 635 nm, respectively. Photomultiplier tube (PMT) voltages were adjusted optimized to produce the largest dynamic range of signal detection, with minimal increase in background intensity.

data_processing: Normalized by median-centering the logarithmic ratios (MOR/PLA), column "Log Ratio" from .gpr file

organism: Mus musculus

source_name: Pituitary 6hour MOR

label_protocol:
Briefly, total RNA (3-5 microgram per array isolated from pools of tissue from three to five mice) was converted to cDNA, amplified, and labeled using Amino Allyl MessageAmp aRNA (Ambion, Austin, TX) according to the manufacturer protocol. The amplified RNA (aRNA) from three independent pools of sample was then coupled to fluorescent dye esters (Cy3 and Cy5). Size exclusion column purification steps preceded and followed the dye-coupling reaction.
For details see http://depts.washington.edu/popctrma/protocols.shtml

extract_protocol: Mice were sacrificed by decapitation and the hypothalamus and pituitary were isolated. Each tissue was rapidly placed in 1 ml RNAlater solution (Ambion, Austin, TX) and stored at -80°C to prevent RNA degradation. RNA was isolated from pooled tissue samples from three to five mice that received the same treatment using Trizol reagent (Invitrogen, San Diego, CA) according to the instructions of the manufacturer. After chloroform extraction, RNA was precipitated with ethanol and further purified with RNeasy Micro Kit (Qiagen, Valencia, CA) according to the instructions provided by the manufacturer. The concentration of total RNA was measured by ultraviolet (UV) spectrophotometry at 260/280 nm, and RNA quality was assessed by electrophoresis on a 1% agarose gel. Only the samples with a 260/280 ratio greater then or equal to 1.9 and no signs of degradation on agarose electrophoresis were used for analysis.

tag: Strain

value: C57BL/6, Gender:male, Tissue:pituitary

source_name: Pituitary 6hour PLA


title: CD4+ miR-181a - mAdbID:88056

description: mAdb experiment ID: 88056

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.18;; 4.14 Temperature: 29.1

source_name: CD4+ miR-181a

treatment_protocol:
Treatment type: small molecule
Agent: MDH1-miR-181a-1-PGK-GFP
In-vivo treatment: CD4 cells from PBL were positively selected using microbeads and magnetic columns according to manufacture’s instructions (Miltenyi Biotec Inc.) Six million HEK-293T cells were placed in 10 cm poly-L-Lysine coated dishes (BD Biosciences) with 10% FCS DMEM. One day later, the HEK-293T monolayer was cotransfected with the plasmid MDH1-miR-181a-1-PGK-GFP and the helper plasmid VSVG. Lipofectamine 2000 (Invitrogen Corp.) was used for transfection according to manufacture’s instructions. Briefly, 9 ug of retroviral vector plus 6.3 ug of VSVG were added to 1.5 ml of OPTI-MEM. In a separate tube, 60 ul of Lipofectamine 2000 were added to 1.5 ml of OPTI-MEM. These two solutions were combined, incubated for 20 minutes at room temperature, and added dropwise to HEK-293T cells cultured in 10 ml of DMEM plus 10% FCS (without antibiotics). The following day, the supernatant was replaced with fresh medium and incubated at 37C overnight. Retroviral supernatant was then collected from the transfected HEK-293T and used for T cell transduction.


title: pmel-miR-181a mix - repeat 2 - mAdbID:87630

description: mAdb experiment ID: 87630

hyb_protocol: Hybridization Protocol (mouse) Other: Hybridization was done in a water bath at 42°C for 18-24 hrs.

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.2;; 4.42 Temperature: 30.29

source_name: mouse control

label_protocol:
Cy3 Labeling Protocol (mouse)
Other: RNA was directly labeled using ULS aRNA Fluorescent labeling Kit (Kreatech, Netherlands) with Cy3.

value: multiple organs

tag: Developmental stage

value: adult

value: normal multi-organ mixture

source_name: pmel-Mir-181a Mix

label_protocol:
Cy5 Labeling Protocol (mouse)
Other: RNA was directly labeled using ULS aRNA Fluorescent labeling Kit (Kreatech, Netherlands) with Cy5.

treatment_protocol:
Treatment type: small molecule
Agent: MDH1-miR-181a-1-PGK-GFP
In-vivo treatment: Six million plat-E cells were placed in 10 cm poly-L-Lysine coated dishes (BD Biosciences) with 10% FCS DMEM. One day later, the Plat-E monolayer was cotransfected with the plasmid MDH1-miR-181a-1-PGK-GFP and the helper plasmid pCL-Eco (Imgenex). Lipofectamine 2000 (Invitrogen Corp.) was used for transfection according to manufacture's instructions. Briefly, 9 ug of retroviral vector plus 6.3 ug of pCL-Eco were added to 1.5 ml of OPTI-MEM. In a separate tube, 60 ul of Lipofectamine 2000 were added to 1.5 ml of OPTI-MEM. These two solutions were combined, incubated for 20 minutes at room temperature, and added dropwise to Plat-E cells cultured in 10 ml of DMEM plus 10% FCS (without antibiotics). The following day, the supernatant was replaced with fresh medium and incubated at 37C overnight. Retroviral supernatant was then collected from the transfected Plat-E and used for T cell transduction.

value: spleen

value: Sorted lymphocytes


title: CD4+ miR-181a mutant - mAdbID:88058

description: mAdb experiment ID: 88058

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.15;; 4.4 Temperature: 26.91

source_name: CD4+ miR-181a mutant

treatment_protocol:
Treatment type: small molecule
Agent: MDH1- MiR-181amut -1-PGK-GFP
In-vivo treatment: CD4 cells from PBL were positively selected using microbeads and magnetic columns according to manufacture’s instructions (Miltenyi Biotec Inc.) Six million HEK-293T cells were placed in 10 cm poly-L-Lysine coated dishes (BD Biosciences) with 10% FCS DMEM. One day later, the HEK-293T monolayer was cotransfected with the plasmid MDH1- MiR-181amut -1-PGK-GFP and the helper plasmid VSVG. Lipofectamine 2000 (Invitrogen Corp.) was used for transfection according to manufacture’s instructions. Briefly, 9 ug of retroviral vector plus 6.3 ug of VSVG were added to 1.5 ml of OPTI-MEM. In a separate tube, 60 ul of Lipofectamine 2000 were added to 1.5 ml of OPTI-MEM. These two solutions were combined, incubated for 20 minutes at room temperature, and added dropwise to HEK-293T cells cultured in 10 ml of DMEM plus 10% FCS (without antibiotics). The following day, the supernatant was replaced with fresh medium and incubated at 37C overnight. Retroviral supernatant was then collected from the transfected HEK-293T and used for T cell transduction.


title: Pituitary 6hour (P2s/S2s);biological replicate_dye swap


title: Pituitary 6hour(P1s/S1s);dye swap


title: Pituitary 6hour (P1/S1)


title: Pituitary 4day(L2s);biological replicate_dye swap

data_processing: Normalized by median-centering the logarithmic ratios, column "Log Ratio" from .gpr file

source_name: Pituitary 4day MOR

source_name: Pituitary 4day PLA


title: Shoot apical mersietm 4

city: Parkville

first: Chui

middle: E

last: WONG

state: Victoria

address: University of Melbourne

department: Land and Food

country: Australia

institute: University of Melbourne

description:
The Cy5- or Cy3-labelled cDNA was then hybridized to different sector of the chip according to a balanced block design dual label experiment scheme (Cochran & Cox, 1992):
Sector 1: Cy3-SAM A vs Cy5-NM A
Sector 2: Cy5-SAM B vs Cy3-NM B
Sector 3: Cy3-SAM C vs Cy5-NM C
Sector 4: Cy5-SAM D vs Cy3-NM D

hyb_protocol: Carried out according to protocol at www.combimatrix.com

scan_protocol: The Cy5- and Cy3-hybridized chip was then scanned using Genepix 4000B microarray scanner (Axon Instruments, CA, USA) according to manufacturer’s instructions. The generated tiff image files were then imported into Combimatrix Microarray Imager to produce intensity data.

data_processing: The LimmaGUI software, which is an implementation of the Empirical Bayes linear modelling approach, was used for subsequent statistical analysis of the resulting data (Wettenhall & Smyth, 2004). A robust spline method was chosen for within array normalization and a least-square linear model fit was computed with the p-value adjusted using the Benjamini- Hochberg procedure.

organism: Lathyrus oleraceus

source_name: Non-apical meristem tissues

label_protocol: Target preparation and hybridization were performed in Australian Genome Research Facility Ltd (AGRF) according to the standard CombiMatrix protocol described in detail at www.combimatrix.com/docs/CustomArray4x2KProtocol.pdf. One microgram of total RNA from SAM or NM was labelled using the Kreatech’s ULS™ RNA ampULSe kit to generate Cy5 or Cy3 labelled targets.

extract_protocol: Qiagen RNeasy Mini Kit was used for all RNA extraction

tag: non-apical- meristem (NM) tissue consisted of primary stem, primary roots and mature leaves from 10-day-old garden pea (cultivar Torsdag) grown under greenhouse conditions in the uNiversity of Melbourne.

source_name: Shoot apical meristem

tag: micro-dissected shoot apical meristem from 10-day-old garden pea (cultivar Torsdag) grown under the greenhouse conditions in the university of Melbourne.


title: pmel-ctrl Neg - repeat 1 - mAdbID:86304

description: mAdb experiment ID: 86304

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.22;; 4.16 Temperature: 29.99

source_name: pmel-CTRL-

treatment_protocol:
Treatment type: small molecule
Agent: MDH1-PGK-GFP-2.0
In-vivo treatment: Six million plat-E cells were placed in 10 cm poly-L-Lysine coated dishes (BD Biosciences) with 10% FCS DMEM. One day later, the Plat-E monolayer was cotransfected with the plasmid MDH1-PGK-GFP-2.0 and the helper plasmid pCL-Eco (Imgenex). Lipofectamine 2000 (Invitrogen Corp.) was used for transfection according to manufacture's instructions. Briefly, 9 ug of retroviral vector plus 6.3 ug of pCL-Eco were added to 1.5 ml of OPTI-MEM. In a separate tube, 60 ul of Lipofectamine 2000 were added to 1.5 ml of OPTI-MEM. These two solutions were combined, incubated for 20 minutes at room temperature, and added dropwise to Plat-E cells cultured in 10 ml of DMEM plus 10% FCS (without antibiotics). The following day, the supernatant was replaced with fresh medium and incubated at 37C overnight. Retroviral supernatant was then collected from the transfected Plat-E and used for T cell transduction. Cells were FACS sorted according to GFP expression and negative population was selected.


