title: 338_12

source_name: Dp(11)17/+, hippocampus, individual 338


title: Rat_prefrontal_cortex-rep7-expt1

status: Public on Nov 24 2009

type: RNA

city: Toronto

first: Paul

middle: C

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: experiment 1

hyb_protocol: Hybridization was performed according to manufacturer's instructions at the TCAG facility (Toronto, Canada).

scan_protocol: Array images were captured with the Agilent 2500 scanner using the Affymetrix Microarray Suite software (v5.0).

data_processing: Data were loaded into the R statistical environment (v2.6.2) using the affy pacakge (v1.16.0) of the BioConductor open-source library. Arrays were tested for spatial and distributional heterogeneity; none were excluded. Pre-processing employed the GCRNA algorithm, as implemented in the gcrma package of BioConductor (v2.10.0).

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: Rat Prefrontal cortex, individual #7

label_protocol: Labeling was performed according to manufacturer's instructions at the TCAG facility (Toronto, Canada).

growth_protocol: Experiment 1: 20 male Lewis rats (200-250g, Charles River, Montreal, Canada) underwent three behavioural tests: SF, locomotion, and ASR. Experiment 2: 40 male Lewis rats (200-250g, Charles River) underwent four behaviour tests: SF, locomotion, ASR, and PPI.  Rats were acclimated one week before testing, singly housed in clear Plexiglas cages with food and water ad libitum, except as described during the SF test. Light cycle was from 0800-2000h, temperature at 21°C +/-1°C. Testing occurred between 0900-1700h. Procedures were approved by the Department of Zoology animal care committee, and conformed to ethical standards of the University of Toronto and the Canadian Council on Animal Care.

extract_protocol: Rats were sacrificed in a random order by decapitation 12 days (Experiment 1) and 6 days after the last testing day (Experiment 2). Brains were removed, and PFC dissected: Fr1and Fr2 anterior to Bregma +4.0mm without olfactory bulb, snap frozen on dry ice and stored at -80°C until RNA extraction. 30-35mg of PFC was added to a pre-chilled cuvette containing 600μl Trizol (Invitrogen, Carlsbad, CA) and mechanically homogenized. The homogenate was then centrifuged at 14,000rpm for 10min, 4°C. Chloroform (VWR International, Mississauga, ON) was added to the supernatant (20% v/v Trizol), shaken and incubated 15s at 21°C, then centrifuged at 14,000rpm for 15min at 4°C. RNA was precipitated by adding an equal volume of 70% ethanol at room temperature then vortexed. The Absolutely RNeasy® RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) was used to purify precipitated RNA, and RNA was eluted then concentrated to 1.2μg/μl using the Microcron YM-10 centrifugal filter device kit (Millipore Corp., Bedford, MA). RNA quality assurance was obtained via the Agilent BioAnalyzer 2100 (Agilent Technologies, Palo Alto, CA) or NanoDrop ND-8000 (Wilmington, DE) spectrophotometer, verifying the 18s and 28s ribosomal RNA bands. Quality assurance was conducted at the Centre for Applied Genomics TCAG facilities at the Hospital for Sick Children (Toronto, ON, Canada) before preparation for microarray hybridization at the same facility.

treatment_protocol: No treatments applied

tag: gender

value: Male

tag: strain

value: Lewis

tag: tissue

value: prefrontal cortex

tag: weight

tag: light cycle

tag: startle

tag: plus maze

tag: sugar feeding


title: Rat_prefrontal_cortex-rep3-expt1

description: experiment 1

source_name: Rat Prefrontal cortex, individual #3


title: Rat_prefrontal_cortex-rep2-expt1

description: experiment 1

source_name: Rat Prefrontal cortex, individual #2


title: Rat_prefrontal_cortex-rep4-expt1

description: experiment 1

source_name: Rat Prefrontal cortex, individual #4


title: Rat_prefrontal_cortex-rep5-expt1

description: experiment 1

source_name: Rat Prefrontal cortex, individual #5


title: Rat_prefrontal_cortex-rep1-expt1

description: experiment 1

source_name: Rat Prefrontal cortex, individual #1


title: H3K27me3 Yaswen1A RenLab ENCODE PCR tiling array replicate 1 llee_enc_H3K27me3_Yaswen1A_031608.gpr

status: Public on Dec 01 2009

type: genomic

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Drive

country: USA

institute: University of California, San Diego

description: ChIP-chip analyses were performed for various transcription factors and chromatin modifications in various cell types. Details to be described in publications.

hyb_protocol: GenePix

scan_protocol: GenePix

data_processing: raw data

molecule: genomic DNA

organism: Homo sapiens

source_name: Chromatin immunoprecipitated DNA from Yaswen1A cells using H3K27me3 antibody

label_protocol: Cy3 input Cy5 ChIP sample

extract_protocol: GenePix

source_name: Input DNA from Yaswen1A cells

tag: Input DNA from Yaswen1A cells


title: Rat_prefrontal_cortex-rep6-expt1

description: experiment 1

source_name: Rat Prefrontal cortex, individual #6


title: 227_3

status: Public on Nov 30 2009

city: Lausanne

first: Alexandre

last: Reymond

address: Genopode building

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

hyb_protocol: Twelve micrograms of biotinylated cRNA from each sample were fragmented and hybridized to GeneChip Mouse 430 2.0 arrays, according to standard procedures. Washing and staining was performed using the EuGE-WS2v5 protocol.

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G and hybridization quality control were assessed using RACE (Psarros et al., 2005), a web service based on Bioconductor affy and affyPLM packages (Gautier et al., 2004).

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003).

organism: Mus musculus

source_name: C57BL/6-Tyr c-Brd, hippocampus, individual 227

label_protocol: Target preparations were performed as described by the Affymetrix GeneChip Expression Analysis Technical Manual (http://www.affymetrix.com), and were conducted at the DNA array facility of the University of Lausanne (Switzerland). 3 ug of each pool was used.

extract_protocol: Mice were sacrificed by cervical dislocation. RNA from whole brain, testis, kidney, heart, liver and lung was isolated with TRIzol (Invitrogen) and purified on Qiagen RNeasy Mini columns (Qiagen), according to manufacturers' instructions.

tag: Strain

value: C57BL/6-Tyr c-Brd, Genotype:+/+, Gender:male, Age:11-14 weeks of age, Tissue:hippocampus


title: H3K4me3 Yaswen1B RenLab ENCODE PCR tiling array replicate 1 llee_enc_H3K4me3_Yaswen1B_061708.gpr

source_name: Chromatin immunoprecipitated DNA from Yaswen1B cells using H3K4me3 antibody

source_name: Input DNA from Yaswen1B cells

tag: Input DNA from Yaswen1B cells


title: LungXenograft-A549-Myc-rep2

hyb_protocol: The 158 µL were mixed with 50 µL of 1 mg/mL of Human Cot-1 DNA, 52 µL of 10x Agilent Blocking Agent, 260 µL of 2x Agilent Hybridization Buffer. Samples were heated at 95°C for 3 minutes, and then incubated at 37°C for 30 minutes. 490 µL of the sample were applied to the 1x244 promoter array assembled in a chamber and incubated in a rotisserie hybridization oven at 65°C and 20 RPM for 40 hours. After hybridization the microarray slide was washed with Oligo aCGH/ChIP-on-chip Wash Buffer for 5 minutes at room temperature, followed by a wash for 5 minutes at 31°C. QC metrics used were based on the ChIP-on-chip requirements and no arrays were removed or repeated.

scan_protocol: Microarray data was scanned using a G2565BA DNA Scanner; Agilent Scan Control software (v7.0) with the following settings:  5 um scan, 100% PMT (both channels), 100% laser power (both channels), scan area 61 x 21.6 mm.

data_processing: Raw microarray data were loaded into the limma package (v2.12.0) of the BioConductor open-source library for the R statistical environment (v2.6.2). Data were assessed for spatial and distributional homogeneity; no arrays were excluded. Pre-processing used the variance-stabilizing normalization (vsn) algorithm, as implemented in the vsn package (v3.2.1) of BioConductor using 10,000 iterations to ensure convergence.

source_name: DNA ChIPed from A549 Xenografts using a polyclonal antibody directed against the N-terminal 262 residues of c-Myc

label_protocol: Arrays were labeled using the Agilent Genomic DNA Labelling Kit and hybridized using the aCGH Hybridization Kit following the ChIP-on-chip v10 protocol as follows: for each 1x244 promoter array, 2 µg of DNA was brought to 26 µL final volume. 5 µL of Random Primers (supplied with Agilent Genomic DNA Labeling Kit PLUS) was added and the mix was incubated at 95°C for 3 minutes, then on ice for 5 minutes. The 31 µL were mixed with the Labeling Mix to a final volume of 50 µL (10 µL of 5x Buffer, 5 µL of 10x dNTP, 3 µL of 1 mM Cyanine 3-UTP or 1 mM Cyanine 5-dUTP, 1 µL of Exo-Klenow fragment) and incubated at 37 °C for 2 hours. The enzyme was then inactivated at 65°C for 10 minutes. The labeled Genomic DNA was cleaned with Microcon columns (Millipore, Microcon YM-30) and eluted with 80.5 µL of 1x TE. 5 µg Cy5-labeled and 5 µg of Cy3-labeled DNAs were combined in a total volume of 158 µL.

growth_protocol: Seven-week old female severe combined immunodefiicent (SCID) mice (Ontario Cancer Institute) were sub-cutaneously injected into the right flank with 5 x 106 A549, MGH8, MGH24 or RVH6849 cells suspended in 0.1 mL of sterile PBS.  Mice were monitored daily. At maximal tumor burden, mice were sacrificed by CO2 inhalation and tumors were excised and immediately snap-frozen in liquid N2 for later analysis.

