title: JY_met1whole_polyA_02_F0333_11162005.CEL

city: La Jolla

first: Joseph

middle: R.

last: Ecker

address: 10010 N. Torrey Pines Road

department: Genomic Analysis Laboratory

institute: The Salk Institute

description: Arabidopsis thaliana (ecotype Columbia) seeds were surface sterilized in 75% Ethanol 10 min, rinsed in distilled water. The seeds were cold-treated at 4 degrees C for 2 days and then incubated in the light for 40 days at 25 degrees C. Whole plant and mature leaves were collected from mature Arabidopsis plants (40 days old) which were grown as described in the Arabidopsis Biological Resources Center manual (ABRC; http://www.biosci.ohio-state.edu/~plantbio/Facilities/abrc/abrchome.htm).Total RNA was isolated from whole plant tissue and leaves using the Qiagen RNeasy kit (Valencia,CA) according to the manufacturer's instructions with DNase I treatment step. The quality and quantity of RNA isolated was checked by both gel electrophoresis and spectrophotometry. Five micro g total RNA was converted into double-stranded cDNA using Affymetrix T7-oligo(dT) primers. Biotin-labeled cRNA was generated by in vitro transcription reactions, fragmented, and then approximately 15 micro g of fragmented cRNA were hybridized to the tiling arrays according to Affymetrix (Santa Clara, CA) instructions. The arrays were washed and stained using an Affymetrix fluidics station as instructed in the manufacturer's user manual. CELTM files from scanned arrays were used for further analysis by TileMap software.

hyb_protocol: Whole Genome Tiling Array  was hybridized for 16 hrs, washed and stained with a streptavidin-phycoerythrin conjugate on the Affymetrix Fluidics Station 400 according to the standard Affymetrix protocol.

scan_protocol: Whole Genome Tiling array were scanned on Affymetrix scanner G7

data_processing: The following procedure was used to process and analyze tiling microarray data for RNA expression and DNA methylation. First, CEL files of the each three biological replicate (total 6 CEL files) within genotype comparison (e.g., comparison between wt and __t1 of poly-A RNA profiling) were subject to quantile normalization. Next, to identify significant difference regions between wt and mutant, probe-level t-statistics was calculated using a recently proposed method (1). Regions statistically different between two groups were identified using the Hidden Markov Models (HMM) option. 1. H. Ji and W. H. Wong, Bioinformatics 21, 3629-3636 (2005).

organism: Arabidopsis thaliana

source_name: Whole plant

extract_protocol: total RNA was isolated from whole plant tissues using RNAeasy kit following instructions from the manufacturer (QIAGEN)

treatment_protocol: Untreated

tag: Strain;met1 mutant on colmbia back ground segregated from heterozygote, Tissue; whole plant w/o root, Age; 40days, Growth; on soil under continuous light condition


title: CML-BM 2

status: Public on Aug 17 2006

type: RNA

city: Duesseldorf

first: Michael

last: Rosskopf

address: Universitaetsstrasse 1

department: Bioinformatics

country: Germany

institute: University of Duesseldorf

description: bone marrow CD34+ cells

data_processing: Using the affy package of functions of statistical scripting language 'R' integrated into the Bioconductor project data from cel files of each sample were normalized by variance stabilizing transformations (VSN) Ref.: Huber W, von Heydebreck A, Sultmann H, et al. Bioinformatics 2002;18:96-104.

label: Biotin/Streptavidin-PE

molecule: total RNA

organism: Homo sapiens

source_name: bone marrow

tag: age	42

tag: gender	female

tag: disease	CML

tag: disease phase	chronic phase

tag: previous therapy	no

tag: bcr-abl/G6PDH ratio (%)	5.4

tag: leukocyte count (/nl)	180

tag: hemoglobin (g/dl)	12.1

tag: platelet count (/nl)	476


title: CML-BM 1

description: bone marrow CD34+ cells

tag: age	26

tag: bcr-abl/G6PDH ratio (%)	9.3

tag: leukocyte count (/nl)	25.7

tag: hemoglobin (g/dl)	13.9

tag: platelet count (/nl)	915


title: Normal-BM 8

description: bone marrow CD34+ cells

tag: age	34

tag: gender	male

tag: disease	healthy control

tag: disease phase

tag: bcr-abl/G6PDH ratio (%)	n.a.

tag: leukocyte count (/nl)	6.3

tag: hemoglobin (g/dl)	14.5

tag: platelet count (/nl)	293


title: Platelet activating factor receptor and innate immunity: 1601186017644

city: San Antonio

first: Deepak

last: Kaushal

state: TX

address: 8715 W Military Dr

department: HPI

country: USA

institute: Texas Biomedical Research Institute

description: Replicate two: differential expression analysis of CW treatment on RBEC6 cells

organism: Rattus norvegicus

source_name: RBCEC Replicate 2

extract_protocol: Qiagen RNeasy

tag: cy3 labeled aa-cDNA from RBCEC Replicate 2 RNA

source_name: RBCEC + CW Replicate 2

tag: cy5 labeled aa-cDNA from RBCEC + CW Replicate 2 RNA


title: Plate activating factor receptor and innate immunity: 16011866017643

description: Replicate one: differential expression analysis of CW treatment on RBEC6 cells

source_name: RBCEC Replicate 1

tag: Cy3 labeled aa-cDNA from RBCEC Replicate 1 RNA

source_name: RBCEC + CW Replicate 1 RNA

tag: Cy5 labeled aa-cDNA from RBCEC + CW Replicate 1 RNA


title: JY_tripleWhole_polyA_03_F0461_22022006.CEL

state: CA

label: biotin

tag: Strain;drm1 drm2 cmt3 mutant on colmbia back ground segregated from heterozygote, Tissue; whole plant w/o root, Age; 40days, Growth; on soil under continuous light condition


title: ORMES6_biological repB

city: Beaverton

first: James

middle: Anthony

last: Byrne

state: OR

address: 505 NW 185th Ave

department: Reproductive Sciences

institute: ONPRC

description: Probe level measurements produced by Affymetrix Microarray Suite 5.0. Analysis performed at level of raw signal. (See Affymetrix Microarray Suite 5.0 reference on web site for description).

scan_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001).Scanning Hardware – HP GeneArray Scanner

data_processing: MAS 5.0; Data was normalized with Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001)

label: Biotin

organism: Macaca mulatta

source_name: Rhesus monkey embryonic stem cell lines ORMES6B

growth_protocol: ORMES cells were grown at 37°C in 5% CO2 atmosphere on mitotically inactivated mouse embryonic fibroblasts (MEF) feeder cells in Dulbecco’s Modified Eagle’s Medium/F12 (DMEM/F12) (Invitrogen) supplemented with 15% foetal bovine serum (FBS) (Hyclone), 0.1 mM ß-mercaptoethanol (Sigma), 1% nonessential amino acids (Invitrogen), 4ng/ml FGF2, 2 mM L-glutamine (Invitrogen) and a pH of 7.2 (altered with 4N NaOH). ES cell colonies were manually passaged every 4-5 days.

extract_protocol: Total RNA was isolated using the Invitrogen RNA purification kit (Cat No.12183-018) with the optional DNase I treatment.

treatment_protocol: Embryonic stem cells with good morphology were manually removed from culture for total RNA purification.

tag: Undifferentiated rhesus monkey Oregon Rhesus Macaque Embryonic Stem (ORMES) cell line 6, biological replicate B (passage 41).


title: Normal-BM 7

description: bone marrow CD34+ cells

tag: age	24

tag: gender	female

tag: previous therapy	no

tag: leukocyte count (/nl)	5.2

tag: hemoglobin (g/dl)	12.5

tag: platelet count (/nl)	235


title: Normal-BM 6

description: bone marrow CD34+ cells

tag: age	31

tag: gender	male

tag: disease	healthy control

tag: disease phase

tag: leukocyte count (/nl)	8.3

tag: hemoglobin (g/dl)	14.9

tag: platelet count (/nl)	269


title: Normal-BM 5

description: bone marrow CD34+ cells

tag: age	43

tag: bcr-abl/G6PDH ratio (%)	n.a.

tag: leukocyte count (/nl)	6.8

tag: hemoglobin (g/dl)	14

tag: platelet count (/nl)	311


title: Platelet activated factor receptor and innate immunity: 251186821692

description: Replicate two: differential expression analysis of CW vs Lyt44 treatment

source_name: Lyt44 Replicate 3

tag: Cy3 labeled cDNA from Lyt44 Replicate 3 RNA

source_name: CW Replicate 2

tag: Cy5 labeled cDNA from CW Replicate 3 RNA


title: JY_met1Whole_polyA_03_F0451_10012006.CEL

tag: Strain;met1 mutant on colmbia back ground segregated from heterozygote, Tissue; whole plant w/o root, Age; 40days, Growth; on soil under continuous light condition


title: ORMES6_biological repA

hyb_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001)

source_name: Rhesus monkey embryonic stem cell lines ORMES6A

tag: Undifferentiated rhesus monkey Oregon Rhesus Macaque Embryonic Stem (ORMES) cell line 6, biological replicate A (passage 41).


title: Normal-BM 4

description: bone marrow CD34+ cells

tag: age	29

tag: gender	female

tag: previous therapy	no

tag: leukocyte count (/nl)	7.3

tag: hemoglobin (g/dl)	12.9

tag: platelet count (/nl)	257


title: Normal-BM 3

description: bone marrow CD34+ cells

tag: age	54

tag: disease	healthy control

tag: disease phase

tag: leukocyte count (/nl)	5.1

tag: hemoglobin (g/dl)	13.8

tag: platelet count (/nl)	284


title: ORMES10

source_name: Rhesus monkey embryonic stem cell lines ORMES10

label_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001)

tag: Undifferentiated rhesus monkey Oregon Rhesus Macaque Embryonic Stem (ORMES) cell line 10.


title: Platelet activating factor receptor and innate immunity

description: Replicate one: differential expression analysis of CW vs Lyt1 treatment

source_name: Lyt44 Replicate 1

tag: Cy3 labeled aa-cDNA from Lyt44 Replicate 1 RNA

source_name: CW Replicate 1

tag: Cy5 labeled aa-cDNA from CW Replicate 1 RNA


title: Platelet activating factor receptor and innate immunity: 251186821691

source_name: Lyt44 Replicate 2

tag: Cy3 labeled aa-cDNA from Lyt44 replicate 2

tag: Cy5 labeled aa-cDNA from CW replicate 2


title: Normal-BM 1

description: bone marrow CD34+ cells

tag: age	24

tag: gender	male

tag: bcr-abl/G6PDH ratio (%)	n.a.

tag: leukocyte count (/nl)	4.7

tag: hemoglobin (g/dl)	14.2

tag: platelet count (/nl)	192


title: ORMES13

source_name: Rhesus monkey embryonic stem cell lines ORMES13

tag: Undifferentiated rhesus monkey Oregon Rhesus Macaque Embryonic Stem (ORMES) cell line 13.


title: Normal-BM 2

description: bone marrow CD34+ cells

tag: age	26

tag: disease	healthy control

tag: previous therapy	no

tag: leukocyte count (/nl)	6.1

tag: hemoglobin (g/dl)	14.6

tag: platelet count (/nl)	217


title: GFP control rep 2

status: Public on Aug 16 2006

city: St. Louis

first: Brian

last: Finck

state: MO

address: 660 S. Euclid Ave

institute: Washington University

description: control for lipin overexpressing

organism: Mus musculus

source_name: liver

tag: adult male C57Bl6 mouse overexpressing green fluorescent protein as a control for lipin overexpression


title: Pooled differentiated EBs

description: Probe level measurements produced by Affymetrix Microarray Suite 5.0.  Analysis performed at level of raw signal.  (See Affymetrix Microarray Suite 5.0 reference on web site for description).

scan_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001). Scanning Hardware – HP GeneArray Scanner

source_name: Rhesus monkey pooled differentiated EBs, 30 days spontaneous differentiation

growth_protocol: ORMES ES cells were grown at 37°C in 5% CO2 atmosphere on mitotically inactivated mouse embryonic fibroblasts (MEF) feeder cells in Dulbecco’s Modified Eagle’s Medium (DMEM/F12) (Invitrogen) supplemented with 15% foetal bovine serum (FBS) (Hyclone), 0.1 mM ß-mercaptoethanol (Sigma), 1% nonessential amino acids (Invitrogen), and 2 mM L-glutamine (Invitrogen), 4ng/ml FGF2, and with a 7.2 pH with NaOH. ES cell colonies were manually passaged every 4-5 days.  To induce embryoid body (EB) formation, rhesus monkey ESCs were manually harvested and incubated in ultra-low adhesion dishes for 30 days in ES culture media without FGF2.

treatment_protocol: EB formation for 1 week in suspension, then culture in gelatin coated dishes for 30 days with the removal of FGF2 from culture media.

tag: Pooled differentiated rhesus monkey Oregon Rhesus Macaque Embryonic Stem (ORMES) cell line 6 embryoid bodies.  Obtained by pooling 20 EBs.


