title: Control cells, 48 h post-supplementation.

description: HMVEC (Cambrex, Walkersville, MD, USA) were cultured in endothelial growth medium 2-microvascular (bulletkit, BioWhittaker, Walkersville, MD, USA) supplemented as directed with 5% fetal bovine serum. The cells (passage 9) were plated at 2.5 x 104 cells/cm^2 at 37 degrees Celsius in a humidified chamber with 5% carbon dioxide. They were grown to confluence. After confluence, medium was refreshed, and 0.6% dimethyl sulfoxide (DMSO) vehicle control was added to the sample. Total RNA from the cultures was isolated 48 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.

source_name: Human microvascular endothelial cells (HMVEC), 48 h post-supplementation with 0.6% dimethyl sulfoxide (DMSO) vehicle control.


title: pqsE rep3

status: Public on Jul 17 2009

type: RNA

city: Boston

first: Laurence

middle: G

last: Rahme

state: MA

address: 50 Blosson St, Thier 340

department: Surgery

country: USA

institute: Massachusetts General Hospital

description: pqsE is a key gene in virulence of P. aeruginosa.

hyb_protocol: According to Affymetrix GeneChip® Fluidics Station 450 protocol.

scan_protocol: According to Affymetrix scanner 3000 protocol

data_processing: Affymetrix Microarray Suite version 5.0

label: biotin

molecule: total RNA

organism: Pseudomonas aeruginosa

source_name: pqsE mutant OD 3

label_protocol: According to Enzo Life sciences BioArray terminal labeling kit with biotin ddUTP.

growth_protocol: Cells were inoculated from -80C stock, grown in LB at 37C over night, diluted 1:100 and grown to OD600nm of 3.0

extract_protocol: According to Qiagen RNAeasy mini kit

tag: mutant

value: pqsE

tag: bacteria

value: Pseudomonas aeruginosa

tag: strain

tag: protocol

value: LB at 37C until OD 3


title: 6CABA rep3

description: 2-amino-6-chlorobenzoic acid (6CABA) is a halogenated anthranilic acid analog that specifically inhibits intercellular signals and virulence mediated by the MvfR pathway (PLoS Pathog. 2007 September; 3(9): e126).

source_name: Pseudomonas aeruginosa PA14

growth_protocol: Cells were inoculated from -80C stock, grown in LB at 37C over night, diluted 1:100 and grown to OD600nm of 2.5

treatment_protocol: 6CABA was added at concentration of 6mM dissolved in LB medium.

value: treated with 6mM of 6CABA


title: Control cells, 1 h post-supplementation.

city: Charlottesville

first: Erwin

middle: P

last: Gianchandani

state: VA

department: Office of the Vice President for Research

institute: University of Virginia

description: HMVEC (Cambrex, Walkersville, MD, USA) were cultured in endothelial growth medium 2-microvascular (bulletkit, BioWhittaker, Walkersville, MD, USA) supplemented as directed with 5% fetal bovine serum. The cells (passage 9) were plated at 2.5 x 104 cells/cm^2 at 37 degrees Celsius in a humidified chamber with 5% carbon dioxide. They were grown to confluence. After confluence, medium was refreshed, and 0.6% dimethyl sulfoxide (DMSO) vehicle control was added to the sample. Total RNA from the cultures was isolated 1 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.

hyb_protocol: Biotin-labeled cRNA was generated from the total RNA samples and fragmented in preparation for array hybridization, according to standard Affymetrix GeneChip protocols. Fragmented cRNA (10 µg) was hybridized to Affymetrix Human Genome U133 Plus 2.0 probe arrays for 16 h.

scan_protocol: The arrays were washed and stained in an Affymetrix Automated Fluidics Station 400 and scanned with the Affymetrix GeneArray Scanner. Scanned images were examined for visible defects and checked for proper grid alignment, and acceptable image files were analyzed to generate raw data in the form of ‘CEL’ files. Quality control, including replicate analysis, measurement of noise and background levels, and assessment of the 3'/5' ratio of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and beta-actin (β-actin) was performed with Microarray Analysis Suite 5.0 (MAS 5.0, Affymetrix).

data_processing: Using MAS 5.0, each gene transcript was detected as ‘present’, ‘absent’ or ‘marginal’, and the change between the experimental (PNF1-stimulated) and baseline (control) conditions at each timepoint was assigned to one of several standard categories, i.e., increase, marginal increase, no change, marginal decrease and decrease, depending on the P-value (calculated using the Wilcoxon signed rank test). The ranges for each call were 0.0000–0.0025, 0.0025–0.0030, 0.0030–0.9970, 0.9970–0.9975 and 0.9975 to 1.0000, respectively. These data were then inputted into dChip version 1.3 (Li and Wong, 2001), where they were normalized using the invariant set approach.

label: Biotin

organism: Homo sapiens

source_name: Human microvascular endothelial cells (HMVEC), 1 h post-supplementation with 0.6% dimethyl sulfoxide (DMSO) vehicle control.

label_protocol: RNA samples were prepared for hybridization using the GeneChip One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA, USA).  Total RNA integrity was assessed by analysis with an Agilent Bioanalyzer using RNA 6000 Nano chips (Agilent Technologies, Santa Clara, CA, USA).

tag: cell line

value: HMVEC


title: Control cells, 24 h post-supplementation.

description: HMVEC (Cambrex, Walkersville, MD, USA) were cultured in endothelial growth medium 2-microvascular (bulletkit, BioWhittaker, Walkersville, MD, USA) supplemented as directed with 5% fetal bovine serum. The cells (passage 9) were plated at 2.5 x 104 cells/cm^2 at 37 degrees Celsius in a humidified chamber with 5% carbon dioxide. They were grown to confluence. After confluence, medium was refreshed, and 0.6% dimethyl sulfoxide (DMSO) vehicle control was added to the sample. Total RNA from the cultures was isolated 24 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.

source_name: Human microvascular endothelial cells (HMVEC), 24 h post-supplementation with 0.6% dimethyl sulfoxide (DMSO) vehicle control.


title: Control cells, 4 h post-supplementation.

description: HMVEC (Cambrex, Walkersville, MD, USA) were cultured in endothelial growth medium 2-microvascular (bulletkit, BioWhittaker, Walkersville, MD, USA) supplemented as directed with 5% fetal bovine serum. The cells (passage 9) were plated at 2.5 x 104 cells/cm^2 at 37 degrees Celsius in a humidified chamber with 5% carbon dioxide. They were grown to confluence. After confluence, medium was refreshed, and 0.6% dimethyl sulfoxide (DMSO) vehicle control was added to the sample. Total RNA from the cultures was isolated 4 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.

source_name: Human microvascular endothelial cells (HMVEC), 4 h post-supplementation with 0.6% dimethyl sulfoxide (DMSO) vehicle control.


title: Expression profiling of Bmal -/- littermate dorsal skin_rep2

city: Irvine

first: Kevin

middle: K

last: Lin

state: CA

address: 250 Sprague Hall

department: Biological Chemistry & Medicine

institute: University of California, Irvine

description: Hair cycle staging: telogen

hyb_protocol: Following the recommended procedure, 0.54 ug of this fragmented target single-stranded cDNA was hybridized at 45c with rotation for 17 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix Mouse Gene 1.0 ST array.  The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fludics Station 450 (Fluidics protocol FS450_007).

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 7G and GeneChip Operating Software v. 1.4 to produce .CEL intensity files.

data_processing:
These probe cell intensity files (*.CEL) were analyzed in Affymetrix Expression Console software v1.1 using the PLIER algorithm to generate probe level summarization files (*.CHP).
(Algorithm: PLIER v 2.0; Quantification Scale: Linear; Quantification Type: Signal and Detection P-Value; Background: PM-GCBG; Normalization Method: Sketch-Quantile).

organism: Mus musculus

source_name: Bmal -/- dorsal skin at P22, biological replicate 2

label_protocol:
Single-stranded, then double-stranded cDNA was synthesized from the poly(A)+mRNA present in the isolated total RNA (typically 100ng total RNA starting material each sample reaction) using the GeneChip WT cDNA synthesis Kit (Affymetrix, Inc., Santa Clara, CA) and random hexamers tagged with a T7 promoter sequence.  The double-stranded cDNA is then used as a template to generate many copies of antisense cRNA from an in vitro transcription reaction (IVT) of 16hrs in the presence of T7 RNA Polymerase using the Affymetrix Genechip WT cDNA Amplification Kit.  10 ug of cRNA were input into the second cycle cDNA reaction with random hexamers that are used to reverse transcribe the cRNA from the first cycle to produce single-stranded DNA in the sense orientation.
The single-stranded DNA sample is fragmented (WT Terminal Labeling Kit, Affymetrix, Inc, Santa Clara, CA) to an average strand length of 60 bases (range 40-70bp) following prescribed protocols (Affymetrix GeneChip WT Sense Target Labeling Assay Manual).  The fragmented single-stranded DNA is subsequently labeled with recombinant terminal deoxynucleotidyl transferase (TdT) and the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin.

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

tag: Age

value: postnatal day 22

tag: Gender

value: female

tag: Tissue

value: dorsal skin


title: Control cells, 2 h post-supplementation.

description: HMVEC (Cambrex, Walkersville, MD, USA) were cultured in endothelial growth medium 2-microvascular (bulletkit, BioWhittaker, Walkersville, MD, USA) supplemented as directed with 5% fetal bovine serum. The cells (passage 9) were plated at 2.5 x 104 cells/cm^2 at 37 degrees Celsius in a humidified chamber with 5% carbon dioxide. They were grown to confluence. After confluence, medium was refreshed, and 0.6% dimethyl sulfoxide (DMSO) vehicle control was added to the sample. Total RNA from the cultures was isolated 2 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.

source_name: Human microvascular endothelial cells (HMVEC), 2 h post-supplementation with 0.6% dimethyl sulfoxide (DMSO) vehicle control.


title: Expression profiling of Bmal +/- littermate dorsal skin_rep3

description: Hair cycle staging: telogen

source_name: Bmal +/- dorsal skin at P22, biological replicate 3


title: Retina DBA/2J 2 days rep3

status: Public on Jul 16 2009

city: Memphis

first: William

middle: Edwin

last: Orr

state: TN

address: 930 Madison Avenue, Suite 757

department: Ophthalmology

institute: University of Tennessee Health Science Center

description: DBA/2J retina, total RNA isolation 2 days after optic nerve crush

hyb_protocol: Standard Protocol for Illumina Sentrix 6 Mouse BeadChip microarrays

scan_protocol: Illumina BeadArray Reader and BeadScan scan protocol

data_processing: Using Microsoft Excel, we normalized the data using the formula 2 (z-score of log2 [intensity]) + 8

source_name: retina, DBA/2J, 2 days post crush

label_protocol: The RNA from each sample was processed with the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX) to produce labeled cRNA.