extract_protocol: 0.03g of snap-frozen tissue per antibody was chopped into small pieces in 1X PBS, formaldehyde was added to a final concentration of 1% at room temperature for 15 minutes. The crosslinking reaction was quenched by addition of glycine to a final concentration of 0.125 M for 5 minutes, followed by two washes with phosphate-buffered saline (PBS). Samples were washed one time in 1X PBS. The tissues were disaggregated in 1X PBS using a dounce homogenizer, Brinkmann Homogenizer. Model PT 10/35 (110volts, 6Amps, 60Hz). Polytron. Switzerland. Cells were resuspended in cell lysis buffer (5 mM PIPES pH 8, 85 mM KCl, 0.5% [v/v] NP40, 1 mM PMSF, 10  g/mL aprotinin, 10  g/mL leupeptin) for 10 minutes on ice and then pelleted (5000 rpm, 5 minutes, 4  C). The pellet was resuspended in 1 mL of nuclei lysis buffer (50mM Tris-HCl pH 8.1, 10mM EDTA, 1% SDS, 1 mM PMSF, 10  g/mL aprotinin, 10  g/mL leupeptin) for 10 minutes on ice. Prior to sonication, 0,1g of glass beads (Sigma G-1277) were added to each sample. The samples were sonicated on ice at setting 7 pulses (12-13 Watts, setting 10, 10 seconds per pulse, 45 seconds on ice between pulses) from a Model 60 Sonic Dismembrator (Fisher Scientific 15-338-53) to generate fragments between 600 bp and 1000 bp and then were microcentrifuged. Lysates were centrifuged for 10 minutes at 21,000 x g at 4 °C. Supernatants were diluted into an equal volume with IP dilution buffer (0.01% SDS, 1.1% Triton-X100, 1.2mN EDTA, 16.7mM Tris-HCl pH 8.1, 0.2% Sarkosyl, 1 mM PMSF, 10  g/mL aprotinin, 10  g/mL leupeptin) and pre-cleared for 30 minutes at 4 °C with protein G-PLUS agarose beads (Santa Cruz Biotechnology sc-2002). Prior to use, G-PLUS agarose beads were blocked with salmon sperm DNA at a final concentration of 50 µg/mL and rotated overnight at 4 °C. Diluted and cleared extracts corresponding to 10 x 106 HL60 cells were incubated and rotated at 4°C for approximately 12 to 16 hours with each of the following antibodies: 0.7 µg normal rabbit IgG (Santa Cruz Biotechnology sc-2027), 0.7 µg N262 home made, as described elsewhere (Ponzielli et al. NAR.2008. 36(21):e144). 50  L of salmon sperm DNA pre-blocked Protein G-PLUS agarose beads were added to each sample, incubated on a rotating platform at 4 °C for 3 hours. Each pellet was washed once with 1.4 mL of sonication buffer and then twice with 1.4 mL of high salt buffer (0.1% [v/v] SDS, 1% [v/v] Triton X-100, 1 mM EDTA, 50 mM HEPES, 500 mM NaCl, 0.1% [w/v] sodium deoxycholate) and then once with 1.4 mL LiCl Buffer (250 mM LiCl, 1% [v/v] NP-40, 1% [w/v] sodium deoxycholate, 1 mM EDTA, 1 mM Tris pH 8) and finally twice with 1.4 mL TE pH 8 (10 mM Tris pH8, 1 mM EDTA). For each wash, the pellets were mixed for 5 minutes at room temperature then pelleted (3000 rpm, 30 seconds, room temperature). After the last wash, the pellets were eluted in 300 µL of Elution buffer (1% [w/v] SDS, 10 mM Tris pH 8, 5 mM EDTA), incubated at 65 °C for 15 minutes, and then pelleted (3000 rpm, 3 minutes, room temperature). Cross-links were reversed in the presence of 200 mM NaCl at 65 °C over-night and samples were treated with RNase A (Sigma R5500). After ethanol precipitation, the samples were resuspended in 100 µ of TE (10 mM Tris, pH 7.5, 1 mM EDTA), 25 µ of 5x proteinase K buffer (1.25% SDS, 50 mM Tris, pH 7.5, 25 mM EDTA), and 1.5 µ of proteinase K (Roche 1413783) and incubated at 42 °C for 2 hours. DNA was isolated using the QIAquick PCR purification kit (Qiagen 28106)  and resuspended in 60 µ of H2O. The DNA amplification was performed following a protocol described elsewhere (O'Geen et al. Biotechniques 2006. 41: 577-580) This method efficiently primes the DNA fragments to generate a library of DNA fragments with defined 3' and 5' termini. The library is then replicated using linear amplification in the initial steps followed by a limited round of geometric amplifications. Entire ChIP samples with an average size of 500-1,000 bp of DNA fragments were used for the library generation and subsequent amplification. For the library preparation and the amplification (round 1), GenomePlex Complete Whole Genome Amplification (WGA) kit was used (Sigma WGA2) as follows. Library Preparation step: 2  L of Library Preparation Buffer was added to the ChIP material that has been concentrated to 10  L. 1  L of Library Stabilization Solution was added and heated at 95 °C for 2 minutes in a thermal cycler and immediately cooled on ice. 1  L of Library Preparation Enzyme was added and incubated in a thermal cycler precooled to 16 °C (16 °C for 20 minutes, 24 °C for 20 minutes, 37 °C for 20 minutes, 75 °C for 5 minutes). Amplification step (round 1): the following master mix was added to each sample prepared on the previous step, 7.5  L of 10x Amplification Master Mix, 47.5  L of nuclease-free H2O and 5  L of WGA DNA Polymerase. Samples were incubated in a thermal cycler (95 °C for 3 minutes, then 14 cycles of 94 °C for 15 seconds, and 65 °C for 5 minutes). Samples were then purified using QIAquick PCR Purification kit (Qiagen 28106). 10 ng of each amplified sample was tested for specificity as described above under the PCR title. For the reamplification step (round 2), GenomePlex WGA amplification Kit was used (Sigma WGA3). A master mix of 7.5  L of 10x Amplification Master Mix, 47.5  L of nuclease-free H2O and 5  L of WGA DNA Polymerase was added to 15 ng of purified amplification product previously diluted in nuclease-free H2O to 10  L volume. Samples were then purified using QIAquick PCR Purification kit (Qiagen 28106). Amplified sample (10 ng) was tested for specificity as described above. WGA amplified DNA (4  g) was hybridized to Agilent 2x244 promoter arrays at the UHN microarray center (Toronto, Canada). Based on our previous results a single batch of arrays was used with lot number 19585.

treatment_protocol: Not Applicable

tag: cell-line

tag: antibody

value: c-Myc

source_name: DNA ChIPed from A549 Xenografts using a non-specific IgG antibody

value: non-specific IgG


title: Rat_prefrontal_cortex-rep8-expt2

description: experiment 2

source_name: Rat Prefrontal cortex, individual #8

tag: locomotion

tag: ppi


title: Rat_prefrontal_cortex-rep9-expt2

description: experiment 2

source_name: Rat Prefrontal cortex, individual #9


title: LungXenograft-MGH8-Myc-rep1

source_name: DNA ChIPed from MGH8 Xenografts using a polyclonal antibody directed against the N-terminal 262 residues of c-Myc

source_name: DNA ChIPed from MGH8 Xenografts using a non-specific IgG antibody


title: LungXenograft-RVH6849-Myc-rep3

source_name: DNA ChIPed from RVH6849 Xenografts using a polyclonal antibody directed against the N-terminal 262 residues of c-Myc

source_name: DNA ChIPed from RVH6849 Xenografts using a non-specific IgG antibody


title: LungXenograft-RVH6849-Myc-rep2


title: Rat_prefrontal_cortex-rep7-expt2

description: experiment 2

source_name: Rat Prefrontal cortex, individual #7


title: Rat_prefrontal_cortex-rep10-expt2

description: experiment 2

source_name: Rat Prefrontal cortex, individual #10


title: LungXenograft-RVH6849-Myc-rep1


title: LungXenograft-A549-Myc-rep3


title: LungXenograft-MGH24-Myc-rep1

source_name: DNA ChIPed from MGH24 Xenografts using a polyclonal antibody directed against the N-terminal 262 residues of c-Myc

source_name: DNA ChIPed from MGH24 Xenografts using a non-specific IgG antibody


title: LungXenograft-MGH24-Myc-rep2


title: 334_4

source_name: Dp(11)17/+, hippocampus, individual 334

value: C57BL/6-Tyr c-Brd, Genotype:Dp(11)17/+, Gender:male, Age:11-14 weeks of age, Tissue:hippocampus


title: LungXenograft-MGH24-Myc-rep3


title: 192_11

source_name: C57BL/6-Tyr c-Brd, hippocampus, individual 192


title: Rat_prefrontal_cortex-rep4-expt2

description: experiment 2

source_name: Rat Prefrontal cortex, individual #4


title: Rat_prefrontal_cortex-rep5-expt2

description: experiment 2

source_name: Rat Prefrontal cortex, individual #5


title: LungXenograft-MGH8-Myc-rep2


title: Rat_prefrontal_cortex-rep6-expt2

description: experiment 2

source_name: Rat Prefrontal cortex, individual #6


title: 1927_LowSplitting_rep2

status: Public on Oct 01 2009

city: Pretoria

first: Eugenia

last: Barros

state: Gauteng

address: Meiring Naude Rd

department: Building 20

country: South Africa

institute: CSIR

description:
Technical replicate
1927_LS2

hyb_protocol: Microarray slides were pre-hybridized for 20 min at 60°C in a solution containing 3.5× SSC, 0.2% SDS, and 1% BSA (Roche Diagnostics). Slides were rinsed three times in deionized water and dried with N2 gas. The Cy3-labeled probe was then dissolved in hybridization solution containing 50% formamide (SIGMA), 25% 2× hybridization buffer (Amersham Pharmacia Biotech), and 25% deionized water. The mixture was denatured at 92°C for 5 min and quickly cooled on ice. The denatured probe (approximately 35 μl) was pipetted directly onto the microarray surface and covered with a glass coverslip (24×60 mm, No.1, Marienfeld, Germany). Slides were placed in a custom-made hybridization chamber (N.B. Engineering Works, Pretoria, South Africa) and incubated for 16–18 h in a 42°C water bath. After hybridization, slides were washed once in 1× SSC, 0.2% SDS at 37°C for 4 min, twice in 0.1× SSC, 0.2% SDS at 37°C for 4 min, twice in 0.1× SSC at room temperature for 1 min, and then rinsed in deionized water for 2 s. Slides were dried using N2 gas.

scan_protocol: Arrays were scanned with an Axon GenePix 4000A scanner and the images were analyzed with GenePix Pro 6.0 software (Axon Instruments).

data_processing:
Raw data processing was performed with GenePix Pro 6.0. Signal intensities of duplicate spots were averaged and spots with a signal-to-noise ratio of less than two were rejected.  Intensity values were normalized across slides by global regression on the median spot intensity data for tree 1/23/4-HS, which was used as a reference for normalization of all spot intensity data (reference design). Subtracted data obtained from log10 of processed Sample signal/processed Reference signal. The statistical significance of changes in transcript abundance was estimated using two successive mixed models as previously described [Wolfinger, R. D., Gibson, G., Wolfinger, E. D., Bennett, L., Hamadeh, H., Bushel, P., Afshari, C., Paules, R. S. (2001)  J. Comput. Biol.  8(6):625-637]. Only genes with an average fold-change of 1.4 in biological replicates and a p value of 0.01 were considered to be differentially expressed and sequenced. For genotyping, normalized signal intensity values were used to identify polymorphic fragments based on their bimodal distribution of their intensity values across slides. Polymorphic markers identified were then scored for the absence (0) or presence (1) of the fragment in each of the respective E. grandis trees. Cluster analysis was performed on all the normalized and mean-centered signal intensities using Pearson’s correlation in the Cluster program and visualized in TreeView (CLUSTER, available at http://rana.lbl.gov/). Only cDNA clones showing high differential expression were assigned putative identities by BLAST searches against the non-redundant protein database of the National Center for Biotechnology Information (NCBI) database (www.ncbi.nlm.nih.gov). For the cDNA-AFLP fragments, normalized signal intensity values were used to identify polymorphic fragments based on their bimodal distribution of their intensity values across slides as described by Lezar et al. [42]. Polymorphic markers identified were then scored for the absence (0) or presence (1) of the fragment in each of the respective E. grandis trees.