title: Ad-lipin rep 1

description: lipin overexpressing

tag: 6 week old C57Bl6 male mouse with adenoviral driven lipin 1 protein over expressed


title: GFP control rep 1

description: control sample for lipin overexpressing

tag: 6 week old C57Bl6 mouse infected with adenoviral-driven green fluorescent protein


title: JY_met1whole_polyA_02_R0143_11162005.CEL

source_name: Whole plant

tag: Strain;met1 mutant on colmbia back ground segregated from heterozygote, Tissue; whole plant w/o root, Age; 40days, Growth; on soil under continuous light condition


title: untreated_24hr_rep4

status: Public on Aug 15 2006

city: Bloomington

first: Milton

middle: W

last: Taylor

state: IN

address: 343 Jordan Hall

department: Biology

institute: Indiana University

description: Gene expression data 5-aza-dC plus Trichostatin A  treated HepG2 cells.

hyb_protocol: Following fragmentation, 15 microg of cRNA were mixed with spike controls and 2/3 was hybridized for 17 hr at 45C on GeneChip Human Genome 133 plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station per manufacturer's instructions.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 1000.

source_name: A549 cells (lung epithelial cells, a common cell line used in IFN assays)

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Cell culture, EMEM (Sigma, St. Louis, MO) with 10% fetal bovine serum (FBS) (Omega Scientific Inc. Tarzana, CA)

extract_protocol: TRI Reagent® according to the manufacturer's instructions, followed by RNeasy columns (Qiagen, Valencia, CA.)

tag: untreated 24 hr


title: JY_tripleWhole_polyA_02_F0407_11282005.CEL

tag: Strain;drm1 drm2 cmt3 mutant on colmbia back ground segregated from heterozygote, Tissue; whole plant w/o root, Age; 40days, Growth; on soil under continuous light condition


title: Eulgem_1-2_Col-0-MKK2-EE4_Rep1_AG

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

data_processing: The data were analysed using Affymetrix Microarray Suite 5.0 (MAS5)

tag: Developmental stage

value: 2 week old plants

tag: Tissue

value: Leaves


title: Infergen+IFN_Gamma_24hr_rep4

treatment_protocol: 200 IU of Infergen (Intermune, Inc., Brisbane, CA) + 200 IU IFN-g1b (Actimmune, Intermune Inc)


title: Ad-lipin rep 2

description: lipin 1 overexpressing

molecule: polyA RNA

tag: adult male C57Bl6 mouse overexpressing lipin 1 in liver using an adenovirus


title: JY_tripleWhole_polyA_02_R0204_11282005.CEL


title: Infergen_24hr_rep4

treatment_protocol: 500 IU of Infergen (Intermune, Inc., Brisbane, CA)


title: IFN_Gamma_6hr_rep4

treatment_protocol: 500 IU IFN-g1b (Actimmune, Intermune Inc)


title: IFN_Gamma_24hr_rep4


title: Infergen+IFN_Gamma_6hr_rep4


title: JY_tripleWhole_polyA_01_F0405_11282005.CEL


title: JY_tripleWhole_polyA_01_R0203_11282005.CEL


title: JY_colWhole_polyA_01_F0414_11302005.CEL

tag: Strain;wild type colmbia, Tissue; whole plant w/o root, Age; 40days, Growth; on soil under continuous light condition


title: JY_met1Whole_polyA_03_R0226_10012006.CEL


title: Infergen_6hr_rep4


title: Infergen_24hr_rep1


title: untreated_24hr_rep2

treatment_protocol: untreated


title: untreated_6hr_rep4


title: JY_colWhole_polyA_03_F0452_10012006.CEL


title: JY_colWhole_polyA_02_R0207_11302005.CEL


title: Infergen+IFN_Gamma_24hr_rep2


title: JY_met1whole_polyA_01_F0344_11102005.CEL


title: Infergen_24hr_rep2


title: Infergen+IFN_Gamma_6hr_rep2


title: IFN_Gamma_24hr_rep2


title: IFN_Gamma_6hr_rep2


title: untreated_24hr_rep1

tag: untreated


title: untreated_6hr_rep2


title: Infergen_6hr_rep2


title: untreated_24hr_rep3


title: JY_colWhole_polyA_03_R0227_10012006.CEL


title: IFN_Gamma_24hr_rep3


title: Infergen_24hr_rep3


title: Underwood_1-21_Mock-Inoculum-10h_Rep3_ATH1

institute: Nottingham Arabidopsis Stock Centre (NASC)

description:
stratification: Stratified 3 days at 4degC
growth protocol: Arabidopsis thaliana accession Col-0 plants were grown in soil in growth chambers with a day/night cycle of 12 h/12 h, a light intensity of 100 µE, and a constant temperature of 20°C. Four- to 5-week-old plants were used for experiments.
Location: Growth chamber
Growth  substrate: Commercial soil
Watering: flats were watered every 2-3 days

treatment_protocol: Plants were inoculated by vacuum infiltration with a mock inoculum of distilled/deionized water. Inoculated leaf tissue from at least 15 plants was collected 10 hours after inoculation for RNA isolation.

tag: Stock Code


title: JY_met1whole_polyA_01_R0144_11102005.CEL


title: Infergen+IFN_Gamma_24hr_rep3


title: JY_tripleWhole_polyA_03_R0231_22022006.CEL


title: untreated_6hr_rep3


title: Infergen_6hr_rep3

description: Gene expression data Trichostatin A  treated HepG2 cells.


title: Infergen+IFN_Gamma_6hr_rep3


title: IFN_Gamma_24hr_rep1

description: Gene expression data 5-aza-dC treated HepG2 cells.


title: untreated_6hr_rep1


title: IFN_Gamma_6hr_rep3


title: IFN_Gamma_6hr_rep1

description: Gene expression data untreated HepG2 cells (control).


title: Infergen+IFN_Gamma_24hr_rep1


title: Underwood_1-9_DC3000-10e6-24h_Rep3_ATH1

treatment_protocol: Plants were inoculated by vacuum infiltration with Pseudomonas syringae pv. tomato strain DC3000 bacteria at a concentration of 10e6 cfu/ml. Inoculated leaf tissue from at least 15 plants was collected for RNA isolation.


title: Yeast FAIRE_set2_1

status: Public on Aug 11 2006

type: genomic

city: Chapel Hill

first: Jason

middle: D

last: Lieb

state: NC

address: 203 Fordham Hall

department: Department of Biology

institute: University of North Carolina at Chapel Hill

scan_protocol: Images were acquired using a GenePix 4000B scanner and Genepix software (Axon Instruments)

data_processing: Data were uploaded to the UNC Microarray Database and retrieved as the log2 normalized ratio of (median intensity of sample pixels / median intensity of reference pixels). Only spots with a regression correlation >0.6 (i.e. those comprised of pixels with consistent ratio values). Spots that either failed from PCR or that were flagged in Genepix were not downloaded. Data were then z-score transformed such that the mean of all spots became 0 and the standard deviation became 1.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: genomic set2 KO in BY4741 background

label_protocol: samples and references were amplified using a T7 RNA polymerase–based linear method (see Liu et al., 2003 BMC Genomics)

tag: genomic set2 KO in BY4741 background

source_name: fixed set2 KO in BY4741 background

tag: fixed set2 KO in BY4741 background


title: myoblast_treated_rep1

status: Public on Aug 12 2006

city: Cambridge

first: Reza

last: Halse

state: MA

address: 100 Technology Square

institute: Novartis Institutes for BioMedical Research

description: Gene expression data from undifferentiated C2C12 myoblasts incubated in pyruvate test media for 72 hr.

hyb_protocol: Following fragmentation, 10?g of labeled cRNA were hybridized at 45°C for approximately 16 hr to Gene Chip Mouse Genome 430 2.0 Expression Array (Affymetrix).  The arrays were stained on Gene Chip Fluidics Workstation 450.

scan_protocol: Gene Chips were scanned using the GeneArray Scanner 3000.

data_processing: The scanned image was converted into numerical values of the signal intensity (Signal) and into categorical expression level measurement (Absolute Call) using the Affymetrix MAS 5.0 software.  The MAS 5.0 statistical algorithm parameters used to attribute the Absoute Calls were set to 0.05 for Alpha 1, 0.065 for Alpha 2 and 0.015 for Tau.  The software scaled the average intensity of all genes of each chip to a target intenisty of 150.

source_name: C2C12 myoblasts, treated with 50 mM sodium pyruvate for 72 hr

label_protocol: Biotinylated cRNA were prepared according to the manufacturer's instructions (Bioarray High yield T7 DNA transcirption kit, ENZO Life Sciences, Inc.)

growth_protocol: C2C12 myoblasts were incubated in pyruvate test media for 72 hr at 37°C.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: C2C12 myoblasts were seeded in 100 mm dishes in pyruvate test media and incubated for 72 hr at 37°C.  Pyruvate test media:  DMEM with no sodium pyruvate supplemented with 10% fetal bovine serum, 1% antibiotics, 4 mM L-glutamine and 50 mM sodium pyruvate.

tag: Undifferentiated C2C12 myoblasts, passage #11


title: myoblast_treated_rep3


title: JY_colWhole_polyA_02_F0415_11302005.CEL


title: myoblast_treated_rep2


title: myoblast_untreated_rep3

description: Gene expression data from undifferentiated C2C12 myoblasts incubated in basal media for 72 hr.

source_name: C2C12 myoblasts, untreated, replicate 3

growth_protocol: C2C12 myoblasts were incubated in basal media for 72 hr at 37°C.

treatment_protocol: Sample_treatment_protocol_ch1 = C2C12 myoblasts were seeded in 100 mm dishes in basal media and incubated for 72 hr at 37°C.  Basal media: Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum, 1% antibiotics and 4 mM L-glutamine.


title: Infergen+IFN_Gamma_6hr_rep1


title: Yeast FAIRE_set1_1

source_name: genomic set1 KO in AS4 background

tag: genomic set1 KO in AS4 background

source_name: fixed set1 KO in AS4 background

tag: fixed set1 KO in AS4 background


title: myoblast_untreated_rep1

source_name: C2C12 myoblasts, untreated

treatment_protocol: C2C12 myoblasts were seeded in 100 mm dishes in basal media and incubated for 72 hr at 37°C.  Basal media: Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum, 1% antibiotics and 4 mM L-glutamine.


title: Yeast FAIRE_HDACs_2

source_name: genomic hda1 hos1 hos2 hos3 rpd3 quintuple KO in W303 background

source_name: fixed hda1 hos1 hos2 hos3 rpd3 quintuple KO in W303 background


title: Yeast FAIRE_HDACs_1

tag: genomic hda1 hos1 hos2 hos3 rpd3 quintuple KO in W303 background

tag: fixed hda1 hos1 hos2 hos3 rpd3 quintuple KO in W303 background


title: Yeast FAIRE_set1_2


title: Yeast FAIRE_hat1_2

source_name: genomic hat1 KO in BY4741 background

tag: genomic hat1 KO in BY4741 background

source_name: fixed hat1 KO in BY4741 background

tag: fixed hat1 KO in BY4741 background


title: Yeast FAIRE_hat2_1

source_name: genomic hat2 KO in BY4741 background

tag: genomic hat2 KO in BY4741 background

source_name: fixed hat2 KO in BY4741 background

tag: fixed hat2 KO in BY4741 background


title: Yeast FAIRE_hat2_2


title: Infergen_6hr_rep1

description: Gene expression data Infergen_6hr on A549 cells.


title: Yeast FAIRE_hat1_1


title: Yeast FAIRE_h4_3

source_name: genomic h4 N-terminal tail truncation mutant

source_name: fixed h4 N-terminal tail truncation mutant


title: Yeast FAIRE_h4_2

tag: genomic h4 N-terminal tail truncation mutant

tag: fixed h4 N-terminal tail truncation mutant


title: Yeast FAIRE_h3_2

source_name: genomic h3 N-terminal tail truncation mutant

source_name: fixed h3 N-terminal tail truncation mutant


title: Yeast FAIRE_h3_1

tag: genomic h3 N-terminal tail truncation mutant

tag: fixed h3 N-terminal tail truncation mutant


title: Yeast FAIRE_h2b_1

source_name: genomic h2b N-terminal tail truncation mutant

source_name: fixed h2b N-terminal tail truncation mutant


title: Yeast FAIRE_h2a_2

source_name: genomic h2a N-terminal tail truncation mutant

source_name: fixed h2a N-terminal tail truncation mutant


title: Yeast FAIRE_h2a_1

tag: genomic h2a N-terminal tail truncation mutant

tag: fixed h2a N-terminal tail truncation mutant


title: Yeast FAIRE_gcn5_2

source_name: genomic gcn5 KO in BY4741 background

tag: genomic gcn5 KO in BY4741 background

source_name: fixed gcn5 KO in BY4741 background

tag: fixed gcn5 KO in BY4741 background


title: Yeast FAIRE_BY4741_8

source_name: genomic unfixed BY4741

tag: genomic unfixed BY4741

source_name: fixed BY4741

tag: fixed BY4741


title: Yeast FAIRE_gcn5_1


title: JY_colWhole_polyA_01_R0206_11302005.CEL

data_processing: The following procedure was used to process and analyze tiling microarray data for RNA expression and DNA methylation. First, CEL files of the each three biological replicate (total 6 CEL files) within genotype comparison (e.g., comparison between wt and met1 of poly-A RNA profiling) were subject to quantile normalization. Next, to identify significant difference regions between wt and mutant, probe-level t-statistics was calculated using a recently proposed method (1). Regions statistically different between two groups were identified using the Hidden Markov Models (HMM) option. 1. H. Ji and W. H. Wong, Bioinformatics 21, 3629-3636 (2005).