title: pmel-miR-181a mix - repeat 1 - mAdbID:87629

description: mAdb experiment ID: 87629

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.2;; 4.46 Temperature: 30.45


title: Pituitary 4day(L2);biological replicate


title: Hypothalamus 6hour (H2s/S2s);biological replicate_dye swap

source_name: Hypothalamus 6hour MOR

source_name: Hypothalamus 6hour PLA


title: Hypothalamus 6hour(H1s/S1s);dye swap


title: pmel-ctrl Pos - repeat 2 - mAdbID:86305

description: mAdb experiment ID: 86305

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.2;; 4.51 Temperature: 28.8

source_name: pmel-CTRL+

treatment_protocol:
Treatment type: small molecule
Agent: MDH1-PGK-GFP-2.0
In-vivo treatment: Six million plat-E cells were placed in 10 cm poly-L-Lysine coated dishes (BD Biosciences) with 10% FCS DMEM. One day later, the Plat-E monolayer was cotransfected with the plasmid MDH1-PGK-GFP-2.0 and the helper plasmid pCL-Eco (Imgenex). Lipofectamine 2000 (Invitrogen Corp.) was used for transfection according to manufacture's instructions. Briefly, 9 ug of retroviral vector plus 6.3 ug of pCL-Eco were added to 1.5 ml of OPTI-MEM. In a separate tube, 60 ul of Lipofectamine 2000 were added to 1.5 ml of OPTI-MEM. These two solutions were combined, incubated for 20 minutes at room temperature, and added dropwise to Plat-E cells cultured in 10 ml of DMEM plus 10% FCS (without antibiotics). The following day, the supernatant was replaced with fresh medium and incubated at 37C overnight. Retroviral supernatant was then collected from the transfected Plat-E and used for T cell transduction. Cells were FACS sorted according to GFP expression and positive population was selected.


title: pmel-miR-181a Pos - repeat 2 - mAdbID:86306

description: mAdb experiment ID: 86306

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.2;; 4.63 Temperature: 28.46

source_name: pmel-Mir-181a +

treatment_protocol:
Treatment type: small molecule
Agent: MDH1-miR-181a-1-PGK-GFP
In-vivo treatment: Six million plat-E cells were placed in 10 cm poly-L-Lysine coated dishes (BD Biosciences) with 10% FCS DMEM. One day later, the Plat-E monolayer was cotransfected with the plasmid MDH1-miR-181a-1-PGK-GFP and the helper plasmid pCL-Eco (Imgenex). Lipofectamine 2000 (Invitrogen Corp.) was used for transfection according to manufacture's instructions. Briefly, 9 ug of retroviral vector plus 6.3 ug of pCL-Eco were added to 1.5 ml of OPTI-MEM. In a separate tube, 60 ul of Lipofectamine 2000 were added to 1.5 ml of OPTI-MEM. These two solutions were combined, incubated for 20 minutes at room temperature, and added dropwise to Plat-E cells cultured in 10 ml of DMEM plus 10% FCS (without antibiotics). The following day, the supernatant was replaced with fresh medium and incubated at 37C overnight. Retroviral supernatant was then collected from the transfected Plat-E and used for T cell transduction. Cells were FACS sorted according to GFP expression and positive population was selected.


title: Hypothalamus 6hour (H2/S2);biological replicate


title: pmel-miR-181a Neg - repeat 2 - mAdbID:86307

description: mAdb experiment ID: 86307

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.18;; 3.67 Temperature: 27.88

source_name: pmel-Mir-181a -

treatment_protocol:
Treatment type: small molecule
Agent: MDH1-miR-181a-1-PGK-GFP
In-vivo treatment: Six million plat-E cells were placed in 10 cm poly-L-Lysine coated dishes (BD Biosciences) with 10% FCS DMEM. One day later, the Plat-E monolayer was cotransfected with the plasmid MDH1-miR-181a-1-PGK-GFP and the helper plasmid pCL-Eco (Imgenex). Lipofectamine 2000 (Invitrogen Corp.) was used for transfection according to manufacture's instructions. Briefly, 9 ug of retroviral vector plus 6.3 ug of pCL-Eco were added to 1.5 ml of OPTI-MEM. In a separate tube, 60 ul of Lipofectamine 2000 were added to 1.5 ml of OPTI-MEM. These two solutions were combined, incubated for 20 minutes at room temperature, and added dropwise to Plat-E cells cultured in 10 ml of DMEM plus 10% FCS (without antibiotics). The following day, the supernatant was replaced with fresh medium and incubated at 37C overnight. Retroviral supernatant was then collected from the transfected Plat-E and used for T cell transduction. Cells were FACS sorted according to GFP expression and negative population was selected.


title: pmel-miR-181a mutant - mAdbID:87631

description: mAdb experiment ID: 87631

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.21;; 5.16 Temperature: 32.25

source_name: pmel-Mir-181a Mutant

treatment_protocol:
Treatment type: small molecule
Agent: MDH1- MiR-181amut -1-PGK-GFP
In-vivo treatment: Six million plat-E cells were placed in 10 cm poly-L-Lysine coated dishes (BD Biosciences) with 10% FCS DMEM. One day later, the Plat-E monolayer was cotransfected with the plasmid MDH1- MiR-181amut -1-PGK-GFP and the helper plasmid pCL-Eco (Imgenex). Lipofectamine 2000 (Invitrogen Corp.) was used for transfection according to manufacture's instructions. Briefly, 9 ug of retroviral vector plus 6.3 ug of pCL-Eco were added to 1.5 ml of OPTI-MEM. In a separate tube, 60 ul of Lipofectamine 2000 were added to 1.5 ml of OPTI-MEM. These two solutions were combined, incubated for 20 minutes at room temperature, and added dropwise to Plat-E cells cultured in 10 ml of DMEM plus 10% FCS (without antibiotics). The following day, the supernatant was replaced with fresh medium and incubated at 37C overnight. Retroviral supernatant was then collected from the transfected Plat-E and used for T cell transduction.


title: pmel-ctrl Pos - repeat 1 - mAdbID:86300

description: mAdb experiment ID: 86300

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.18;; 4.68 Temperature: 27.06


title: DissectedShootApicalMeristem_10-day-oldPea

source_name: Dissected Shoot Apical Meristem

label_protocol: Target preparation and hybridization were performed in Australian Genome Research Facility Ltd (AGRF) according to the standard CombiMatrix protocol described in detail at www.combimatrix.com/docs/CustomArray4x2KProtocol.pdf. One microgram of total RNA from SAM or NM was labelled using the Kreatech’s ULS™ RNA ampULSe kit to generate Cy5 or Cy3 labelled targets. The Cy5- or Cy3-labelled cDNA was then hybridized to different sector of the chip according to a balanced block design dual label experiment scheme (Cochran & Cox, 1992)

growth_protocol: Grown under the greenhouse condition in the University of Melbourne for 10 days after sowing the seeds

extract_protocol: Using Qiagen RNAEasy minikit

tag: Shoot apical meristem micro-dissected from 10-day-old garden pea (cultivar Torsdag)

source_name: Non-apical- meristem tissue

tag: non-apical- meristem tissue consisted of primary stem, primary roots and mature leaves from 10-day-old pea plants


title: Pea_Shoot apical meristem 2

tag: micro-dissected shoot apical mersietm from 10-day-old garden pea (cultivar Torsdag) grown under the greenhouse conditions in teh university fo Melbourne.


title: pmel-ctrl Neg - repeat 2 - mAdbID:86301

description: mAdb experiment ID: 86301

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.21;; 4.36 Temperature: 29.17


title: Pea_Shoot apical meristem 3


title: pmel-miR-181a Pos - repeat 1 - mAdbID:86302

description: mAdb experiment ID: 86302

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.21;; 4.07 Temperature: 29.47


title: pmel-miR-181a Neg - repeat 1 - mAdbID:86303

description: mAdb experiment ID: 86303

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.22;; 4.05 Temperature: 29.74


title: Pituitary 4day(P2s/L1s);biological replicate_dye swap


title: Hypothalamus 6hour(H1/S1)


title: Hypothalamus 4day(H1s/L1s);dye swap

source_name: Hypothalamus 4day MOR

source_name: Hypothalamus 4day PLA


title: Pituitary 4day(P1)


title: Hypothalamus 4day(H2s/L2s);biological replicate_dye swap


title: Hypothalamus 4day(H1/L1)


title: diabetic mother rep3

city: Singapore

first: S Thameem

last: Dheen

address: Medical Drive 10

country: Singapore

institute: National University of Singapore

hyb_protocol: based on Affymetrix genechip hybridization protocol

scan_protocol: based on Affymetrix genechip scaning protocol

data_processing: image captured and processed by Affymetrix GCOS (Gene chip operating system)

label: Biotin

source_name: brain of the E11.5 days embryo from diabetic mother

label_protocol: based on Affymetrix genechip labeling protocol

extract_protocol: based on Affymetrix genechip RNA extraction protocol

value: Swiss Albino mice

value: embryonic brain

tag: Stage

value: E11.5 day embryo

tag: Treatment

value: streptozotocin (STZ) induced maternal diabetes


title: Hypothalamus 4day(H2/L2);biological replicate


title: Pituitary 4day(P2/L1);biological replicate


title: LPS&paeoniflorin(100ug/ml)_6h_rep2

city: Seoul

first: Hoog-Hee

last: Kim

address: 28 Yeongon-Dong, Chongno-Gu,

department: Cell and Developmental Biology

country: South Korea

institute: Seoul National University

description: The RAW264.7 macrophages were either treated with DMSO or with LPS in the presence or absence of albiflorin, paeoniflorin, or paeonol.

hyb_protocol: The microarray chip was pre-hybridized with hybridization buffer (Applied Biosystems) for 1 h at 55℃. cRNA fragmentation was for 30 min at 60℃. The fragmented cRNA was added to prehybridized chip and the chip was incubated for 16 h at 55℃ with constant rocking at 100 rpm.

scan_protocol: The microarray chip  was scanned with Applied Biosystems 1700 Chemiluminescent Microarray Analyzer.

data_processing: The raw data were normalized using median shifting and lowess regression normalization methods by avadis software (India). Log-tansformation algorithm was used.

label: DIG-UTP

source_name: Raw264.7 macrophage cells treated with 6h of LPS in presence of paeoniflorin

label_protocol: Digoxigenin (DIG)-labeled cRNA was generated from the total RNA by using the chemiluminescent RT-IVT labeling kit (Applied Biosystems) as per the manufacturer’s instruction. 2 ug of total RNA was reverse transcribed for 2 h at 42℃. The second strand DNA was synthesized for 2 h at 16℃. The double stranded cDNA was purified and mixed with DIG-UTP (Roche), IVT enzyme mix, and IVT buffer mix. IVT reaction was performed for 9 h at 37℃.

extract_protocol: Cells were treated with LPS in the presence or absence of Paeony root components for 6h. Total RNA was extracted using Trizol reagent.

tag: macrophage-like cell line


title: LPS&paeonol(10ug/ml)_6h_rep2

source_name: Raw264.7 macrophage cells treated with 6h of LPS in presence of paeonol


title: LPS&paeonol(1ug/ml)_6h_rep3


title: LPS&paeoniflorin(100ug/ml)_6h_rep1


title: LPS&paeonol(100ug/ml)_6h_rep3


title: LPS&paeonol(1ug/ml)_6h_rep2


title: Pituitary 4day(P1s);dye swap

scan_protocol: After washing in molecular biology-grade water for 5 times, followed by one wash in isopropanol, hybridized microarrays were scanned for Cy3 and Cy5-labelled probes using a GenePix 4100A confocal scanner (Axon Instruments, Union City, CA) at 532 and 635 nm, respectively. Photomultiplier tube (PMT) voltages were adjusted optimized to produce the largest dynamic range of signal detection, with minimal increase in background intensity.