extract_protocol: The tissue was homogenized and extracted according to the RNA-Stat-60 protocol as described by the manufacturer (Tel-Test, Friendswood, TX). The quality and purity of RNA was assessed using an Agilent Bioanalyzer 2100 system.

treatment_protocol: Optic nerve crush: Mice were deeply anesthetized with a mixture of 13 mg/kg of Rompum and 87 mg/kg of Ketalar.  A small incision was made in the lateral aspect of the conjunctiva.  With a pair of small forceps the edge of the conjunctiva next to the globe was retracted slightly and rotated laterally, allowing visualization of the posterior aspect of the globe where the optic nerve could be observed.  Viewed under a binocular operating microscope, the surrounding connective tissue and muscle was gently separated from the nerve.  The exposed optic nerve was grasped for 10 sec with a pair of Dumont cross-clamp #7 forceps (Roboz, cat. #RS=5027, Gaithersburg, MD).  This instrument was chosen because its spring action applied a moderate yet constant and consistent force to the optic nerve.  The forceps were then removed and the eye was allowed to rotate back into place.

tag: age

tag: gender

value: Male

tag: tissue

value: retina from both eyes


title: Expression profiling of Bmal -/- littermate dorsal skin_rep3

description: Hair cycle staging: telogen

source_name: Bmal -/- dorsal skin at P22, biological replicate 3


title: Expression profiling of Bmal +/- littermate dorsal skin_rep2

description: Hair cycle staging: telogen

source_name: Bmal +/- dorsal skin at P22, biological replicate 2


title: Retina DBA/2J 2 days rep2


title: Retina DBA/2J 5 days rep3

description: DBA/2J retina, total RNA isolation 5 days after optic nerve crush: The exposed optic nerve was grasped for 10 sec with a pair of Dumont cross-clamp #7 forceps

source_name: retina, DBA/2J, 5 days post crush


title: Retina DBA/2J 5 days rep1


title: Expression profiling of Bmal +/- littermate dorsal skin_rep1

description: Hair cycle staging: telogen

source_name: Bmal +/- dorsal skin at P23, biological replicate 1

value: male


title: Retina DBA/2J 2 days rep1

description: DBA/2J retina, total RNA isolation 2 days after optic nerve crush: The exposed optic nerve was grasped for 10 sec with a pair of Dumont cross-clamp #7 forceps


title: P3.a (yr.0)

city: Brussels

first: Karen

last: Willard-Gallo

address: 127 Blvd de Waterloo

department: Institut Bordet

country: Belgium

institute: Université Libre de Bruxelles

description:
CD3- CD4+ T-cells from blood obtained at diagnosis (year 0).
Pre-malignant stage of lymphocytic variant of hypereosinophilic syndrome.

hyb_protocol: 15µg of cRNA was hybridized following the standard protocol for Affymetrix’s Genechips hybridization

scan_protocol: Chips were scanned using GCF3000 scanner and processed using GCOS operating software

data_processing: Data were processed using GCOS operating software

source_name: Patient 3

label_protocol: 1.5µg of total RNA was labeled following the standard protocol for Affymetrix’s Genechips hybridization

extract_protocol: Total RNA was extracted using TriPure Isolation Reagent (Roche Applied Science) as manufacturer's recommendations. ). The quality of the RNA was assessed based on the RNA profile generated by the bioanalyzer (Agilent Inc)

treatment_protocol:
Isolated PBMC were frozen.
Thawed CD3-CD4+ T-cells were purified using magnetic beads and 18h-cultured in X-vivo medium

tag: cell type

value: CD3- CD4+ T-cells

value: blood

tag: time

value: year 0 (diagnosis)

tag: disease state


title: NotSAT_ES3

type: genomic

city: Tokyo

first: Mayumi

last: Oda

address: 35 Shinanomachi, Shinjuku

country: Japan

institute: Keio University

description: data definition: Normalized median log signal intensity

hyb_protocol: Affymetrix Chromatin-Immunoprecipitation Assay Protocol

data_processing: median signal intensity of probe corresponding to a HpyCH4IV-TaqI fragment was defined as the fragment value (= VALUE in main data file)

molecule: genomic DNA

source_name: ES cells derived from native blastocyst.

growth_protocol: Cultured in standard proliferation medium for ES cells.

extract_protocol: genomic DNA was purified using proteinase K, Rnase A and phenol/chroloform, and amplified HpyCH4IV-TaqI fragment using the combination of restriction digestion and linker-mediated PCR (Yagi et al. Genome Res (2008) 18:1969-1978).

treatment_protocol: Day 3 in proliferation medium.

value: ES cells

tag: source

value: native blastocyst


title: Expression profiling of Bmal -/- littermate dorsal skin_rep1

description: Hair cycle staging: telogen

source_name: Bmal -/- dorsal skin at P22, biological replicate 1


title: NotSAT_BDntTS5

scan_protocol: Affymetrix Chromatin-Immunoprecipitation Assay Protocol

source_name: TS cells derived from somatic-cell nuclear-transferred blastocyst

growth_protocol: Cultured in proliferation medium for TS cells (RPMI1640 + 20%FBS + 1 mM Sodium Pyruvate + 2 mM L-glutamine + penicillin/storeptmycin + 25ng/ml bFGF +  heparin)(Tanaka et al. Science (1988) 282:2072-2075)

treatment_protocol: Day 4 in proliferation medium.

value: TS cells


title: Retina DBA/2J control rep1

description: DBA/2J Control retina total RNA isolation

source_name: retina, DBA/2J, control


title: Retina DBA/2J control rep2


title: Retina DBA/2J control rep3


title: Retina C57BL/6J 5 days rep1

description: C57BL/6J retina, total RNA isolation 5 days after optic nerve crush: The exposed optic nerve was grasped for 10 sec with a pair of Dumont cross-clamp #7 forceps

source_name: retina, C57BL/6J, 5 days post crush


title: NotSAT_ES2

source_name: ES cells derived from native blastocyst

label_protocol: Affymetrix Chromatin-Immunoprecipitation Assay Protocol


title: Retina C57BL/6J 2 days rep3

description: C57BL/6J retina, total RNA isolation 2 days after optic nerve crush: The exposed optic nerve was grasped for 10 sec with a pair of Dumont cross-clamp #7 forceps

source_name: retina, C57BL/6J, 2 days post crush


title: Retina C57BL/6J 5 days rep3


title: NotSAT_BDTS2

source_name: TS cells derived from native blastocyst

tag: ts cells, source


title: Retina C57BL/6J 2 days rep2


title: Retina DBA/2J 5 days rep2


title: NotSAT_BDntTS4

source_name: TS cells derived from somatic-cell nuclear-transferred blastocyst, line 4


title: NotSAT_BDTS1


title: NotSAT_ES1


title: L3.6pl.2

city: Houston

first: Woonyoung

last: Choi

state: TX

address: 1515 Holcombe

institute: Md Anderson Cancer center

description: Illumina Human-6 v 2 has 46713 probes.

hyb_protocol: 1.5 ug/array of biotin-labled cRNA was hybridized to Illumina Human-6 v 2 (48K) according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA). Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) was used to develop the array signal.

scan_protocol: BeadStation 500GXDW (Illumina, Inc., San Diego, CA) was used to scan array chips.

data_processing: Signal intensities were quantified with Illumina BeadStudio software.

source_name: Pancreatic Cancer cell line, L3.6pl

label_protocol: cRNA samples were prepared for hybridization according to Illumina's instructions: 500 ng of total RNA from each sample was converted to cDNA synthesis then to biotin labeled cRNA by in vitro transcription using the Illumina TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations were measured using spectrophotometer (Nanodrop, ND-1000) and cRNA size was measured using Agilent bioanalyzer.

extract_protocol: Total RNA was isolated using Trizol reagent (Molecular lab), followed by clean up with RNeasy® Mini kit (Qiagen, Valencia, CA). RNA quality and integrity were confirmed by Bioanalyzer (Agilent technology)

value: pancreatic cancer


title: Retina C57BL/6J control rep1

description: C57BL/6J Control retina total RNA isolation

source_name: retina, C57BL/6J, control


title: Retina C57BL/6J control rep2


title: NotSAT_BDntTS2


title: SU8686.2

description: Illumina Human-6 v 2 has 46713 probes.

source_name: Pancreatic Cancer cell line, SU8686


title: AsPC1

description: Illumina Human-6 v 2 has 46713 probes.

source_name: Pancreatic Cancer cell line, AsPC1


title: Retina C57BL/6J 5 days rep2


title: Retina C57BL/6J 2 days rep1


title: Hs766T.2

description: Illumina Human-6 v 2 has 46713 probes.

source_name: Pancreatic Cancer cell line, Hs766T


title: TER119-negative fetal liver erythroid precursors - Hipk2 knockdown - replicate 2

city: Cambridge

first: Shilpa

middle: Manohar

last: Hattangadi

address: 9 Cambridge Center

department: Lodish Lab

institute: Whitehead Institute (WIBR)

description: Biological replicate 2 of 2. Hipk2 knockdown versus control.

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

scan_protocol: Scanned on an Agilent G2565AA scanner.  Images were quantified using Agilent Feature Extraction Software (version 10.5).

data_processing: Normalized and analyzed using bioconductor and R using the limma function.

label_protocol: 500ng of total RNA were primed with 2 µl of 50 µM T7-oligo(dT) DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 200 U SuperScript II RTase (Invitrogen), and 500 µM each dATP, dTTP, dGTP, with 50 µM dCTP, 50 µM Cy3-label

growth_protocol: shRNA retroviruses against Hipk1, Hipk2, or luciferase (control) were cloned.  TER119-negative fetal liver erythroid precursors were isolated and infected with shRNA at time 0; then differentiated for 36 hours.

extract_protocol: total RNA extracted using Qiagen RNAeasy kit

value: Fetal liver TER119-negative erythroid precursors

tag: shrna

source_name: TER119-negative erythroid precursors

label_protocol: 500ng of total RNA were primed with 2 µl of 50 µM T7-oligo(dT) DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 200 U SuperScript II RTase (Invitrogen), and 500 µM each dATP, dTTP, dGTP, with 50 µM dCTP, 50 µM Cy5-label

value: luciferase


title: SU8686

description: Illumina Human-6 v 2 has 46713 probes.


title: Panc-1.2

description: Illumina Human-6 v 2 has 46713 probes.

source_name: Pancreatic Cancer cell line, Panc-1


title: Retina C57BL/6J control rep3


title: BxPC3

description: Illumina Human-6 v 2 has 46713 probes.

source_name: Pancreatic Cancer cell line, BxPC3


title: TER119-negative fetal liver erythroid precursors - Hipk2 knockdown - replicate 1

description: Biological replicate 1 of 2. Hipk2 knockdown versus control.


title: TER119-negative fetal liver erythroid precursors - Hipk1 knockdown - replicate 1

description: Biological replicate 1 of 2. Hipk1 knockdown versus control.