Tree 1/23/4-HS was used as the reference because it showed the highest hybridization signals in the raw data files. Data of tree 1/23/4-HS was normalized between the slides. The normalized data was then averaged, and these values were used for global normalization for each hybridization for each tree. The resulting ratios were mean-centered using Cluster (CLUSTER, available at http://rana.lbl.gov/). The VALUEs in the data table represent the mean-centered log10 ratio of the sample tree signal/averaged reference tree signal.

organism: Eucalyptus grandis

source_name: E. grandis, vascular cambium, low splitting

label_protocol: The cDNA obtained was divided into aliquots of 2 ug each and where possible one technical array replicate was performed. The 2 ug cDNA was coupled to either Cy3  or Cy5 as described by Lezar et al. [Lezar, S., Myburg, A.A., Berger, D.K., Wingfield, M.J., Wingfield, B.D. (2004) Theor. Appl. Genet. 109:1329-1336]. Free dye was removed with the QIAGEN PCR Purification Kit (QIAGEN, Valencia, CA).

extract_protocol: Total RNA was isolated by a standard protocol [Chang, S., Puryear, J., Cairney, J. (1993)  Plant Mol. Biol. Rep. 11:113-116]. Contaminating genomic DNA was removed with DNase I (Qiagen). Double-stranded cDNA was synthesized from purified RNA using the cDNA Synthesis System (Roche Diagnostics, Mannheim, Germany) according to manufacturer’s protocol. Contaminating RNA was removed by hydrolysis with 0.5 M EDTA and 1 M NaOH at 65°C for 15 min and the reactions were subsequently column-purified using the QIAquick PCR Purification Kit (QIAGEN).

tag: tree

tag: trait

value: Low splitting

tag: age

value: 4 years

value: vascular cambium


title: 1927_LowSplitting_repB

description:
Biological replicate
1927_LSB


title: LungXenograft-MGH8-Myc-rep3


title: LungXenograft-A549-Myc-rep1

source_name: DNA ChIPed from A549 Xenografts using a polyclonal antibody directed against the N-terminal 262 residues of c-Myc

source_name: DNA ChIPed from A549 Xenografts using a non-specific IgG antibody


title: Rat_prefrontal_cortex-rep1-expt2

description: experiment 2

source_name: Rat Prefrontal cortex, individual #1

tag: gender

tag: strain


title: 1917_LowSplitting_rep2

description:
Technical replicate
1917_LS2

tag: tissue


title: 1917_LowSplitting_repB

description:
Biological replicate
1917_LSB


title: 1927_LowSplitting_rep1

description:
Sample
1927_LS1


title: LungXenograft-A549-Myc-rep2


title: 1716_HighSplitting_rep2

description:
Technical replicate
1716_HS2

source_name: E. grandis, vascular cambium, high splitting

value: High splitting


title: 1917_LowSplitting_rep1

description:
Sample
1917_LS1


title: LungXenograft-MGH24-Myc-rep2


title: LungXenograft-A549-Myc-rep3


title: 1716_HighSplitting_repB

description:
Biological replicate
1716_HSB


title: LungXenograft-MGH24-Myc-rep1


title: LungXenograft-RVH6849-Myc-rep3


title: Rat_prefrontal_cortex-rep2-expt2

description: experiment 2

source_name: Rat Prefrontal cortex, individual #2

tag: weight

tag: light cycle


title: LungXenograft-MGH8-Myc-rep1

source_name: DNA ChIPed from MGH8 Xenografts using a polyclonal antibody directed against the N-terminal 262 residues of c-Myc

source_name: DNA ChIPed from MGH8 Xenografts using a non-specific IgG antibody


title: 1234_HighSplitting_rep1

description:
Sample
1234_HS1


title: 1234_HighSplitting_rep2

description:
Technical replicate
1234_HS2


title: Egrandis_243_LowLignin_rep2

description:
Technical replicate
243_LL2

source_name: E. grandis, vascular cambium, low lignin

value: Low lignin content


title: 1716_HighSplitting_rep1

description:
Sample
1716_HS1


title: Egrandis_243_LowLignin_repB

description:
Biological replicate
243_LLB


title: Egrandis_243_LowLignin_rep1

description:
Sample
243_LL1


title: Egrandis_108_LowLignin_rep1

description:
Sample
108_LL1


title: Egrandis_741_HighLignin_repB

description:
Biological replicate
741_HLB

source_name: E. grandis, vascular cambium, high lignin

value: High lignin content


title: Egrandis_108_LowLignin_repB

description:
Biological replicate
108_LLB


title: Egrandis_108_LowLignin_rep2

description:
Technical replicate
108_LL2


title: 1234_HighSplitting_repB

description:
Biological replicate
1234_HSB


title: Egrandis_741_HighLignin_rep2

description:
Technical replicate
741_HL2


title: Egrandis_741_HighLignin_rep1

description:
Sample
741_HL1


title: Rat_prefrontal_cortex-rep3-expt2

description: experiment 2

source_name: Rat Prefrontal cortex, individual #3

tag: startle

tag: plus maze


title: Modioli_negative-control_rep1

status: Public on Sep 16 2009

city: Urbana

first: Richard

last: Kollmar

state: IL

address: 407 S. Goodwin Ave., MC-114

hyb_protocol: The biotinylated cDNA was hybridized to a Mouse Expression Set 430 2.0 array in a Hybridization Oven 640 (Affymetrix, Santa Clara, CA). After 16 hours, the array was stained and washed in a Fluidics Station 450 (Affymetrix) according to protocol EukGE-WS2v4_450.

scan_protocol: The stained array was imaged in a Gene Chip Scanner 3000 (Affymetrix) at a resolution of 1.56 µm per pixel and a wavelength of 570 nm. The probe hybridization signals (cell intensity data) were extracted from the .DAT image file with Affymetrix software and saved as a .CEL file. Both hybridization and scan steps were performed at the Roy J. Carver Biotechnology Center of the University of Illinois at Urbana-Champaign.

data_processing:
The probe hybridization signals of all six samples (files 149_E.CEL to 154_E.CEL) were pre-processed together with Bioconductor tools (release 2.1; www.bioconductor.org) in R software (version 2.6.1; http://www.r-project.org) according to the procedures outlined in Gentleman et al. (2005) by using the following commands:
#################
### Importing ###
# import .CEL files in working directory into Affybatch object RK111904_CELs
> library("affy")
> RK111904_CELs <- ReadAffy()
#######################
### Quality Control ###
# Simple and Affymetrix-style quality control of hybridization data
> library(affyQCReport)
> QCReport(RK111904_CELs,file="affyQCReport.pdf")
# Check for RNA degradation
> RNAdeg <- AffyRNAdeg(RK111904_CELs)
> plotAffyRNAdeg(RNAdeg, col = c(2,3,2,3,3,2))
> summaryAffyRNAdeg(RNAdeg)
# Check for abnormal population distributions of hybridization signals
> library(geneplotter)
> MAplot(RK111904_CELs,pairs=TRUE,plot.method="smoothScatter", cex = 1.2)
# Check for abnormal spatial distributions of hybridization signals
> library(affyPLM)
> options(width = 40)
> Pset <- fitPLM(RK111904_CELs)
> image(Pset, which = 1, type = "sign.resids")
> ...
> RLE(Pset, main = "RLE for RK111904_CELs", ylim = c(-6,7))
> NUSE(Pset, main = "NUSE for RK111904_CELs", ylim = c(0.85,1.5))
######################
### Pre-processing ###
# Background correction, normalization, PM correction, and summarization
> RK111904_fullEset <- expresso(RK111904_CELs,bgcorrect.method="rma", normalize.method="quantiles", pmcorrect.method="pmonly", summary.method="medianpolish")
The quality-control step did not uncover notable defects other than a higher background level in file 154_E.CEL, which was corrected in the pre-processing step. For each sample, the paired Affymetrix probe-set IDs (ID_REF) and pre-processed expression levels (VALUE) were then exported as text files.
Reference: Gentleman R., Huber W., Carey V.J., Irizarry R., Smith C., Zhang J., Li X., Scholtens D., Ding B., and Dudoit S. (eds). Bioinformatics and Computational Biology Solutions Using R and Bioconductor. London: Springer. 2005.

label: Biotin

source_name: Left and right cochlear modiolus, not noise-exposed, animal '8A'

label_protocol: The entire RNA sample was reverse transcribed, linearly amplified, fragmented, and biotinylated with an Ovation Biotin kit version 1.0 (NuGEN, San Carlos, CA). The cDNA concentrations after amplification and labeling were determined by spectrophotometry.

growth_protocol: Noise-exposed and negative-control animals were kept next to each other in the same holding room of the animal facility at the Beckman Institute and maintained according to standard procedures. All experiments were conducted in accordance with protocols approved by the University of Illinois Institutional Animal Care and Use Committee.

extract_protocol: Both treated and untreated animals were sacrificed at 8 weeks of age. Modioli were rapidly dissected in physiological saline (within 8 min after sacrifice), dissolved in Trizol (Invitrogen, Carlsbad, CA) with a small rotor-stator homogenizer (Tissue-Tearor; Biospec Products, Bartlesville, OK), and stored at -80°C. Total RNA was extracted from all samples in parallel, with glycogen added to maximize precipitation. The resuspended RNA was further purified by adsorption to silica-gel-membrane spin columns (RNeasy MinElute Cleanup kit; Qiagen, Valencia, CA) and eluted in a minimal volume of water. The concentration of the RNA was determined by fluorometry (RiboGreen; Invitrogen), and its integrity was confirmed by electrophoresis (2100 Bioanalyzer; Agilent, Santa Clara, CA).

treatment_protocol: At four weeks of age, 'treated' animals were exposed together for five hours to two-octave band-limited noise (5-20 kHz) at 110 dB SPL. The animals were distributed between two empty 10-gallon glass tanks inside an acoustic isolation chamber in a separate room. A model S81-02 noise generator (Coulbourn, Whitehall, PA), a model GFP-555II preamplifier (Adcom, Scottsdale, AZ), and a model XL-600 power amplifier (Hafler, Tempe, AZ) drove one model 100HT high-efficiency horn tweeter with a flat frequency response from 2 to 20 kHz (Fostex, Boonton, NJ) over each tank. The noise level was monitored with a model 2239 sound level meter (Brüel & Kjær, Nærum, Denmark). The animals' behavior did not change during the noise exposure. 'Untreated' (negative-control) animals remained in the holding room throughout the experiment  and were not exposed to elevated noise levels.

tag: aliases

tag: biological replicate

value: 1 of 3

value: CBA/CaJ

value: male

tag: date of birth

tag: litter number

tag: individual number

tag: date of noise exposure

tag: date of sacrifice

value: left and right modioli dissected from cochlea

tag: total rna

value: 21 ng

tag: amplified cdna

value: 6.4 micrograms

tag: fragmented and biotinylated cdna

value: 5.1 micrograms


title: Modioli_negative-control_rep3

institute: University of Illinois at Urbana-Champaign

source_name: Left and right cochlear modiolus, not noise-exposed, animal '11-3'

value: 3 of 3

tag: gender

value: 8 ng

value: 5.8 micrograms

value: 3.7 micrograms


title: Modioli_negative-control_rep2

source_name: Left and right cochlear modiolus, not noise-exposed, animal '10-1'

value: 2 of 3

tag: strain

value: female

value: 5.2 micrograms

value: 3.5 micrograms


title: Modioli_noise-exposed_rep2

source_name: Left and right cochlear modiolus, previously noise-exposed, animal 'DB'

tag: tissue

value: 18 ng

value: 5.7 micrograms

value: 4.2 micrograms


title: slide3 array4

status: Public on Sep 01 2009

city: College Station

first: Huaijun

last: Zhou

state: TX

address: Rm 418D Kleberg Center,Texas A&M University

institute: Texas A&M University

description: Four arrays are included in one slide

hyb_protocol: A 825 ng of labeled cRNA with specificity over 8 were used for the hybridization reaction using the in situ hybridization kit plus (Agilent Technologies). A 100 ul hybridization solution was loaded on each of array in Agilent 4x44K microarrays. Arrays were incubated at 65 ℃ for 17h in Agilent’s microarray hybridization chambers. After hybridization, arrays were washed according to the Agilent protocol.