source_name: Pituitary 4day MOR

source_name: Pituitary 4day PLA


title: LPS&paeonol(1ug/ml)_6h_rep1


title: LPS&paeonol(100ug/ml)_6h_rep1


title: LPS&paeoniflorin(100ug/ml)_6h_rep3


title: LPS&paeonol(100ug/ml)_6h_rep2


title: LPS&paeoniflorin(10ug/ml)_6h_rep3


title: LPS&paeoniflorin(10ug/ml)_6h_rep2


title: LPS&paeoniflorin(1ug/ml)_6h_rep3


title: D. Melanogaster AF Larvae 5

city: La Jolla

first: Dan

last: Zhou

address: CMG 103, 9500 Gilman Drive, MC0735

department: Pediatrics

institute: University of California, San Diego, School of Medicine

description: Biological replicate 5 of 8 AF 3rd instar larval samles

hyb_protocol: Hybridization buffer were added, and samples were applied to microarrays and hybridized for 18 hours at 64°C in a chamber, after hybridization, slides were washed sequentially with 1.14x SSC/0.0285% SDS, 1.14xSSC, 0.228xSSC, and 0.057x SSC before scanning

scan_protocol: Scanned on an GenePix 4000B scanner Images were quantified using GenePix Pro software

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of ratio of medians

organism: Drosophila melanogaster

source_name: cRNA from 3rd instar larvae labeled with Cyanine-5 (red)

label_protocol: 4 µg of cRNA were primed with 7.5 µg random hexamer at 70°C for 10 min, then reversed transcripted at 42°C for 180 min in the presence of 400 U SuperScript II RTase, 500 µM each dATP, dCTP, dGTP, with 200 µM dUTP, 100 µM Cy5-labeled dUTP, and RNase inhibitor. RNA was then degraded with 35 mM NaOH/  600 µM EDTA, and labeled cDNAs were purified using QIAquick PCR columns

extract_protocol: TriZol procedure

value: 3rd instar larvae

source_name: Reference cRNA, labeled with Cyanine-3 (green)

label_protocol: 4 µg of cRNA were primed with 7.5 µg random hexamer at 70°C for 10 min, then reversed transcripted at 42°C for 180 min in the presence of 400 U SuperScript II RTase, 500 µM each dATP, dCTP, dGTP, with 200 µM dUTP, 100 µM Cy3-labeled dUTP, and RNase inhibitor. RNA was then degraded with 35 mM NaOH/  600 µM EDTA, and labeled cDNAs were purified using QIAquick PCR columns


title: normal control rep3

source_name: brain of the E11.5 days embryo from normal mice


title: LPS&paeonol(10ug/ml)_6h_rep3


title: LPS&paeoniflorin(10ug/ml)_6h_rep1


title: LPS&paeoniflorin(1ug/ml)_6h_rep1


title: LPS&paeonol(10ug/ml)_6h_rep1


title: LPS&albiflorin(10ug/ml)_6h_rep2

source_name: Raw264.7 macrophage cells treated with 6h of LPS in presence of albiflorin


title: LPS&albiflorin(100ug/ml)_6h_rep1


title: LPS&albiflorin(100ug/ml)_6h_rep2


title: LPS&albiflorin(1ug/ml)_6h_rep3


title: LPS&albiflorin(100ug/ml)_6h_rep3


title: LPS&albiflorin(10ug/ml)_6h_rep1


title: LPS&albiflorin(10ug/ml)_6h_rep3


title: vehicle_6h_rep2

source_name: Raw264.7 macrophage cells as vehicle controls


title: vehicle_6h_rep3


title: LPS_6h_rep1

source_name: Raw264.7 macrophage cells treated with 6h of LPS


title: vehicle_6h_rep1


title: LPS&albiflorin(1ug/ml)_6h_rep1


title: LPS&albiflorin(1ug/ml)_6h_rep2


title: LPS_6h_rep3


title: LPS_6h_rep2


title: WT dendritic cell PAK6

city: New York

first: Stefan

last: Worgall

state: NY

address: 515 East 71st Street

department: Genetic Medicine

institute: Weill Cornell Medical College

description: Gene expression data from WT dendritic cell with Pseudosmonas aeruginosa infection

hyb_protocol: The labeled cRNA was first hybridized to the test chip and then, when satisfactory, to the MG-U74Av2 GeneChip for 16 hr.

scan_protocol: The GeneChips were processed in the fluidics station under the control of the Microarray Suite software (Affymetrix) to receive the appropriate reagents and washed for detection of hybridized biotinylated cRNA and then manually transferred to the scanner for data acquisition.

data_processing: The image data on each individual microarray chip was scaled to arbitrary target intensity, using the Microarray Suite version 5.0. The raw data was normalized using the GeneSpring GX 7.3.1 software (Agilent Technologies, Santa Clara, CA) by setting measurements <0.01 to 0.01, followed by per-chip normalization to the 50th percentile of the measurements for the array, and per-gene by normalizing to the median measurement for the gene across all the arrays in the data set. Data from probe sets representing genes that failed the Affymetrix detection criterion (labeled “Absent ”or  “A”, or   “Marginal”or  “M”) in over 90% of microarrays were eliminated from further assessment. All further analyses were carried out on the remaining 6,474 genes selected using this criterion.

label: biotin

source_name: WT dendritic cell PAK

label_protocol: Double stranded cDNA was purified by phenol chloroform extraction and precipitation and the size distribution assessed by agarose gel electrophoresis. This material was then used for synthesis of the biotinylated RNA transcript using the BioArray HighYield reagents (Enzo, New York, NY), purified by the RNeasy kit (Qiagen, Valencia, CA) and fragmented immediately before use.

growth_protocol: Bone marrow-derived DC, generated from mouse bone marrow precursors from the CF mice and their WT littermates, were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), penicillin (100 U/ml), streptomycin (100ug/ml) (Invitrogen Corporation, CA), recombinant murine granulocyte-macrophage colony-stimulating factor (GM-CSF, 10ng/ml; R&D System, Minneapolis, Minn) and recombinant murine interleukin-4 (IL-4, 2 ng/ml; R&D System, Minneapolis, Minn).

extract_protocol: Total RNA was extracted from the DC using TRIzol followed by RNeasy (Qiagen, Valencia, CA) to remove residual DNA. First strand cDNA was synthesized using the T7-(dT)24 primer (sequence 5'-GGC CAG TGA ATT GTA ATA CGA CTC ACT ATA GGG AGG CGG-(dT)24-3', HPLC purified from Oligos Etc., Wilsonville, OR) and converted to double stranded cDNA using Superscript Choice system (Life Technologies). Double stranded cDNA was purified by phenol chloroform extraction and precipitation and the size distribution assessed by agarose gel electrophoresis.

treatment_protocol: The P.aeruginosa strain used was the laboratory strain PAK (kindly provided by A. Prince, Columbia University, NY). Bacteria were grown from frozen stocks in tryptic soy broth (Difco, Detroit, MI) at 37  C to mid-log phase, washed three times with phosphate buffered saline (PBS) pH 7.4 (Invitrogen Corporation, CA), and resuspended in the infection media at the desired concentration as determined by spectrophotometry. DC were incubated for 4 h with 10 CFU of PAK per cell in RPMI 1640 supplemented with 25mM Hepes (Biosource International, MD) and then harvested for RNA extraction.

tag: dendritic cell control from WT mice with Pseudosmonas aeruginosa infection


title: Arabidopsis mutant seedlings (cerk1) with/without elicitor treatment

city: Kawasaki

first: Hanae

last: Kaku

state: Kanagawa

address: 1-1-1, Higashi-Mita, Tama-ku

department: Life Sciences

country: Japan

institute: Meiji University

description: Arabidopsis seeds were surface-sterilized and germinated on the petri plates containing MGRL nutrients supplemented with 0.1% agarose and 1% sucrose. Seedlings were grown for 8-10 days under 16/8 h light/dark cycle at 22ºC (light) or 15ºC (dark). The seedlings were pre-incubated in the fresh MGRL medium in a 48-well microtiter plate for 2 h. One hundred of (GlcNAc)8 was added to the culture medium and incubated for 2h. Total RNA was extracted from the Arabidopsis seedlings using RNeasy Plant Mini kit (QIAGEN).

hyb_protocol: The microarrays were hybridized according to the Agilent manufacture’s protocol.

scan_protocol: The slides were scanned by an Agilent scanner.

data_processing: The obtained results were analyzed using Rosetta Luminator software (Rosetta Inpharmatics LLC).

organism: Arabidopsis thaliana

source_name: Arabidopsis mutant seedlings (cerk1) without elicitor treatment

label_protocol: RNA extracts from Arabidopsis seedlings were fluorescence labeled according to the Agilent manufacture’s protocol.

tag: Arabidopsis mutant seedlings (cerk1) treated with DW for 2h

source_name: Chitin oligosaccharide treated Arabidopsis mutant seedlings (cerk1)

tag: Arabidopsis mutant seedlings (cerk1) treated with chitinoligosaccharide for 2h


title: WT dendritic cell control6

description: Gene expression data from WT dendritic cell control without Pseudosmonas aeruginosa infection

source_name: WT dendritic cell control

tag: dendritic cell control from WT mice without Pseudosmonas aeruginosa infection


title: Arabidopsis seedlings (WT) with/without elicitor treatment

description: Arabidopsis seeds were surface-sterilized and germinated on the petri plates containing MGRL nutrients supplemented with 0.1% agarose and 1% sucrose. Seedlings were grown for 8-10 days under 16/8 h light/dark cycle at 22ºC (light) or 15ºC (dark). The seedlings were pre-incubated in the fresh MGRL medium in a 48-well microtiter plate for 2 h. (GlcNAc)8 was  added to the culture medium and incubated for 2h. Total RNA was extracted from the Arabidopsis seedlings using RNeasy Plant Mini kit (QIAGEN).

source_name: Arabidopsis seedlings (WT) without elicitor treatment

tag: Arabidopsis seedlings treated with DW for 2h

source_name: Chitin oligosaccharide treated Arabidopsis seedlings (WT)

tag: Arabidopsis seedlings treated with chitinoligosaccharide for 2h


title: WT dendritic cell control5


title: Arabidopsis mutant seedlings (cerk1) with/without elicitor treatment (color swap)

extract_protocol: Total RNA was extracted from the Arabidopsis seedlings using RNeasy Plant Mini kit (QIAGEN).


title: pmel-ctrl mix - mAdbID:87628

description: mAdb experiment ID: 87628

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.17;; 4.25 Temperature: 28.92

source_name: mouse control

tag: Tissue

tag: Cell type

source_name: pmel-CTRL Mix

treatment_protocol:
Treatment type: small molecule
Agent: MDH1-PGK-GFP-2.0
In-vivo treatment: Six million plat-E cells were placed in 10 cm poly-L-Lysine coated dishes (BD Biosciences) with 10% FCS DMEM. One day later, the Plat-E monolayer was cotransfected with the plasmid MDH1-PGK-GFP-2.0 and the helper plasmid pCL-Eco (Imgenex). Lipofectamine 2000 (Invitrogen Corp.) was used for transfection according to manufacture¡¦s instructions. Briefly, 9 ug of retroviral vector plus 6.3 ug of pCL-Eco were added to 1.5 ml of OPTI-MEM. In a separate tube, 60 ul of Lipofectamine 2000 were added to 1.5 ml of OPTI-MEM. These two solutions were combined, incubated for 20 minutes at room temperature, and added dropwise to Plat-E cells cultured in 10 ml of DMEM plus 10% FCS (without antibiotics). The following day, the supernatant was replaced with fresh medium and incubated at 37C overnight. Retroviral supernatant was then collected from the transfected Plat-E and used for T cell transduction.