title: Panc-1

description: Illumina Human-6 v 2 has 46713 probes.


title: TER119-negative fetal liver erythroid precursors - Hipk1 knockdown - replicate 2

description: Biological replicate 2 of 2. Hipk1 knockdown versus control.


title: CFPAC1

description: Illumina Human-6 v 2 has 46713 probes.

source_name: Pancreatic Cancer cell line, CFPAC1


title: MIApaca-2

description: Illumina Human-6 v 2 has 46713 probes.

source_name: Pancreatic Cancer cell line, MIApaca-2


title: L3.6pl

description: Illumina Human-6 v 2 has 46713 probes.


title: HPDE

description: Illumina Human-6 v 2 has 46713 probes.

source_name: Normal Pancreatic cell line, HPDE

value: HPDE

value: pancreatic ductal epithelial


title: 1170-I tumorigenic lung epithelial cells replicate number 2

first: Humam

last: Kadara

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

description:
The 1170-I tumorigenic lung epithelial cells were isolated and cultured from xenografts in mice (by Klein-Szanto et al, 1992) after introduction of de-epitheliazed tracheas containing the immortalized human BEAS-2B cells and a beeswax pellet containing a tobacco-specific carcinogen. The tumorigenic 1170-I cells developed in vivo rather than in vitro and were tumorigenic as they formed invasive lung adenocarcinomas when injected into nude mice.
This sample is the second replicate of tumorigenic 1170-I cells.

hyb_protocol: One vial of the 20X eukaryotic hybridization controls and a vial of oligo B2 (included in the GeneChip Eukaryotic hybridization control kit) were thawed by heating the vials at 65°C for 5 minutes. A hybridization cocktail consisting of 15 micrograms of the cRNA, 5 ul of the control oligo B2, 15 ul of eukaryotic hybridization controls, 3 ul of Herring sperm DNA, 3 ul of acetylated BSA, 150 ul of 2 x hybridization buffer and 300 ul of water. Probe arrays were then equilibrated to room temperature. The hybridization cocktail was heated to 99°C for 5 minutes, spun briefly and transfered to 45°C for 5 minutes. Hybridization/cocktail was spun at maximum speed for 5 minutes to remove any insoluble material. The probe array was wetted by filling it through one of the septa with 1X hybridization buffer and incubated at 45°C for 10 minutes with rotation. The buffer solution was then removed from the probe array which was then filled with the appropriate amount of the clarified hybridization cocktail. Hybridization was then performed overnight at 45°C with rotation.

scan_protocol: The array was scanned with a GeneChip® Scanner 3000 from Affymetrix and raw image file was converted to probe set data (*.CEL file), using the Affymetrix GeneChip® Operating Software.

data_processing: The raw data were analyzed by normalization using robust multichip average (RMA). Values were log (base 2) transformed.

source_name: 1170-I tumorigenic lung epithelial cells isolated and cultured from xenografts in mice

label_protocol:
Following clean-up of double-stranded cDNA by phenol/chloroform extraction and ethanol precipitation, biotin-labeled cRNA were synthesized by in vitro transcription (IVT) reaction using the ENZO BioArray High Yield RNA transcript labeling kit (Affymetrix, Santa Clara, CA).
The following were added to a fresh 1.5-mL microcentrifuge tube: 1 µg double-stranded cDNA,  RNase/Dnase free water, 4 µL of 10X HY reaction buffer, 4 µL of 10X Biotin-labeled ribonucleotides, 4 µL of 10X DTT, 4 µL of 10X RNase inhibitor mix and 2 µL of T7 RNA polymerase.
The mixture was incubated at 37°C for 4 – 5 hours, mixing the tube every 30 – 45 minutes.
cRNA were then cleaned with RNeasy spin columns from Qiagen with two rounds of elution for maximum recovery followed by ethanol precipitation and dilution in RNase free water.

extract_protocol: Total RNA was extracted and purified using the RNeasy mini kit from Qiagen according to the manufacturer's instructions. RNA was treated with DNase provided by Qiagen to remove any genomic DNA. a total of 1 microgram of RNA was reverse-transcribed using the Quantitect Reverse Transcription kit from Qiagen for generation of first-strand cDNA.


title: 1198 transformed lung epithelial cells replicate number 2

description:
The 1198 transformed lung epithelial cells were isolated and cultured from xenografts in mice (by Klein-Szanto et al, 1992) after introduction of de-epitheliazed tracheas containing the immortalized BEAS-2B cells and a beeswax pellet containing tobacco-specific carcinogen. The 1198 developed in vivo rather than with in vitro manipulations. The 1198 lung epithelial cells exhibited transformed properties as they were able to grow on soft agar.
This sample is the second replicate of transformed 1198 cells.

source_name: 1198 transformed lung epithelial cells isolated and cultured from xenografts in mice


title: Mpanc 96

description: Illumina Human-6 v 2 has 46713 probes.

source_name: Pancreatic Cancer cell line, Mpanc 96

value: Mpanc 96


title: JS95wt_0.05µg/mlSilCR_10min

city: Jerusalem

first: Ilia

last: Belotserkovsky

address: Ein-Kerem Campus

department: Microbiology and Molecular Genetics

country: Israel

institute: Hebrew University

description: Bacteria were grown to OD=0.2 and then 0.05 µg/ml SilCR was added

hyb_protocol: Hybridization was performed according to NimbleGen protocol (NimbleChip™arrays user 's guide for gene expression analysis) at  420C for 16 h using the NimbleGen MAUI hybridization system.Hybridized arrays were washed as described in NimbleChip™arrays user 's guide for gene expression analysis.

scan_protocol: Slides were scanned using Axon GenePix 4000 B scanner (Axon Instruments) with settings adjusted to obtain similar green and red intensities.

data_processing: The two pair reports of each two-color experiment were imported into a specially written MatLab (R2007b) program.The data underwent a process of flooring (expression data of  less than 20 was assigned a value of 20).Then,a scatter plot was created, plotting log10 of the product of the Data X and Data Y intensities against log2 of their intensity ratios.This was subjected to Lowess normalization method using a linear fit with a window of 0.05 (5%).Since for most of the ORFs there are 7 probes the data was reshaped so that each row contained all the data per each ORF (7 readings of CY3 followed by 7 readings of CY5). At this point a t-test was performed on each row and a p value was calculated using 1000 permutations.

organism: Streptococcus pyogenes

source_name: JS95, 0.05µg/mlSilCR, 10min

label_protocol: cDNA was produced with random hexamer primers (6 µg) from 2µg of total RNA using the superscript III reverse transcriptase (Invitro gen,Carlsbad,CA, USA). The reverse transcription reaction was carried out at 42 °C overnight for 16 h with aminoallyl (aa) labeled dUTP. Coupling of aminoallyl labeled cDNA to Cy-dye esters was performed in 0.1 M sodium carbonate buffer (pH =8.6) for 1 h at room temperature. Free dye was removed from the samples using the Qiagen QIAquick PCR purification columns. Hybridization efficiency was measured using a spectrophotometer (ND-100,Nanodrop Technologies), and labeled cDNA concentration was calculated.Cy3-labeled sample (1 µg) was mixed with an equal amount of Cy5-labeled sample, and themixture was dried using a DNA concentrator.

growth_protocol: Bacteria were grown in Todd Hewitt medium supplemented with 0.2% yeast extract at 37°C in sealed tubes without agitation

extract_protocol: Total RNA from bacteria was isolated by hot acidic phenol extraction

treatment_protocol: Bacteria were grown to OD=0.2 and then 10 µg/ml SilCR was added for 10 minutes

value: JS95 wilde type

source_name: JS95 no SilCR

treatment_protocol: Bacteria were grown to OD=0.2 followed by additional 10 minute growth


title: 1799 immortalized lung epithelial cells replicate number 2

description:
The 1799 immortalized lung epithelial cells were isolated and cultured from xenografts in mice (by Klein-Szanto et al, 1992) after introduction of de-epitheliazed tracheas containing the immortalized BEAS-2B cells and a beeswax pellet containing an organic solvent vehicle.
This sample is the second replicate of immortalized 1799 cells.

source_name: 1799 immortalized lung epithelial cells in culture isolated from xenografts in mice


title: Hs766T

description: Illumina Human-6 v 2 has 46713 probes.


title: 1170-I tumorigenic lung epithelial cells replicate number 1

description:
The 1170-I tumorigenic lung epithelial cells were isolated and cultured from xenografts in mice (by Klein-Szanto et al, 1992) after introduction of de-epitheliazed tracheas containing the immortalized BEAS-2B cells and a beeswax pellet containing a tobacco-specific carcinogen. The tumorigenic 1170-I cells developed in vivo rather than in vitro and were tumorigenic as they formed invasive lung adenocarcinomas when injected into nude mice.
This sample is the first replicate of tumorigenic 1170-I cells.


title: JS95wt_10 µg/mlSilCR_10min_rep1

description: Bacteria were grown to OD=0.2 and then 10 µg/ml SilCR was added. Biological replacate 1 of 2

source_name: JS95, 10 µg/mlSilCR, 10min


title: 1198 transformed lung epithelial cells replicate number 1

description:
The 1198 transformed lung epithelial cells were isolated and cultured from xenografts in mice (by Klein-Szanto et al, 1992) after introduction of de-epitheliazed tracheas containing the immortalized BEAS-2B cells and a beeswax pellet containing tobacco-specific carcinogen. The 1198 therefore developed in vivo rather than by in vitro manipulations. The 1198 exhibit transformed properties as they are able to grow in soft agar.
This sample is the first replicate of immortalized 1198 cells.

source_name: 1198 transformed lung epithelial cells isolated from xenografts in mice


title: JS95wt_10 µg/mlSilCR_10min_rep2

description: Biological replacate 2 of 2


title: 1799 immortalized lung epithelial cells replicate number 1

description:
The 1799 immortalized lung epithelial cells were isolated and cultured from xenografts in mice (by Klein-Szanto et al, 1992) after introduction of de-epitheliazed tracheas containing the immortalized BEAS-2B cells and a beeswax pellet containing an organic solvent vehicle.
This sample is the firstreplicate of immortalized 1799 cells.


title: JS95ΔsilAB_10µg/mSilCR_10min

description: Bacteria were grown to OD=0.2 and then 10 µg/ml SilCR was added

source_name: ΔsilAB, no SilCR, 10min

value: JS95 ΔsilAB

source_name: ΔsilAB,10 µg/mlSilCR, 10min


title: BxPC3.2

description: Illumina Human-6 v 2 has 46713 probes.


title: pBAD_MicC_BR3

type: mixed

city: Norwich

first: Sacha

last: Lucchini

address: Colney Lane

department: Molecular Microbiology

country: United Kingdom

institute: Institute of Food Research

description: Intensity ratios of RNA (channel 2) divided by DNA (channel 1) signals minus respective background signals. Total array is 16 blocks arranged in 4X4 configuration.