source_name: Whole plant

tag: Strain;wild type colmbia, Tissue; whole plant w/o root, Age; 40days, Growth; on soil under continuous light condition


title: Yeast FAIRE_BY4741_3


title: Yeast FAIRE_BY4741_2


title: Yeast FAIRE_BY4741_1


title: Yeast FAIRE_set6_1

source_name: genomic set6 KO in BY4741 background

tag: genomic set6 KO in BY4741 background

source_name: fixed set6 KO in BY4741 background

tag: fixed set6 KO in BY4741 background


title: Yeast FAIRE_W303_2

source_name: genomic W303

tag: genomic W303

source_name: fixed W303

tag: fixed W303


title: Yeast FAIRE_set5_1

source_name: genomic set5 KO in BY4741 background

tag: genomic set5 KO in BY4741 background

source_name: fixed set5 KO in BY4741 background

tag: fixed set5 KO in BY4741 background


title: Yeast FAIRE_set6_2


title: Yeast FAIRE_set4_2

source_name: genomic set4 KO in BY4741 background

tag: genomic set4 KO in BY4741 background

source_name: fixed set4 KO in BY4741 background

tag: fixed set4 KO in BY4741 background


title: Yeast FAIRE_set4_1


title: Yeast FAIRE_set3_2

source_name: genomic set3 KO in BY4741 background

tag: genomic set3 KO in BY4741 background

source_name: fixed set3 KO in BY4741 background

tag: fixed set3 KO in BY4741 background


title: Yeast FAIRE_set2rad6_2

source_name: genomic set2 rad6 double KO in BY4741/2 background

source_name: fixed set2 rad6 double KO in BY4741/2 background


title: Yeast FAIRE_set3_1


title: Yeast FAIRE_h2b_2

source_name: genomic h2b N-terminal tail truncation mutant

source_name: fixed h2b N-terminal tail truncation mutant


title: Yeast FAIRE_set2rad6_1

tag: genomic set2 rad6 double KO in BY4741/2 background

tag: fixed set2 rad6 double KO in BY4741/2 background


title: Yeast FAIRE_set5_2


title: myoblast_untreated_rep2

source_name: C2C12 myoblasts, untreated

tag: Undifferentiated C2C12 myoblasts, passage #11


title: Yeast FAIRE_set2_2

source_name: genomic set2 KO in BY4741 background

tag: genomic set2 KO in BY4741 background

source_name: fixed set2 KO in BY4741 background

tag: fixed set2 KO in BY4741 background


title: Yeast FAIRE_time 0, cell cycle #5

description: FAIRE_time 0, cell cycle #5

source_name: genomic unfixed DBY8724

label_protocol: samples and references were amplified using a random primed PCR-based method (see Bohlander et al., 1992)

tag: genomic unfixed DBY8724

source_name: time 0 fixed DBY8724

tag: time 0 fixed DBY8724


title: Yeast FAIRE_time 54, cell cycle #1

description: FAIRE_time 54, cell cycle #1

source_name: time 54 fixed DBY8724

tag: time 54 fixed DBY8724


title: Yeast FAIRE_time 72, cell cycle #1

description: FAIRE_time 72, cell cycle #1

source_name: time 72 fixed DBY8724

tag: time 72 fixed DBY8724


title: Yeast FAIRE_time 63, cell cycle #5

description: FAIRE_time 63, cell cycle #5

source_name: time 63 fixed DBY8724

tag: time 63 fixed DBY8724


title: Yeast FAIRE_time 63, cell cycle #4 (dye swap)

description: FAIRE_time 63, cell cycle #4 (dye swap)


title: Yeast FAIRE_time 63, cell cycle #4

description: FAIRE_time 63, cell cycle #4


title: Yeast FAIRE_time 54, cell cycle #4 (dye swap)

description: FAIRE_time 54, cell cycle #4 (dye swap)


title: Yeast FAIRE_time 63, cell cycle #3

description: FAIRE_time 63, cell cycle #3


title: Yeast FAIRE_time 54, cell cycle #4

description: FAIRE_time 54, cell cycle #4


title: Yeast FAIRE_time 54, cell cycle #3

description: FAIRE_time 54, cell cycle #3


title: Yeast FAIRE_time 36, cell cycle #4 (dye swap)

description: FAIRE_time 36, cell cycle #4 (dye swap)

source_name: time 36 fixed DBY8724

tag: time 36 fixed DBY8724


title: Yeast FAIRE_time 36, cell cycle #5

description: FAIRE_time 36, cell cycle #5


title: Yeast FAIRE_BY4741_7

source_name: genomic unfixed BY4741

tag: genomic unfixed BY4741

source_name: fixed BY4741

tag: fixed BY4741


title: Yeast FAIRE_time 36, cell cycle #4

description: FAIRE_time 36, cell cycle #4


title: Yeast FAIRE_time 36, cell cycle #2

description: FAIRE_time 36, cell cycle #2


title: Yeast FAIRE_time 18, cell cycle #4 (dye swap)

description: FAIRE_time 18, cell cycle #4 (dye swap)

source_name: time 18 fixed DBY8724

tag: time 18 fixed DBY8724


title: Yeast FAIRE_time 54, cell cycle #5

description: FAIRE_time 54, cell cycle #5


title: Yeast FAIRE_time 18, cell cycle #4

description: FAIRE_time 18, cell cycle #4


title: 57_5dPA_MK02X023

city: Indianapolis

first: Matthew

last: Grow

department: Biochemistry and Molecular Biology

description: Gene expression data from Hindlimbs at either st57 were amputated unilaterally or bilaterally at the mid-zeugopodia level. Five days (5dPA) after amputation tissues were collected 1mm proximal to the original level of amputation.  Total RNA was isolated using RNaqueous micro kit (Ambion, inc.).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Xenopus laevis

source_name: amputation blastema-proximal (1mm) tissue from Xenopus laevis hindlimbs

tag: Stage 57 Xenopus leavis hindlimbs, 5 day post-amputation


title: Yeast FAIRE_time 36, cell cycle #1

description: FAIRE_time 36, cell cycle #1


title: Yeast FAIRE_time 18, cell cycle #2

description: FAIRE_time 18, cell cycle #2


title: Yeast FAIRE_time 18, cell cycle #3

description: FAIRE_time 18, cell cycle #3


title: Yeast FAIRE_time 0, cell cycle #3

description: FAIRE_time 0, cell cycle #3


title: 57_1dPA_MK02X016

description: Gene expression data from Hindlimbs at either st57 were amputated unilaterally or bilaterally at the mid-zeugopodia level. One day (1dPA) after amputation tissues were collected 1mm proximal to the original level of amputation.  Total RNA was isolated using RNaqueous micro kit (Ambion, inc.).

tag: Stage 57 Xenopus leavis hindlimbs, 1 day post-amputation


title: Yeast FAIRE_time 0, cell cycle #2

description: FAIRE_time 0, cell cycle #2


title: Yeast FAIRE_time 0, cell cycle #4

description: FAIRE_time 0, cell cycle #4


title: Yeast FAIRE_time 90, cell cycle #5

description: FAIRE_time 90, cell cycle #5

source_name: time 90 fixed DBY8724

tag: time 90 fixed DBY8724


title: 57_1dPA_MK02X015


title: Yeast FAIRE_time 36, cell cycle #3

description: FAIRE_time 36, cell cycle #3


title: 57_1dPA_MK02X014


title: Yeast FAIRE_time 90, cell cycle #4

description: FAIRE_time 90, cell cycle #4


title: 57_1dPA_MK02X013


title: Yeast FAIRE_time 90, cell cycle #3

description: FAIRE_time 90, cell cycle #3


title: Yeast FAIRE_time 90, cell cycle #4 (dye swap)

description: FAIRE_time 90, cell cycle #4 (dye swap)


title: Yeast FAIRE_time 90, cell cycle #1

description: FAIRE_time 90, cell cycle #1


title: 53_5dPA_MK02X010

description: Gene expression data from Hindlimbs at either st53 were amputated unilaterally or bilaterally at the mid-zeugopodia level. Five days (5dPA) after amputation tissues were collected 1mm proximal to the original level of amputation.  Total RNA was isolated using RNaqueous micro kit (Ambion, inc.).

tag: Stage 53 Xenopus leavis hindlimbs, 5 days post-amputation


title: 53_5dPA_MK02X011


title: 53_5dPA_MK02X009


title: Yeast FAIRE_time 72, cell cycle #5

description: FAIRE_time 72, cell cycle #5


title: 57_5dPA_MK02X022


title: 53_1dPA_MK02X003

description: Gene expression data from Hindlimbs at either st53 were amputated unilaterally or bilaterally at the mid-zeugopodia level. One (1dPA) after amputation tissues were collected 1mm proximal to the original level of amputation.  Total RNA was isolated using RNaqueous micro kit (Ambion, inc.).

tag: Stage 53 Xenopus leavis hindlimbs, 1 day post-amputation


title: Yeast FAIRE_time 72, cell cycle #4

description: FAIRE_time 72, cell cycle #4


title: 57_5dPA_MK02X021


title: Yeast FAIRE_time 72, cell cycle #4 (dye swap)

description: FAIRE_time 72, cell cycle #4 (dye swap)


title: 53_1dPA_MK02X004


title: Yeast FAIRE_time 72, cell cycle #2

description: FAIRE_time 72, cell cycle #2


title: IMR317

status: Public on Aug 10 2006

city: Seattle

first: Andrew

last: Sharp

state: WA

address: 1705 NE Pacific St

department: Genome Sciences

institute: University of Washington

description: BACs for which only one of the triplicates printed on the array yielded data, or for which the standard deviation of log2 ratio for the triplicates was >0.2, were removed from final analysis.

scan_protocol: Slides scanned with ArrayWorX scanner. Image analysis and normalization were performed using UCSF Spot and Sproc software (Jain AN, Tokuyasu TA, Snijders AM, Segraves R, Albertson DG, Pinkel D (2002) Fully automatic quantification of microarray image data. Genome Res 12:325-332)