title: WT dendritic cell control2


title: WT dendritic cell PAK5


title: WT dendritic cell PAK4


title: WT dendritic cell PAK1


title: WT dendritic cell PAK2


title: Arabidopsis seedlings (WT) with/without elicitor treatment (color swap)


title: WT dendritic cell PAK3


title: CF dendritic cell PAK6

description: Gene expression data from CF dendritic cell with Pseudosmonas aeruginosa infection

source_name: CF dendritic cell PAK

tag: dendritic cell control from CF mice with Pseudosmonas aeruginosa infection


title: CF dendritic cell PAK4


title: CF dendritic cell PAK5


title: WT dendritic cell control1


title: CF dendritic cell PAK2


title: CF dendritic cell control6

description: Gene expression data from CF dendritic cell control without Pseudosmonas aeruginosa infection

source_name: CF dendritic cell control

tag: dendritic cell control from CF mice without Pseudosmonas aeruginosa infection


title: CF dendritic cell PAK1


title: CF dendritic cell PAK3


title: CF dendritic cell control2


title: CF dendritic cell control5


status: Public on Sep 30 2008

city: Hamilton

first: Amy

middle: M

last: Palazzolo-Ballance

state: MT

address: 903 S. 4th Street

department: Rocky Mountain Laboratory

institute: NIH/NIAID

description: Gene expression data from_ACME and SCCmec double mutant, stationary phase, biological rep 3

hyb_protocol: Following fragmentation, cDNA were hybridized for 16 hr at 45C on a commercially available array.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Staphylococcus aureus

source_name: double mutant - sta rep3

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from total RNA (Affymetrix Prokaryotic Sample and Array Processing Protocol, Affymetrix).

growth_protocol: For microarray experiments, overnight cultures were diluted into 30 ml of TSB and incubated at 37C with shaking until grown to exponential or stationary growth phase.

extract_protocol: Total RNA was isolated by use of a Bio101 kit (Vista, CA) by the standard protocol with minor modification (e.g. use of Trizol reagent instead of RNApro solution).

treatment_protocol: samples were untreated


description: Gene expression data from_ACME and SCCmec double mutant, stationary phase, biological rep 1

source_name: double mutant - sta rep1


description: Gene expression data from_ACME mutant, exponential phase, biological rep 3

source_name: ACME mutant - exp rep3


title: CF dendritic cell control1


description: Gene expression data from_ACME mutant, stationary phase, biological rep 2

source_name: ACME mutant - sta rep2


description: Gene expression data from_ACME and SCCmec double mutant, stationary phase, biological rep 2

source_name: double mutant - sta rep2


description: Gene expression data from_ACME and SCCmec double mutant, exponential phase, biological rep 1

source_name: double mutant - exp rep1


description: Gene expression data from_ACME and SCCmec double mutant, exponential phase, biological rep 2

source_name: double mutant - exp rep2


description: Gene expression data from_SCCmec mutant, exponential phase, biological rep 3

source_name: SCCmec mutant - exp rep3


description: Gene expression data from_SCCmec mutant, stationary phase, biological rep 2

source_name: SCCmec mutant - sta rep2


description: Gene expression data from_SCCmec mutant, stationary phase, biological rep 1

source_name: SCCmec mutant - sta rep1


description: Gene expression data from_ACME mutant, exponential phase, biological rep 1

source_name: ACME mutant - exp rep1


description: Gene expression data from_ACME mutant, stationary phase, biological rep 1

source_name: ACME mutant - sta rep1


description: Gene expression data from_ACME and SCCmec double mutant, exponential phase, biological rep 3

source_name: double mutant - exp rep3


description: Gene expression data from_SCCmec mutant, stationary phase, biological rep 3

source_name: SCCmec mutant - sta rep3


description: Gene expression data from_ACME mutant, exponential phase, biological rep 2

source_name: ACME mutant - exp rep2


description: Gene expression data from_ACME mutant, stationary phase, biological rep 3

source_name: ACME mutant - sta rep3


description: Gene expression data from_SCCmec mutant, exponential phase, biological rep 1

source_name: SCCmec mutant - exp rep1


description: Gene expression data from_wild type, stationary phase, biological rep 3

source_name: wild type - sta rep3


description: Gene expression data from_wild type, stationary phase, biological rep 2

source_name: wild type - sta rep2


description: Gene expression data from_wild type, stationary phase, biological rep 1

source_name: wild type - sta rep1


description: Gene expression data from_SCCmec mutant, exponential phase, biological rep 2

source_name: SCCmec mutant - exp rep2


description: Gene expression data from_wild type, exponential phase, biological rep 1

source_name: wild type - exp rep1


description: Gene expression data from_wild type, exponential phase, biological rep 3

source_name: wild type - exp rep3


description: Gene expression data from_wild type, exponential phase, biological rep 2

source_name: wild type - exp rep2


title: Ventricle tissue at End-stage, biological replicate 3, technical replicate 3

city: Baltimore

first: Zhong

last: Gao

address: Ross 844 720 Rutland Avenue

institute: Johns Hopkins University

description: Gene expression data from ventricle tissue at tachycardia pacing End-stage

hyb_protocol: 16hrs at 45 C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual, 2004.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual, 2004.

data_processing: Image analysis using GCOS 1.4, using MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.

organism: Canis lupus familiaris

source_name: Ventricle tissue at tachycardia pacing End-stage

label_protocol: One round amplification protocol for total RNA following Affymetrix’ specifications using T7 promoter oligo dT primer for cDNA synthesis, and ENZO IVT kit (www.affymetrix.com, GeneChip Expression Analysis, Technical Manual, 2003).

growth_protocol: All the dogs in this experiment are male and age-matched.

extract_protocol: Myocardial RNA was prepared from canine ventricular tissues using Trizol reagent (GibcoBRL) and Qiagen RNeasy column (Qiagen).

treatment_protocol: HF was induced by rapid pacing from the RV following the protocols approved by Johns Hopkins University Animal Care and Use Committee. A VVI pacemaker (Medtronics) was implanted via a left lateral thoracotomy and the pacing lead was fixed to the RV epicardium under sterile conditions. Rapid pacing at 240 ppm was initiated 1 to 2 days after surgery. Rapid pacing was terminated at different time points, i.e. 3 days, 1 week, and 2 weeks for intermediate stages of HF progression. End stage HF was verified by hemodynamic measurements typically at 4 weeks of rapid pacing. Hearts were harvested by left lateral thoracotomy and immersed in ice-cold saline, tissue sections were quickly frozen in liquid nitrogen and were kept in -80C.

tag: tachycardia paced canine ventricle tissue


title: Ventricle tissue at End-stage, biological replicate 3, technical replicate 1


title: Ventricle tissue at End-stage, biological replicate 2, technical replicate 2


title: Ventricle tissue at End-stage, biological replicate 3, technical replicate 2


title: Ventricle tissue at End-stage, biological replicate 2, technical replicate 3


title: Ventricle tissue at End-stage, biological replicate 1, technical replicate 3


title: Ventricle tissue at Week-1, biological replicate 3, technical replicate 3

description: Gene expression data from ventricle tissue at tachycardia pacing Week-1

source_name: Ventricle tissue at tachycardia pacing Week-1


title: Ventricle tissue at End-stage, biological replicate 2, technical replicate 1


title: Ventricle tissue at Week-2, biological replicate 3, technical replicate 2

description: Gene expression data from ventricle tissue at tachycardia pacing Week-2

source_name: Ventricle tissue at tachycardia pacing Week-2


title: Ventricle tissue at Week-2, biological replicate 3, technical replicate 3


title: Ventricle tissue at Week-2, biological replicate 2, technical replicate 2


title: Ventricle tissue at Week-2, biological replicate 2, technical replicate 1


title: Ventricle tissue at Week-2, biological replicate 1, technical replicate 1


title: Ventricle tissue at Week-1, biological replicate 2, technical replicate 2


title: Ventricle tissue at End-stage, biological replicate 1, technical replicate 1


title: Ventricle tissue at Week-1, biological replicate 2, technical replicate 3


title: Ventricle tissue at Week-2, biological replicate 1, technical replicate 2


title: Ventricle tissue at Week-1, biological replicate 3, technical replicate 1


title: Ventricle tissue at Week-1, biological replicate 3, technical replicate 2


title: Ventricle tissue at Week-1, biological replicate 1, technical replicate 2


title: LPS&paeoniflorin(1ug/ml)_6h_rep2

description: The RAW264.7 macrophages were either treated with DMSO or with LPS in the presence or absence of albiflorin, paeoniflorin, or paeonol.

source_name: Raw264.7 macrophage cells treated with 6h of LPS in presence of paeoniflorin


title: Ventricle tissue at Week-2, biological replicate 3, technical replicate 1


title: Ventricle tissue at Week-2, biological replicate 2, technical replicate 3


title: Ventricle tissue at Week-2, biological replicate 1, technical replicate 3


title: Ventricle tissue at Week-1, biological replicate 1, technical replicate 3


title: Ventricle tissue at End-stage, biological replicate 1, technical replicate 2


title: Ventricle tissue at Day-3, biological replicate 3, technical replicate 2

description: Gene expression data from ventricle tissue at tachycardia pacing Day-3

source_name: Ventricle tissue at tachycardia pacing Day-3


title: Ventricle tissue at Week-1, biological replicate 1, technical replicate 1


title: Ventricle tissue at Day-3, biological replicate 3, technical replicate 3


title: Ventricle tissue at Week-1, biological replicate 2, technical replicate 1


title: Ventricle tissue at Day-3, biological replicate 3, technical replicate 1


title: Ventricle tissue at Day-0, biological replicate 3, technical replicate 3

description: Gene expression data from ventricle tissue at tachycardia pacing Day-0

source_name: Ventricle tissue at tachycardia pacing Day-0


title: Ventricle tissue at Day-0, biological replicate 1, technical replicate 1


title: Ventricle tissue at Day-3, biological replicate 2, technical replicate 1


title: Ventricle tissue at Day-0, biological replicate 2, technical replicate 2


title: Ventricle tissue at Day-3, biological replicate 1, technical replicate 3


title: Ventricle tissue at Day-0, biological replicate 1, technical replicate 2


title: Ventricle tissue at Day-0, biological replicate 3, technical replicate 2


title: Ventricle tissue at Day-3, biological replicate 2, technical replicate 2


title: Ventricle tissue at Day-3, biological replicate 1, technical replicate 1


title: Ventricle tissue at Day-0, biological replicate 2, technical replicate 3


title: Ventricle tissue at Day-3, biological replicate 2, technical replicate 3


title: Ventricle tissue at Day-0, biological replicate 2, technical replicate 1


title: Ventricle tissue at Day-3, biological replicate 1, technical replicate 2


title: 4374

city: Toronto

first: Irene

middle: L

last: Andrulis

state: ON

address: 600 University Avenue

department: Research

country: Canada

institute: Mount Sinai Hospital

hyb_protocol: Array hybridization and washing: Each of the labeled cDNA samples was combined with hybridization solution, which consisted of 5 μl of 10mg/ml tRNA (Roche), 5 μl of 10mg/ml Salmon Sperm DNA (Gibco), and 90 μl DIG Easy Hyb (Roche).  Mixture was incubated at 65oC for 2-5 minutes, cooled at room temperature for 5 minutes, and applied to human cDNA array slide and covered with coverslip.  Arrays were placed in hybridization chamber to prevent drying and incubated at 37oC overnight.   Hybridizations were carried out in duplicates using reverse labeling to avoid dye bias. Following overnight incubation, arrays were washed in 0.1X SSC-0.1% SDS for 5 minutes, and repeated 6 more times using fresh SSC+SDS solution each time.  Slides were then rinsed 5 times using 0.1X SSC, and dried by spinning at 700-1000 rpm for 15 minutes.