hyb_protocol: Slides blocked with DCE according to protocol at PMID 11266573. For hybridisation and washing protocols see http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

scan_protocol: Axon GenePix4000A, 10nm resolution scan & see http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

data_processing: Data centring was performed by bringing the median ratio (Cy5/Cy3) for each of the 16 blocks to one using the following equation: (Ti) = (Cy5i/Cy3i) - c, where T is the centred ratio, i is the gene index, Cy5 and Cy3 are the red and green intensities and c is the 50th percentile of all Cy5/Cy3 ratios.

organism: Salmonella enterica

source_name: Reference genomic DNA

label_protocol: Labelling protocol at http://www.ifr.ac.uk/Safety/Microarrays/default.html#protocols

extract_protocol: Genomic DNA isolated using the Qiagen 'Genomic DNA' Kit (Cat. No.: 19060 for the buffer kit; 10243 for the columns)

tag: reference

value: Salmonella enterica serovar Typhimurium SL1344 genomic DNA

label_protocol: Labelling protocol at http://www.ifr.ac.uk/safety/Microarrays/protocols.html

growth_protocol: S. Typhimurium was grown in LB under aeration until A600=1.5 was reached. L-arabinose was then added to a 0.2% final concentration. Total RNA was isolated 10min after L-arabinose addition.

extract_protocol: Total RNA isolation protocol at http://www.ifr.ac.uk/safety/Microarrays/protocols.html

tag: cell (plasmid)

value: Salmonella enterica serovar Typhimurium SL1344 (pBAD-MicC)


title: immortalized bronchial epithelial cells (BEAS-2B) replicate number 2

description:
The BEAS-2B cells were generated by Klein-Szanto et al in 1992 by introduction of the SV40 large cell T-antigen into normal bronchial epithelial cells rendering them immortalized.
This sample is the second replicate of immortalized BEAS-2B cells.

source_name: SV40 large T-immortalized bronchial epithelial cells


title: AsPC1.2

description: Illumina Human-6 v 2 has 46713 probes.

source_name: Pancreatic Cancer cell line, AsPC1


title: JS95wt_10 µg/mlSilCR_180min

description: Bacteria were grown with 10 µg/ml SilCR for 180 minutes

source_name: JS95, 10 µg/mlSilCR, 180min

treatment_protocol: Over-night culture was diluted 1/50 and grown with 10 µg/ml SilCR for 3 hours

tag: strain

treatment_protocol: Over-night culture was diluted 1/50 and grown for 3 hours


title: Mpanc 96.2

description: Illumina Human-6 v 2 has 46713 probes.


title: HEK293 cells siRNA BAHD1 biological rep2

city: Jouy-en-Josas

first: Helene

last: Bierne

address: Domaine de Vilvert, bat 442, INRA Micalis

department: Micalis Institute

country: France

institute: INRAE - University PARIS SACLAY

description: Gene expression data from HEK293 cells transfected with BAHD1  siRNA

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133Plus2.0  Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: CEL files were generated using GCOS software and preprocessed using GC-RMA method

source_name: HEK293 cells + BAHD1 siRNA 72h

label_protocol: RT on 5 μg of total RNA using oligo(dT) primers and « in vitro » transcription of the cDNA in presence of biotin were performed by using a GeneChip Amplification One-Cycle Target Labeling kit according to Affymetrix (Santa Clara, CA) standard protocols  Labeling kit according to Affymetrix (Santa Clara, CA) standard protocols.

growth_protocol: HEK293 cells(ATCC #CRL 1573) were grown in DMEM supplemented with Glutamax (Gibco) and 10% FCS

extract_protocol: Total RNA from cells  was extracted and purified by using the RNeasy kit according to the manufacturer's instructions.

treatment_protocol: HEK293 cells were  transfected 72h with siRNA BAHD1 or siRNA control (Ambion) using lipofectamine RNAi max (Invitrogen)


title: HPDE.2

description: Illumina Human-6 v 2 has 46713 probes.


title: HEK293 cells siRNA control, biological rep3

description: Gene expression data from HEK293 cells transfected with control  siRNA

source_name: HEK293 cells + control siRNA 72h


title: pBAD_MicC_BR1


title: immortalized bronchial epithelial cells (BEAS-2B) replicate number 1

description:
The BEAS-2B cells were generated by Klein-Szanto et al in 1992 by introduction of the SV40 large cell T-antigen into normal bronchial epithelial cells rendering them immortalized.
This sample is the first replicate of immortalized BEAS-2B cells.


title: pBAD_MicC_BR2


title: MIApaca-2.2

description: Illumina Human-6 v 2 has 46713 probes.

source_name: Pancreatic Cancer cell line, MIApaca-2


title: pBAD_CTRL_BR1

value: Salmonella enterica serovar Typhimurium SL1344 (pBAD-CTRL)


title: CFPAC1.2

description: Illumina Human-6 v 2 has 46713 probes.

source_name: Pancreatic Cancer cell line, CFPAC1


title: pBAD_CTRL_BR3


title: HEK293 cells siRNA BAHD1 biological rep3


title: pBAD_CTRL_BR2


title: normal human bronchial epithelial cells (NHBE) replicate number 1

description:
NHBE cells purchased from Cambrex/Clonetics and used at the second passage.
This sample is the first replicate of two samples of normal human bronchial epithelial cells.

source_name: normal human bronchial epithelial cells in culture

value: NHBE


title: HEK293 cells siRNA BAHD1 biological rep1


title: normal human bronchial epithelial cells (NHBE) replicate number 2

description:
NHBE cells purchased from Cambrex/Clonetics and used at the second passage
This sample is the second replicate of normal human bronchial epithelial cells

source_name: transcriptome of normal human bronchial epithelial cells


title: Set 2 - Sham 24h rep1

status: Public on Jul 15 2009

city: Berkeley

first: Luisa

last: Cacheaux

address: 5155 Valley Life Sciences Building

institute: UC Berkeley

description: Gene expression data from sham operated rat.

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Expression values were determined using GCRMA.

organism: Rattus norvegicus

source_name: Rat somatosensory cortex

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix)

treatment_protocol: sham operated animal

tag: Strain

value: Wistar

value: male

value: adult


title: Set 2 - Albumin plus blockers 24h rep1

description: Gene expression data from rat treated with bovine serum albumin plus TGF-Beta receptor blockers.

treatment_protocol: Somatosensory cortex was perfused with ACSF supplemented with bovine serum albumin plus TGF-Beta receptor blockers (TGF-BetaR2 antibody, 50 μg/ml; SB431542, 100 μM). Animal was sacrificed 24 hours following treatment.


title: Set 2 - Sham 24h rep2


title: Fpr1 X-RIP (1)

city: ETH Hoenggerberg, Zuerich

first: Andre

last: Gerber

address: Wolfgang Pauli Str. 10, HCI H396

department: Institute of Pharmaceutical Science

country: Switzerland

institute: Swiss Federal Institute of Technology

description:
Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82456.gif
Antigenic peptide used in IP: TAP-tag

hyb_protocol: not provided

scan_protocol: GenePix 4200A

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

organism: Saccharomyces cerevisiae

source_name: X-linked total RNA extract (1)

label_protocol: not provided

extract_protocol: not provided

value: X-linked total RNA extract

molecule: other

source_name: X-linked Fpr1 IP RNA (1)

tag: test

value: X-linked Fpr1 IP RNA


title: small airway epithelial cells (SAEC) replicate number 2

description:
epithelial cells from the small airway of the lung purchased fromCambrex/Clonetics and used at the second passage
The sample is one replicate of two small airway epithelial cells (SAEC) which are considered normal (non-malignant) lung epithelial cells from the small airways of the lung.

source_name: small airway epithelial cells in culture

extract_protocol: Total RNA was extracted and purified using the RNeasy mini kit from Qiagen according to the manufacturer's instructions. RNA was treated with DNase provided by Qiagen to elilminate any genomic DNA. a total of 1 microgram of RNA was reverse-transcribed using the Quantitect Reverse Transcription kit from Qiagen for generation of first-strand cDNA.

tag: cell line

value: SAEC


title: Trf4 X-RIP (3)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82455.gif
Antigenic peptide used in IP: TAP-tag

source_name: X-linked total RNA extract (3)

source_name: X-linked Trf4 IP RNA (3)

value: X-linked Trf4 IP RNA


title: Fpr1 X-RIP (2)

description:
Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82457.gif
Antigenic peptide used in IP: TAP-tag

source_name: X-linked total RNA extract (2)

source_name: X-linked Fpr1 IP RNA (2)


title: small airway epithelial cells (SAEC) replicate number 1

description:
airway epithelial cells form the lung and purchased from Cambrex/Clonetics. Cells were used at the second passage.
The sample is one replicate of two small airway epithelial cells (SAEC) which are considered normal (non-malignant) lung epithelial cells from the small airways of the lung.


title: Set 2 - Albumin plus blockers 24h rep3

tag: Gender

tag: Age


title: BY4741 X-RIP

description:
Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82452.gif
Antigenic peptide used in IP: no tag

source_name: X-linked total RNA extract

source_name: X-linked mock IP RNA

value: X-linked mock IP RNA


title: Trf4 X-RIP (1)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82453.gif
Antigenic peptide used in IP: TAP-tag

source_name: X-linked Trf4 IP RNA


title: HEK293 cells siRNA control, biological rep2


title: Set 2 - Albumin plus blockers 24h rep2


title: Set 2 - Albumin 24h rep3

description: Gene expression data from rat treated with bovine serum albumin.

treatment_protocol: Somatosensory cortex was perfused with ACSF supplemented with bovine serum albumin (BSA, 0.1 mM) corresponding to 25% of serum albumin concentration. Animal was sacrificed 24h following treatment.


title: Trf4 delta (1)

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82458.gif
mutated gene: trf4 deletion

hyb_protocol: cDNAs were hybridized on yeast oligo microarrays over night at 42 degrees in formamide-based hybridization buffer

source_name: total RNA WT

extract_protocol: Total RNA was isolated by hot phenol extraction from exponentially growing cells,

value: WT

source_name: total RNA trf4 delta

value: trf4 delta


title: Set 2 - Albumin plus blockers 24h rep4


title: HEK293 cells siRNA control, biological rep1

source_name: HEK293 cells + control siRNA 72h


title: Trf4 X-RIP (2)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82454.gif
Antigenic peptide used in IP: TAP-tag

source_name: X-linked Trf4 IP RNA (2)


title: Set 2 - Albumin 24h rep2


title: TGF-Beta 24h

description: Gene expression data from rat treated with TGF-Beta1.