data_processing: Default parameters within Spot software

extract_protocol: Phenol-chloroform extraction

growth_protocol: Grown as per Coriell recommendations

extract_protocol: Gentra Puregene DNA Isolation system

tag: Lymphoblastoid cell line GM15724


title: IMR316


title: IMR314ds


title: IMR315


title: IMR316ds


title: IMR314


title: 57_5dPA_MK02X024


title: IMR313


title: Yeast FAIRE_time 90, cell cycle #2

description: FAIRE_time 90, cell cycle #2


title: IMR312


title: IMR310ds


title: IMR309


title: IMR308ds


title: Yeast FAIRE_time 72, cell cycle #3

description: FAIRE_time 72, cell cycle #3


title: IMR309ds


title: 53_1dPA_MK02X002


title: IMR307ds


title: IMR307


title: IMR308


title: IMR306ds


title: IMR306


title: IMR305ds


title: IMR300ds


title: IMR298ds


title: IMR315ds


title: IMR313ds


title: IMR283


title: IMR283ds


title: IMR279


title: IMR278


title: IMR310


title: IMR277ds


title: IMR276


title: IMR276ds


title: IMR275ds


title: IMR277


title: IMR275


title: IMR273ds


title: IMR274


title: IMR273


title: IMR298


title: IMR300


title: IMR305


title: IMR271


title: IMR270ds


title: IMR270


title: IMR279ds


title: IMR269ds


title: IMR268ds


title: IMR269


title: IMR274ds


title: IMR278ds


title: IMR268


title: IMR266ds


title: IMR266


title: IMR264ds


title: IMR263ds


title: IMR260ds


title: IMR264


title: IMR260


title: IMR259ds


title: IMR257ds


title: IMR271ds


title: IMR257


title: IMR256


title: IMR253ds


title: IMR256ds


title: IMR255


title: IMR263


title: IMR253


title: IMR249ds


title: IMR248ds


title: IMR249


title: IMR247ds


title: IMR247


title: IMR312ds


title: IMR248


title: IMR246


title: IMR246ds


title: IMR244ds


title: IMR244


title: IMR243


title: IMR243ds


title: IMR259


title: IMR240ds


title: IMR240


title: IMR255ds


title: IMR239ds


title: IMR238ds


title: IMR239


title: IMR236ds


title: IMR235ds


title: IMR236


title: IMR235


title: IMR234ds


title: IMR234


title: IMR232ds


title: IMR231ds


title: IMR231


title: IMR230


title: IMR228ds


title: IMR230ds


title: IMR228


title: IMR227


title: IMR225


title: IMR223ds


title: IMR224


title: IMR222


title: IMR223


title: IMR225ds


title: IMR222ds


title: IMR220


title: IMR220ds


title: IMR218ds


title: IMR238


title: IMR218


title: IMR217ds


title: IMR216ds


title: IMR232


title: IMR217


title: IMR215


title: IMR215ds


title: IMR216


title: IMR214


title: IMR214ds


title: IMR213ds


title: IMR227ds


title: IMR213


title: IMR212


title: IMR211ds


title: IMR212ds


title: 53_1dPA_MK02X001


title: IMR210


title: IMR210ds


title: IMR206ds


title: IMR206


title: IMR207


title: IMR207ds


title: IMR224ds


title: IMR209


title: IMR205


title: IMR204


title: IMR203ds


title: IMR201ds


title: IMR204ds


title: IMR201


title: IMR203


title: IMR198ds


title: IMR198


title: IMR199


title: IMR197ds


title: IMR199ds


title: IMR197


title: IMR211


title: IMR194ds


title: IMR194


title: IMR192ds


title: IMR209ds


title: IMR191ds


title: IMR192


title: IMR190


title: IMR189


title: IMR189ds


title: IMR188ds


title: IMR187ds


title: IMR187


title: IMR188


title: IMR184ds


title: IMR183


title: IMR185ds


title: IMR184


title: IMR185


title: IMR182


title: IMR183ds


title: IMR182ds


title: IMR179ds


title: IMR190ds


title: IMR179


title: IMR178ds


title: IMR177ds


title: IMR176ds


title: IMR176


title: IMR191


title: IMR174ds


title: IMR174


title: IMR175


title: IMR173ds


title: IMR205ds


title: IMR173


title: IMR175ds


title: IMR172


title: IMR172ds


title: IMR171ds


title: IMR169


title: IMR168ds


title: IMR169ds


title: IMR171


title: IMR167ds


title: IMR167


title: IMR166ds


title: IMR166


title: IMR177


title: IMR178


title: IMR163ds


title: IMR164


title: IMR165


title: IMR163


title: IMR168


title: IMR164ds


title: IMR162


title: IMR160ds


title: IMR162ds


title: IMR159ds


title: IMR160


title: IMR158ds


title: IMR159


title: IMR157ds


title: IMR165ds


title: IMR158


title: IMR157


title: IMR156ds


title: IMR155


title: IMR156


title: IMR155ds


title: IMR149


title: IMR153ds


title: IMR154


title: IMR150ds


title: IMR153


title: IMR151ds


title: IMR146ds


title: IMR147ds


title: IMR149ds


title: IMR151


title: IMR147


title: IMR146


title: IMR142


title: IMR141


title: IMR142ds


title: IMR143


title: IMR141ds


title: IMR140ds


title: IMR140


title: IMR138


title: IMR136ds


title: IMR138ds


title: IMR148


title: IMR148ds


title: IMR134ds


title: IMR134


title: IMR131ds


title: IMR129ds


title: IMR131


title: IMR128


title: IMR130


title: IMR154ds


title: IMR127ds


title: IMR128ds


title: IMR129


title: IMR127


title: IMR143ds


title: IMR126ds


title: IMR126


title: IMR124ds


title: IMR136


title: IMR121ds


title: IMR121


title: IMR118ds


title: IMR130ds


title: IMR150


title: IMR118


title: IMR124


title: IMR123ds


title: IMR116ds


title: IMR116


title: IMR123


title: IMR115


title: IMR112


title: IMR111


title: IMR111ds


title: IMR109


title: IMR112ds


title: IMR113


title: IMR109ds


title: IMR108ds


title: IMR106ds


title: IMR107


title: IMR108


title: IMR105


title: IMR106


title: IMR103ds


title: IMR102ds


title: IMR102


title: IMR101ds


title: IMR115ds


title: IMR113ds


title: IMR100ds


title: IMR101


title: IMR103


title: IMR99ds


title: IMR107ds


title: IMR98ds


title: IMR98


title: IMR97


title: IMR96


title: IMR105ds


title: IMR96ds


title: IMR97ds


title: IMR95ds


title: IMR89ds


title: IMR94


title: IMR89


title: IMR94ds


title: IMR90ds


title: IMR86ds


title: IMR85ds


title: IMR86


title: IMR82


title: IMR100


title: IMR85


title: IMR83ds


title: IMR99


title: IMR82ds


title: IMR83


title: IMR81ds


title: IMR81


title: IMR79ds


title: IMR90


title: IMR77ds


title: IMR95


title: IMR79


title: IMR78


title: IMR76ds


title: IMR76


title: IMR75ds


title: IMR75


title: IMR71ds


title: IMR74ds


title: IMR69ds


title: IMR63ds


title: IMR70


title: IMR69


title: IMR71


title: IMR74


title: IMR67ds


title: IMR63


title: IMR61


title: IMR67


title: IMR61ds


title: IMR60ds


title: IMR77


title: IMR60


title: IMR58


title: IMR57ds


title: IMR56ds


title: IMR55ds


title: IMR56


title: IMR55


title: IMR54ds


title: IMR54


title: IMR78ds


title: IMR51


title: IMR52ds


title: IMR52


title: IMR50ds


title: IMR51ds


title: IMR50


title: IMR48ds


title: IMR48


title: IMR58ds


title: IMR49


title: IMR47ds


title: IMR47


title: IMR46ds


title: IMR46


title: IMR57


title: IMR45


title: IMR44ds


title: IMR43ds


title: IMR44


title: IMR42ds


title: IMR41ds


title: IMR70ds


title: IMR41


title: IMR39ds


title: IMR37


title: IMR37ds


title: IMR38ds


title: IMR34ds


title: IMR49ds


title: IMR36


title: IMR35


title: IMR35ds


title: IMR36ds


title: IMR33ds


title: IMR38


title: 312 (rma)

city: Durham

last: Nevins

address: 2133 CIEMAS, 101 Science Dr.

department: IGSP

institute: Duke University

description: frozen tissue of primary lung tumors

data_processing: Affymetrix U133 RMA DATA

source_name: frozen tissue of primary lung tumor

tag: STATUS(0=alive, 1=dead)


title: IMR34


title: IMR45ds


title: 310 (rma)

description: frozen tissue of primary lung tumors


title: IMR33


title: IMR43


title: IMR32


title: IMR32ds


title: 307 (rma)

description: frozen tissue of primary lung tumors


title: IMR39


title: IMR28ds


title: 311 (rma)

description: frozen tissue of primary lung tumors


title: 305 (rma)

description: frozen tissue of primary lung tumors


title: IMR27ds


title: 306 (rma)

description: frozen tissue of primary lung tumors


title: IMR26ds


title: 304 (rma)

description: frozen tissue of primary lung tumors


title: IMR27


title: 300 (rma)

description: frozen tissue of primary lung tumors


title: IMR26


title: IMR28


title: IMR25ds


title: IMR25


title: IMR24ds


title: IMR24


title: 295 (rma)

description: frozen tissue of primary lung tumors


title: 296 (rma)

description: frozen tissue of primary lung tumors


title: 309 (rma)

description: frozen tissue of primary lung tumors


title: 297 (rma)

description: frozen tissue of primary lung tumors


title: IMR23ds


title: 293 (rma)

description: frozen tissue of primary lung tumors


title: IMR22ds


title: IMR23


title: 292 (rma)

description: frozen tissue of primary lung tumors


title: 294 (rma)

description: frozen tissue of primary lung tumors


title: 291 (rma)

description: frozen tissue of primary lung tumors


title: IMR22


title: IMR21ds


title: 289 (rma)

description: frozen tissue of primary lung tumors


title: IMR20ds


title: 290 (rma)

description: frozen tissue of primary lung tumors


title: 287 (rma)

description: frozen tissue of primary lung tumors


title: 288 (rma)

description: frozen tissue of primary lung tumors


title: IMR20


title: IMR21


title: IMR19ds


title: 285 (rma)

description: frozen tissue of primary lung tumors


title: IMR42


title: 286 (rma)

description: frozen tissue of primary lung tumors


title: IMR18ds


title: IMR19


title: 299 (rma)

description: frozen tissue of primary lung tumors


title: 283 (rma)

description: frozen tissue of primary lung tumors


title: IMR18


title: IMR17ds


title: IMR17


title: 282 (rma)

description: frozen tissue of primary lung tumors


title: 280 (rma)

description: frozen tissue of primary lung tumors


title: 278 (rma)

description: frozen tissue of primary lung tumors


title: IMR16ds


title: 277 (rma)

description: frozen tissue of primary lung tumors


title: IMR15ds


title: 275 (rma)

description: frozen tissue of primary lung tumors


title: 274 (rma)

description: frozen tissue of primary lung tumors


title: IMR13ds


title: IMR15


title: 273 (rma)

description: frozen tissue of primary lung tumors


title: IMR13


title: 271 (rma)

description: frozen tissue of primary lung tumors


title: IMR12ds


title: IMR12


title: 272 (rma)

description: frozen tissue of primary lung tumors


title: IMR10ds


title: 270 (rma)

description: frozen tissue of primary lung tumors


title: 281 (rma)

description: frozen tissue of primary lung tumors


title: 269 (rma)

description: frozen tissue of primary lung tumors


title: 268 (rma)

description: frozen tissue of primary lung tumors


title: IMR10


title: 267 (rma)

description: frozen tissue of primary lung tumors


title: IMR9


title: 263 (rma)

description: frozen tissue of primary lung tumors


title: IMR8ds


title: IMR16


title: 259 (rma)

description: frozen tissue of primary lung tumors


title: 276 (rma)

description: frozen tissue of primary lung tumors


title: IMR7


title: IMR7ds


title: 258 (rma)

description: frozen tissue of primary lung tumors


title: 257 (rma)

description: frozen tissue of primary lung tumors


title: IMR6ds


title: IMR6


title: IMR5


title: 248 (rma)

description: frozen tissue of primary lung tumors


title: IMR5ds


title: 247 (rma)

description: frozen tissue of primary lung tumors


title: 246 (rma)

description: frozen tissue of primary lung tumors


title: IMR4


title: IMR4ds


title: 245 (rma)

description: frozen tissue of primary lung tumors


title: 240 (rma)

description: frozen tissue of primary lung tumors


title: IMR3ds


title: 239 (rma)

description: frozen tissue of primary lung tumors


title: IMR3


title: 238 (rma)

description: frozen tissue of primary lung tumors


title: 237 (rma)

description: frozen tissue of primary lung tumors


title: IMR2


title: 236 (rma)

description: frozen tissue of primary lung tumors


title: IMR400


title: 249 (rma)

description: frozen tissue of primary lung tumors


title: IMR400ds


title: IMR2ds


title: 235 (rma)

description: frozen tissue of primary lung tumors


title: IMR397ds


title: 232 (rma)

description: frozen tissue of primary lung tumors


title: IMR397


title: IMR8


title: 231 (rma)

description: frozen tissue of primary lung tumors


title: IMR396ds


title: IMR396


title: IMR394ds


title: 229 (rma)

description: frozen tissue of primary lung tumors


title: IMR9ds


title: 228 (rma)

description: frozen tissue of primary lung tumors


title: 250 (rma)

description: frozen tissue of primary lung tumors


title: 227 (rma)

description: frozen tissue of primary lung tumors


title: 224 (rma)

description: frozen tissue of primary lung tumors


title: IMR393ds


title: IMR393


title: IMR392ds


title: 221 (rma)

description: frozen tissue of primary lung tumors


title: 222 (rma)

description: frozen tissue of primary lung tumors


title: IMR392


title: 234 (rma)

description: frozen tissue of primary lung tumors


title: IMR391ds


title: 220 (rma)

description: frozen tissue of primary lung tumors


title: 298 (rma)

description: frozen tissue of primary lung tumors


title: IMR391


title: IMR390


title: 218 (rma)

description: frozen tissue of primary lung tumors


title: 230 (rma)

description: frozen tissue of primary lung tumors


title: IMR390ds


title: 216 (rma)

description: frozen tissue of primary lung tumors


title: 215 (rma)

description: frozen tissue of primary lung tumors


title: IMR389ds


title: IMR394


title: IMR388ds


title: 214 (rma)

description: frozen tissue of primary lung tumors


title: IMR389


title: 213 (rma)

description: frozen tissue of primary lung tumors


title: 212 (rma)

description: frozen tissue of primary lung tumors


title: IMR388


title: IMR387ds


title: 209 (rma)

description: frozen tissue of primary lung tumors


title: 210 (rma)

description: frozen tissue of primary lung tumors


title: 208 (rma)

description: frozen tissue of primary lung tumors


title: IMR386ds


title: 219 (rma)

description: frozen tissue of primary lung tumors


title: IMR386


title: 207 (rma)

description: frozen tissue of primary lung tumors


title: IMR385ds


title: 205 (rma)

description: frozen tissue of primary lung tumors


title: 206 (rma)

description: frozen tissue of primary lung tumors


title: IMR385


title: 203 (rma)

description: frozen tissue of primary lung tumors


title: IMR384


title: 204 (rma)

description: frozen tissue of primary lung tumors


title: 202 (rma)

description: frozen tissue of primary lung tumors


title: IMR382ds


title: 8852 0234_7093_h133+_8852.cel 1 (rma)

description: frozen tissue of primary lung tumors


title: IMR381ds


title: IMR382


title: IMR383


title: 8849 0234_7091_h133+_8849.cel 1 (rma)

description: frozen tissue of primary lung tumors


title: 8853 0234_7094_h133+_8853.cel 1 (rma)

description: frozen tissue of primary lung tumors


title: 8843 0234_7087_h133+_8843.cel 1 (rma)