scan_protocol: All microarray slides were scanned using the GenePix 4000B scanner (Axon Instruments).  The PhotoMultiplier Tube (PMT) gain for each laser was adjusted to give an average ratio of Cy3 to Cy5 of 1.0.  Images were analyzed using the GenePix Pro 4.0 software (Axon Instruments).

data_processing: Pre-processing and Normalization: Pre-processing and normalization were carried out using R (http://cran.r-project.org) and the Bioconductor (http://www.bioconductor.org) package LIMMA (Smyth, 2005). Briefly, the foreground pixels were summarized by their mean and the background pixels were summarized by their median. For each spot, the foreground intensity was corrected by subtracting the background intensity. Clones are printed in duplicate side-by-side on the arrays. If the log2 ratio for one of the pair was missing because the background intensity exceeded the foreground intensity, the non-missing duplicate was imputed. As proposed by Yang et al. (2002), the log2 ratios were normalized by a within-array print-tip loess adjustment followed by a between-array scale adjustment. Poor quality spots as flagged by the GenePix image analysis software were excluded from the normalization. The log2 ratios were averaged across duplicate spots and across tumor replicates.

label_protocol: Labeling of cDNA targets: For Cy3/Cy5 coupling, cDNA was resuspended in 9 μl of 0.1M NaHCO3 (pH 9.0) and mixed with 1.25 μl of Cy3 or Cy5 (Amersham) that was resuspended with 18 μl of DMSO.  Following 45 minutes of incubation at room temperature, uncoupled Cy3/Cy5 was quenched by the addition of 4.5 μl of 4M hydroxylamine and incubated for 15 minutes at room temperature.  Removal of unincorporated and quenched dyes from cDNA was performed using High Pure PCR product Purification Kit (Qiagen).  Two differentially labeled cDNA (tumor and reference pool) were then combined and vacuumed-dried and resuspended in 5 μl of water (Sigma).

extract_protocol: RNA Extraction & Reverse Transcription: Total RNA from flash-frozen tumor samples was extracted using Trizol according to manufacturer’s instructions (Life Technologies).  The purity of RNA was confirmed by A260/A280 ratio of 1.8-2.2, while the integrity of RNA was verified by 1% agarose gel electrophoresis. RNA from each tumor sample, as well as reference RNA that is composed of 13 pooled cell lines, were reverse-transcribed to generate complementary DNA.  In brief, 5 μg of mRNA was first combined with 1.5 μl of 100 pmol/μl AncT mRNA primer (Qiagen), 8 μl of 5x first strand buffer, and 4 μl of 100 mM DTT, to a total volume of 34.35 μl, and incubated at 65oC for 5 minutes, followed by 47oC for 5 minutes.  While at 47oC, the following reagents were added to each of the reaction and were incubated for two hours:  1 μl of dGTP, dATP, dCTP mix (20 mM each), 1.3 μl of 5mM dTTP, 1.35 μl of 10 mM aa-dUTP, 2 μl of 200 units/μl superscript III reverse transcriptase (Invitrogen), in a total volume of 40 μl.  Each of the reactions were stopped and hydrolyzed by adding 4 μl of 50 mM EDTA and 2 μl of 10N NaOH and incubated at 65oC for 20 minutes, followed by neutralization with the addition of 4 μl of 5 M acetic acid.  Reaction purifications were performed using PCR purification kit (Qiagen) to remove all traces of tris, thus preventing reaction of the amine groups on tris with monofunctional NHS-ester of the Cyanine dye.  Samples were then vacuumed-dried, and stored at –20oC until ready for labeling.

tag: Mutation

tag: type

value: Ductal and No special type

tag: agedx

tag: grade

tag: Lymphatic Invasion

value: yes

tag: ER

value: negative

tag: PR

tag: NTERA-2 (Human testis cancer teratoma derived cell line), Hs578T (Human breast carcinosarcoma), HepG2 (Human Hepatoblastoma), Ht1080 (Human Fibrosarcoma), SW872 (Human Liposarcoma), T47D (Human mammary gland ductal carcinoma derived from pleural effusion), MCF-12A (Human mammary gland

value: epithelial mucin), Fetal Normal Muscle Cells, Colo-205 (Human colorectal adenocarcinoma), MOLT-4 (Human T lymphoblast acute lymphoblastic leukemia), RPMI 8226 (Human plasmocytoma myeloma), SK-MEL-28 (Human skin.  Malignant melanoma) ,SKOV3 (Human ovary adenocarcinoma)


title: 4472

value: IVS16+3 A-C

value: no


title: 4326

value: not available


title: Ventricle tissue at Day-0, biological replicate 1, technical replicate 3


title: 3435


title: 4080

value: equivocal

value: positive


title: Ventricle tissue at Day-0, biological replicate 3, technical replicate 1


title: 2172


title: 1834


title: 3627


title: 3242


title: IL-18 stimulated, in vitro differentiated MMC_rep4

status: Public on Sep 26 2008

city: Budapest

first: Zoltan

last: Wiener

address: Nagyvarad ter 4.

department: Dept of Genetics, Cell- and Immunobiology

country: Hungary

institute: Semmelweis University

description:
Gene expression profiling of IL-18 stimulated, in vitro differentiated mouse mucosal mast cells (MMC), replicate No4
fourth biological replicate out of four

hyb_protocol: Hybridization was carried out according to Agilent Two-Color Expression Microarray Protocol 5.5. Washing was done with Agilent Gene Expression Wash Buffer 1 and 2 and Stabilization and Drying Solution according to Agilent’s Protocol.

scan_protocol: Slides were scanned by Agilent Scanner and data were normalized by Feature Extraction 9.1 with default settings for two-color expression microarrays with 4x44K format (GE2_v5_91_0806).

data_processing: Data are the text file presented by Agilent Feature Extraction Software 9.1 with the above mentioned normalization.

source_name: Unstimulated MMC

label_protocol: cDNA and labelled cRNA synthesis was carried out according to Agilent Two-Color Expression Microarray Protocol 5.5. Washing was done with Agilent Gene Expression Wash Buffer 1 and 2 and Stabilization and Drying Solution according to Agilent’s Protocol. Slides were scanned by Agilent Scanner and data were normalized by Feature Extraction 9.1 with default settings for two-color expression microarrays with 4x44K format.

extract_protocol: Total RNA was isolated from cells and purified by the Qiagen RNeasy Mini Kit with on-column DNase digestion. The RNA quality was checked by Agilent Bioanalyzer.

tag: Cell (Balb/c mice) were cultured in the presence of SCF, IL-3, IL-9 and TGFbetaI for more than 4 weeks. The stimulation experiment lasted for 2 hours.

source_name: IL-18 stimulated MMC

tag: Cell (Balb/c mice) were cultured in the presence of SCF, IL-3, IL-9 and TGFbetaI for more than 4 weeks. The stimulation experiment lasted for 2 hours with 100 ng/ml IL-18.


title: 2528


title: 4324

description: 4324CY34324CY5Pool_12697659_24.02.04.gpr; 4324CY3PoolCY54324l_12683409_0012.gpr

value: present


title: 3078


title: 1693

description: 1693CY31693CY5Pool_12730333_5.5.04.gpr; 1693CY3PoolCY51693_12730334_5.5.04.gpr


title: IL-18 stimulated, in vitro differentiated MMC_rep3

description:
Gene expression profiling of IL-18 stimulated, in vitro differentiated mouse mucosal mast cells (MMC), replicate No3
third biological replicate out of four


title: Human primary TM cells expressing Adenivirus GFP

status: Public on Sep 25 2008

city: Durham

first: Vasantha

middle: P

last: Rao

state: NC

address: 2351 Erwin Rd

department: Ophthalmology

institute: Duke University Medical Center

description: Purchased from Stratagen Cat no: 740000

hyb_protocol: see series supplementary file

scan_protocol: Arrays were scanned with a GenePix 4000B scanner (Axon Instruments, Foster City, CA) and analyzed using GenePix Pro v4.0

data_processing: Agilent's GeneSpring GX 7.3.1 software

source_name: Total RNA from Human TM cells labeled with Cy-5 (red).

label_protocol: see series supplementary file

growth_protocol: Human primary trabecular meshwork cells were isolated from from 2-month-old donor eyes by collagenase IV digestion. Cells were cultured at 37°C under 5% CO2, in DMEM containing 10% FBS and penicillin (100 Units/ml)-streptomycin (100 µg/ml).

extract_protocol: Total RNA was extracted using RNeasy Micro Kit from Qiagen (Valencia, CA) as per manufacturers instructions. The quality and concentration of RNA was determined using the Nanodrop chip (Wilmington, DL) and the Agilent bioanalyzer (Agilent Technologies, Santa Clara, CA), respectively,

treatment_protocol: Passage- 4 cells were cultured to 80% confluence and infected with adenoviral vectors expressing either the GFP alone or RhoAV14/GFP for 48 hrs earlier and serum starved for 24 hrs prior to harvesting them.

tag: Primary cell cultures

source_name: Stratagen's Universal Human Reference RNA

tag: Comprised of 10 different cell lines for broad gene coverage on human microarrays


title: Human primary TM cells expressing Adenivirus GFP with Constitutively active RhoA

description: Purchased from Stratagen Cat no: 740000

source_name: Total RNA from Human TM cells labeled with Cy-5 (red)


title: IL-18 stimulated, in vitro differentiated MMC_rep1

description:
Gene expression profiling of IL-18 stimulated, in vitro differentiated mouse mucosal mast cells (MMC), replicate No1
first biological replicate out of four

tag: Cell (Balb/c mice) were cultured int he presence of SCF, IL-3, IL-9 and TGFbetaI for more than 4 weeks. The stimulation experiment lasted for 2 hours with 100 ng/ml IL-18.


title: IL-18 stimulated, in vitro differentiated MMC_rep2

description:
Gene expression profiling of IL-18 stimulated, in vitro differentiated mouse mucosal mast cells (MMC), replicate No2
second biological replicate out of four


title: SON WKY 4

status: Public on Sep 22 2008

city: Bristol

first: DAVID

last: MURPHY

state: AVON

address: Whitson Street

department: Medicine and Dentistry

country: United Kingdom

institute: University of Bristol

description: Sample represents the Supraoptic nucleus from 5 untreated Wistar-Kyoto rats

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: GCOS version 1.2

label: MessageAmpII aRNA Amplification kit (Ambion)

organism: Rattus norvegicus

source_name: Supraoptic nucleus

label_protocol: Protocol available at http://www.AMBION.com/catalog/CatNum.php?1753

extract_protocol: Tissue was dissected in an RNase free manner and stored in RNAlater (Ambion) at -20C for no more than 1 month. Homogenisation in QIAzol was conducted mechanically and the aqueous phase separated using a PLG column (Eppendorf). RNA was further purified using RNeasy minelute cleanup kit (Qiagen). RNA quality was confirmed using nanodrop and bioanylizer 2100 (Agilent).