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

treatment_protocol: Somatosensory cortex was perfused with ACSF supplemented with TGF-Beta1 (10 ng/ml). Animal was sacrificed 24 hours following treatment.


title: Sham 24h

treatment_protocol: Sham operated animal


title: Albumin 24h

treatment_protocol: Somatosensory cortex was perfused with ACSF supplemented with bovine serum albumin (BSA, 0.1 mM) corresponding to 25% of serum albumin concentration. Animal was sacrificed 24 hours following treatment.


title: TGF-Beta 8h

treatment_protocol: Somatosensory cortex was perfused with ACSF supplemented with TGF-Beta1 (10 ng/ml). Animal was sacrificed 8 hours following treatment.


title: Trf4 delta (2)

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82459.gif
mutated gene: trf4 deletion

source_name: total RNA WT  (2)

source_name: total RNA trf4 delta (2)


title: Trf5 delta (1)

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82460.gif
mutated gene: trf5 deletion

source_name: total RNA WT  (1)

source_name: total RNA trf5 delta (1)

value: trf5 delta


title: TGF-Beta 48h

source_name: Rat somatosensory cortex

treatment_protocol: Somatosensory cortex was perfused with ACSF supplemented with TGF-Beta1 (10 ng/ml). Animal was sacrificed 48 hours following treatment.


title: Albumin 48h

treatment_protocol: Somatosensory cortex was perfused with ACSF supplemented with bovine serum albumin (BSA, 0.1 mM) corresponding to 25% of serum albumin concentration. Animal was sacrificed 48 hours following treatment.


title: DOC 48h

description: Gene expression data from rat treated with deoxycholic acid (DOC).

treatment_protocol: Somatosensory cortex was perfused with ACSF supplemented with deoxycholic acid (DOC, 2 mM) and animal was sacrificed 48 hours following treatment.


title: Trf5 delta (2)

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82461.gif
mutated gene: trf5 deltion

source_name: total RNA trf5 delta (2)


title: DOC 24h

treatment_protocol: Somatosensory cortex was perfused with ACSF supplemented with deoxycholic acid (DOC, 2 mM) and animal was sacrificed 24 hours following treatment.


title: DOC 7h

treatment_protocol: Somatosensory cortex was perfused with ACSF supplemented with deoxycholic acid (DOC, 2 mM) and animal was sacrificed 7 hours following treatment.


title: Disc Tissue 9- 27ts

city: Charlotte

first: Helen

last: Gruber

state: NC

address: 1542 Graden Terrace

department: Orthopaedic Surgery

institute: Carolinas HealthCare System

description: Disc Tissue 9- 27ts

hyb_protocol: Fragmented cRNA was hybridized to the  X3P chip in the Affymetrix hybridiztion buffer for 16 hrs at 45oC. X3P chips were washed and labeled in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned once via the Affymetrix 3000G scanner.

data_processing: The data were analyzed with the GCOS Affymetrix GeneChip Operating System (version 1.2) and Microarray Suite version 5.0 (MAS 5.0). Affymetrix default analysis settings and global scaling as normalization were used. Further normalization was acheived using GC-RMA (robust multiarray average) via GeneSifter analysis software (Viz Labs LLC, Seattle , WA; http://www.genesifter.net).

source_name: Disc Tissue

label_protocol: Biotin-labeled cRNA were prepard according to the Affymetrix protocol for IVT labeling.

extract_protocol: Cells were collected via laser capture mircodissection (LCM) and total RNA was isolated according to the Paradise reagent system.

tag: senescent or non-senescent

value: non-senescent

tag: tissue grade

value: III


title: Disc Tissue 8- 123s

description: Disc Tissue 8- 123s

value: senescent


title: Disc Tissue 7- 05s

description: Disc Tissue 7- 05s

value: V


title: Disc Tissue 9- 27s

description: Disc Tissue 9- 27s


title: Set 2 - Albumin 24h rep1


title: Disc Tissue 11- 84ts

description: Disc Tissue 11- 84ts


title: Disc Tissue 10- 28ts

description: Disc Tissue 10- 28ts


title: Disc Tissue 10- 28s

description: Disc Tissue 10- 28s


title: Disc Tissue 8- 123ts

description: Disc Tissue 8- 123ts


title: Albumin 8h

treatment_protocol: Somatosensory cortex was perfused with ACSF supplemented with bovine serum albumin (BSA, 0.1 mM) corresponding to 25% of serum albumin concentration. Animal was sacrificed 8 hours following treatment.


title: Disc Tissue 11- 84s

description: Disc Tissue 11- 84s


title: Disc Tissue 7- 05ts

description: Disc Tissue 7- 05ts


title: Definite MS_411AV54

city: Ramat Gan

first: Michael

last: Gurevich

address: Tel Hashomer

department: Multiple Sclerosis Center

institute: Sheba Medical Center

description: working set54

hyb_protocol: cDNA was synthesized, labeled, hybridized to either HU-133A or HU133A-2 containing 22,215 gene-transcripts according to Affymetrix (Inc, Santa Clara, CA) protocol

scan_protocol: Hewlett Packard, GeneArray-TM scanner G2500A

data_processing: Data analysis was performed by Partek Genomics Solution software (www.partek.com ). Expression values were computed from raw CEL files by applying the Robust Multi-Chip Average (RMA) background correction algorithm. The RMA correction included: 1) values background correction; 2) quantile normalization; 3) log2 transformation; 4) median polish summarization. In order to avoid the noise caused by variable set effects we normalized each set to pre-saved distribution pattern of a well balanced set used as a reference distribution. To reduce batch effect, Analysis of  Variance (ANOVA) multiple model analysis was applied. Source of variation was analyzed; non-relevant batches effects such as array type, working batch, patient age and gender were eliminated.

source_name: PBMC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA

extract_protocol: Total RNA was isolated using the TRIzol Reagent (Invitrogen, Carlsbad, CA)

treatment_protocol: Peripheral blood mononuclear cells (PBMC) were separated on ficoll-hypaque gradient

value: Definite MS

value: Peripheral blood mononuclear cells

tag: age

tag: gender

value: Female

tag: time to next relapse(days)


title: Disc Tissue 6- 04ts

description: Disc Tissue 6- 04ts

value: IV


title: Definite MS_678MS

description: working set32

tag: disease state

tag: cell type


title: Disc Tissue 5- 03ts

description: Disc Tissue 5- 03ts


title: Disc Tissue 6- 04s

description: Disc Tissue 6- 04s


title: CIS_1067PMS

description: working set35

value: CIS

value: Male


title: Definite MS_1306IVIG53

description: working set53


title: Definite MS_1080AV56

description: working set56


title: Disc Tissue 4- 347ts

description: Disc Tissue 4- 347ts


title: Disc Tissue 5- 03s

description: Disc Tissue 5- 03s


title: CIS_655PMS

description: working set35


title: Definite MS_1401IVIG52

description: working set52


title: Definite MS_410AV54

description: working set54


title: Definite MS_621COP47

description: working set47


title: Definite MS_1278IVIG53

description: working set53


title: CIS_826PMS

description: working set35


title: Disc Tissue 2 -272

description: Disc Tissue 2 -272


title: Definite MS_882COP48

description: working set48


title: Definite MS_1343AV55

description: working set55


title: CIS_968DMS

description: working set34


title: Definite MS_551AV54

description: working set54


title: Definite MS_1727AV55

description: working set55


title: Disc Tissue 3- 346

description: Disc Tissue 3- 346


title: Disc Tissue 1- 271

description: Disc Tissue 1- 271


title: Disc Tissue 4- 347s

description: Disc Tissue 4- 347s


title: Definite MS_310MS

description: working set33


title: Definite MS_896COP49

description: working set49


title: Definite MS_2883AV55

description: working set55


title: Definite MS_2586REB54

description: working set54


title: Definite MS_1612AV54

description: working set54


title: CIS_2721PR58

description: working set58


title: Definite MS_1187COP49

description: working set49


title: Definite MS_817COP47

description: working set47


title: CIS_3094PR58

description: working set58


title: Definite MS_2121IVIG52

description: working set52


title: Definite MS_1554IVIG52

description: working set52


title: Definite MS_341REB51

description: working set51


title: Definite MS_1091REB50

description: working set50


title: Definite MS_2309COP75

description: working set75


title: Definite MS_970COP48

description: working set48


title: Definite MS_1210MS

description: working set32


title: Definite MS_186MS

description: working set32


title: Definite MS_950COP75

description: working set75


title: Definite MS_2771AV54

description: working set54


title: Trf4-DADA (3)

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82466.gif
mutated gene: trf4 (DADA) mutant

source_name: total RNA WT  (3)

source_name: total RNA from trf4-DADA cells (3)

value: from trf4-DADA cells


title: Definite MS_529MS

description: working set33


title: Trf4 delta (3)

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82463.gif
mutated gene: trf4 deletion

source_name: total RNA trf4 delta (3)


title: Trf5 delta (3)

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82462.gif
mutated gene: trf5 deletion

source_name: total RNA trf5 delta (3)


title: Definite MS_785COP49

description: working set49


title: CIS_1312DMS

description: working set34


title: Trf4-DADA (1)

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82464.gif
mutated gene: trf4 (DADA) mutant

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1400, 6320; Software: type: feature extraction; Performer: Andre,,Gerber

source_name: total RNA from trf4-DADA cells (1)


title: CIS_956DMS

description: working set34


title: CIS_1206DMS

description: working set35


title: Definite MS_2580IVIG52

description: working set52


title: Definite MS_545MS

description: working set32


title: Definite MS_468DIAG73

description: working set73


title: Trf4-DADA (2)