description: frozen tissue of primary lung tumors


title: IMR381


title: IMR387


title: IMR380ds


title: 8840 0234_7085_h133+_8840.cel 1 (rma)

description: frozen tissue of primary lung tumors


title: 201 (rma)

description: frozen tissue of primary lung tumors


title: IMR379ds


title: IMR378ds


title: 8839 0234_7084_h133+_8839.cel 1 (rma)

description: frozen tissue of primary lung tumors


title: 8833 0234_7080_h133+_8833.cel 1 (rma)

description: frozen tissue of primary lung tumors


title: IMR379


title: IMR383ds


title: IMR380


title: IMR384ds


title: 8835 0234_7082_h133+_8835.cel 1 (rma)

description: frozen tissue of primary lung tumors


title: 8832 0234_7079_h133+_8832.cel 1 (rma)

description: frozen tissue of primary lung tumors


title: IMR378


title: 8847 0234_7090_h133+_8847.cel 1 (rma)

description: frozen tissue of primary lung tumors


title: IMR377ds


title: IMR376ds


title: IMR377


title: 8826 0234_7075_h133+_8826.cel 1 (rma)

description: frozen tissue of primary lung tumors


title: IMR376


title: 8825 0234_7074_h133+_8825.cel 1 (rma)

description: frozen tissue of primary lung tumors


title: 8829 0234_7077_h133+_8829.cel 1 (rma)

description: frozen tissue of primary lung tumors


title: 6787 0234_7071_h133+_6787.cel 1 (rma)

description: frozen tissue of primary lung tumors


title: IMR375ds


title: IMR375


title: IMR374


title: IMR374ds


title: IMR373ds


title: 6705 0234_7065_h133+_6705.cel 1 (rma)

description: frozen tissue of primary lung tumors


title: 6692 0234_7063_h133+_6692.cel 1 (rma)

description: frozen tissue of primary lung tumors


title: IMR373


title: 6523 0234_7057_h133+_6523.cel 1 (rma)

description: frozen tissue of primary lung tumors


title: IMR371ds


title: 6587 0234_7059_h133+_6587.cel 1 (rma)

description: frozen tissue of primary lung tumors


title: 6503 0234_7053_h133+_6503.cel 1 (rma)

description: frozen tissue of primary lung tumors


title: 8827 0234_7076_h133+_8827.cel 1 (rma)

description: frozen tissue of primary lung tumors


title: 6511 0234_7054_h133+_6511.cel 1 (rma)

description: frozen tissue of primary lung tumors


title: IMR371


title: IMR370


title: IMR370ds


title: IMR369ds


title: 97-0930 (rma)

description: frozen tissue of primary lung tumors


title: 6271 0234_7051_h133+_6271.cel 1 (rma)

description: frozen tissue of primary lung tumors


title: 01-139 (rma)

description: frozen tissue of primary lung tumors


title: 8822 0234_7072_h133+_8822.cel 1 (rma)

description: frozen tissue of primary lung tumors


title: IMR367


title: 01-0534 (rma)

description: frozen tissue of primary lung tumors


title: 01-0424 (rma)

description: frozen tissue of primary lung tumors


title: 6714 0234_7067_h133+_6714.cel 1 (rma)

description: frozen tissue of primary lung tumors


title: 6785 0234_7070_h133+_6785.cel 1 (rma)

description: frozen tissue of primary lung tumors


title: 01-0369 (rma)

description: frozen tissue of primary lung tumors


title: IMR364ds


title: IMR365


title: IMR365ds


title: 01-0284 (rma)

description: frozen tissue of primary lung tumors


title: 01-0331 (rma)

description: frozen tissue of primary lung tumors


title: IMR363ds


title: IMR364


title: IMR363


title: IMR367ds


title: IMR362ds


title: IMR369


title: 01-0189 (rma)

description: frozen tissue of primary lung tumors


title: 01-0236 (rma)

description: frozen tissue of primary lung tumors


title: 01-0646 (rma)

description: frozen tissue of primary lung tumors


title: IMR361ds


title: IMR362


title: IMR361


title: IMR360ds


title: 00-0941 (rma)

description: frozen tissue of primary lung tumors


title: IMR360


title: 00-0827 (rma)

description: frozen tissue of primary lung tumors


title: 00-1072 (rma)

description: frozen tissue of primary lung tumors


title: 01-0181 (rma)

description: frozen tissue of primary lung tumors


title: 00-0398 (rma)

description: frozen tissue of primary lung tumors


title: 00-0452 (rma)

description: frozen tissue of primary lung tumors


title: IMR358


title: IMR359


title: IMR358ds


title: 00-0334 (rma)

description: frozen tissue of primary lung tumors


title: 00-0479 (rma)

description: frozen tissue of primary lung tumors


title: IMR359ds


title: IMR357ds


title: IMR356ds


title: IMR357


title: IMR356


title: 00-0253 (rma)

description: frozen tissue of primary lung tumors


title: IMR355


title: IMR355ds


title: 96-353 (rma)

description: frozen tissue of primary lung tumors


title: 99-706 (rma)

description: frozen tissue of primary lung tumors


title: IMR354


title: IMR353ds


title: 97-608 (rma)

description: frozen tissue of primary lung tumors


title: 00-550 (rma)

description: frozen tissue of primary lung tumors


title: IMR352ds


title: 97-666 (rma)

description: frozen tissue of primary lung tumors


title: 98-956 (rma)

description: frozen tissue of primary lung tumors


title: IMR351


title: 96-264 (rma)

description: frozen tissue of primary lung tumors


title: 98-417 (rma)

description: frozen tissue of primary lung tumors


title: IMR353


title: IMR350


title: 97-829 (rma)

description: frozen tissue of primary lung tumors


title: 00-909 (rma)

description: frozen tissue of primary lung tumors


title: IMR352


title: IMR351ds


title: 00-0145 (rma)

description: frozen tissue of primary lung tumors


title: IMR349


title: 00-1082 (rma)

description: frozen tissue of primary lung tumors


title: 97-792 (rma)

description: frozen tissue of primary lung tumors


title: 00-703 (rma)

description: frozen tissue of primary lung tumors


title: IMR349ds


title: 00-440 (rma)

description: frozen tissue of primary lung tumors


title: IMR354ds


title: IMR350ds


title: 98-828 (rma)

description: frozen tissue of primary lung tumors


title: 98-197 (rma)

description: frozen tissue of primary lung tumors


title: IMR348ds


title: IMR347ds


title: IMR347


title: 98-723 (rma)

description: frozen tissue of primary lung tumors


title: 98-186 (rma)

description: frozen tissue of primary lung tumors


title: 98-1277 (rma)

description: frozen tissue of primary lung tumors


title: 98-691 (rma)

description: frozen tissue of primary lung tumors


title: IMR346ds


title: 98-343 (rma)

description: frozen tissue of primary lung tumors


title: IMR345ds


title: 98-438 (rma)

description: frozen tissue of primary lung tumors


title: 98-1063 (rma)

description: frozen tissue of primary lung tumors


title: 99-137 (rma)

description: frozen tissue of primary lung tumors


title: 99-301 (rma)

description: frozen tissue of primary lung tumors


title: IMR344


title: IMR345


title: IMR348


title: 99-1067 (rma)

description: frozen tissue of primary lung tumors


title: 00-151 (rma)

description: frozen tissue of primary lung tumors


title: 00-327 (rma)

description: frozen tissue of primary lung tumors


title: IMR343ds


title: IMR344ds


title: 99-1017 (rma)

description: frozen tissue of primary lung tumors


title: IMR341ds


title: IMR346


title: IMR340ds


title: 98-967 (rma)

description: frozen tissue of primary lung tumors


title: IMR340


title: 98-1296 (rma)

description: frozen tissue of primary lung tumors


title: IMR341


title: 98-375 (rma)

description: frozen tissue of primary lung tumors


title: IMR339ds


title: 98-1293 (rma)

description: frozen tissue of primary lung tumors


title: 98-152 (rma)

description: frozen tissue of primary lung tumors


title: IMR338ds


title: IMR338


title: 00-011 (rma)

description: frozen tissue of primary lung tumors


title: IMR335


title: IMR339


title: IMR335ds


title: 99-830 (rma)

description: frozen tissue of primary lung tumors


title: 98-1216 (rma)

description: frozen tissue of primary lung tumors


title: 98-771 (rma)

description: frozen tissue of primary lung tumors


title: IMR334


title: 98-1146 (rma)

description: frozen tissue of primary lung tumors


title: IMR332ds


title: IMR331ds


title: 98-657 (rma)

description: frozen tissue of primary lung tumors


title: 99-440 (rma)

description: frozen tissue of primary lung tumors


title: IMR330ds


title: 99-692 (rma)

description: frozen tissue of primary lung tumors


title: 00-1059 (rma)

description: frozen tissue of primary lung tumors


title: IMR331


title: IMR330


title: 99-728 (rma)

description: frozen tissue of primary lung tumors


title: 97-587 (rma)

description: frozen tissue of primary lung tumors


title: 98-1014 (rma)

description: frozen tissue of primary lung tumors


title: 97-403 (rma)

description: frozen tissue of primary lung tumors


title: IMR329ds


title: IMR328ds


title: IMR328


title: IMR334ds


title: 98-683 (rma)

description: frozen tissue of primary lung tumors


title: IMR329


title: 99-671 (rma)

description: frozen tissue of primary lung tumors


title: 96-475 (rma)

description: frozen tissue of primary lung tumors


title: IMR327ds


title: 98-933 (rma)

description: frozen tissue of primary lung tumors


title: IMR332


title: 97-1026 (rma)

description: frozen tissue of primary lung tumors


title: IMR326ds


title: IMR326


title: 96-3 (rma)

description: frozen tissue of primary lung tumors


title: 98-543 (rma)

description: frozen tissue of primary lung tumors


title: IMR325ds


title: IMR325


title: 98-711 (rma)

description: frozen tissue of primary lung tumors


title: IMR324ds


title: 98-401 (rma)

description: frozen tissue of primary lung tumors


title: IMR323


title: IMR323ds


title: 98-506 (rma)

description: frozen tissue of primary lung tumors


title: IMR322ds


title: 99-927 (rma)

description: frozen tissue of primary lung tumors


title: 98-853 (rma)

description: frozen tissue of primary lung tumors


title: IMR324


title: 98-320 (rma)

description: frozen tissue of primary lung tumors


title: IMR322


title: 36800 (rma)

description: frozen tissue of primary lung tumors


title: IMR321ds


title: IMR327


title: 00-315 (rma)

description: frozen tissue of primary lung tumors


title: IMR321


title: IMR343


title: 98-0679 (rma)

description: frozen tissue of primary lung tumors


title: 99-0077 (rma)

description: frozen tissue of primary lung tumors


title: 98-985 (rma)

description: frozen tissue of primary lung tumors


title: IMR318


title: 98-0292 (rma)

description: frozen tissue of primary lung tumors


title: IMR317ds


title: 97-0949 (rma)

description: frozen tissue of primary lung tumors


title: Chicken day six liver, Corticosterone rep6 vs. reference RNA pool

status: Public on Aug 09 2006

city: Newark

first: Larry

middle: Albert

last: Cogburn

state: DE

address: 531 South College Ave.

department: Animal and Food Sciences

institute: University of Delaware

description: Chicken day six liver, Corticosterone replicate 6

hyb_protocol: After pre-hybridization of the microarray slides in blocking reagent (1% BSA, 5 x SSC, 0.2% SDS), each slide was hybridized with a sample labeled with Alexa Fluor 555 (green) and a reference RNA sample labeled with Alexa Fluor 647 (red) in a reference hybridization design. Slides were hybridized overnight in a 42 degree C water bath under a light-tight box. On the following day, slides were sequentially washed with 1 x SSC, 0.2% SDS, and 0.5% DTT at 55 degrees C for 10 min, then 0.1 x SSC, 0.2% SDS, and 0.5% DTT for 5 min at room temperature, and finally 0.1 x SSC and 0.5% DTT for 1 min at room temperature, with nitrogen gas bubbled through each of the washes to prevent interference of ozone. The slides were subsequently rinsed in dH2O and dried by centrifugation. Before scanning, slides were stored in individual 50 ml tubes covered in aluminum foil and filled with nitrogen gas.

scan_protocol: Slides were scanned using an Axon 4100A Microarray Scanner (Axon Instruments) with GenePix Pro 5.0 software (Axon Instruments) and at a PMT count ratio (635/532) of about 1.

data_processing: The results of image analysis were automatically merged with Excel files containing the clone identification number/plate address and gene name/function (from the highest BLAST score).  Data in the VALUE column is based on the loess-normalized ratio of the loess-normalized log2 Alexa 555 and Alexa 647 values.  The values are based on non-background corrected median values.

label: Alex Fluor 555

organism: Gallus gallus

source_name: Chicken liver, day six of treatment

label_protocol: Chicken cDNA targets were synthesized with the SuperScript? Plus Indirect cDNA Labeling System (Invitrogen). First, total RNA samples (20 micrograms) were reverse transcribed using an anchored oligo(dT)20 primer, amino-modified dNTPs, and SuperScript III Reverse Transcriptase in 30 microliter volume. Next, the RNA template was destroyed by incubation with sodium hydroxide at 70 degrees C. First strand cDNA was purified with a Low-Elution Volume Spin Cartridge and then labeled with Alexa Fluor 555 (green) in a fluorsecent dye coupling reaction. Dye-incorporated cDNAs were purified to remove un-reacted dye and analyzed for their labeling efficiency with a NanoDrop spectrophotometer.