tag: Strain

value: Wistar-Kyoto

tag: Gender

value: Male

tag: Age

value: 10-12 weeks

tag: Tissue

value: Hypothalamic supraoptic nucleus


title: PVN WISTAR CONTROL

description: Sample represents the paraventricular nucleus from 5 untreated Wistar rats

source_name: Paraventricular nucleus Wistar

value: Wistar

value: Hypothalamic Paraventricular nucleus


title: PVN WISTAR CONTROL 4


title: PVN WISTAR CONTROL 3


title: PVN WISTAR CONTROL 5


title: SON WKY 3


title: SON WKY 5


title: SON WKY 2


title: PVN WKY 3

description: Sample represents the Paraventricular nucleus from 5 untreated Wistar-kyoto rats

source_name: Paraventricular nucleus WKY


title: SON WKY

value: Hypothalamic Supraoptic nucleus


title: NIL WKY 5

description: Sample represents the Neurointermediate lobe of the Pituitary from 5 untreated Wistar-kyoto rats

source_name: Neurointermediate lobe

value: Neurointermediate lobe of the Pituitary


title: PVN WKY 5


title: PVN WKY


title: NIL WKY 2


title: PVN WKY 2


title: NIL WKY


title: PVN WKY 4


title: PVN WISTAR CONTROL 2


title: NIL WKY 4


title: NIL WKY 3


title: Normal (N-08_FF_04)

status: Public on Sep 18 2008

type: genomic

city: Houston

first: Ralf

last: Krahe

state: TX

address: 1515 Holcombe Blvd., Unit #1010

department: Cancer Genetics

institute: University of Texas M.D. Anderson Cancer Center

description: fresh frozen tissue

hyb_protocol: Following fragmentation, 90 ug of DNA were hybridized for 16 hr at 49C on 250K StyI mapping Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 7000.

data_processing: The data were analyzed with CNAG v2.0, AsCNAR and CNATv4.0.1.

molecule: genomic DNA

source_name: Human tumor tissue

label_protocol: Biotinylated DNA were prepared according to the standard Affymetrix protocol from 90 ug total DNA (250K StyI Mapping Asssay Technical Manual, 2006, Affymetrix).

extract_protocol: Protocol 1 and 2 are new DNA extraction protocols, protocol 3 is modified Qiagen extraction protocol and 4 is Qiagen DNA extraction protocol.

tag: Female, breast normal


title: Normal (N-06_PBL_04)

description: peripheral blood

tag: Female, peripheral blood


title: Normal (N-08_PBL_04)

description: peripheral blood


title: Normal (N-09_PBL_04)

description: peripheral blood


title: Normal (N-08_FF_03)

description: fresh frozen tissue


title: Normal (N-07_FF_04)

description: fresh frozen tissue


title: Normal (N-09_FF_04)

description: fresh frozen tissue


title: Normal (N-03_PBL_04)

description: peripheral blood


title: Normal (N-04_PBL_04)

description: peripheral blood


title: Normal (N-07_PBL_04)

description: peripheral blood


title: Tumor (T-02_FFPE_03)

description: formalin fixed parafin embedded tissue

tag: Female, primary breast tumor


title: Tumor (T-06_FF_03)

description: fresh frozen tissue


title: Tumor (T-03_FFPE_03)

description: formalin fixed parafin embedded tissue


title: Tumor (T-07_FFPE_03)

description: formalin fixed parafin embedded tissue


title: Tumor (T-06_FF_02)

description: fresh frozen tissue


title: Tumor (T-08_FF_03)

description: fresh frozen tissue


title: Normal (N-06_FF_03)

description: fresh frozen tissue


title: Tumor (T-01_FFPE_02)

description: formalin fixed parafin embedded tissue


title: Tumor (T-06_FFPE_03)

description: formalin fixed parafin embedded tissue


title: Tumor (T-08_FFPE_02)

description: formalin fixed parafin embedded tissue


title: Tumor (T-09_FFPE_03)

description: formalin fixed parafin embedded tissue


title: Tumor (T-05_FFPE_03)

description: formalin fixed parafin embedded tissue


title: Tumor (T-02_FFPE_02)

description: formalin fixed parafin embedded tissue


title: Normal (N-06_FF_04)

description: fresh frozen tissue


title: Tumor (T-08_FF_02)

description: fresh frozen tissue


title: Brain-cerebellum_subject3b_dye-swap

status: Public on Sep 16 2008

city: Birmingham

first: Jan

last: Dumanski

state: AL

department: Department of Genetics

institute: University of Alabama at Birmingham

hyb_protocol: The 32K slides were prehybridized in 5x SCC, 0.1% SDS at 45 ºC for at least one hour, washed with ddH20 and dried using compressed dust-free air. The dried pellets from the labeling steps were re-suspended in 50 µl of hybridization solution (50% Formamide, 4% SDS, 10 %, Dextran Sulfate, M.W. 500 000, 2 X SSC) and denatured for 5 min at 95°C, followed by incubation at 45°C for 2 h to block repetitive sequences. Subsequently, the probe mixture was applied to the slide surface, covered with a lifterslip (22x60mm, Erie Scientific, Portsmouth, NH) and hybridized at 45 °C for 20 hours in a slide chamber (Corning Inc. Life Sciences, Big Flats, NY). After hybridization the lifterslip was rinsed off using 1xPBS. Washing was performed in 25 % formamide, 2 X SSC, 0.1% SDS, at 45ºC, for 15 min, followed by 10 min in 1 X PBS at room temperature, and brief rinse in 0.2 X SSC. The array was immersed in deionized H2O and immediately dried using pressurized dust-free air.

scan_protocol: Image acquisition was performed using the GenePix 4000B scanner (Axon Instruments Inc, Union City, CA), and image analysis was carried out using the GenePixPro v6 software (Axon Instruments).

data_processing: We uploaded the GPR files from GenePix pro into a pearl script called colloactor. This script links the information about clones to the array position. It also uploads the raw data to the BASE platform. These raw data files are attached as tables. Filtering and normalization was done using the LCB Data-WareHouse (dw.lcb.uu.se). The filters applied on the raw data removed spots containing more than 5% oversaturated pixels, spots with low Signal-to-Noise Ratio (SNR<3) and spots automatically and manually flagged as bad, absent or not found in GenePixPro program. Normalization was done using a print-tip loess method.

source_name: Genomic DNA isolated from cerebellum of subject 3 labeled with Cy5-dCTP.

label_protocol: Labeling was done using 2 mcg DNA, according to the BioPrime® Array CGH Genomic Labeling System protocol supplied by the manufacturer (Invitrogen, Carlsbad, CA). We used CY3 dCTP and CY5 dCTP respectively (PA53021 and PA55021, GE Healthcare, Piscataway, NJ). The labeled DNA probes were mixed together and combined with 200 µg human Cot-1 DNA (Invitrogen, Carlsbad, CA) and dried using a vacufuge concentrator (Eppendorf, Westbury, NY).

extract_protocol: genomic DNA isolation with phenol extraction according to standard protocol (Sambrook, J., Fritsch, E. F. & Maniatis, T. Molecular cloning; a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1989)

value: male

value: brain-cerebellum

tag: Cause of death

value: suicide (hanging)

source_name: Genomic DNA isolated from cerebellum of subject 3 labeled with Cy3-dCTP.


title: Brain-cerebellum_subject3a_regular


title: Brain-cerebellum_subject3a_dye-swap


title: Brain-cerebellum_subject3b_regular


title: Tumor (T-05_FFPE_02)

description: formalin fixed parafin embedded tissue


title: Tumor (T-07_FF_03)

description: fresh frozen tissue


title: Brain-cerebellum_subject2a_dye-swap

source_name: Genomic DNA isolated from cerebellum of subject 2 labeled with Cy5-dCTP.

value: acute ethanol intoxication

source_name: Genomic DNA isolated from cerebellum of subject 2 labeled with Cy3-dCTP.


title: Brain-cerebellum_subject2a_regular


title: Brain-cerebellum_subject1b_dye-swap

source_name: Genomic DNA isolated from cerebellum of subject 1 labeled with Cy5-dCTP.

value: acute cardiovascular failure

source_name: Genomic DNA isolated from cerebellum of subject 1 labeled with Cy3-dCTP.


title: Brain-cerebellum_subject2b_dye-swap


title: Tumor (T-02_FFPE_01)

description: formalin fixed parafin embedded tissue


title: Brain-cerebellum_subject2b_regular


title: Brain-cerebellum_subject1b_regular


title: Brain-cerebellum_subject1a_regular


title: Brain-cerebellum_subject1a_dye-swap


title: Tumor (T-04_FFPE_03)

description: formalin fixed parafin embedded tissue


title: Tumor (T-05_FFPE_01)

description: formalin fixed parafin embedded tissue


title: Tumor (T-09_FFPE_01)

description: formalin fixed parafin embedded tissue


title: Tumor (T-03_FFPE_02)

description: formalin fixed parafin embedded tissue


title: Adrenal_gland_subject3_dye-swap

source_name: Genomic DNA isolated from adrenal gland of subject 3 labeled with Cy5-dCTP.

value: adrenal gland


title: Liver_subject3_dye-swap

source_name: Genomic DNA isolated from liver of subject 3 labeled with Cy5-dCTP.

value: liver


title: Tumor (T-06_FFPE_01)

description: formalin fixed parafin embedded tissue


title: Spleen_subject3_regular

source_name: Genomic DNA isolated from spleen of subject 3 labeled with Cy3-dCTP.

value: spleen


title: Tumor (T-08_FFPE_01)

description: formalin fixed parafin embedded tissue


title: Spleen_gland_subject3_dye-swap

source_name: Genomic DNA isolated from spleen of subject 3 labeled with Cy5-dCTP.


title: Tumor (T-06_FFPE_02)

description: formalin fixed parafin embedded tissue


title: Liver_subject3_regular

source_name: Genomic DNA isolated from liver of subject 3 labeled with Cy3-dCTP.


title: Tumor (T-01_FFPE_01)

description: formalin fixed parafin embedded tissue


title: Heart_subject3_dye-swap

source_name: Genomic DNA isolated from heart of subject 3 labeled with Cy5-dCTP.

value: heart


title: Kidney_subject3_regular

source_name: Genomic DNA isolated from kidney of subject 3 labeled with Cy3-dCTP.

value: kidney


title: Tumor (T-03_FFPE_01)

description: formalin fixed parafin embedded tissue


title: Kidney_subject3_dye-swap

source_name: Genomic DNA isolated from kidney of subject 3 labeled with Cy5-dCTP.


title: Tumor (T-04_FFPE_01)

description: formalin fixed parafin embedded tissue


title: Normal (N-05_PBL_04)

description: peripheral blood


title: Tumor (T-09_FFPE_02)

description: formalin fixed parafin embedded tissue


title: Heart_subject3_regular

source_name: Genomic DNA isolated from heart of subject 3 labeled with Cy3-dCTP.


title: Tumor (T-09_FF_03)

description: fresh frozen tissue


title: Tumor (T-07_FFPE_01)

description: formalin fixed parafin embedded tissue


title: Skeletal_muscle_m.iliopsoas_subject3_regular

source_name: Genomic DNA isolated from skeletal muscle (m.iliopsoas) of subject 3 labeled with Cy3-dCTP.

value: skeletal muscle (m.iliopsoas)


title: Skin_subject3_dye-swap

source_name: Genomic DNA isolated from skin of subject 3 labeled with Cy5-dCTP.