scan_protocol: Slides were scanned at 5-μm resolution using GenePix Personal 4100A (Molecular Devices Corporation, Sunnyvale, CA) and were saved as TIFF images. Auto Photomultiplier tube (PMT) were selected and adjusted to get the ratio of the overall intensities between the two channels (Cy3 and Cy5) was 0.9~1.1. The intensities of the spots on each image were quantified by Genepix pro 6.0 software (Molecular Devices Corporation, Downingtown, PA), and data were saved as .txt files for further analyses.

data_processing: The signal intensity of each gene was globally normalized using LOWESS by R program (Yang et al, 2002).

organism: Gallus gallus

source_name: Spleen

label_protocol: A 400 ng of aliquot of total RNA was reverse transcribed into cDNA using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). The synthesized cDNA was transcribed into cRNA labeled with one of two cyanine-labeled nucleotides (Perkin Elmer, Wellesley, MA). Labeled cRNA was purified with RNeasy Mini columns (Qiagen, Valecia, CA). The quality of each cRNA sample was verified by total yield and specificity measured with ND-100 spectrophotometer (NanoDrop Technologies).

extract_protocol: Tissue sample was homogenized within lysis buffer(Qiagen RNeasy mini RNA extraction kit, Qiagen Inc., Valencia, CA).Total RNA was extracted from the homogenized lysate according to the manufacturer’s instructions, eluted with 30 µl RNase-free water and stored at -80°C.

tag: Ross broilers, Day 19, challenged with Clostridium Perfringens, fed with medicated (bacitracin) starter diets

tag: Ross broilers, Day 19, challenged with Clostridium Perfringens, fed with non-medicated starter diets


title: slide4 array3

description: Four arrays are included in one slide

tag: Ross broilers, Day 22, challenged with Clostridium Perfringens, fed with medicated (bacitracin) starter diets

tag: Ross broilers, Day 22, challenged with Clostridium Perfringens, fed with non-medicated starter diets


title: slide4 array2

description: Four arrays are included in one slide

tag: Ross broilers, Day 22, challenged with Clostridium Perfringens, fed with medicated (bacitracin) starter diets.


title: slide5 array3

description: Four arrays are included in one slide

tag: Ross broilers, Day 18, before Clostridium perfringens infection, fed with medicated (bacitracin) starter diets

tag: Ross broilers, Day 18, before Clostridium perfringens infection, fed with non-medicated starter diets


title: slide5 array2

description: Four arrays are included in one slide


title: slide5 array1

description: Four arrays are included in one slide


title: Modioli_noise-exposed_rep3

source_name: Left and right cochlear modiolus, previously noise-exposed, animal 'DD'

tag: aliases

tag: biological replicate

value: CBA/CaJ

tag: date of birth

tag: litter number

value: 10 ng

value: 5.5 micrograms

value: 4.1 micrograms


title: slide3 array3

description: Four arrays are included in one slide

tag: Ross broilers, Day 19, challenged with Clostridium Perfringens, fed with non-medicated starter diets.


title: Evolved Engineered Methylobacterium methanol batch exponential

status: Public on Oct 30 2009

city: Cambridge

first: HSIN-HUNG

last: CHOU

state: MA

address: 16 Divinity Avenue, Biolab 3079

department: Organismic and Evolutionary Biology

institute: Harvard University

description: Strain CM1145 is an evolved isolate of strain CM702 after 600 generations of experimental evolution. Evolution experiments proceeded at 30 degrees C with 225 rpm shaking in 9.6 ml batch culture supplemented with 15 mM of methanol.Strain cm702 strain is distinguished from the wt by the following genetic characteristics: deletion of the mptG gene, carrying the the disrupted crtI502 allele, and expressing flhA and fghA genes from Paracoccus denitrificans.

hyb_protocol: Hybridization was performed according to the Agilent 60-mer oligo microarray processing protocol (Sure-Hyb chamber/SSPE wash with the Agilent Stabilization and Drying Solution) except that a microhybridization oven (Bellco Biotechnology, Vienland, NJ) was used. The appropriate amount of labeled cDNA to use for hybridizations was examined by generating a Ratio-Intensity (RI) plot. The condition in which the majority of the values of [1/2 log2(R*G)] showed 10 to 12 (1024 to 4096) was selected to strike a good balance between intensities that are too close to background and those that approach the limits of the dynamic range of the assay. Alexa Fluor 555- and Alexa Fluor 647-labeled cDNAs (40 pmol) were cohybridized. After hybridized slides had been washed and dried, they were kept in a nitrogen-purged SmartDesiccator (Terra Universal, Fullerton, CA) until scanning. Unused array slides were also kept under the nitrogen purged SmartDesiccator.

scan_protocol: Microarray slides were sent to the Mogene (Saint Louis, MO) and scanned using an Agilent G2565AA microarray scanner. Scanned images were processed by Agilent Feature Extraction software Ver. 7.5.1 using the default settings for Agilent arrays, the Linear & Lowess method for normalization, and PMT settings of 10, 50, and 100 to obtain usable signal intensities from weak through strong signals. These results showed that for most of the probes, data from the 100 PMT setting were optimal. However, data from the 10-PMT setting were used for the signals (g and r mean) whose intensities were >50,000 at the 100-PMT setting.

data_processing: The data in the VALUE column in the table were computed by taking the Log10 of the ratio of the lowess normalized Alexa_647 signal (rDyeNormSignal) divided by the lowess normalized Alex_555 signal (gDyeNormSignal) for each spot.

label: Alexa Fluor 555

organism: Methylorubrum extorquens AM1

label_protocol: The cDNA synthesis and labeling reactions were carried out by using an Amino Allyl cDNA Labeling Kit (Ambion) and Alexa Fluor 555 and Alexa Fluor 647 Reactive Dyes (Invitrogen Corporation, Carlsbad, CA) according to the manufacture’s manual with the following modifications: 5 ug DNaseI-treated total RNA and 4 ug random decamers were used for cDNA synthesis. Ethanol precipitated cDNA incorporating amino allyl dUTP was incubated overnight at  80°C and microcentrifuged for 45 min at 20,800 g at 4°C. Precipitated cDNA was coupled to either Alexa Fluor 555 or Alexa Fluor 647 reactive dye dissolved in 3 uL high-quality DMSO. Dye-labeled cDNA was purified using a QIAquick PCR Purification Kit (QIAGEN) following the instructions in the kit except for performing three washes instead of one. cDNA samples were eluted into 50 uL Nuclease-free water. The incorporation of dyes, the nucleic acid concentration, and the labeling efficiency of dye-labeled cDNA were measured and calculated as described above.

growth_protocol: 10 uL frozen culture were inoculated in 9.6 mL Hypho media supplemented with 15 mM of methanol. The culture was incubated at 30 °C with 225 rpm shaking for 4 days. 0.15 mL culture was then transferred to 9.45 mL of fresh Hypho media and grown under the same conditions for 4 days. From this acclimated culture, 6.25 mL was inoculated into 393.75 mL fresh Hypho media in a 2 liter flask and grown under the same conditions. Bacterial cells were harvested at mid log phase (OD600~0.21).

extract_protocol:
To obtain individual replicates for RNA extraction, samples from cultures were harvested under exponential growth phase and taken as rapidly as possible to limit any potential changes in transcript profiles. A culture volume of 50 mL was sampled directly from the 400 mL batch culture into a conical tube containing 1/10th the culture volume of ice-cold “Stop Solution” (5% water saturated phenol (pH 7.0), 95% absolute ethanol). Cultures were immediately harvested by centrifugation at 4500 g for 8 min at 4°C. Total RNA was extracted from M. extorquens AM1 pellets using the RNeasy Mini Kit (QIAGEN) according to the manufacture’s Yeast III protocol. Lysis was achieved by 3 min of bead-beating in the Mini-Beadbeater 8 (BioSpec Products, Bartlesville, OK) with 600 uL of 0.1-mm zirconium-silica beads (BioSpec Products). SUPERase•In (Ambion, Austin, TX) was added at a final concentration of 1 U/uL to prevent RNA degradation after the elution of RNA with RNase-free water. RNA concentration and purity were determined by using a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies). RNA integrity was assessed by using a Bioanalyzer (Agilent Technologies) as per manufacturer’s instructions. Residual DNA was removed from isolated RNA samples by treating 60 ug RNA with 36 units of RNasefree DNaseI (Ambion) in a 300-uL reaction volume for 1 h at 37°C. DNaseI-treated total RNA samples were purified by using the RNeasy Mini Kit (QIAGEN) according to the manufacture’s RNA cleanup protocol with a slight modification. Briefly, 1050 uL Buffer RLT and 750 uL ethanol were added to the 300
uL RNA samples and subsequently loaded onto an RNeasy mini column and centrifuged. The remaining RNA sample was successively loaded onto the same column and processed until the rest of the RNA sample was collected on the column. The column was washed three times with 700 uL buffer RW1, and then three times with 500 uL RPE buffer. DNaseI-treated total RNA was eluted with 30 uL of RNase-free water. RNA concentration, purity, and integrity were determined as above. The presence of DNA contamination was examined by PCR. DNaseI-treated total RNA (100 ng) was used as a template in a 50-uL reaction. PCR was done using Taq DNA polymerase (Promega, Madison, WI) with 40 cycles. Only RNA that did not result in a PCR product was used for cDNA synthesis and labeling.

tag: genotype

value: strain CM1145

label: Alexa Fluor 647

growth_protocol: 10 uL frozen culture were inoculated in 9.6 mL Hypho media supplemented with 15 mM of methanol. The culture was incubated at 30 °C with 225 rpm shaking for 4 days. 0.15 mL culture was then transferred to 9.45 mL of fresh Hypho media and grown under the same conditions for 4 days. From this acclimated culture, 6.25 mL was inoculated into 393.75 mL fresh Hypho media in a 2 liter flask and grown under the same conditions. Bacterial cells were harvested at mid log phase (OD600~0.13).

value: strain CM702


title: Modioli_noise-exposed_rep1

source_name: Left and right cochlear modiolus, previously noise-exposed, animal 'DA'

value: 1 of 3

tag: individual number

tag: date of noise exposure

tag: date of sacrifice

value: left and right modioli dissected from cochlea

tag: total rna

value: 15 ng

tag: amplified cdna

value: 5.4 micrograms

tag: fragmented and biotinylated cdna

value: 4.0 micrograms


title: slide4 array4

description: Four arrays are included in one slide

tag: Ross broilers, Day 22, challenged with Clostridium Perfringens, fed with medicated (bacitracin) starter diets


title: CSC-exposed human PBMC 8

status: Public on Aug 28 2009

city: Washington

first: Jinguo

last: Chen

state: DC

address: 3800 Reservoir Road NW

department: Cancer Genetics and Epidemiology

institute: Georgetown University Lombardi Cancer Center

description: Gene expression data from CSC treatment 8

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Agilent Scanner 3000.