growth_protocol: Chicks were fed a broiler starter ration and raised in a controlled-environment animal room under a 20-h light:4-h darkness photoperiod in a heated battery-brooder until 3 weeks of age. At 3 weeks of age, 72 birds of uniform body weight (within 1 SD) were randomly assigned to wire cages within two identical controlled-temperature rooms with three birds per pen. Rooms were maintained under the same 20L:4D light/dark cycle throughout the duration of the experiment. The birds were provided with water and a commercial grower/finisher ration ad libitum until the end of the experiment.

extract_protocol: Total RNA from liver samples of birds that received six days of treatment was isolated using a RNeasy Midi kit (Qiagen, Valencia, CA) following the manufacturer's protocol with some modifications. The quantity of extracted total RNA was determined using a NanoDrop spectrophotometer (Wilmington, DE), and the quality of extracted total RNA was examined by microcapillary electrophoresis on a BioAnalyzer 2100 (Agilent, Wilmington, DE), where the rRNA ratio (28S/18S) was observed for integrity.

treatment_protocol: At 29 days of age, broiler cockerels (Ross x Cobb) were given a subcutaneous implant of an osmostic minipump (Alzet, model 2001; ALZA, Mountain View, CA) to continuously release hormone for seven days at a rate of 1.0 microliter/hour. Birds received a vehicle (50% DMSO and 50% propylene glycol) as control (VC), exogenous corticosterone (600 micrograms CS/kg/day), exogenous L-tri-idothyronine (192 micrograms T3/kg/day), or both CS and T3. After six days of treatment, liver tissue was excised immediately, snap frozen in liquid nitrogen, and stored in -80 degrees C until RNA isolation.

tag: Chicken liver, day six of treatment

label: Alexa Fluor 647

source_name: Reference pool of hepatic RNA from five-week-old control chickens

label_protocol: 23 aliquots of the reference RNA were labelled with Alexa Fluor 647 (red) as decribed above for channel 1. A pool was made of all Alexa Fluor 647 -labeled cDNA to be split among the 23 slides in the reference hybridization experiment.

extract_protocol: Extraction was conducted as described above for channel 1. Equal amounts of total RNA from six control birds were combined to form a reference RNA pool.


title: 99-1033 (rma)

description: frozen tissue of primary lung tumors


title: Chicken day six liver, Corticosterone rep4 vs. reference RNA pool

description: Chicken day six liver, Corticosterone replicate 4

tag: Reference pool of hepatic RNA from five-week-old control chickens


title: Chicken day six liver, Thyroid Hormone rep6 vs. reference RNA pool

description: Chicken day six liver, Thyroid Hormone replicate 6


title: 98-821 (rma)

description: frozen tissue of primary lung tumors


title: Chicken day six liver, Thyroid Hormone rep4 vs. reference RNA pool

description: Chicken day six liver, Thyroid Hormone replicate 4


title: Chicken day six liver, Corticosterone + Thyroid Hormone rep4 vs. reference RNA pool

description: Chicken day six liver, Corticosterone + Thyroid Hormone replicate 4


title: Chicken day six liver, Corticosterone + Thyroid Hormone rep5 vs. reference RNA pool

description: Chicken day six liver, Corticosterone + Thyroid Hormone replicate 5


title: Chicken day six liver, Thyroid Hormone rep5 vs. reference RNA pool

description: Chicken day six liver, Thyroid Hormone replicate 5


title: Chicken day six liver, Vehicle Control rep5 vs. reference RNA pool

description: Chicken day six liver, Vehicle Control replicate 5


title: Chicken day six liver, Vehicle Control rep6 vs. reference RNA pool

description: Chicken day six liver, Vehicle Control replicate 6


title: Chicken day six liver, Vehicle Control rep4 vs. reference RNA pool

description: Chicken day six liver, Vehicle Control replicate 4


title: Chicken day six liver, Thyroid Hormone rep2 vs. reference RNA pool

description: Chicken day six liver, Thyroid Hormone replicate 2


title: IMR318ds


title: Chicken day six liver, Corticosterone + Thyroid Hormone rep1 vs. reference RNA pool

description: Chicken day six liver, Corticosterone + Thyroid Hormone replicate 1


title: Effect of 9 hours of cycle stretch on normal human spinal ligament cells-2

city: Hirosaki

first: Ken-Ichi

last: Furukawa

address: Zaifucho 5

department: Pharmacology

country: Japan

institute: Hirosaki University School of Medicine

description: Total RNA was extracted from each cell monolayer. A quality check of each total RNA sample was carried out using an Agilent 2100 Bioanalyzer. Two micrograms of total RNA was reverse-transcribed into cDNA. Target cDNAs transcribed from non-stretched control cells and stretched cells were labeled with Cy3 and Cy5, respectively, and then hybridized with an Agilent Human 1 cDNA Microarray that included 18,564 cDNA elements. The microarrays were scanned in both the Cy3 and Cy5 channels with an Affymetrix 428 Array Scanner, and then analyzed using the ImaGene and GeneSight-Lite Software packages. The change in expression of each gene was shown as the ratio (Cy5 fluorescence/Cy3 fluorescence).

data_processing: After background subtraction and dye bias normalization, poor quality features were excluded from further analysis. Features with low signal intensity in the reference channel were filtered if the signal-to-noise ratio was less than 2.5. ANOVA was used to identify genes with a statistically different expression level in at least one of the experimental groups.

source_name: human spinal ligament cells in 9 hour static culture

tag: Human spinal ligament cells from patients with ossification of the posterior longitudinal ligament of the spine cultured for 9 hours in static condition.

source_name: human spinal ligament cells exposed to 9 hour cyclic stretch

tag: Human spinal ligament cells from patients with ossification of the posterior longitudinal ligament of the spine exposed to cyclic stretch for 9 hours.


title: Chicken day six liver, Corticosterone + Thyroid Hormone rep2 vs. reference RNA pool

description: Chicken day six liver, Corticosterone + Thyroid Hormone replicate 2


title: Chicken day six liver, Thyroid Hormone rep1 vs. reference RNA pool

description: Chicken day six liver, Thyroid Hormone replicate 1


title: Chicken day six liver, Corticosterone rep1 vs. reference RNA pool

description: Chicken day six liver, Corticosterone replicate 1


title: Effect of 9 hours of cycle stretch on human spinal ligament cells from patients with ossification-2


title: Effect of 9 hours of cycle stretch on normal human spinal ligament cells

description: Total RNA was extracted from each cell monolayer. A quality check of each total RNA sample was carried out using an Agilent 2100 Bioanalyzer.  Two micrograms of total RNA was reverse-transcribed into cDNA. Target cDNAs transcribed from non-stretched control cells and stretched cells were labeled with Cy3 and Cy5, respectively, and then hybridized with an Agilent Human 1 cDNA Microarray that included 18,564 cDNA elements. The microarrays were scanned in both the Cy3 and Cy5 channels with an Affymetrix 428 Array Scanner, and then analyzed using the ImaGene and GeneSight-Lite Software packages.  The change in expression of each gene was shown as the ratio (Cy5 fluorescence/Cy3 fluorescence).

data_processing: After background subtraction and dye bias normalization, poor quality features were excluded from further analysis.  Features with low signal intensity in the reference channel were filtered if the signal-to-noise ratio was less than 2.5.  ANOVA was used to identify genes with a statistically different expression level in at least one of the experimental groups.

source_name: Normal human spinal ligament cells in 9 hour static culture

tag: Human spinal ligament cells from patients with other cervical diseases with no relation to OPLL (ossification of the posterior longitudinal ligament of the spine)

source_name: Normal human spinal ligament cells exposed to 9 hour cyclic stretch

tag: same as channel 1


title: Effect of 9 hours of cycle stretch on human spinal ligament cells from patients with ossification


title: Chicken day six liver, Corticosterone rep3 vs. reference RNA pool

description: Chicken day six liver, Corticosterone replicate 3


title: Chicken day six liver, Vehicle Control rep3 vs. reference RNA pool

description: Chicken day six liver, Vehicle Control replicate 3


title: Chicken day six liver, Corticosterone rep5 vs. reference RNA pool

description: Chicken day six liver, Corticosterone replicate 5


title: Chicken day six liver, Corticosterone + Thyroid Hormone rep3 vs. reference RNA pool

description: Chicken day six liver, Corticosterone + Thyroid Hormone replicate 3


title: Chicken day six liver, Vehicle Control rep1 vs. reference RNA pool

description: Chicken day six liver, Vehicle Control replicate 1

hyb_protocol: After pre-hybridization of the microarray slides in blocking reagent (1% BSA, 5 x SSC, 0.2% SDS), each slide was hybridized with a sample labeled with Alexa Fluor 555 (green) and a reference RNA sample labeled with Alexa Fluor 647 (red) in a reference hybridization design.  Slides were hybridized overnight in a 42 degree C water bath under a light-tight box.  On the following day, slides were sequentially washed with 1 x SSC, 0.2% SDS, and 0.5% DTT at 55 degrees C for 10 min, then 0.1 x SSC, 0.2% SDS, and 0.5% DTT for 5 min at room temperature, and finally 0.1 x SSC and 0.5% DTT for 1 min at room temperature, with nitrogen gas bubbled through each of the washes to prevent interference of ozone.  The slides were subsequently rinsed in dH2O and dried by centrifugation.  Before scanning, slides were stored in individual 50 ml tubes covered in aluminum foil and filled with nitrogen gas.

label_protocol: Chicken cDNA targets were synthesized with the SuperScript Plus Indirect cDNA Labeling System (Invitrogen).  First, total RNA samples (20 micrograms) were reverse transcribed using an anchored oligo(dT)20 primer, amino-modified dNTPs, and SuperScript III Reverse Transcriptase in 30 microliter volume.  Next, the RNA template was destroyed by incubation with sodium hydroxide at 70 degrees C.  First strand cDNA was purified with a Low-Elution Volume Spin Cartridge and then labeled with Alexa Fluor 555 (green) in a fluorsecent dye coupling reaction.  Dye-incorporated cDNAs were purified to remove un-reacted dye and analyzed for their labeling efficiency with a NanoDrop spectrophotometer.

growth_protocol: Chicks were fed a broiler starter ration and raised in a controlled-environment animal room under a 20-h light:4-h darkness photoperiod in a heated battery-brooder until 3 weeks of age.  At 3 weeks of age, 72 birds of uniform body weight (within 1 SD) were randomly assigned to wire cages within two identical controlled-temperature rooms with three birds per pen.  Rooms were maintained under the same 20L:4D light/dark cycle throughout the duration of the experiment.  The birds were provided with water and a commercial grower/finisher ration ad libitum until the end of the experiment.

extract_protocol: Total RNA from liver samples of birds that received six days of treatment was isolated using a RNeasy Midi kit (Qiagen, Valencia, CA) following the manufacturer’s protocol with some modifications.  The quantity of extracted total RNA was determined using a NanoDrop spectrophotometer (Wilmington, DE), and the quality of extracted total RNA was examined by microcapillary electrophoresis on a BioAnalyzer 2100 (Agilent, Wilmington, DE), where the rRNA ratio (28S/18S) was observed for integrity.

treatment_protocol: At 29 days of age, broiler cockerels (Ross x Cobb) were given a subcutaneous implant of an osmostic minipump (Alzet, model 2001; ALZA, Mountain View, CA) to continuously release hormone for seven days at a rate of 1.0 microliter/hour.  Birds received a vehicle (50% DMSO and 50% propylene glycol) as control (VC), exogenous corticosterone (600 micrograms CS/kg/day), exogenous L-tri-idothyronine (192 micrograms T3/kg/day), or both CS and T3.  After six days of treatment, liver tissue was excised immediately, snap frozen in liquid nitrogen, and stored in –80 degrees C until RNA isolation.

label_protocol: 23 aliquots of the reference RNA were labelled with Alexa Fluor 647 (red) as decribed above for channel 1.  A pool was made of all Alexa Fluor 647 -labeled cDNA to be split among the 23 slides in the reference hybridization experiment.

extract_protocol: Extraction was conducted as described above for channel 1.  Equal amounts of total RNA from six control birds were combined to form a reference RNA pool.