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82465.gif
mutated gene: trf4 (DADA) mutant

source_name: total RNA from trf4-DADA cells (2)


title: Definite MS_83MS

description: working set33

value: NoRelapse


title: Definite MS_4344DIAG73

description: working set73


title: Definite MS_383AV55

description: working set55


title: Definite MS_1493MS

description: working set33


title: CIS_1308DMS

description: working set35


title: Definite MS_526MS

description: working set33


title: Definite MS_698COP49

description: working set49


title: CIS_129DMS

description: working set35


title: Definite MS_391BFER54

description: working set54


title: Definite MS_515AV56

description: working set56


title: CIS_626PMS

description: working set34


title: CIS_441PMS

description: working set34


title: CIS_967PMS

description: working set35


title: Definite MS_1174REB50

description: working set50


title: CIS_450PMS

description: working set10


title: Definite MS_333AV56

description: working set56


title: Definite MS_532COP47

description: working set47


title: Definite MS_1076COP48

description: working set48


title: Definite MS_871RMS

description: working set20


title: Definite MS_1371MS

description: working set32


title: Definite MS_975COP75

description: working set75


title: CIS_563PMS

description: working set11


title: CIS_605PMS

description: working set15


title: Definite MS_679RMS

description: working set12


title: Definite MS_1009REB50

description: working set50


title: CIS_458PMS

description: working set10


title: Definite MS_857RMS

description: working set20


title: Definite MS_778RMS

description: working set16


title: Definite MS_807RMS

description: working set20


title: CIS_160PMS

description: working set9


title: Definite MS_767COP49

description: working set49


title: Definite MS_946RMS

description: working set23


title: Definite MS_781RMS

description: working set16


title: Definite MS_518RMS

description: working set12


title: Definite MS_568RMS

description: working set12


title: CIS_55PMS

description: working set9


title: CIS_642PMS

description: working set14


title: CIS_459PMS

description: working set15


title: CIS_658PMS

description: working set14


title: CIS_665PMS

description: working set14


title: CIS_511PMS

description: working set11


title: Definite MS_1064COP48

description: working set48


title: CIS_457PMS

description: working set10


title: CIS_452PMS

description: working set15


title: CIS_667PMS

description: working set14


title: Definite MS_670RMS

description: working set12


title: CIS_170PMS

description: working set9


title: CIS_939PMS

description: working set14


title: CIS_911PMS

description: working set15


title: CIS_682PMS

description: working set14


title: 58M0

status: Public on Jul 14 2009

city: Rotterdam

first: Peter

last: Valk

address: Postbus 2040

department: Hematology

country: Netherlands

institute: ErasmusMC

hyb_protocol: PMID: 15084694 -Valk PJM, Verhaak RGW, Beijen MA, Erpelinck CAJ, Barjesteh van Waalwijk van Doorn - Khosrovani S, Boer JM, Beverloo HB, Moorhouse MJ, van der Spek PJ, Löwenberg B, Delwel R - Prognostically Useful Gene-Expression Profiles in Acute Myeloid Leukemia. New Engl.J.Med. 2004, 350: 1617-1628.

source_name: PBMC isolated from bone marrrow and blood

label_protocol: 2ug RNA, labelled according to PMID: 15084694- Valk PJM, Verhaak RGW, Beijen MA, Erpelinck CAJ, Barjesteh van Waalwijk van Doorn - Khosrovani S, Boer JM, Beverloo HB, Moorhouse MJ, van der Spek PJ, Löwenberg B, Delwel R - Prognostically Useful Gene-Expression Profiles in Acute Myeloid Leukemia. New Engl.J.Med. 2004, 350: 1617-1628.

extract_protocol: QIAamp RNA Blood Mini Kit

tag: who fab classification


title: 55M0

scan_protocol: PMID: 15084694- Valk PJM, Verhaak RGW, Beijen MA, Erpelinck CAJ, Barjesteh van Waalwijk van Doorn - Khosrovani S, Boer JM, Beverloo HB, Moorhouse MJ, van der Spek PJ, Löwenberg B, Delwel R - Prognostically Useful Gene-Expression Profiles in Acute Myeloid Leukemia. New Engl.J.Med. 2004, 350: 1617-1628.

value: PBMC isolated from bone marrrow and blood


title: 56M0


title: 7M0


title: 41M0


title: Definite MS_996RMS

description: working set23


title: 6M0


title: 8M0


title: 45M0


title: 60M0


title: 52M0


title: 5M0


title: 39M0


title: 34M0


title: 35M0


title: 42M0


title: 9M0


title: 57M0


title: 33M0


title: Thyroid tissue cultured with NaI 10-5M 3 hours

city: Shinjuku-ku

first: Kanji

last: Sato

state: Tokyo

address: Kawada-cho 8-1

department: Institute of Clinical Endocrinology

institute: Tokyo Women's Medical University

description: Thyroid follicles were cultured with NaI 10-8 M or 10-5 M for 3 hours.

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

scan_protocol: Images were quantified using Agilent Microarray Scanner

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

source_name: human thyroid follicles

label_protocol: 0.5 µg of total RNA were primed with 1.2 µl of 100 µM T7 promoter primer at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of Low RNA input linear amplification (Agilent), and 10mM dNDP.

growth_protocol: Thyroid follicles  prepared from patients with Graves' disease  were cultured in medium containing NaI (10e-8 M) and 0.5% serum in 10cm-dishes coated with agarose gel.

extract_protocol: Total RNA was extracted from thyroid follicles using the RNeasy Minikit (Quiagen, Tokyo, Japan)

treatment_protocol: Total RNA was prepared from thyroid follicles treated with NaI 10e-8M or 10e-5M for 3 hours or 48 hours.

tag: tissue

value: thyroid follicles

tag: agent

value: NaI

tag: concentration

value: 10e-8M NaI

tag: time

value: 3 hours

value: 10e-5M NaI


title: 30M0


title: 32M0


title: 31M0


title: 2M0


title: 25M0


title: 23M0


title: 22M0


title: 21M0


title: 18M0


title: 1M0


title: 20M0


title: 19M0


title: 28M0


title: 3M0


title: 24M0


title: 26M0


title: Majeti_NBM_HSC_001

city: Seattle

first: Qiang

last: Tian

state: WA

institute: Institute for Systems Biology

hyb_protocol: Following fragmentation, ten micrograms of adjusted cRNA fromeach sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip

scan_protocol: Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.

data_processing: Raw CEL intensity data were GCRMA normalized using R/Bioconductor

source_name: Normal human bone marrow hematopoietic stem cells

label_protocol: Standard Affymetrix IVT labeling protocol. See Affymetrix Expression Analysis Technical Manual

extract_protocol: Total RNA was extracted using TRIzol reagent containing either glycogen or linear acrylamide according to the manufacturer's protocol, and then treated with DNaseI (Ambion).


title: Majeti_LSC_SU018

source_name: Human acute myeloid leukemia stem cells

value: Human acute myeloid leukemia stem cells


title: Majeti_LSC_SU031


title: Majeti_NBM_HSC_007

value: Normal human bone marrow hematopoietic stem cells


title: Majeti_NBM_HSC_010


title: Majeti_LSC_SU008


title: Majeti_LSC_SU004


title: Majeti_NBM_HSC_004


title: Majeti_LSC_SU032


title: Majeti_LSC_SU014


title: Majeti_LSC_SU028


title: Majeti_LSC_SU006


title: T84 4twd5

city: Kumamoto

first: Soken

last: Tsuchiya

address: 5-1 Oe-honmachi, Chuo-ku

institute: Kumamoto University

description: T84 cells were seeded onto polycarbonate filters with 24 mm diameter and 0.4 µm pores in transwell chambers at a density of 5E+5 cells per well, and were transfected with 15 pmol of oligonucleotides for miR-210, miR-338-3p, miR-33a and miR-451. Cultured cell media were changed into fresh medium on alternate days. After 5 days, total RNA was extracted by the acid guanidinium thiocyanate-phenol-chloroform method.

hyb_protocol: According to manufacture’s instructions, fragmented RNA was hybridized on the GeneChip Human Genome U133 Plus 2.0 array for 16 hour at 45˚C.

scan_protocol: Genechips were scanned using GeneChip scanner 3000.

label_protocol: Biotinylated cRNA were prepared from 5 µg of total RNA according to manufacture’s instructions.

extract_protocol: Total RNA was extracted by the acid guanidinium thiocyanate-phenol-chloroform method.

value: human colorectal carcinoma cell line

tag: treatment

value: 5 days post-transfection


title: GK_Liver_Replicate 1

city: Oxford

first: Cecilia

last: Lindgren

address: Roosevelt Drive

institute: Wellcome Trust Centre for Human Genetics, University of Oxford

hyb_protocol: Hybridisation to Illumina ratRef-12  v1 (11222119_A) expression beadchips  was  carried  out  using  750ng  of  each  biotinylated  cRNA  in  a  58ºC hybridisation oven for 18 hours. Arrays were subsequently washed and stained with Streptavidin-Cy3.

scan_protocol: Arrays were scanned on the Illumina® BeadArray Reader (Illumina Inc., San Diego, USA). Illumina® BeadStudio Application software (version 1.5.1.3) was used to check the quality of the resulting data and generate raw signal intensities.

data_processing: Raw intensity data were imported into the R statistical package for further processing. An array-specific background measure, based on the average signal  from negative control probes, was subtracted from all probes on the array. Data  were  then  transformed  and  normalized  using  the  vsn2 package from BioConductor.

source_name: GK liver

label_protocol: Double-stranded  cDNA  and  purified  biotin-labelled  cRNA were  synthesised  from  300ng  high  quality total  RNA  using  the  Illumina®  TotalPrep  RNA  Amplification  Kit  (Ambion  Inc.,  Austin,  Texas,  USA).

growth_protocol: Seven-month-old male rats from the GK (n=4) and BN (n=4) colonies (Oxford) were fed with standard laboratory chow pellets (B&K Universal, Hull, UK) and kept on a 12h light/dark cycle.

extract_protocol: Total RNA was extracted from homogenized tissue samples using TRI Reagent (Sigma, UK) following manufacturer's instructions.

treatment_protocol: Liver and adipose tissue samples were obtained from the rats, snap-frozen in liquid nitrogen and stored at -80oC prior to use.

tag: rat id

tag: strain

value: Goto-Kakizaki

value: Liver

value: 7 months


title: GK_Liver_Replicate 3


title: Majeti_LSC_SU001


title: GK_Liver_Replicate 2


title: BN_Liver_Replicate 4

source_name: BN liver

value: Brown-Norway


title: T84 NCtwd7

description: T84 cells were seeded onto polycarbonate filters with 24 mm diameter and 0.4 µm pores in transwell chambers at a density of 5E+5 cells per well, and were transfected with 15 pmol of short RNA which sequence has minimal homology with human miRNAs (negative control). Cultured cell media were changed into fresh medium on alternate days. After 7 days, total RNA was extracted by the acid guanidinium thiocyanate-phenol-chloroform method.

tag: cell line

value: negative control

value: 7 days post-transfection


title: T84 2twd5

description: T84 cells were seeded onto polycarbonate filters with 24 mm diameter and 0.4 µm pores in transwell chambers at a density of 5E+5 cells per well, and were transfected with 15 pmol of oligonucleotides for miR-338-3p and miR-451. Cultured cell media were changed into fresh medium on alternate days. After 5 days, total RNA was extracted by the acid guanidinium thiocyanate-phenol-chloroform method.

value: miR-338-3p and miR-451


title: BN_Liver_Replicate 5

value: Male


title: BN_Liver_Replicate 2


title: BN_Liver_Replicate 3


title: T84 NCtwd5

description: T84 cells were seeded onto polycarbonate filters with 24 mm diameter and 0.4 µm pores in transwell chambers at a density of 5E+5 cells per well, and were transfected with 15 pmol of short RNA which sequence has minimal homology with human miRNAs (negative control). Cultured cell media were changed into fresh medium on alternate days. After 5 days, total RNA was extracted by the acid guanidinium thiocyanate-phenol-chloroform method.