data_processing: The R language affy package , that implements the RMA (Robust Multichip Average) procedure, was used to convert probe signal data (.CEL files) to expression values through the following sequence: 1) convolution model background correction; 2) cyclic Loess normalization; and 3) summarization by taking log2 of the probe values and fitting a robust multi-chip linear model using the median polish algorithm.

source_name: Human PBMC from smokers who smoked 4 cig/last 24h, 5.6 pack-years

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

growth_protocol: Blood samples from eight light smokers were collected into BD Vacutainer® CPT tubes, and peripheral blood mononuclear cells were segregated according to the manufacturer’s instructions. The PBMC from each light smoker were cultured in RPMI 1640 medium, supplemented with 1.5% phytohemagglutinin, 1000 U/ml heparin, 2 mM L-glutamine, and 15% fetal bovine serum.

extract_protocol: Trizol extraction of total RNA and clean-up step using RNeasy Micro Kit were performed according to the manufacturer's instructions.

treatment_protocol: The cultures were then exposed to 2R4F CSC at a final concentration of 40 ug/ml (CSC-treated) for 18h. The CSC-exposed lymphocyte expression was compared to lymphocyte cultures without exposure from the same phlebotomy and subject (paired control cultures).

tag: treatment

value: CSC exposure

tag: age

tag: gender

value: Male

tag: race

value: white


title: slide2 array3

description: Four arrays are included in one slide

tag: Ross broilers, Day 20, challenged with Clostridium Perfringens, fed with medicated (bacitracin) starter diets

tag: Ross broilers, Day 20, challenged with Clostridium Perfringens, fed with non-medicated starter diets


title: slide5 array4

description: Four arrays are included in one slide

tag: Ross broilers, Day 18, before Clostridium perfringens infection, fed with medicated (bacitracin) starter diets

tag: Ross broilers, Day 18, before Clostridium perfringens infection, fed with non-medicated starter diets


title: Cultured human PBMC 8

description: Gene expression data from culture control 8

value: culture only


title: slide3 array2

description: Four arrays are included in one slide

tag: Ross broilers, Day 19, challenged with Clostridium Perfringens, fed with non-medicated starter diets

tag: Ross broilers, Day 19, challenged with Clostridium Perfringens, fed with medicated (bacitracin) starter diets


title: slide2 array1

description: Four arrays are included in one slide


title: slide1 array4

description: Four arrays are included in one slide


title: slide3 array1

description: Four arrays are included in one slide


title: slide4 array1

description: Four arrays are included in one slide

tag: Ross broilers, Day 22, challenged with Clostridium Perfringens, fed with non-medicated starter diets


title: slide1 array3

description: Four arrays are included in one slide

tag: Ross broilers, Day 22, challenged with Clostridium Perfringens, fed with non-medicated starter diets.


title: slide1 array1

description: Four arrays are included in one slide


title: slide2 array2

description: Four arrays are included in one slide


title: CSC-exposed human PBMC 7

description: Gene expression data from CSC treatment 7

source_name: Human PBMC from smokers who smoked 10 cig/last 24h, 11.5 pack-years

value: Female


title: slide2 array4

description: Four arrays are included in one slide


title: Cultured human PBMC 7

description: Gene expression data from culture control 7


title: CSC-exposed human PBMC 5

description: Gene expression data from CSC treatment 5

source_name: Human PBMC from smokers who smoked 10 cig/last 24h, 15.55 pack-years

value: black


title: Cultured human PBMC 1

description: Gene expression data from culture control 1

source_name: Human PBMC from smokers who smoked 10 cig/last 24h, 4.5 pack-years


title: Light smoker 11, biological rep11

description: Gene expression data from light smoker

data_processing: The R language affy package , that implements the RMA (Robust Multichip Average) procedure, was used to convert probe signal data (.cel files) to expression values through the following sequence: 1) convolution model background correction; 2) cyclic Loess normalization; and 3) summarization by taking log2 of the probe values and fitting a robust multi-chip linear model using the median polish algorithm.

source_name: Human PBMC from smokers who smoked 8 cig/last 24h, 15.6 pack-years

growth_protocol: no culture in vitro

treatment_protocol: Subjects were recruited through local print advertising, and screened for eligibility.  Only healthy smokers without current infections, medication use or illnesses that can affect the immune system were included in this study. All smokers had to have been smoking for at least 5 years and had a stable smoking pattern for the prior 6 months (cigarette brand and cigarettes per day, and no smoking-cessation attempts).  Blood samples from each subject were collected into CPT tubes, and peripheral blood mononuclear cells (PBMC), predominantly lymphocytes, were segregated according to the manufacturer’s instructions. The lymphocyte pellets were immediately placed in TRIzol reagent and kept at –80C until RNA isolation (uncultured). All blood samples were delivered and processed within 2 h of phlebotomy.


title: CSC-exposed human PBMC 4

description: Gene expression data from CSC treatment 4

source_name: Human PBMC from smokers who smoked 8 cig/last 24h, 4 pack-years


title: CSC-exposed human PBMC 2

description: Gene expression data from CSC treatment 2

source_name: Human PBMC from smokers who smoked 4 cig/last 24h, 1.25 pack-years


title: CSC-exposed human PBMC 1

description: Gene expression data from CSC treatment 1


title: Light smoker 8, biological rep8

description: Gene expression data from light smoker

source_name: Human PBMC from smokers who smoked 7 cig/last 24h, 2.1 pack-years


title: slide1 array2

description: Four arrays are included in one slide


title: Light smoker 6, biological rep6

description: Gene expression data from light smoker


title: Cultured human PBMC 6

description: Gene expression data from culture control 6


title: Light smoker 12, biological rep12

description: Gene expression data from light smoker


title: Cultured human PBMC 3

description: Gene expression data from culture control 3


title: Light smoker 13, biological rep13

description: Gene expression data from light smoker


title: Cultured human PBMC 5

description: Gene expression data from culture control 5


title: Light smoker 10, biological rep10

description: Gene expression data from light smoker


title: Light smoker 1, biological rep1

description: Gene expression data from light smoker

source_name: Human PBMC from smokers who smoked 10 cig/last 24h, 10 pack-years


title: Light smoker 5, biological rep5

description: Gene expression data from light smoker


title: Cultured human PBMC 4

description: Gene expression data from culture control 4


title: Heavy smoker 10, biological rep10

description: Gene expression data from heavy smoker

source_name: Human PBMC from smokers who smoked 30 cig/last 24h, 61.5 pack-years


title: Light smoker 7, biological rep7

description: Gene expression data from light smoker

source_name: Human PBMC from smokers who smoked 10 cig/last 24h, 18.55 pack-years


title: CSC-exposed human PBMC 6

description: Gene expression data from CSC treatment 6


title: Cultured human PBMC 2

description: Gene expression data from culture control 2


title: CSC-exposed human PBMC 3

description: Gene expression data from CSC treatment 3


title: Light smoker 9, biological rep9

description: Gene expression data from light smoker


title: Heavy smoker 8, biological rep8

description: Gene expression data from heavy smoker

source_name: Human PBMC from smokers who smoked 23 cig/last 24h, 40.25 pack-years


title: Light smoker 3, biological rep3

description: Gene expression data from light smoker

source_name: Human PBMC from smokers who smoked 12 cig/last 24h, 27.6 pack-years


title: Light smoker 4, biological rep4

description: Gene expression data from light smoker

source_name: Human PBMC from smokers who smoked 10 cig/last 24h, 175 pack-years


title: Heavy smoker 9, biological rep9

description: Gene expression data from heavy smoker

source_name: Human PBMC from smokers who smoked 25 cig/last 24h, 35 pack-years


title: Heavy smoker 4, biological rep4

description: Gene expression data from heavy smoker

source_name: Human PBMC from smokers who smoked 23 cig/last 24h, 26.45 pack-years


title: Heavy smoker 3, biological rep3

description: Gene expression data from heavy smoker

source_name: Human PBMC from smokers who smoked 40 cig/last 24h, 88 pack-years


title: Heavy smoker 7, biological rep7

description: Gene expression data from heavy smoker

source_name: Human PBMC from smokers who smoked 50 cig/last 24h, 122.5 pack-years


title: NC17D8 T15 Isotype Monoclonal IgM (dendritic cell study)

status: Public on Aug 25 2009

type: protein

first: Gregg

last: Silverman

address: 9500 Gilman Dr

department: Medicine

institute: UC San Diego School of Medicine

description:
2000 ng/ml
NC17D8 Isotype Monoclonal IgM Antibody at a Concentration of 2000 ng/ml

hyb_protocol: On each slide were two nitrocellulose pads, with most antigens printed at 200 mg/ml on each pad in six replicates at known positions that alternated with printing of buffer alone to eliminate carry-over. Slides were then blocked (Whatman blocking buffer) and incubated for 2 h with 400 ml of serum diluted at 1 : 200 in phosphate-buffered saline (PBS), pH 7·4.

scan_protocol: Slides were washed with PBS, water-rinsed and then scanned (Genepix 4000B; Molecular Devices, Sunnyvale, CA, USA) using Genepix Pro version 6·0 software at 532 and 635 nm to detect IgG and IgM reactivity, respectively, with images saved as tiff files.

data_processing: Genepix Pro version 6·0 software was used to analyse the intensity of each spot with foreground and background fluorescence intensities determined for each spot on the slide, with output as a gpr file. Data were extracted from the gpr files with r software (http://www.r-project.org). Background correction used a Matlab script, and the mean values for replicate spots determined with jmp version 7·0 software (http://www.jmp.com). Comparisons of array data for subjects and controls were performed and visual depictions generated with Cluster version 3·0 (Stanford University)  and Java TreeView (http://rana.lbl.gov/EisenSoftware.htm). Background levels were therefore determined based on replicate slides developed without antibodies, and with sera from healthy adult controls (not shown). In these studies, a level of 600 digital fluorescence intensity units was set as a threshold for significant reactivity, which was greater than the mean background plus 2 standard deviations (s.d.).

molecule: protein

source_name: Hybridoma

label_protocol: After washing with Tris-buffered saline/0·1% Tween 20, the slides were reacted with Cy-5 labelled anti-human IgG and Cy-3- labelled anti-human IgM (Jackson Immunoresearch, West Grove, PA, USA) for 1 h incubation, then washed with PBS/0·05% Tween20.

growth_protocol: The mice were from a 14-week old C57BL/6 strain, as well as a 20-week old female MRL/lpr strain. The monoclonal antibodies were derived from hybridoma supernatant

extract_protocol: At the end of the injection courses, the mice were bled for their serum. Monoclonal antibodies were purified using standard protocols for IgM purifications.

treatment_protocol: The mouse serum was either naive, injected with either saline (PBS), 25 million apoptotic thymocytes, or 1 mg of T15 IgM antibody at three weekly timepoints.