title: Chicken day six liver, Vehicle Control rep2 vs. reference RNA pool

description: Chicken day six liver, Vehicle Control replicate 2


title: Double_positive_thymocytes_Dexamethasone (1E-07M) _3h_rep2

status: Public on Aug 08 2006

city: Perugia

first: Carlo

last: Riccardi

state: Perugia

address: via del Giochetto

department: Clinical and Experimetal Medicine

country: Italy

institute: Università degli Studi di Perugia

description: Thymi from 4 week old C3H/HeN mice were teased in culture medium, CD4+CD8+ double positive (DP) thymocytes were sorted with microbeads Miltenyi Biotech methods and were plated in 6 well plates with 3 ml of the culture medium at a concentration of 5.0E+06 cell/ml together with 1E-07 M Dexamethasone or a corresponding volume of PBS. DP thymocytes were kept at 37°C, 5% CO2 in a humidified atmosphere for 3 hours

data_processing: MAS 5.0

source_name: CD4+CD8+ double positive (DP) thymocytes 3h Dexamethasone(DEX) (final concentration 1E-07 M) treated

growth_protocol: CD4+CD8+ double positive thymocytes were plated in 6 well plates  with 3 ml of the  culture  medium at a concentration of 5.0 E+06 cell/ml and kept at 37°C , 5%CO2 in a humidified atmosphere for 3 hours

treatment_protocol: CD4+CD8+ double positive thymocytes were treated with medium and Dexamethasone (final concentration 1E-07 M) in PBS for 3 hours

tag: Strain

tag: Gender

value: female

tag: Age

value: 4 weeks

tag: Tissue

value: thymus


title: Double_positive_thymocytes_Dexamethasone (1E-07 M) _3h_rep1

growth_protocol: CD4+CD8+ double positive thymocytes were plated in 6 well plates  with 3 ml of the  culture  medium at a concentration of 5.0E+06 cell/ml and kept at 37°C , 5% CO2 in a humidified atmosphere for 3 hours

extract_protocol: Total RNA was isolated with TRIzol LS reagent(Invitrogen)


title: Double_positive_thymocytes_medium _3h_rep1

source_name: CD4+CD8+ double positive (DP) thymocytes 3h medium treated

treatment_protocol: CD4+CD8+ double positive thymocytes were treated with medium and 0.1% PBS for 3 hours


title: Double_positive_thymocytes_medium _3h_rep2


title: 20_LAC_FOS

status: Public on Aug 07 2006

city: Raleigh

first: Todd

middle: Robert

last: Klaenhammer

department: Department of Food, Bioprocessing, and Nutrition Sciences

institute: North Carolina State University

description: L. acidophilus cells, transferred at least five times in modified MRS medium (Barrangou et al, 2003) containing the carbohydrate of interest, were grown to an OD600 of 0.6, harvested and processed for microarray experiments (Azcarate-Peril et al, 2005).

organism: Lactobacillus acidophilus

source_name: L. acidophilus, lactose

source_name: L. acidophilus, fructooligosaccharides


title: 21_FOS_GAL

source_name: L. acidophilus, galactose


title: 19_FOS_RAF

source_name: L. acidophilus, raffinose


title: Chicken day six liver, Thyroid Hormone rep3 vs. reference RNA pool

description: Chicken day six liver, Thyroid Hormone replicate 3


title: 15_RAF_SUC

source_name: L. acidophilus, sucrose


title: 17_GAL_SUC


title: 16_SUC_LAC


title: 14_SUC_FOS


title: 13_TRE_FRU

source_name: L. acidophilus, trehalose

source_name: L. acidophilus, fructose


title: 12_FRU_GAL


title: 9_FOS_FRU


title: 11_LAC_FRU


title: 6_GAL_GLC

source_name: L. acidophilus, glucose


title: 10_FRU_RAF


title: 8_FRU_SUC


title: 4_RAF_GLC


title: 2_SUC_GLC


title: 1_GLC_FRU


title: 3_GLC_FOS

source_name: L. acidophilus, fructooligosaccharide


title: 26_LAC_GAL


title: 27_TRE_LAC


title: 24_GAL_RAF


title: hippocampus_FVBNJ_4_271102

city: Utrecht

first: Cathy

last: Fernandes

address: Universiteitsweg 100

department: Pharmacology & Anatomy

country: Netherlands

institute: Rudolf Magnus Institute of Neuroscience

description: For full description of the experiment, refer to Fernandes et al (2004) Eur J Neuroscience 19:2576-2582

hyb_protocol: Using standard Affymetrix protocols (Affymetrix 1999 Genechip Expression Technical Manual, Affymetrix Santa Clara USA)

data_processing: Using Affymetrix global scaling (TGT 100) and MAS5 algorithm

label: Streptavidin

source_name: Hippocampal total RNA

growth_protocol: Every effort was made to keep the environment constant for all study mice. Mice were killed by cervical dislocation.

extract_protocol: Guanidium thiocyanate method of Chomczynski and Sacchi (Anal Biochem, 1987, 162:156-159) using Trizol reagent.

treatment_protocol: No treatment was given as the study was an inbred strain comparision.

tag: strain (FVB/NJ)

tag: gender (male)

tag: age (13-14 weeks)

tag: tissue (hippocampus)


title: 25_RAF_TRE


title: 22_TRE_FOS


title: 23_RAF_LAC


title: hippocampus_BALBcByJ_3_271102

scan_protocol: Using standard Affymetrix protocols (Affymetrix 1999 Genechip Expression Technical Manual, Affymetrix Santa Clara USA)

tag: strain (BALB/cByJ)


title: hippocampus_SJLJ_4_130902

label_protocol: Using standard Affymetrix protocols (Affymetrix 1999 Genechip Expression Technical Manual, Affymetrix Santa Clara USA)

tag: strain (SJL/J)


title: 18_SUC_TRE


title: hippocampus_129S1SvImJ_4_130902

tag: strain (129S1/SvImJ)


title: 5_GLC_LAC


title: hippocampus_SJLJ_3_120902


title: hippocampus_129S1SvImJ_3_120902


title: 7_GLC_TRE


title: hippocampus_C3HHeJ_4_130902

tag: strain (C3H/HeJ)


title: hippocampus_FVBNJ_3_130902


title: hippocampus_C3HHeJ_3_120902


title: 28_GAL_TRE


title: hippocampus_AJ_4_130902

tag: strain (A/J)


title: hippocampus_DBA2J_4_130902

tag: strain (DBA/2J)


title: hippocampus_AJ_3_120902


title: hippocampus_C57BL6J_4_130902

tag: strain (C57BL/6J)


title: hippocampus_C57BL6J_3_120902


title: hippocampus_DBA2J_3_120902


title: hippocampus_DBA2J_2_110702


title: hippocampus_129S1SvImJ_2_110702


title: hippocampus_SJLJ_2_110702


title: hippocampus_C3HHeJ_1_040702


title: hippocampus_SJLJ_1_040702


title: hippocampus_C3HHeJ_2_110702


title: hippocampus_FVBNJ_1_040702


title: hippocampus_FVBNJ_2_120902


title: hippocampus_C57BL6J_1_040702


title: hippocampus_C57BL6J_2_110702


title: hippocampus_AJ_2_110702


title: hippocampus_BALBcByJ_2_110702

extract_protocol: Extraction protocol Guanidium thiocyanate method of Chomczynski and Sacchi (Anal Biochem, 1987, 162:156-159) using Trizol reagent.


title: hippocampus_AJ_1_040702


title: hippocampus_BALBcByJ_1_040702


title: AAkata_exposure_TGFbeta1_rep2

status: Public on Aug 05 2006

city: Dublin

first: Andrea

middle: Patricelli

last: Malizia

address: 21, Nelson Street

country: Ireland

institute: University College Dublin

description: Microarray gene chip analysis performed by Genome Explorations www.genome-explorations.com

data_processing: MAS5.0, RMA

source_name: AAkata TGFbeta1 4hours

tag: EBV infected A549 (AAkata) cultured in RPMI1640+5%FCS, exposed to TGFbeta1 10ng/ml for 4hours.


title: AAkata_exposure_TGFbeta1_rep1

tag: EBV infected A549 (AAkata) cultured in RPMI1640+5%FCS, exposed to 10ng/ml TGFbeta1 for 4hours


title: PA_WT - 120 Min - Replicate 2

status: Public on Aug 04 2006

city: La Jolla

first: Floyd

last: Romesberg

address: 10550 N. Torrey Pines Road

department: Chemistry

institute: The Scripps Research Institute

description: Present (P) and Absent (A) calls were determined with the Affymetrix algorithm (GCOS, Affymetrix, Santa Clara, CA).  All marginal (M) calls were treated as absent (A).  Probesets were considered present for a given condition if they had been assigned a present call in at least two of the three replicate samples for that condition.

scan_protocol: standard Affymetrix Prokaryotic Target Preparation protocol as described at the Affymetrix website Chips were scanned using the Affymetrix ScanArray 3000 using default settings and a target intensity of 250 for scaling

organism: Pseudomonas aeruginosa

source_name: P. aeruginosa PAO1, 120 min post ciprofloxacin addition

growth_protocol: Luria broth at 37 C with shaking

extract_protocol: Qiagen RNeasy mini kit with RNAprotect reagent and on-column DNAse digestion

treatment_protocol: Grow to mid-log in luria broth, treat with 1 ug/ml ciprofloxacin (~8x MIC).  Take samples at 0, 30, 120 minutes post drug addition

tag: P. aeruginosa strain PAO1


title: PA_WT - 120 Min - Replicate 1

hyb_protocol: standard Affymetrix Prokaryotic Target Preparation protocol as described at the Affymetrix website

data_processing: Present (P) and Absent (A) calls were determined with the Affymetrix algorithm (GCOS, Affymetrix, Santa Clara, CA).  All marginal (M) calls were treated as absent (A).  Probesets were considered present for a given condition if they had been assigned a present call in at least two of the three replicate samples for that condition.


title: PA_WT - 30 min - Replicate 1

source_name: P. aeruginosa PAO1, 30 min post ciprofloxacin addition

label_protocol: standard Affymetrix Prokaryotic Target Preparation protocol as described at the Affymetrix website


title: PA_WT - 30 Min - Replicate 2


title: PA_WT - 120 Min - Replicate 3


title: PA_WT - 0 Min - Replicate 2

source_name: P. aeruginosa PAO1, 0 min post ciprofloxacin addition


title: PA_LexA Mutant - 120 Min - Replicate 3

source_name: P. aeruginosa LexA Mutant, 120 min post ciprofloxacin addition

tag: P. aeruginosa strain PAO1 mutant with Ser125Ala mutation in lexA and a gentamciin resistance marker from vector pBBR1MCS-5


title: PA_LexA Mutant - 120 Min - Replicate 2


title: hippocampus_129S1SvImJ_1_040702


title: Linoleate+TNF100 sample2

city: East Lansing

first: Zheng

last: Li

state: MI

address: 2527 Engineering Building

department: Chemical Engineering and Materials Science

institute: Michigan State University

description: TNFa(0, 20,100 ng/ml), and FFA( palm, oleate, linoleate,BSA, control) combinations treated HepG2 cells to study the cytotoxicity

data_processing: log2 ratio of the cy3 by cy5

source_name: HepG2 cells treated with lnoleate medium +tnf100 for 24 hours

source_name: HepG2 cells treated with HepG2 medium 24 hours


title: PA_LexA Mutant - 0 Min - Replicate 2

source_name: P. aeruginosa LexA Mutant, 0 min post ciprofloxacin addition


title: hippocampus_DBA2J_1_040702


title: Linoleate+TNF100


title: PA_LexA Mutant - 120 Min - Replicate 1


title: PA_LexA Mutant - 30 Min - Replicate 1

source_name: P. aeruginosa LexA Mutant, 30 min post ciprofloxacin addition

tag: P. aeruginosa strain PAO1 mutant with Ser125Ala mutation in lexA and a gentamicin resistance marker from vector pBBR1MCS-5


title: BSA+TNF100 sample2

source_name: HepG2 cells treated with BSA medium +tnf100 for 24 hours


title: Ole+TNF100 sample2

source_name: HepG2 cells treated with oleate medium +tnf100 for 24 hours

tag: 0.7 mM oleate 100ng/ml tnf-alpha


title: Ole+TNF100


title: HepG2 medium+TNF100

source_name: HepG2 cells treated with hepg2 medium +tnf100 for 24 hours

tag: hepg2 medium + 100ng/ml tnf-alpha


title: Linoleate+TNF20 sample2

source_name: HepG2 cells treated with linoleate medium +tnf20 for 24 hours

tag: 0.7mM linoleate


title: palm+TNF100 sample2

source_name: HepG2 cells treated with palmitate medium +tnf100 for 24 hours


title: HepG2 medium+TNF100 sample2


title: palm+TNF100


title: PA_WT - 0 Min - Replicate 1


title: PA_lexA(S125A) - 0 Minutes - Replicate 1

source_name: lexA(S125A) mutant, 0 minutes after ciprofloxacin addition

tag: P. aeruginosa PAO1 mutant containing a Ser125Ala mutation in the lexA gene and a gentamicin-resistance marker from vector pBBR1MCS-5


title: Ole+TNF20 sample2

source_name: HepG2 cells treated with oleate medium +tnf20 for 24 hours


title: Ole+TNF20


title: Linoleate+TNF20


title: Stem cell sample 5 (B)

city: London

first: Kim

middle: B.

last: Jensen

address: 44 Lincoln's Inn Fields

department: London Research Institute

institute: Cancer Research UK

description: Gene expression data from single cultured human epidermal keratinocytes

hyb_protocol: Following fragmentation, 10 microg of cDNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array HU133. GeneChips were washed and stained using an Affymetrix GeneChip Instrument System.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

source_name: Cultured human keratinocytes at passage 3

label_protocol:
amplified mRNA from single cultured epidermal keratinocytes
Biotinylated cDNA were prepared according to Tietjen et al. 2003, Neuron.