title: 27M0

value: PBMC isolated from bone marrrow and blood


title: GK_Adipose tissue_Replicate 3

source_name: GK adipose tissue

value: Adipose tissue


title: GKvsBN_Adipose tissue_Replicate 1

description: GKvsBN_Adipose tissue_Replicate 1

hyb_protocol: Samples were hybridised to Ambion mirVana miRNA Probe Set 1564v1 arrays for 4 hours at 62oC in dark conditions and subsequently washed.

scan_protocol: Arrays were scanned on an Axon® GenePix 4000B scanner and GenePix Pro software v4.0 was used to obtain raw probe intensities.

data_processing: Background subtracted data were summarised across the 16 replicates of each probe by taking the median value. Data were normalised using the loess regression-based method within arrays to generate log2 ratios (expt (Alexa5)/expt (Alexa3) using the BioConductor package 'marray' and R statistical software.

label: Alexa Fluor 5

source_name: BN adipose tissue

label_protocol: Poly-A tailing was added to 400ng of each small RNA fraction using Ncode miRNA labelling system (Invitrogen), which also adds the fluorescent labels Alexa Fluor 3 and Alexa Fluor 5. For each tissue, half the samples (n=2 for each strain) were labelled with Alexa Fluor 5 and the other half with Alexa Fluor 3.

extract_protocol: Total RNA was extracted from homogenized tissue samples using TRI Reagent (Sigma, UK) following manufacturer's instructions. MiRNAs were isolated and purified using mirVana miRNA isolation kit (Ambion).

tag: ratid

label: Alexa Fluor 3


title: GKvsBN_Adipose tissue_Replicate 2

description: GKvsBN_Adipose tissue_Replicate 2


title: GKvsBN_Adipose tissue_Replicate 4

description: GKvsBN_Adipose tissue_Replicate 4


title: BN_Adipose tissue_Replicate 3


title: GKvsBN_Adipose tissue_Replicate 3

description: GKvsBN_Adipose tissue_Replicate 3


title: GKvsBN_Liver_Replicate 4

description: GKvsBN_Liver_Replicate 4


title: GK_Adipose tissue_Replicate 4


title: GK_Adipose tissue_Replicate 2


title: BN_Adipose tissue_Replicate 5


title: BN_Adipose tissue_Replicate 4


title: GK_Adipose tissue_Replicate 1


title: BN_Liver_Replicate 1


title: GKvsBN_Liver_Replicate 3

description: GKvsBN_Liver_Replicate 3


title: BN_Adipose tissue_Replicate 2


title: GKvsBN_Liver_Replicate 1

description: GKvsBN_Liver_Replicate 1


title: BN_Adipose tissue_Replicate 1


title: GKvsBN_Liver_Replicate 2

description: GKvsBN_Liver_Replicate 2


title: Thyroid tissue cultured with NaI 10-5M 48 hours

description: Thyroid follicles were cultured with NaI 10-8 M or 10-5 M for 48 hours.

value: thyroid follicles

value: NaI

value: 10e-8M NaI

value: 48 hours


title: S_mansoni_adult_worms_treated_with_quinine_left_replicate4

status: Public on Jul 13 2009

city: Campos dos Goytacazes

first: Thiago

middle: Motta

last: Venancio

state: RJ

address: Av Alberto Lamego 2000

country: Brazil

institute: UENF

description: No additional information

scan_protocol: Slides were air dried and scanned using a microarray dual channel laser scanner (GenePix 4000B, Molecular Devices, USA) at 5 Ìm resolution, 100 % laser power and PMT levels were adjusted in order to obtain similar average intensities of red and green signal.

data_processing: Data was extracted from images using the Array Vision 8.0 program. Unreliable spots, having intensities too similar to local background (ie, low intensity) or saturated, were filtered out. Saturated signals  were also discarded. Normalization was carried out by LOWESS fitting on a M versus A plot.

organism: Schistosoma mansoni

source_name: S. mansoni adult worms treated with 30.0% ethanol alone(control).

label_protocol: One microgram of total RNA from each sample was amplified using the T7-RNA polymerase-based linear amplification protocol. Three micrograms of aminoallyl-modified amplified RNA was labeled with Cy3 or Cy5 by indirect labeling (GE Healthcare). The Cy3- and Cy5-labeled samples were then combined, dried and re-suspended in hybridization buffer (50 % formamide, 25 % RNase free water and 25 % Microarray Hybridization buffer 4x from GE Healthcare).

extract_protocol: Total RNA was obtained using Trizol reagent (Invitrogen) according to the manufacturer's instructions. The RNA was quantified using the Nanodrop ND-1000 UV/Vis spectrophotometer and RNA integrity was checked by electrophoresis with an Agilent 2100 Bioanalyzer.

tag: The Schistosoma mansoni adult female worms were recovered forty two days after infection of female swiss mice treated from day 11 to 17 after infection, with daily intraperitoneal injections of 30.0% ethanol alone (control).

source_name: S. mansoni adult worms treated with quinine hydocholride dihydrate in 30.0% ethanol (QN).

tag: The Schistosoma mansoni adult female worms were recovered forty two days after infection of female swiss mice treated from day 11 to 17 after infection, with daily intraperitoneal injections of 75 mg/kg quinine hydrochloride dihydrate in 30.0% ethanol (QN).


title: K562 miR-34a 24h

city: Boston

first: Francisco

last: Navarro

address: 200 Longwood Ave

institute: Immune Disease Institute

description: Gene expression data from miR-34a tranfected K562 cells

hyb_protocol: Following fragmentation, cRNA was hybridized overnight at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with dCHIP software using default settings

source_name: K562 transfected with miR-34a 24h

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 15 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Human erythroleukemia K562 cells (ATCC) were grown in RPMI-1640 medium supplemented with 10% FCS and penicillin/streptomycin (Invitrogen).

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

treatment_protocol: K562 cells were transfected by nucleofection (Amaxa) with 3 ug of miR-34a mimic or control mimic (Dharmacon) as per manufacturer’s protocol.


title: S_mansoni_adult_worms_treated_with_quinine_left_replicate3

description: No additional information

hyb_protocol: The Cy3- and Cy5-labeled samples were then combined, dried and re-suspended in hybridization buffer (50 % formamide, 25 % RNase free water and 25 % Microarray Hybridization buffer 4x from GE Healthcare).


title: K562 control miRNA 24h

description: Gene expression data from control tranfected K562 cells

source_name: K562 transfected with control miRNA 24h


title: S_mansoni_adult_worms_treated_with_quinine_left_replicate2

description: No additional information


title: S_mansoni_adult_worms_treated_with_quinine_right_replicate1

description: No additional information


title: S_mansoni_adult_worms_treated_with_quinine_right_replicate2

description: No additional information


title: S_mansoni_adult_worms_treated_with_quinine_left_replicate1

description: No additional information


title: S_mansoni_adult_worms_treated_with_quinine_right_replicate3

description: No additional information

source_name: S. mansoni adult worms treated with quinine hydocholride dihydrate in 30.0% ethanol (QN)


title: S_mansoni_adult_worms_treated_with_quinine_right_replicate4

description: No additional information


title: JHB-blood-N-F-079

city: Kiel

first: Paul-Martin

last: Holterhus

address: Campus Kiel, Schwanenweg 20

department: Pädiatrische Endokrinologie und Diabetologie

country: Germany

institute: Universitätsklinikum Schleswig-Holstein

description:
Simple annotation: Development, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58773.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1600, 5480; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus

source_name: Stratagene Reference (0810006)

label_protocol: We subsequently used 3 ug aRNA, 7.5 ug random-hexamer-primers (Roche), and Cy5-dUTP (0,1 mM) (Amersham, Freiburg, Germany) for Cy5-labeling (pseudo-color red) and 50 ug of human universal reference-RNA (Stratagene; Amsterdam; The Netherlands), 4.5 ug T20VN-primer (TIB MolBiol, Berlin, Germany), and Cy3-dUTP (0,1 mM) (Amersham) for Cy3-labeling (pseudo-color green) to prepare the microarray-probes.

tag: Stratagene Reference (0810006)

extract_protocol:
Blood samples were taken at 1:00 pm +/- 1 h (Potassium-EDTA-monovettes, Sarstedt, Numbrecht, Germany) to control for circadian influences on gene expression. Blood was taken from normal male controls, normal female controls as well as different patients with disorders of sex development leading to a dissection of sex chromosomes and external genital phenotype.
All samples were analyzed by a blood cell counter (Beckmann-Coulter, Krefeld, Germany) and white blood cell counts did not differ between the normal males and the normal females (by t-test).
PBMCs were isolated from whole blood using PBS (pH 7.2) and Ficoll (Biochrom, Berlin, Germany) gradient centrifugation. In essence, serum was extracted from whole blood by centrifugation (720 g; 10 min), diluted with 3 ml of PBS and pipetted on top of 5 ml Ficoll. After centrifugation (950 g; 20 min), the cellular interphase was transferred and washed twice with PBS (460 g; 10 min). Total RNA was extracted by TRIZOL (Invitrogen, Karlsruhe, Germany) according to the manufacturer's manual. After extraction and clean-up (RNeasy-Mini-columns, Qiagen, Hilden, Germany), RNA was quantified by spectrophotometry and additionally analyzed for quality by 1% denaturating gel electrophoresis.
Three micrograms of total RNA and 1 ug of T7-oligo(dT)15 were used for linear RNA-amplification. Reverse transcription was done by SuperScript II (400 U) (Invitrogen, Karlsruhe, Germany) at 42degrees C for 90 min. The second-strand synthesis buffer containing RNaseH (2U), DNA-Polymerase-I (40 U), and dNTPs (1 mM) (Roche, Mannheim, Germany) was mixed with the first reaction mixture and subsequently incubated for 2 h at 15degrees C. The reaction was deactivated with 0.05 M NaOH (Merck, Darmstadt, Germany) and 0.1 M EDTA (Merck) and the reaction product was cleaned by phenol-chlorofom-isoamylalcohol (25:24:1) (Merck) and Phase-Lock-Gel-Tubes (Eppendorf, Hamburg, Germany). Subsequently, the in-vitro-transcription-mixture containing T7-RNA-Polymerase (60 U) and NTPs (1 mM) (Roche) was added to the cleaned reaction product and incubated for 5 h at 37degrees C. The resulting aRNA was purified with RNeasy-Mini-columns and quantified by spectrophotometry.

tag: Disease State

value: female control

tag: Genotype

tag: Measurement

value: time(absolute) 22;6 years

tag: Phenotype

value: normal female


title: JHB-blood-N-M-080

description:
Simple annotation: Development, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58418.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1560, 6160; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus

value: male control

value: time(absolute) 33;2 years

value: normal male


title: JHB-blood-N-M-016

description:
Simple annotation: Development, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58485.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1640, 5720; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus

value: time(absolute) 42;0 years


title: MDA-MB-436

first: Antoinette

last: Hollestelle

address: Dr. Molenwaterplein 50

department: Medical Oncology

institute: Erasmus University Medical Center

description: Gene expression of MDA-MB-436.