tag: sample

value: IgM

tag: genotype


title: T15 B (dendritic cell study)

description:
1:200 Dilution
Serum from a second mouse with directly injected T15 antibody

value: Serum


title: Heavy smoker 2, biological rep2

description: Gene expression data from heavy smoker

source_name: Human PBMC from smokers who smoked 25 cig/last 24h, 45 pack-years


title: T15 125 ng/ml (dendritic cell study)

description:
125 ng/ml
T15 Monoclonal IgM Antibody at a concentration of 125 ng/ml


title: Apoptotic A (dendritic cell study)

description:
1:200 Dilution
Serum from a mouse immunized with apoptotic cells


title: Apoptotic B (dendritic cell study)

description:
1:200 Dilution
Serum from a second mouse immunized with apoptotic cells


title: PBS A (dendritic cell study)

description:
1:200 Dilution
Serum from a mouse immunized with saline solution


title: T15 A (dendritic cell study)

description:
1:200 Dilution
Serum from a mouse with directly injected T15 antibody


title: Heavy smoker 5, biological rep5

description: Gene expression data from heavy smoker

source_name: Human PBMC from smokers who smoked 40 cig/last 24h, 22 pack-years


title: Heavy smoker 1, biological rep1

description: Gene expression data from heavy smoker

source_name: Human PBMC from smokers who smoked 40 cig/last 24h, 86 pack-years


title: Blank (dendritic cell study)

type: other

description:
None
No Antibody (Negative Control)

molecule: other

organism: unidentified

value: blank


title: MRL/Lpr 1:50 (dendritic cell study)

description:
1:50 Dilution
Serum from a mouse with a lupus prone disease model

source_name: MRL/Lpr

value: MRL/Lpr


title: MRL/Lpr 1:200 (dendritic cell study)

description:
1:200 Dilution
Serum from a second mouse with a lupus prone disease model


title: PBS B (dendritic cell study)

description:
1:200 Dilution
Serum from a second mouse immunized with saline solution


title: Heavy smoker 6, biological rep6

description: Gene expression data from heavy smoker

source_name: Human PBMC from smokers who smoked 36 cig/last 24h, 54 pack-years


title: Naïve B (dendritic cell study)

description:
1:200 Dilution
Serum from a second naïve mouse


title: T15 31.25 ng/ml (dendritic cell study)

description:
31.25 ng/ml
T15 Monoclonal IgM Antibody at a concentration of 31.25 ng/ml


title: T15 500 ng/ml (dendritic cell study)

description:
500 ng/ml
T15 Monoclonal IgM Antibody at a concentration of 500 ng/ml


title: Naïve A (dendritic cell study)

description:
1:200 Dilution
Serum from a Naïve mouse


title: NASP Overexpression, sample #3

status: Public on Aug 24 2009

city: Chapel Hill

first: Oleg

middle: M

last: Alekseev

state: NC

address: 210 Taylor Hall

department: Cell and Developmental Biology

institute: University of North Carolina at Chapel Hill

description: RNA samples representing four separate experiments from cells overexpressing tNASP and four experiments from cells treated with NASP siRNA, along with appropriate controls, were submitted for analysis.

hyb_protocol: The labeled cRNA samples were then fragmented in fragmentation buffer at 60°C for 30 min before the microarray hybridization. Each sample was hybridized to a whole separate Human Genome (4×44K) microarray (Agilent Technologies, Wilmington, DE) overnight at 65°C in a hybridization oven.

scan_protocol: The hybridization slides were washed, stabilized, dried, and immediately scanned by Agilent Technologies Microarray Scanner (Agilent Technologies, Wilmington, DE).

data_processing: During the initial analysis at UNC Microarray Database, all genes were retrieved, appropriately annotated, and filtered. Eventually, only genes with an absolute value of a Log2 Red/Green Lowess Normalized Ratio of at least 1 (doubled in intensity) for all 4 arrays were selected.

source_name: reference, mock treated sample

extract_protocol: Total cellular RNA was purified from HeLa cells using RNeasy ® Mini Kit (Qiagen, Valencia, CA) according to manufacturers instructions.

tag: cell type

value: HeLa cells

source_name: experimental, NASP Overexpression sample #3


title: NASP Overexpression, sample #2

source_name: experimental, NASP Overexpression sample #2


title: NASP Overexpression, sample #4

source_name: experimental, NASP Overexpression sample #4


title: NASP siRNA treatment, sample #3

source_name: reference, C2siRNA treated sample

source_name: experimental, NASP siRNA treated sample #3


title: Lymph nodes_Infected animal 1 vs reference

status: Public on Aug 01 2009

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

institute: ETH Zurich / University of Zurich

description: Biological replicate 1 of 2

hyb_protocol: Agilent Gene Expression kit for oligo microarrays (Agilent, order number 5188-5242, protocol G4140-90050).

scan_protocol: Agilent Feature Extraction software 8.5.1.1.

data_processing: GeneSpring 7.3.1 default loading and normalization routines (dye-swap normalization, normalization to reference).

organism: Bos taurus

source_name: Ovine Herpesvirus 2-infected lymph nodes

label_protocol: 1.6 - 5 μg of total RNA were reverse transcribed to cDNA, and amplified and labeled to cRNA with the Agilent Low RNA Input Linear Amplification Kit PLUS (order number 5184-3525, Agilent).

growth_protocol: Not applicable.

extract_protocol: Lymph node tissue was frozen in liquid nitrogen and homogenized using a mortar and pistil. Total RNA was isolated using the RNeasy Kit by Qiagen (order number 74106, RNeasy, Qiagen, Hombrechtikon, Switzerland). Immediately upon homogenization the samples were taken up in RLT buffer with 1% β-mercaptoethanol (Sigma, Buchs, Switzerland). DNA was digested using RNase-free DNase (Qiagen, order number 79254) at room temperature for 15 minutes.

treatment_protocol: Not applicable.

tag: Infection

source_name: uninfected lymph nodes


title: NASP siRNA treatment, sample #4

source_name: experimental, NASP siRNA treated sample #4


title: NASP siRNA treatment, sample #2

source_name: experimental, NASP siRNA treated sample #2


title: NASP siRNA treatment, sample #1

source_name: experimental, NASP siRNA treated sample #1


title: Lymph nodes_Infected animal 2 vs reference

description: Biological replicate 2 of 2


title: Lymph nodes_Uninfected_R:04

description: Biological replicate 4 of 6

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

scan_protocol: Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).


title: Lymph nodes_Infected animal 1 vs reference_dye-swap

description: Biological replicate 1 of 2


title: Lymph nodes_Infected animal 2 vs reference_dye-swap

description: Biological replicate 2 of 2


title: Lymph nodes_Infected_R:03

description: Biological replicate 3 of 3


title: Lymph nodes_Uninfected_R:01

description: Biological replicate 1 of 6


title: Lymph nodes_Uninfected_R:02

description: Biological replicate 2 of 6


title: Lymph nodes_Uninfected_R:05

description: Biological replicate 5 of 6


title: Lymph nodes_Infected_R:02

description: Biological replicate 2 of 3


title: NASP Overexpression, sample #1

source_name: experimental, NASP Overexpression sample #1


title: Lymph nodes_Infected_R:01

description: Biological replicate 1 of 3


title: H9_undifferentiated_3

city: Charleston

first: Stephen

middle: A

last: Duncan

state: SC

address: 173 Ashley Avenue, BSB 6th Floor, Room 657A

department: Regenerative Medicine and Cell Biology

institute: Medical University South Carolina

description: Reprogrammed somatic cells offer a valuable source of pluripotent cells that have the potential to differentiate into many cells types and provide a new tool for regenerative medicine. In the present study we differentiated induced pluripotent stem cells (iPS cells) into hepatic cells. We first showed that mouse iPS cells could from a complete liver in mouse embryo (E14.5) including hepatocytes, endothelial cells, sinusoidal cells and resident macrophages. We then designed a highly efficient hepatocyte differentiation protocol using defined factors on human embryonic stem cells (ES cells). This protocol was found to generate more than 80% albumin expressing cells that show hepatic functions and express most of liver genes as shown by microarray analyses. Similar results were obtained when human iPS cells were induced to differentiate following the same procedure.

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Standard Affymetrix protocol, standard GCOS data processing produced the values in the accompanying table

source_name: WAO9 human embryonic stem cells

label_protocol: Affymetrix One-Cycle Target Labeling

extract_protocol: Rneasy (Qiagen)

value: WAO9 human embryonic stem cells, undifferentiated


title: H9_undifferentiated_1


title: Lymph nodes_Uninfected_R:06

description: Biological replicate 6 of 6


title: LP/J_saline_pool2_liver_2

status: Public on Jul 01 2009

city: Denver

first: Ivana

middle: V

last: Yang

state: CO

address: 1400 Jackson Street

institute: National Jewish Health

hyb_protocol: Agilent hyb reagents and protocol.

scan_protocol: Agilent scanner - default settings.

data_processing: Feature Extraction Version A.7.5.1

source_name: Universal mouse reference RNA

label_protocol: Agilent low-input kit.

extract_protocol: Trizol

treatment_protocol: Each mouse was injected with 125,000 EU/kg LPS or saline control intraperitoneally.  Organs were collected and flash frozen six hours post-treatment.

tag: Stratagene cat number 740100

source_name: liver, 6 hrs post-saline

tag: strain

value: LP/J

value: male

value: 6-8 weeks

tag: route

value: i.p. injection

tag: time

value: 6 hours

tag: tissue

value: liver


title: C57(TLR4-/-)_LPS_pool1_lung_1

source_name: lung, 6 hrs post-LPS

tag: gender

tag: age

value: lung


title: H9_d20_hepatic differentiated_2

value: WAO9 human embryonic stem cells subjected to a hepatic differentiation protocol