growth_protocol: Keratinocytes were cultured on a feeder layer of J2-3T3 cells in FAD medium (1 part HAM’S F12, 3 parts Dulbecco’s modified Eagle’s medium, 1.8x10-4 M adenine), supplemented with 10% fetal calf serum (FCS), 0.5 µg/ml hydrocortisone, 5 µg/ml insulin, 10-10 M cholera enterotoxin and 10ng/ml EGF

extract_protocol: Single cells were seeded in amplification buffer

treatment_protocol: Keratinocyte were picked upon putting them in suspension and seeded in single cell amplification buffer

tag: Human epidermal keratinocyte from healthy donor


title: palm+TNF20

source_name: HepG2 cells treated with palmitate medium +tnf20 for 24 hours


title: BSA+TNF20 sample2

source_name: HepG2 cells treated with BSA medium +tnf20 for 24 hours


title: Stem cell sample 4 (B)


title: palm+TNF20 sample2


title: Stem cell sample 1 (B)


title: BSA+TNF20


title: PA_LexA Mutant - 30 Min - Replicate 2


title: Stem cell sample 2 (B)


title: Stem cell sample 3 (B)


title: Transit amplifying cell sample 6 (B)


title: hippocampus_BALBcByJ_4_291102

source_name: Hippocampal total RNA

tag: strain (BALB/cByJ)

tag: gender (male)

tag: age (13-14 weeks)

tag: tissue (hippocampus)


title: Chicken day six liver, Corticosterone rep2 vs. reference RNA pool

description: Chicken day six liver, Corticosterone replicate 2

source_name: Chicken liver, day six of treatment

tag: Chicken liver, day six of treatment

source_name: Reference pool of hepatic RNA from five-week-old control chickens


title: HepG2 medium+TNF20

source_name: HepG2 cells treated with hepg2 medium +tnf20 for 24 hours


title: Transit amplifying cell sample 3 (B)


title: Stem cell sample 6 (B)


title: Transit amplifying cell sample 2 (B)


title: Transit amplifying cell sample 5 (B)


title: BSA+TNF100

tag: bsa + 100ng/ml

source_name: HepG2 cells treated with HepG2 medium 24 hours


title: Transit amplifying cell sample 4 (B)


title: Linoleate+TNF0 sample2

source_name: HepG2 cells treated with Linoleate for 24 hours


title: A.thaliana with the RNAi silenced Myosin XI-K, Group 3

city: Corvallis

first: Valera

last: Peremyslov

address: 2082 Cordley Hall

department: Botany and Plant Pathology

institute: Oregon State University

description: RNA integrity screening, Probe synthesis, hybridization and scanning were conducted by the Center for Genome Research and Biocomputing Core Laboratories at Oregon State University, Corvallis OR.

hyb_protocol: Prior to hybridization, the cRNA was purified with GeneChip Sample Cleanup Modules (Affymetrix, Santa Clara, CA), and fragmented. 10 mkg from each experimental sample along with Affymetrix eukaryotic hybridization controls were hybridized for 16 hours to Affymetrix ATH1 array in an Affymetrix GeneChip Hybridization Oven 640. Affymetrix GeneChip Fluidics Station 450 was used to wash and stain the arrays with streptavidin-phycoerythrin (Moleculer Probes, Eugene, OR), biotinylated anti-streptavidin (Vector Laboratories, Burlingame, CA) according to the standard antibody amplification protocol for eukaryotic targets.

scan_protocol: Arrays were scanned with an Affymetrix GeneChip Scanner 3000 at 570nm.

data_processing: Data were generated with GCOS software (MAS5.0 method) with a scale factor of 500.

label: phycoerythrin

source_name: Mixture of rosette, cauline leaves and flowers in equal proportions

label_protocol: Biotinylated cRNA was synthesized from the double stranded cDNA using T7 RNA polymerase and a biotin-conjugated pseudouridine containing nucleotide mixture provided in the IVT Labeling Kit (Affymetrix, Santa Clara, CA) .

extract_protocol: Total RNA was purified using RNeasy Plant Mini kit (QIAGEN). 5 mkg of total RNA was used to generate biotinylated complementary RNA (cRNA) using the One-Cycle Target Labeling protocol (Affymetrix, Santa Clara, CA) from the GeneChip Expression Analysis Technical Manual ( 701021 Rev. 5 ).

tag: A.thaliana cv. Col-0 with the RNAi silenced Myosin XI-K


title: Transit amplifying cell sample 1 (B)


title: A.thaliana with the RNAi silenced Myosin XI-K, Group 2


title: Ole+TNF0 sample2

source_name: HepG2 cells treated with Oleate for 24 hours


title: A.thaliana expressing GUS transgene

tag: A.thaliana cv. Col-0 constitutively expressing GUS driven by 35S promoter


title: A.thaliana with the RNAi silenced Myosin XI-K, Group 1


title: A549_exposure_TGFbeta1_rep1

description: Microarray chip analysis performed by Genome Explorations

data_processing: Normalization method

source_name: A549 TGFbeta1 4hours

tag: A549 cell line exposed to 10ng/ml TGFbeta1 4hours in RPMI1640+5%FCS.


title: HeLa, mock, 24 hr vs. HeLa, SOD1 SNP at position 18

city: Boston

first: Julja

last: Burchard

address: 33 Avenue Louis Pasteur

department: Computational & Systems Biology

institute: Merck & Co., Inc.

description:
For details please see: Dianne S. Schwarz, Hongliu Ding, Lori Kennington,
Jessica T. Moore, Janell Schelter, Julja Burchard, Peter S. Linsley,
Neil Aronin, Zuoshang Xu and Phillip D. Zamore  (2006) PLoS Genetics.

data_processing: custom

label: Cy3/Cy5 (fluor-reversed pair)

source_name: HeLa cells

tag: Cells transfected with siRNA to SOD1, SNP at position 18

label: Cy5/Cy3 (fluor-reversed pair)

tag: Cells mock-transfected


title: HepG2 medium+TNF20 sample2


title: HeLa, mock, 24 hr vs. HeLa, SOD1 SNP at position 19

tag: Cells transfected with siRNA to SOD1, SNP at position 19


title: AAKata_rep2

source_name: AAKata

tag: AAKata cultured in RPMI1640+5%FCS


title: HeLa, mock, 24 hr vs. HeLa, SOD1 SNP at position 16

tag: Cells transfected with siRNA to SOD1, SNP at position 16


title: FFA+TNF HepG2 cells(BSA0_1)

source_name: HepG2 cells treated with BSA for 24 hours


title: HeLa, mock, 24 hr vs. HeLa, SOD1 SNP at position 15

tag: Cells transfected with siRNA to SOD1, SNP at position 15


title: BSA0_2


title: AAKata_rep1

tag: AAkata cultured in RPMI 1640 + 5%FCS


title: A549_rep2

source_name: A549 control

tag: A549 cell line cultured in RPMI 1640 + 5%FCS


title: A549_rep1

description: Microarray chip analysis supplied by Genome Explorations, www.genome-explorations.com


title: Linoleate+TNF0


title: Auratus goldfish genome project: Slide 30; Fluoxetine on the reproductive axis of female goldfish

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

description: Further details for techniques and protocols for our microarray hybridizations and normalizations can be found in Mennigen et al. The effects of fluoxetine on the reproductive axis of female goldfish (Carassius auratus)(to be submitted) and Martyniuk et al. Gene expression profiling in the brain of male goldfish exposed to 17alphaEE2(in press; Physiological Genomics).  Sequence information found at www.auratus.ca

data_processing: Array quality filter test used; Intensity-dependent Lowess normalization

organism: Carassius auratus

source_name: Carassius auratus; hypothalamus; i.p injection fluoxetine

tag: Female adult goldfish

tag: tissue

value: hypothalamus

tag: Fish were treated twice a week for 17 days with 5 μg fluoxetine/g of body weight

tag: Sexually regressed animals (December)

tag: Adults approx. 2-3 years of age

source_name: Carassius auratus; hypothalamus; i.p. saline control

tag: Fish were treated twice a week for 17 days with 0.6%saline


title: Auratus goldfish genome project: slide 39; The effects of fluoxetine on female goldfish

description: Further details for techniques and protocols for our microarray hybridizations and normalizations can be found in Mennigen et al. ?The effects of fluoxetine on the reproductive axis of female goldfish (Carassius auratus)? (to be submitted) and Martyniuk et al. Gene expression profiling in the brain of male goldfish exposed to 17α-EE2 (in press Physiological Genomics).  Sequence information found at www.auratus.ca

tag: Dye swap with slide 36


title: HeLa, mock, 24 hr vs. HeLa, SOD1 SNP at position 11

tag: Cells transfected with siRNA to SOD1, SNP at position 11


title: Stem cell sample 4 (A)

source_name: Cultured human keratinocytes at passage 3

growth_protocol: Keratinocytes were cultured on a feeder layer of J2-3T3 cells in FAD medium (1 part HAM’S F12, 3 parts Dulbecco’s modified Eagle’s medium, 1.8x10-4 M adenine), supplemented with 10% fetal calf serum (FCS), 0.5 µg/ml hydrocort

tag: Human epidermal keratinocyte from healthy donor


title: palm0

source_name: HepG2 cells treated with palmitate for 24 hours


title: Stem cell sample 5 (A)


title: HeLa, mock, 24 hr vs. HeLa, SOD1 SNP at position 14

tag: Cells transfected with siRNA to SOD1, SNP at position 14


title: HeLa, mock, 24 hr vs. HeLa, SOD1 SNP at position 12

tag: Cells transfected with siRNA to SOD1, SNP at position 12

tag: Cells mock-transfected


title: Auratus goldfish genome project:slide50_MuscTel

description: Further details for techniques and protocols for our microarray hybridizations and normalizations can be found in

source_name: Carassius auratus; telencephalon; i.p injection 1 ug/gram muscimol

value: telencephalon

tag: single i.p. injection muscimol 1 ug/gram body weight

tag: 6 hour treatment

tag: Sexually regressed animals (mid-August)

source_name: Carassius auratus; telencephalon; saline control

tag: Control i.p. injection of 0.6% saline


title: A549_exposure_TGFbeta1_rep2

tag: A549 cell line exposed to 10ng/ml TGFbeta1 4hours in RPMI1640+5%FCS


title: Ole+TNF0


title: HeLa, mock, 24 hr vs. HeLa, SOD1 SNP at position 10

tag: Cells transfected with siRNA to SOD1, SNP at position 10


title: HeLa, mock, 24 hr vs. HeLa, SOD1 SNP at position 9

tag: Cells transfected with siRNA to SOD1, SNP at position 9


title: Auratus goldfish genome project:slide33_MuscTel

tag: Female adult goldfish

tag: tissue

tag: dye swap with slide22


title: Stem cell sample 2 (A)


title: Auratus goldfish genome project:slide22_Muscimol expt.

tag: Adults approx. 2-3 years of age

tag: dye swap with slide 33


title: AURATUS goldfish genome project:Slide16_MuscTel


title: Stem cell sample 1 (A)


title: Stem cell sample 3 (A)


title: HeLa, mock, 24 hr vs. HeLa, SOD1 SNP at position 7

tag: Cells transfected with siRNA to SOD1, SNP at position 7


title: HeLa, mock, 24 hr vs. HeLa, SOD1 SNP at position 13

tag: Cells transfected with siRNA to SOD1, SNP at position 13


title: HeLa, mock, 24 hr vs. HeLa, SOD1 SNP at position 6

tag: Cells transfected with siRNA to SOD1, SNP at position 6


title: HeLa, mock, 24 hr vs. HeLa, SOD1 SNP at position 8

tag: Cells transfected with siRNA to SOD1, SNP at position 8


title: Transit amplifying cell sample 5 (A)

tag: Human epidermal keratinocyte from healthy donor


title: HeLa, mock, 24 hr vs. HeLa, SOD1 SNP at position 5

tag: Cells transfected with siRNA to SOD1, SNP at position 5

tag: Cells mock-transfected


title: Transit amplifying cell sample 3 (A)


title: HeLa, mock, 24 hr vs. HeLa, SOD1 SNP at position 3

tag: Cells transfected with siRNA to SOD1, SNP at position 3


title: Stem cell sample 6 (A)


title: HeLa, mock, 24 hr vs. HeLa, SOD1 SNP at position 2

tag: Cells transfected with siRNA to SOD1, SNP at position 2


title: HeLa, mock, 24 hr vs. HeLa, SOD1 SNP at position 1

tag: Cells transfected with siRNA to SOD1, SNP at position 1


title: Transit amplifying cell sample 6 (A)


title: Arctic ground squirrel skeletal muscle of torpor animal rep9 on 2A array on 16-sample beadchip

status: Public on Aug 03 2006

city: Fairbanks

first: Jun

last: Yan

state: AK

address: 311 Irving Building

department: Institute of Arctic Biology

institute: University of Alaska Fairbanks

description: Gene expression data from arctic ground squirrel skeletal muscle of torpor animal sampled by saw-dust method during hibernation

data_processing: The data were analyzed with Illumina Inc. BeadStudio version 1.5.1.3 and normalized by rank invariant method.

label: Biotin Streptavidin-Cy3

organism: Urocitellus parryii

source_name: Arctic ground squirrel skeletal muscle of torpor animal sampled by saw-dust method during hibernation

tag: torpor skeletal muscle