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: Intensity values for all genes were scaled using the global normalization factor as specified by GCOS 1.1.

source_name: breast cancer cell line

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 10 ug total RNA.

growth_protocol: Cell lines were grown to optimal cell density in RPMI 1640 supplemented with 10% FBS at 37C. Medium was changed 24h prior to RNA isolation.

extract_protocol: Cells were washed with PBS at 37C prior to isolation. Total RNA was isolated using the Rneasy kit from Qiagen. Lysis of the cells was performed in the culture flask directly after washing with PBS. Total RNA was DNAseI-treated for 1 hour at 37C. RNA QC using Agilent Technologies 2100 Bioanalyzer.

tag: cell type

value: breast cancer

tag: morphology

value: spindle


title: JHB-blood-P-115

description:
Simple annotation: Development, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59118.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1400, 5680; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus

value: XY-DSD due to unknown defect of testosterone biosynthesis

value: time(absolute) 14;6 years


title: JHB-blood-P-110

description:
Simple annotation: Development, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58421.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 5480; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus

value: time(absolute) 2;11 years


title: JHB-blood-N-F-034

description:
Simple annotation: Development, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56088.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 4880; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus

value: time(absolute) 24;11 years


title: JHB-blood-P-089

description:
Simple annotation: Development, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-12/58119.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1240, 5680; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus

value: gonadal dysgenesis

value: time(absolute) 15;1 years


title: JHB-blood-P-088

description:
Simple annotation: Development, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58419.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1390, 5520; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus

value: mixed gonadal dysgenesis

value: time(absolute) 1;4 years


title: JHB-blood-N-M-028

description:
Simple annotation: Development, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52865.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1200, 5120; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus

value: time(absolute) 5;10 years


title: JHB-blood-P-027

description:
Simple annotation: Development, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/52452.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1200, 5040; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus

value: 17?-hydroxysteroid-dehydrogenase type III deficiency

value: time(absolute) 19;8 years


title: JHB-blood-P-113

description:
Simple annotation: Development, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58447.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 5680; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus

value: 21-hydroxylase deficiency,salt wasting CAH

value: time(absolute) 10;8 years


title: JHB-blood-P-112

description:
Simple annotation: Development, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58838.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 5480; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus

value: time(absolute) 14;5 years


title: JHB-blood-N-M-035

description:
Simple annotation: Development, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54272.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1240, 5080; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus

value: male control

value: time(absolute) 28;2 years

value: normal male


title: JHB-blood-P-103

description:
Simple annotation: Development, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58430.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 5960; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus

value: time(absolute) 9;3 years


title: JHB-blood-N-M-003

description:
Simple annotation: Development, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58621.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1840, 5400; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus

value: time(absolute) 40;4 years


title: JHB-blood-P-105

description:
Simple annotation: Development, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-12/58118.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 5600; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus

value: time(absolute) 10;2 years


title: JHB-blood-P-033

description:
Simple annotation: Development, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54154.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 5000; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus

value: P450scc deficiency

value: time(absolute) 7;11 years

value: normal female


title: JHB-blood-N-F-031

description:
Simple annotation: Development, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53845.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1240, 5400; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus

value: female control

value: time(absolute) 35;6 years


title: JHB-blood-P-032

description:
Simple annotation: Development, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55042.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1720, 4880; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus

value: 5α-reductase type II deficiency

value: time(absolute) 0;4 years


title: JHB-blood-N-F-036

description:
Simple annotation: Development, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54153.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 4920; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus

value: time(absolute) 24;5 years


title: JHB-blood-N-F-029

description:
Simple annotation: Development, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53447.gif

value: time(absolute) 8;3 years


title: JHB-blood-N-F-021

description:
Simple annotation: Development, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/52073.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 5760; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus

value: time(absolute) 30;3 years


title: JHB-blood-N-F-012

description:
Simple annotation: Development, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58417.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1960, 5640; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus

value: time(absolute) 23;6 years


title: small airways, smoker 199

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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.

source_name: airway epithelial cells obtained by bronchoscopy and brushing

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: Age

tag: Sex

value: F

tag: Ethnic group

value: hispanic

tag: Smoking status

value: smoker, 38 pack-years


title: small airways, smoker 183

value: M

value: black


title: JHB-blood-N-M-104

description:
Simple annotation: Development, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58424.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1400, 5400; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus

value: male control

value: time(absolute) 43;7 years

value: normal male


title: JHB-blood-N-F-020

description:
Simple annotation: Development, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51592.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 5760; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus

value: normal female


title: NRVC1, 12_01_06

city: East Lansing

first: Theodora

last: Szasz

state: MI

address: B 445 Life Sciences

department: Pharmacology and Toxicology

institute: Michigan State University

description: Biological replicate 6 of 6

hyb_protocol: Hybridization was performed according to the "CodeLink Gene Expression System: Single-Assay Bioarray Hybridization and Detection" protocol provided by Amersham/GE Healthcare. Ten µg cRNA were fragmented and hybridized to array. Streptavidin-Cy5 conjugate was used for detection.

scan_protocol: Arrays were scanned using the GenePix Array Scanner (Axon Instruments/Molecular Devices) using standard procedures detailed in the "CodeLink Gene Expression System: Single-Assay Bioarray Hybridization and Detection" protocol provided by Amersham/GE Healthcare.

data_processing: Images were acquired using GenePix Pro 6.0 software (Axon Instruments/Molecular Devices), which runs automatic spot-finding algorithms, subtracts background, filters absent and flags low (near background), saturated, noisy or otherwise poor quality spots. Raw intensities of the ~34,000 spots on each array (N=6 for aorta, N=6 for vena cava) were median-normalized as a batch. Normalized intensity values of each spot were averaged and p values were calculated in Microsoft Excel.

source_name: Sprague-Dawley rat vena cava

label_protocol: Labeling was performed according to the "CodeLink Gene Expression System: Manual Labelled cRNA Target Preparation" protocol provided by Amersham/GE Healthcare. Briefly, first-strand cDNA was synthesized starting with one µg DNase-treated total RNA and diluted bacterial mRNA controls. After second-strand synthesis and cDNA purification, cRNA was in vitro transcribed with incorporation of biotin-labeled UTP, purified and assessed for concentration, purity and quality.

extract_protocol: Total RNA was isolated from ~10 mg sections of rat aorta tissue using the MELT TM Total RNA Isolation System (Ambion/Applied Biosystems) according to the manufacturer’s protocol. RNA was then quantified on a NanoDrop spectrophotometer (NanoDrop Technologies/Thermo Fisher Scientific).

tag: Normal (untreated) male Sprague-Dawley rat vena cava


title: NRVC1, 11_30_06

description: Biological replicate 5 of 6


title: NRA1, 12_01_06

description: Biological replicate 6 of 6

source_name: Sprague-Dawley rat aorta

tag: Normal (untreated) male Sprague-Dawley rat aorta


title: JHB-blood-P-018

description:
Simple annotation: Development, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51732.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 920, 6160; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus

extract_protocol: not provided

value: gonadal dysgenesis

value: time(absolute) 12;5 years


title: small airways, non-smoker 088

value: white

value: non-smoker


title: NRVC2, 11_17_06

description: Biological replicate 4 of 6


title: PCA_wildtype_rpoN_BR3B

city: Amherst

first: Derek

last: Lovley

address: University of Massachusetts at Amherst, Dept. of Microbiology, Morrill IV north room 202

department: Microbiology

institute: University of Massachusetts Amherst

description: Total RNA (10 ug) was directly labeled with cy5 (pCDrpoN) or cy3 (pCD341)

hyb_protocol: Combimatrix 100 ul volume cap.

scan_protocol: Slide was scanned using GenePix software and a GenePix 4000b scanner.

data_processing:
The raw total intensities were treated as follows to generate the M Log2 ratios for this work.  Background signal was calculated from a set of negative control spots incorporated into the array.  As the negative control sequences are not design specific (ie. are found in all of the ESOAs independent of the organism being sampled) some will inevitably demonstrate strong cross hybridization with the sample of interest.  To avoid this issue the negative control spots were ranked according to their total intensity.  The average of the lowest 30% was calculated.  Background signal was calculated as this mean + 2 standard deviations.  The background signal was then subtracted from the total intensity for each spot.  Probes whose signal was not greater than zero after background subtraction were omitted from further analysis.  For the remaining data, the logged ratios [M=log2 (Ex/Ct)] are then calculated and Lowess global normalization is performed. During the data preprocessing, M vs. A plots before and after normalization, and side-by-side box plots for all arrays are used to assess array quality.(3)  LIMMA mixed model analysis (R-package LIMMA(2))is applied to the normalized logged ratios to identify differentially expressed genes.  Specifically, biological replicates are treated as a randomized block to allow for modeling correlations within them. LIMMA calculates a moderated t statistic for each probe, which is the ratio of the estimated mean logged intensity ratio and the Empirical Bayes estimate of its standard error. The P-value of each oligo is then corrected for multiple comparisons according to Benjamini and Hockberg's procedure(1) to control the false discovery rate. Oligos are ranked according to the adjusted P-values and were called differentially expressed if the adjusted P-values are < 0.001.  Note that multiple oligonucleotide probes from the same gene are analyzed separately and a gene is called differentially expressed if at least half of its probes are called differentially expressed.
1.	Benjamini, Y., and Y. Hochberg. 1995. Controlling the False Discovery Rate - a Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society Series B-Methodological 57:289-300.
2.	Smyth, G. K. 2004. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3:Article3.
3.	Smyth, G. K., and T. Speed. 2003. Normalization of cDNA microarray data. Methods 31:265-73.

organism: Geobacter sulfurreducens

source_name: rpoN overexpressor

label_protocol: Micromax ASAP direct RNA labeling kit

extract_protocol: Qiagen RNEasy Midi protocol

tag: DL1/pCDrpoN was grown in medium containing acetate as the electron donor and fumarate as the electron acceptor.  1mM IPTG was added to induce

tag: rpoN overexpression from plasmid pCDrpoN.

source_name: wildtype (pCD341)

label_protocol: Micromax direct RNA labeling kit

tag: DL1/pCD341 was grown in medium containing acetate as the electron donor and fumarate as the electron acceptor.  1mM IPTG was added to induce

tag: control plasmid pCD341.


title: small airways, smoker 186


title: NRA1, 11_30_06

description: Biological replicate 5 of 6


title: JHB-blood-N-M-007

description:
Simple annotation: Development, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/49965.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1680, 7760; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus

tag: Stratagene Reference (0810006)

value: time(absolute) 36;7 years


title: NRVC1, 7_8_06

description: Biological replicate 2 of 6


title: NRVC1, 11_17_06

description: Biological replicate 3 of 6


title: PCA_wildtype_rpoN_BR3A


title: NRVC1, 6_23_06

description: Biological replicate 1 of 6