value: skin-neck


title: Smooth_muscle_colon_subject3_regular

source_name: Genomic DNA isolated from smooth muscle (colon) of subject 3 labeled with Cy3-dCTP.

value: smooth muscle (colon)

source_name: Genomic DNA isolated from cerebellum of subject 3 labeled with Cy5-dCTP.


title: Liver_subject2_dye-swap

source_name: Genomic DNA isolated from liver of subject 2 labeled with Cy5-dCTP.


title: Brain-cortex_subject3_dye-swap

source_name: Genomic DNA isolated from brain (cortex) of subject 3 labeled with Cy5-dCTP.

value: brain (cortex)

source_name: Genomic DNA isolated from cerebellum of subject 3 labeled with Cy3-dCTP.


title: Spleen_gland_subject2_dye-swap

source_name: Genomic DNA isolated from spleen of subject 2 labeled with Cy5-dCTP.

source_name: Genomic DNA isolated from cerebellum of subject 2 labeled with Cy3-dCTP.


title: Brain-cortex_subject3_regular

source_name: Genomic DNA isolated from brain (cortex) of subject 3 labeled with Cy3-dCTP.


title: Liver_subject2_regular

source_name: Genomic DNA isolated from liver of subject 2 labeled with Cy3-dCTP.

source_name: Genomic DNA isolated from cerebellum of subject 2 labeled with Cy5-dCTP.


title: Adrenal_gland_subject2_regular

source_name: Genomic DNA isolated from adrenal gland of subject 2 labeled with Cy3-dCTP.


title: Kidney_subject2_dye-swap

source_name: Genomic DNA isolated from kidney of subject 2 labeled with Cy5-dCTP.


title: Brain-pons_subject3_regular

source_name: Genomic DNA isolated from brain (pons) of subject 3 labeled with Cy3-dCTP.

value: brain (pons)


title: Brain-pons_subject3_dye-swap

source_name: Genomic DNA isolated from brain (pons) of subject 3 labeled with Cy5-dCTP.


title: Spleen_subject2_regular

source_name: Genomic DNA isolated from spleen of subject 2 labeled with Cy3-dCTP.


title: Skin_subject3_regular

source_name: Genomic DNA isolated from skin of subject 3 labeled with Cy3-dCTP.


title: Kidney_subject2_regular

source_name: Genomic DNA isolated from kidney of subject 2 labeled with Cy3-dCTP.


title: Smooth_muscle_colon_subject2_dye-swap

source_name: Genomic DNA isolated from smooth muscle (colon) of subject 2 labeled with Cy5-dCTP.


title: Smooth_muscle_colon_subject2_regular

source_name: Genomic DNA isolated from smooth muscle (colon) of subject 2 labeled with Cy3-dCTP.


title: Skeletal_muscle_m.iliopsoas_subject2_regular

source_name: Genomic DNA isolated from skeletal muscle (m.iliopsoas) of subject 2 labeled with Cy3-dCTP.


title: Brain-pons_subject2_dye-swap

source_name: Genomic DNA isolated from brain (pons) of subject 2 labeled with Cy5-dCTP.


title: Skeletal_muscle_m.iliopsoas_subject2_dye-swap

source_name: Genomic DNA isolated from skeletal muscle (m.iliopsoas) of subject 2 labeled with Cy5-dCTP.


title: Brain-cortex_subject2_regular

source_name: Genomic DNA isolated from brain (cortex) of subject 2 labeled with Cy3-dCTP.


title: Adrenal_gland_subject1_dye-swap

source_name: Genomic DNA isolated from adrenal gland of subject 1 labeled with Cy5-dCTP.

source_name: Genomic DNA isolated from cerebellum of subject 1 labeled with Cy3-dCTP.


title: Mucosa_stomach_subject1_regular

source_name: Genomic DNA isolated from mucosa (stomach) of subject 1 labeled with Cy3-dCTP.

value: mucosa (stomach)

source_name: Genomic DNA isolated from cerebellum of subject 1 labeled with Cy5-dCTP.


title: Heart_subject2_dye-swap

source_name: Genomic DNA isolated from heart of subject 2 labeled with Cy5-dCTP.

source_name: Genomic DNA isolated from cerebellum of subject 2 labeled with Cy3-dCTP.


title: Liver_subject1_dye-swap

source_name: Genomic DNA isolated from liver of subject 1 labeled with Cy5-dCTP.


title: Liver_subject1_regular

source_name: Genomic DNA isolated from liver of subject 1 labeled with Cy3-dCTP.


title: Heart_subject2_regular

source_name: Genomic DNA isolated from heart of subject 2 labeled with Cy3-dCTP.

source_name: Genomic DNA isolated from cerebellum of subject 2 labeled with Cy5-dCTP.


title: Spleen_subject1_regular

source_name: Genomic DNA isolated from spleen of subject 1 labeled with Cy3-dCTP.


title: Spleen_gland_subject1_dye-swap

source_name: Genomic DNA isolated from spleen of subject 1 labeled with Cy5-dCTP.


title: Brain-cortex_subject2_dye-swap

source_name: Genomic DNA isolated from brain (cortex) of subject 2 labeled with Cy5-dCTP.


title: Brain-pons_subject2_regular

source_name: Genomic DNA isolated from brain (pons) of subject 2 labeled with Cy3-dCTP.


title: Smooth_muscle_colon_subject1_dye-swap

source_name: Genomic DNA isolated from smooth muscle (colon) of subject 1 labeled with Cy5-dCTP.


title: Adrenal_gland_subject1_regular

source_name: Genomic DNA isolated from adrenal gland of subject 1 labeled with Cy3-dCTP.


title: Kidney_subject1_dye-swap

source_name: Genomic DNA isolated from kidney of subject 1 labeled with Cy5-dCTP.


title: Skin_subject2_dye-swap

source_name: Genomic DNA isolated from skin of subject 2 labeled with Cy5-dCTP.


title: Heart_subject1_regular

source_name: Genomic DNA isolated from heart of subject 1 labeled with Cy3-dCTP.


title: Adrenal_gland_subject2_dye-swap

source_name: Genomic DNA isolated from adrenal gland of subject 2 labeled with Cy5-dCTP.


title: Smooth_muscle_colon_subject1_regular

source_name: Genomic DNA isolated from smooth muscle (colon) of subject 1 labeled with Cy3-dCTP.

source_name: Genomic DNA isolated from cerebellum of subject 1 labeled with Cy5-dCTP.


title: Skeletal_muscle_m.iliopsoas_subject1_dye-swap

source_name: Genomic DNA isolated from skeletal muscle (m.iliopsoas) of subject 1 labeled with Cy5-dCTP.

source_name: Genomic DNA isolated from cerebellum of subject 1 labeled with Cy3-dCTP.


title: Adrenal_gland_subject3_regular

source_name: Genomic DNA isolated from adrenal gland of subject 3 labeled with Cy3-dCTP.

source_name: Genomic DNA isolated from cerebellum of subject 3 labeled with Cy5-dCTP.


title: Kidney_subject1_regular

source_name: Genomic DNA isolated from kidney of subject 1 labeled with Cy3-dCTP.


title: Brain-cortex_subject1_dye-swap

source_name: Genomic DNA isolated from brain (cortex) of subject 1 labeled with Cy5-dCTP.


title: Brain-pons_subject1_regular

source_name: Genomic DNA isolated from brain (pons) of subject 1 labeled with Cy3-dCTP.


title: Skeletal_muscle_m.iliopsoas_subject1_regular

source_name: Genomic DNA isolated from skeletal muscle (m.iliopsoas) of subject 1 labeled with Cy3-dCTP.


title: Heart_subject1_dye-swap

source_name: Genomic DNA isolated from heart of subject 1 labeled with Cy5-dCTP.


title: Skeletal_muscle_m.iliopsoas_subject3_dye-swap

source_name: Genomic DNA isolated from skeletal muscle (m.iliopsoas) of subject 3 labeled with Cy5-dCTP.

source_name: Genomic DNA isolated from cerebellum of subject 3 labeled with Cy3-dCTP.


title: Brain-cortex_subject1_regular

source_name: Genomic DNA isolated from brain (cortex) of subject 1 labeled with Cy3-dCTP.


title: Smooth_muscle_colon_subject3_dye-swap

source_name: Genomic DNA isolated from smooth muscle (colon) of subject 3 labeled with Cy5-dCTP.


title: Skin_subject1_dye-swap

source_name: Genomic DNA isolated from skin of subject 1 labeled with Cy5-dCTP.


title: Brain-pons_subject1_dye-swap

source_name: Genomic DNA isolated from brain (pons) of subject 1 labeled with Cy5-dCTP.


title: Primary graft dysfunction case 90

status: Public on Sep 15 2008

first: Masaki

last: Anraku

state: Ontario

address: 101 College Street, TMDT 2-816

department: Surgery

institute: Toronto General Research Institute

description: Patients with PGD

hyb_protocol: The reaction mixture was heated to 65°C for 5 minutes and then placed at 42°C for 5 minutes. Subsequently, reverse transcription was performed at 42°C for 2 hours by adding 2 µl of reverse transcriptase (Superscript II, Life Technologies, Inc., Burlington, Canada) to each sample. RNA was hydrolyzed by adding 4 µl of 50 mM EDTA and 2 µl of 10 N NaOH, and then incubated at 65°C for 20 minutes. Samples were neutralized with 4 µl of 50 M of acetic acid and 50 µl of isopropanol. At this point, the two reactions to be hybridized to the same slide (i.e. control and experimental) were combined together. Air dried pellets of labeled cDNA were obtained after removing isopropanol; the samples were then resuspended with 5 µl of distilled water. Samples were resuspended in 100 µl of DIGeasy hybridization buffer (Roche, Basel, Switzerland) combined with 5 µl of 10 mg/ml yeast tRNA (Life Technologies, Inc.) and 5 µl of 10 mg/ml salmon sperm (boiled 10 minutes prior to use), denatured at 65°C for 2 minutes, then hybridized to the arrays overnight at 37°C in humid hybridization chambers. Arrays were washed next day, three times for 15 minutes each at 50°C in slide staining boxes containing pre-warmed 1× SSC, 0.1% SDS, and then rinsed two times with 1× SSC. Slides were dried by centrifugation at 1000 rpm for 5 minutes.

scan_protocol: Hybridized arrays were scanned using a GenePix 4000 scanner (Axon Instruments Inc., Union City, CA), and fluorescent images were analyzed with GenePix Pro version 5.0 (Molecular Devices Corp., Sunnywale, CA).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Microarray Data Analysis System version 2.19 (The Institute for Genomic Research) was used.

source_name: Total RNA from human donor lung tissues labeled with Cyanine-5 (red).

label_protocol: Total RNA was added to 8 µl of 5× first strand reaction buffer, 0.75 µl of 200 µM AncT mRNA primer (5’-T20VN-3’) and 4 µl of 0.1 M DTT. Three µl of 20 mM ddNTP (dATP, dGTP, and dTTP mix), 1 µl of 2 mM dCTP, 1 ng of control RNA and 1 µl of 1 mM Cyanine 3 or Cyanine 5 dCTP were added to each RNA sample to a total volume of 40 µl in the dark.