title: H9_d20_hepatic differentiated_3


title: H9_undifferentiated_2


title: LP/J_saline_pool2_liver_1


title: LP/J_saline_pool1_liver_2


title: LP/J_LPS_pool2_liver_2

source_name: liver, 6 hrs post-LPS


title: H9_d20_hepatic differentiated_1


title: LP/J_LPS_pool1_liver_1


title: LP/J_LPS_pool1_liver_2


title: LP/J_LPS_pool2_liver_1


title: Lymph nodes_Uninfected_R:03

description: Biological replicate 3 of 6


title: NZW/LacJ_saline_pool2_liver_1

value: NZW/LacJ


title: NZW/LacJ_saline_pool2_liver_2


title: NZW/LacJ_saline_pool1_liver_2


title: LP/J_saline_pool1_liver_1


title: NZW/LacJ_saline_pool1_liver_1


title: NZW/LacJ_LPS_pool1_liver_2


title: DBA/2J_saline_pool2_liver_1


title: DBA/2J_saline_pool1_liver_2


title: DBA/2J_saline_pool1_liver_1


title: NZW/LacJ_LPS_pool2_liver_2


title: NZW/LacJ_LPS_pool1_liver_1


title: NZW/LacJ_LPS_pool2_liver_1


title: DBA/2J_LPS_pool2_liver_1


title: DBA/2J_LPS_pool1_liver_2


title: C3H/HeJ_saline_pool2_liver_2


title: DBA/2J_LPS_pool1_liver_1


title: C3H/HeJ_LPS_pool2_liver_2


title: DBA/2J_LPS_pool2_liver_2


title: BALB/cJ_saline_pool1_liver_2

value: BALB/cJ


title: C3H/HeJ_saline_pool2_liver_1


title: C3H/HeJ_LPS_pool2_liver_1


title: C3H/HeJ_LPS_pool1_liver_1


title: C3H/HeJ_saline_pool1_liver_2


title: C3H/HeJ_LPS_pool1_liver_2


title: BALB/cJ_saline_pool2_liver_2


title: BALB/cJ_saline_pool1_liver_1


title: BALB/cJ_LPS_pool2_liver_2


title: DBA/2J_saline_pool2_liver_2


title: BALB/cJ_saline_pool2_liver_1


title: BALB/cJ_LPS_pool2_liver_1


title: FVB/NJ_saline_pool2_liver_2

value: FVB/NJ


title: BALB/cJ_LPS_pool1_liver_2


title: FVB/NJ_LPS_pool1_liver_2


title: FVB/NJ_saline_pool2_liver_1


title: BALB/cJ_LPS_pool1_liver_1


title: FVB/NJ_saline_pool1_liver_2


title: 129/SvIm_saline_pool2_liver_2


title: FVB/NJ_LPS_pool1_liver_1


title: FVB/NJ_LPS_pool2_liver_2


title: FVB/NJ_LPS_pool2_liver_1


title: FVB/NJ_saline_pool1_liver_1


title: 129/SvIm_LPS_pool1_liver_1


title: 129/SvIm_LPS_pool1_liver_2


title: 129/SvIm_saline_pool2_liver_1


title: AKR/J_saline_pool2_liver_2

value: AKR/J


title: AKR/J_saline_pool1_liver_1


title: 129/SvIm_saline_pool1_liver_2


title: 129/SvIm_LPS_pool2_liver_1


title: AKR/J_LPS_pool2_liver_2


title: 129/SvIm_saline_pool1_liver_1


title: 129/SvIm_LPS_pool2_liver_2


title: AKR/J_LPS_pool2_liver_1


title: AKR/J_saline_pool1_liver_2


title: AKR/J_saline_pool2_liver_1


title: AKR/J_LPS_pool1_liver_2


title: AKR/J_LPS_pool1_liver_1


title: A/HeJ_saline_pool2_liver_2

value: A/HeJ


title: A/HeJ_saline_pool1_liver_1


title: A/HeJ_saline_pool2_liver_1


title: A/HeJ_LPS_pool2_liver_2


title: A/HeJ_saline_pool1_liver_2


title: C57/B6_saline_pool2_liver_1


title: A/HeJ_LPS_pool1_liver_1


title: C57/B6_saline_pool1_liver_2


title: A/HeJ_LPS_pool1_liver_2


title: C57/B6_saline_pool1_liver_1


title: C57/B6_LPS_pool2_liver_2


title: C57/B6_saline_pool2_liver_2


title: C57(TLR4-/-)_saline_pool2_liver_2


title: A/HeJ_LPS_pool2_liver_1


title: C57/B6_LPS_pool1_liver_1


title: C57(TLR4-/-)_saline_pool2_liver_1


title: C57/B6_LPS_pool1_liver_2


title: C57(TLR4-/-)_LPS_pool2_liver_2


title: C57/B6_LPS_pool2_liver_1


title: C57(TLR4-/-)_saline_pool1_liver_2


title: C57(TLR4-/-)_saline_pool1_liver_1


title: LP/J_LPS_pool2_spleen_2

source_name: spleen, 6 hrs post-LPS

value: spleen


title: LP/J_saline_pool2_spleen_2

source_name: spleen, 6 hrs post-saline


title: LP/J_saline_pool1_spleen_1


title: C57(TLR4-/-)_LPS_pool1_liver_2


title: LP/J_LPS_pool1_spleen_1


title: C3H/HeJ_saline_pool1_liver_1


title: LP/J_saline_pool1_spleen_2


title: LP/J_LPS_pool1_spleen_2


title: FNA16_POST_PRE

first: Dong-Yu

last: Wang

address: 610 University Ave

institute: UHN-PMH-OCI

description:
Four replicated data were combined for analysis
IDC, invasive ductal carcinoma; ILC, invasive lobular carcinoma; LVI, lymphovascular invasion; EIC, extensive intraductal component; ER, estrogen receptor; PR, progesterone receptor; ERBB2, HER2 status. ER, PR, and HER2 status as reported on standard surgical pathology reports were determined by immunohistochemistry, or by fluorescent in situ hybridization for HER2 according to our institutional standard of practice.

hyb_protocol: The generated cDNA probes were then purified and denatured. The labeled targets were hybridized to UHN h19k cDNA microarrays.

scan_protocol: Scanned at 16 bits using the Genepix Axon Scanner 4000A (Molecular Devices Corp) at 635 nm (Cy5) and 532 nm (Cy3) using Genepix Pro 6.0 analysis software (Molecular Devices Corp).

data_processing: Each quantified output file in GenePix report (GPR) format was directly transferred into Acuity 4.0 (Molecular Devices Corp.) for analysis. After Lowess slide normalization, any uninformative microarray data were flagged and filtered. The dye-swaped signal log2 ratios were inverted and four replicates were combined, resulting in 16 specimens for analysis finally. Probes with minimal changes in expression level (Log2 ratio >=1 or <=-1 in not more than 2 tumors) and with different expression between the samples taken before and after surgeries (t-Test, P<0.05) were removed, resulting in a list of 4,042 probes in the matrix dataset.

label: Cy5, Cy3

source_name: Post-operative, Pre-operative, palpable invasive breast cancer

label_protocol: The amplified RNA species from FNABs and an amplified Universal Human Reference RNA (Stratagene; La Jolla, CA) were directly labeled using cyanine 5 and cyanine 3 fluorescent dyes from 5 to 10μg of RNA according to the UHN Microarray Centre instructions. Dye-swap technical replicate was carried out for every FNABs.

extract_protocol: Total RNA was extracted using RNAeasy Micro kit (Qiagen) then amplified using the MessageAmp aRNA kit (Ambion) according to the manufacturer's instructions.

tag: Patient No.

tag: Tumor Type

value: IDC

tag: Tumor Size(cm)

tag: Tumor Grade

tag: LVI

tag: EIC

tag: ER

tag: PR

tag: palpable invasive breast cancer

label: Cy3, Cy5

source_name: Universal RNA

tag: Stratagene Universal RNA


title: NZW/LacJ_saline_pool2_spleen_2

tag: Stratagene cat number 740100


title: NZW/LacJ_LPS_pool1_spleen_2

tag: strain


title: NZW/LacJ_LPS_pool2_spleen_1

tag: route


title: NZW/LacJ_saline_pool1_spleen_1

tag: time


title: DBA/2J_saline_pool2_spleen_1

tag: tissue


title: LP/J_LPS_pool2_spleen_1

tag: gender


title: NZW/LacJ_LPS_pool2_spleen_2

tag: age


title: FNA13_POST_PRE

tag: Patient No.


title: FNA14_POST_PRE

tag: Tumor Type


title: LP/J_saline_pool2_spleen_1


title: FNA09_POST_PRE

tag: Tumor Size(cm)


title: FNA07_POST_PRE

tag: Tumor Grade


title: FNA05_POST_PRE

tag: LVI


title: FNA15_POST_PRE

tag: EIC


title: C3H/HeJ_saline_pool2_spleen_2


title: FNA03_POST_PRE

tag: ER


title: DBA/2J_saline_pool1_spleen_2


title: FNA12_POST_PRE

tag: PR


title: FNA11_POST_PRE

value: IDC/ILC

tag: palpable invasive breast cancer


title: FNA10_POST_PRE

tag: Stratagene Universal RNA


title: FNA04_POST_PRE


title: FNA06_POST_PRE


title: FNA08_POST_PRE


title: NZW/LacJ_saline_pool2_spleen_1

tag: Stratagene cat number 740100


title: C3H/HeJ_saline_pool2_spleen_1

tag: strain


title: C3H/HeJ_LPS_pool1_spleen_2

tag: route


title: DBA/2J_saline_pool1_spleen_1

tag: time


title: C3H/HeJ_LPS_pool1_spleen_1

tag: tissue


title: NZW/LacJ_LPS_pool1_spleen_1

tag: gender


title: DBA/2J_LPS_pool1_spleen_1

tag: age


title: FNA02_POST_PRE

tag: Patient No.


title: C3H/HeJ_LPS_pool2_spleen_1


title: C3H/HeJ_saline_pool1_spleen_2


title: DBA/2J_LPS_pool1_spleen_2


title: DBA/2J_LPS_pool2_spleen_2


title: FNA01_POST_PRE

tag: Tumor Type


title: E8-9 SMART cDNA

city: Santiago

first: Alejandro

last: Zúñiga

address: Macul 5540

country: Chile

institute: INTA - Universidad de Chile

description: SMART cDNA was synthesized from total RNA from 8-9 staged embryos, labeled with 32P in a random primers labeling method.

hyb_protocol: The labeled cDNA products were denatured and immediately used for membrane hybridization. Hybridization conditions were as follows: pre-hybridization in 5 ml of hybridization buffer (5X SSC, 5X Denhardt solution, 1% SDS, and 50% formamide) for 1–3 h at 42 ºC. Hybridization was performed in the same buffer for 16–18 h at 42 ºC. Membranes were washed at room temperature with two 10-min changes of 2× SSC and 2× SSC plus 0.1% SDS, then with two 15-min changes of 1× SSC plus 0.1% SDS at 60 °C and finally with two 15-min changes of 0.1× SSC.

scan_protocol: Membranes were sealed in plastic bags and placed in Imaging Screen-K (Biorad) for 12-24 hours. Radioactive images were obtained using a scanner Personal Molecular Image FX (BioRad) at 50 µm/pixel resolution. Intensities values were measured using VersArray Analizer v.4.5.1.46 (BioRad).

data_processing: Raw values were measured as the volume of pixels within a circle encompassing the spot. Local background values were measured in the corners of spot and were subtracted from the signal intensity values for each spot. Pearson´s correlation coefficient was used to establish the quality of replicated membranes. Spots that showed: (1) Signal Mean < (Background Mean + (1 x Background Standard Deviation); (2) coefficient of variation (CV) > 0.5 between duplicate spots within membranes (Dudoit et al. 2000) or (3) qcom < 0.8 (Wang et al. 2001) were considered as low-quality spots and were removed. After data filtering, net intensity values were normalized against Dap spike mRNA (membranes A, B and C) or RP49 housekeeping gene (membrane D) intensity values. When genes were represented by more than one clone, mean intensity values were calculated.

organism: Drosophila melanogaster

source_name: 8-9 staged embryos

label_protocol: The 32P-labeled probes were prepared from SMART-cDNAs by incorporation of [α-32P]dCTP using the Random Primers DNA Labelling System (Invitrogen), according to manufacturer´s indications. Unincorporated radioactive nucleotides were removed using the QIAquick Nucleotide Removal (Qiagen).

growth_protocol: D. melanogaster (Canton-S strain) flies were grown at 22 °C on standard cornmeal, molasses, agar and yeast medium. To obtain staged embryos, females were allowed to lay eggs for 2 h on 2% apple juice agar plates spread with live brewer's yeast. The plates were replaced several times, and finally 1-h embryos were collected, dechorionated and washed with Ringer Drosophila solution (182 mM KCl, 46 mM NaCl, 3 mM CaCl2, 10 mM Tris–Hcl, pH 7.2). Embryos were selected at stages 2–3 (syncytial blastoderm) or 5 (cellular blastoderm) and then allowed to continue their development in a humidified chamber at 25 °C. We hand-selected embryos at different developmental stages based on their morphological characters (Campos-Ortega and Hartenstein, 1985) and rapidly froze them in liquid N2. Embryos were kept at −80 °C for 1–2 weeks.