extract_protocol: Total RNA (10 μg) was prepared from lung tissue sample using Trizol Reagent (Invitrogen, Carlsbad, CA) and further purified using an RNeasy kit (Qiagen, Valencia, CA) with a DNase treatment (RNase-free DNase Set, Qiagen) according to the manufacturer’s instructions.

tag: Human lung

tag: End cold ischemic period

source_name: Human Universal Reference RNA (Stratagene), labeled with Cyanine-3 (green).

tag: reference RNA


title: Primary graft dysfunction case 130

description: Patients with PGD


title: Primary graft dysfunction case 293

description: Patients with PGD


title: Primary graft dysfunction case 127

description: Patients with PGD


title: Primary graft dysfunction case 27

description: Patients with PGD


title: Control (Good outcome) -matched to 121_PGD_2

description: Patients without PGD


title: Skin_subject2_regular

source_name: Genomic DNA isolated from skin of subject 2 labeled with Cy3-dCTP.

source_name: Genomic DNA isolated from cerebellum of subject 2 labeled with Cy5-dCTP.


title: Control (Good outcome) -matched to 293_PGD_2

description: Patients without PGD


title: Primary graft dysfunction case 138

description: Patients with PGD


title: Control (Good outcome) -matched to 27_PGD_2

description: Patients without PGD


title: Primary graft dysfunction case 50

description: Patients with PGD


title: Mucosa_stomach_subject1_dye-swap

source_name: Genomic DNA isolated from mucosa (stomach) of subject 1 labeled with Cy5-dCTP.

source_name: Genomic DNA isolated from cerebellum of subject 1 labeled with Cy3-dCTP.


title: Primary graft dysfunction case 237

description: Patients with PGD


title: Pst mutant K3 exp. 3

city: St-Hyacinthe

first: Sébastien

last: Crépin

state: Québec

address: 3200 Sicotte

department: Microbiologie et pathologie

institute: Université de Montréal

description: The cDNA of the K3 strain from experience 3 was hybridized onto the GeneChip.

hyb_protocol: Hybridization was carried out at McGill University & Genome Quebec Innovation Centre according to Affymetrix recommendation (Affymetrix Expression Manual Section 3 701029 rev. 4).

scan_protocol: Scan procedure was carried out at McGill University & Genome Quebec Innovation Centre according to Affymetrix recommendation (Affymetrix Expression Manual Section 3 701029 rev. 4).

data_processing: Data were processed using the FlexArray software (Blazejczyk, M., M. Miron and R. Nadon. 2007. FlexArray: A statistical data analysis software for gene expression microarrays. Genome Quebec, Montreal, Canada. Genome Quebec, Montreal, Canada). Raw data were normalized using the RMA algorithm and log2 were generated. The expression value was generated by subtracting the mean value of each replicate of the mutant strain by wild-type strain.

organism: Escherichia coli

source_name: Pst mutant (K3) strain experiment 3

label_protocol: Fragmented cDNA was 3’ biotynylated using GeneChip DNA Labelling Reagent, 7.5 mM (Affymetrix, Santa Clara, CA) and 60 U of Terminal Deoxynucleotidyl Transferase (Promega, Madison, WI) at 37°C for 60 min, as recommended by Affymetrix (www.affymetrix.com). The reaction was stopped by adding 2 µl of 0.5 M EDTA (Sigma) to the reaction mix.

extract_protocol: An overnight culture grown at 37°C was diluted 100-fold into 5 ml of LB broth and was allowed to grow to mid-log phase (OD600 0,6). Cultures were centrifuged and RNAs were isolated by using the RiboPure™-Bacteria Kit (Ambion, Austin, TX), according to the manufacturer’s recommendations, with the exception that the DNAse 1 treatment was performed twice.

tag: E. coli serotype O78:K80:H9, K3 strain grown in LB media [LB broth, per liter, is composed of 10 g of Bacto tryptone, 5 g of yeast extract, 10 g of NaCl and the pH is adjusted to 7.5 by 10 N of NaOH].


title: Pst mutant K3 exp. 1

description: The cDNA of the K3 strain from experience 1 was hybridized onto the GeneChip.

source_name: Pst mutant (K3) strain experiment 1

tag: E. coli serotype O78:K80:H9, K3 strain grown in LB media [LB broth, per liter, is composed of 10 g of Bacto tryptone, 5 g of yeast extract, 10 g of NaCl and the pH is adjusted to 7.5 by 10 N of NaOH]


title: Skin_subject1_regular

source_name: Genomic DNA isolated from skin of subject 1 labeled with Cy3-dCTP.

source_name: Genomic DNA isolated from cerebellum of subject 1 labeled with Cy5-dCTP.


title: Pst mutant K3 exp. 4

description: The cDNA of the K3 strain from experience 4 was hybridized onto the GeneChip.

source_name: Pst mutant (K3) strain experiment 4


title: Primary graft dysfunction case 279

description: Patients with PGD


title: Primary graft dysfunction case 121

description: Patients with PGD


title: Control (Good outcome) -matched to 127_PGD_2

description: Patients without PGD


title: Pst mutant K3 exp. 2

description: The cDNA of the K3 strain from experience 2 was hybridized onto the GeneChip.

source_name: Pst mutant (K3) strain experiment 2


title: Wild-type strain chi7122 exp. 4

description: The cDNA of the chi7122 strain from experience 4 was hybridized onto the GeneChip.

source_name: Wild-type strain chi7122 experiment 4

tag: E. coli serotype O78:K80:H9, avian pathogenic strain chi7122 grown in LB media [LB broth, per liter, is composed of 10 g of Bacto tryptone, 5 g of yeast extract, 10 g of NaCl and the pH is adjusted to 7.5 by 10 N of NaOH]


title: Wild-type strain chi7122 exp. 1

description: The cDNA of the chi7122 strain from experience 1 was hybridized onto the GeneChip.

source_name: chi7122 exp. 1


title: Wild-type strain chi7122 exp. 2

description: The cDNA of the chi7122 strain from experience 2 was hybridized onto the GeneChip.

source_name: Wild-type strain chi7122 experiment 2


title: Control (Good outcome) -matched to 90_PGD

description: Patients without PGD


title: Control (Good outcome) -matched to 293_PGD_1

description: Patients without PGD


title: Wild-type strain chi7122 exp. 3

description: The cDNA of the chi7122 strain from experience 3 was hybridized onto the GeneChip.

source_name: Wild-type strain chi7122 experiment 3


title: Control (Good outcome) -matched to 121_PGD_1

description: Patients without PGD


title: Control (Good outcome) -matched to 27_PGD_1

description: Patients without PGD


title: Control (Good outcome) -matched to 237_PGD_1

description: Patients without PGD


title: Control (Good outcome) -matched to 50_PGD

description: Patients without PGD


title: Control (Good outcome) -matched to 130_PGD

description: Patients without PGD


title: Control (Good outcome) -matched to 279_PGD

description: Patients without PGD


title: Control (Good outcome) -matched to 237_PGD_2

description: Patients without PGD


title: Control (Good outcome) -matched to 138_PGD_2

description: Patients without PGD


title: Control (Good outcome) -matched to 138_PGD_1

description: Patients without PGD


title: Control (Good outcome) -matched to 127_PGD_1

description: patients without PGD


title: wt SF8300 grown in CCY media to stationary phase biological replicate 2

status: Public on Sep 12 2008

description: gene expression data from_wtSF8300 grown in CCY media to stationary phase biological rep 2

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 40C on our custom Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus.

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis with a scale filter for Se genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: wt8300 CCY sta rep2

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Overnight cultures of bacteria were diluted 1:200 into 20 ml of either TSB or CCY media and cultured to exponential (exp, OD600 = 1.0) or stationary (sta, OD600 = 2.0) phases of growth

extract_protocol: Total RNA was isolated by use of an RNeasy Mini Kit (Qiagen) recommended by a standard protocol.

treatment_protocol: no treatments were performed


title: wt SF8300 grown in CCY media to stationary phase biological replicate 3

description: gene expression data from_wtSF8300 grown in CCY media to stationary phase biological rep 3

source_name: wt8300 CCY sta rep3


title: wt SF8300 grown in TSB media to stationary phase biological replicate 3

description: gene expression data from_wtSF8300 grown in TSB media to stationary phase biological rep 3

source_name: wt8300 TSB sta rep 3


title: wt SF8300 grown in TSB media to stationary phase biological replicate 1

description: gene expression data from_wtSF8300 grown in TSB media to stationary phase biological rep 1

source_name: wt8300 TSB sta rep 1


title: PVL mutant in SF8300 grown in CCY media to stationary phase biological replicate 3

description: gene expression data from_mutSF8300 grown in CCY media to stationary phase biological rep 3

source_name: mut8300 CCY sta rep3


title: PVL mutant in SF8300 grown in TSB media to exponential phase biological replicate 2

description: gene expression data from_mutSF8300 grown in TSB media to exponential phase biological rep 2

source_name: mut8300 TSB log rep2


title: wt SF8300 grown in CCY media to stationary phase biological replicate 1

description: gene expression data from_wtSF8300 grown in CCY media to stationary phase biological rep 1

source_name: wt8300 CCY sta rep1


title: PVL mutant in SF8300 grown in TSB media to stationary phase biological replicate 3

description: gene expression data from_mutSF8300 grown in TSB media to stationary phase biological rep 3

source_name: mut8300 TSB sta rep 3


title: wt SF8300 grown in TSB media to exponential phase biological replicate 3

description: gene expression data from_wtSF8300 grown in TSB media to exponential phase biological rep 3

source_name: wt8300 TSB log rep3


title: wt SF8300 grown in TSB media to stationary phase biological replicate 2

description: gene expression data from_wtSF8300 grown in TSB media to stationary phase biological rep 2

source_name: wt8300 TSB sta rep 2


title: PVL mutant in SF8300 grown in TSB media to exponential phase biological replicate 3

description: gene expression data from_mutSF8300 grown in TSB media to exponential phase biological rep 3

source_name: mut8300 TSB log rep3


title: PVL mutant in SF8300 grown in TSB media to stationary phase biological replicate 2

description: gene expression data from_mutSF8300 grown in TSB media to stationary phase biological rep 2

source_name: mut8300 TSB sta rep 2


title: PVL mutant in SF8300 grown in TSB media to exponential phase biological replicate 1

description: gene expression data from_mutSF8300 grown in TSB media to exponential phase biological rep 1

source_name: mut8300 TSB log rep1


title: wt SF8300 grown in TSB media to exponential phase biological replicate 2

description: gene expression data from_wtSF8300 grown in TSB media to exponential phase biological rep 2

source_name: wt8300 TSB log rep2


title: PVL mutant in MW2 grown in TSB media to stationary phase biological replicate 1

description: gene expression data from_mutMW2 grown in TSB media to stationary phase biological rep 1

source_name: mutMW2 TSB sta rep1


title: PVL mutant in SF8300 grown in CCY media to stationary phase biological replicate 2

description: gene expression data from_mutSF8300 grown in CCY media to stationary phase biological rep 2

source_name: mut8300 CCY sta rep2


title: PVL mutant in MW2 grown in CCY media to stationary phase biological replicate 3

description: gene expression data from_mutMW2 grown in CCY media to stationary phase biological rep 3

source_name: mutMW2 CCY sta rep3


title: PVL mutant in SF8300 grown in TSB media to stationary phase biological replicate 1

description: gene expression data from_mutSF8300 grown in TSB media to stationary phase biological rep 1

source_name: mut8300 TSB sta rep 1