extract_protocol: Embryos were collected at 5 developmental intervals (stages 2-3, 5, 6-7, 8-9 and 10-12, according to Campos-Ortega & Harstenstein, 1985). Total RNA was extracted from staged embryos (n=100) using the RNAWIZ reagent (Ambion). Embryos were carefully homogenized in a 1.5 mL eppendorf tube with 1 mL of RNAWIZ reagent using a plastic tissue grinder. To improve RNA yield, the homogenized was passed throughout Qiashreder columns (Qiagen) by centrifugation at room temperature for 2 min at 10,000 x g. The quantity and quality of the RNA were assessed by OD260/280 and by electrophoresis on a 1.2% formaldehyde-agarose gel. Typical yield was 0.18-0.23 µg RNA/embryo. Total RNA was used to synthesize double strand cDNA using SMART cDNA Synthesis kit (Clontech)  according to manufacturer´s indications.

value: Canton S wild type

tag: developmental stage

value: 8-9 staged embryos


title: E10-12 SMART cDNA

description: SMART cDNA was synthesized from total RNA from 10-12 staged embryos, labeled with 32P in a random primers labeling method.

source_name: 10-12 staged embryos

value: 10-12 staged embryos


title: E6-7 SMART cDNA

description: SMART cDNA was synthesized from total RNA from 6-7 staged embryos, labeled with 32P in a random primers labeling method.

source_name: 6-7 staged embryos

value: 6-7 staged embryos


title: BALB/cJ_saline_pool2_spleen_2

value: male

value: 6-8 weeks

value: i.p. injection


title: DBA/2J_LPS_pool2_spleen_1

value: 6 hours


title: C57(TLR4-/-)_LPS_pool1_liver_1

value: liver


title: DBA/2J_saline_pool2_spleen_2


title: C3H/HeJ_saline_pool1_spleen_1


title: E2-3 SMART cDNA

description: SMART cDNA was synthesized from total RNA from 2-3 staged embryos, labeled with 32P in a random primers labeling method.

source_name: 2-3 staged embryos

value: 2-3 staged embryos


title: E5 SMART cDNA

description: SMART cDNA was synthesized from total RNA from 5 staged embryos, labeled with 32P in a random primers labeling method.

source_name: 5 staged embryos

value: 5 staged embryos


title: BALB/cJ_saline_pool2_spleen_1

value: BALB/cJ


title: NZW/LacJ_saline_pool1_spleen_2

value: NZW/LacJ


title: BALB/cJ_LPS_pool2_spleen_2


title: C57(TLR4-/-)_LPS_pool2_liver_1


title: BALB/cJ_saline_pool1_spleen_2


title: BALB/cJ_LPS_pool2_spleen_1


title: C3H/HeJ_LPS_pool2_spleen_2


title: BALB/cJ_saline_pool1_spleen_1


title: FVB/NJ_saline_pool1_spleen_1

value: FVB/NJ


title: FVB/NJ_saline_pool2_spleen_1

value: spleen


title: FVB/NJ_LPS_pool1_spleen_1


title: BALB/cJ_LPS_pool1_spleen_2


title: FVB/NJ_saline_pool2_spleen_2


title: 129/SvIm_saline_pool2_spleen_2


title: FVB/NJ_LPS_pool2_spleen_1


title: 129/SvIm_saline_pool1_spleen_2


title: FVB/NJ_LPS_pool2_spleen_2


title: BALB/cJ_LPS_pool1_spleen_1


title: 129/SvIm_saline_pool2_spleen_1


title: 129/SvIm_LPS_pool1_spleen_1


title: 129/SvIm_LPS_pool1_spleen_2


title: FVB/NJ_saline_pool1_spleen_2


title: 129/SvIm_LPS_pool2_spleen_2


title: 129/SvIm_LPS_pool2_spleen_1


title: AKR/J_saline_pool2_spleen_2

value: AKR/J


title: FVB/NJ_LPS_pool1_spleen_2


title: AKR/J_saline_pool1_spleen_2


title: AKR/J_LPS_pool1_spleen_1


title: AKR/J_saline_pool2_spleen_1


title: 129/SvIm_saline_pool1_spleen_1


title: AKR/J_LPS_pool1_spleen_2


title: AKR/J_saline_pool1_spleen_1


title: AKR/J_LPS_pool2_spleen_1


title: A/HeJ_LPS_pool2_spleen_2

value: A/HeJ


title: A/HeJ_saline_pool2_spleen_1


title: A/HeJ_LPS_pool2_spleen_1


title: AKR/J_LPS_pool2_spleen_2


title: C57/B6_LPS_pool2_spleen_1


title: A/HeJ_LPS_pool1_spleen_1


title: C57/B6_LPS_pool2_spleen_2


title: C57/B6_saline_pool1_spleen_1


title: A/HeJ_LPS_pool1_spleen_2


title: C57/B6_saline_pool1_spleen_2


title: C57/B6_LPS_pool1_spleen_2


title: A/HeJ_saline_pool1_spleen_2


title: C57/B6_saline_pool2_spleen_2


title: C57(TLR4-/-)_saline_pool2_spleen_2


title: C57/B6_saline_pool2_spleen_1


title: A/HeJ_saline_pool1_spleen_1


title: C57(TLR4-/-)_saline_pool2_spleen_1


title: C57(TLR4-/-)_LPS_pool2_spleen_2


title: C57(TLR4-/-)_LPS_pool1_spleen_2


title: C57(TLR4-/-)_saline_pool1_spleen_1


title: LP/J_saline_pool2_lung_1

source_name: lung, 6 hrs post-saline

value: LP/J

value: lung


title: C57(TLR4-/-)_saline_pool1_spleen_2


title: C57(TLR4-/-)_LPS_pool1_spleen_1


title: LP/J_saline_pool2_lung_2


title: C57/B6_LPS_pool1_spleen_1


title: LP/J_LPS_pool2_lung_2


title: Oral108

city: Vancouver

first: T

last: Buys

state: BC

address: 675 W.10th Avenue

department: Cancer Genetics and Developmental Biology

institute: British Columbia Cancer Research Centre

hyb_protocol: Probes were combined, denatured and annealed in a solution containing 100 ug human Cot-1 DNA (Invitrogen) and 48 ul DIG Easy hybridization solution (Roche) containing sheared herring sperm DNA (Sigma-Aldrich) and yeast tRNA (Calbiochem). Probe was denautred at 85°C for 5 minutes, and repetitive sequences were blocked at 45°C for 1 hour prior to hybridization. The probe mixture was applied to the slide surface and hybridized for 36 hrs at 45°C. The arrays were washed 5 times in 0.1X SSC, 0.1% SDS at room temperature with agitation. Each array was then rinsed repeatedly in 0.1X SSC and dried by centrifugation.

scan_protocol: A charge-coupled device (CCD) scanner system (ARrayworx eAuto, API, Issaquah, WA) was used to determine the signal intensities of the Cyanine 5/Cyanine3 channels. Arrays were scanned at a 9.75um resolution; exposure times for each image wavelength were usually between 0.2 to 2 sec. Images were analyzed by SoftWoRx Tracker analysis software (Applied Precision, Issaquah, WA, USA).

data_processing: A three-step normalization procedure [Khojasteh et al. BMC Bioinformatics 6:274, 2005] was performed to each raw data.

label_protocol: Random prime probe labeling was performed to label sample and reference genomic DNA (250ng each).  Each reaction was labeled with either 2 nmol of cyanine-3 or cyanine-5 dCTP.

extract_protocol: All lesions were microdissected, and the dissected tissues were places in sodium dodecyl sulfate/proteinase K at 55°C and spiked twice a day for 72 hours with fresh proteinase K. Genomic DNA was extracted with phenol/chloroform and  with ethanol.

tag: Formalin-fixed paraffin-embedded oral specimen.

source_name: Normal female

extract_protocol: Purchased genomic DNA.

tag: Novagen pooled normal female genomic DNA.


title: LP/J_saline_pool1_lung_1


title: LP/J_LPS_pool1_lung_1


title: LP/J_LPS_pool1_lung_2


title: LP/J_saline_pool1_lung_2


title: LP/J_LPS_pool2_lung_1


title: NZW/LacJ_saline_pool2_lung_2


title: NZW/LacJ_saline_pool1_lung_2


title: NZW/LacJ_LPS_pool2_lung_2


title: NZW/LacJ_saline_pool2_lung_1


title: NZW/LacJ_LPS_pool2_lung_1


title: NZW/LacJ_LPS_pool1_lung_1


title: NZW/LacJ_LPS_pool1_lung_2


title: Oral110

source_name: Normal male

label_protocol: Random prime probe labeling was performed to label sample and reference genomic DNA (250ng each). Each reaction was labeled with either 2 nmol of cyanine-3 or cyanine-5 dCTP.

tag: Novagen pooled normal male genomic DNA


title: DBA/2J_saline_pool2_lung_1


title: DBA/2J_saline_pool1_lung_2


title: NZW/LacJ_saline_pool1_lung_1


title: Oral100

tag: Novagen pooled normal male genomic DNA.


title: DBA/2J_saline_pool2_lung_2


title: DBA/2J_saline_pool1_lung_1


title: DBA/2J_LPS_pool2_lung_2


title: Oral117


title: Oral101

source_name: normal male


title: Oral97

source_name: normal female


title: Oral116


title: Oral95


title: Oral102


title: DBA/2J_LPS_pool1_lung_2

source_name: Universal mouse reference RNA


title: DBA/2J_LPS_pool2_lung_1

source_name: lung, 6 hrs post-LPS


title: C57(TLR4-/-)_LPS_pool2_spleen_1


title: DBA/2J_LPS_pool1_lung_1


title: Oral107


title: Oral113


title: Oral114


title: Oral112


title: C3H/HeJ_saline_pool2_lung_1


title: Oral115


title: Oral98


title: Oral96


title: A/HeJ_saline_pool2_spleen_2


title: C3H/HeJ_LPS_pool1_lung_2


title: C3H/HeJ_saline_pool1_lung_1


title: C3H/HeJ_LPS_pool2_lung_2


title: Oral109

tag: Formalin-fixed paraffin-embedded oral specimen


title: BALB/cJ_saline_pool2_lung_2


title: Oral111


title: C3H/HeJ_saline_pool1_lung_2


title: BALB/cJ_saline_pool1_lung_2


title: BALB/cJ_saline_pool1_lung_1


title: BALB/cJ_LPS_pool2_lung_2


title: C3H/HeJ_LPS_pool2_lung_1


title: BALB/cJ_saline_pool2_lung_1


title: C3H/HeJ_LPS_pool1_lung_1


title: BALB/cJ_LPS_pool2_lung_1


title: BALB/cJ_LPS_pool1_lung_2


title: FVB/NJ_saline_pool2_lung_1


title: FVB/NJ_saline_pool2_lung_2


title: BALB/cJ_LPS_pool1_lung_1


title: FVB/NJ_LPS_pool2_lung_2


title: FVB/NJ_LPS_pool2_lung_1


title: 129/SvIm_saline_pool2_lung_2


title: FVB/NJ_saline_pool1_lung_1


title: 129/SvIm_saline_pool2_lung_1


title: FVB/NJ_saline_pool1_lung_2


title: FVB/NJ_LPS_pool1_lung_2


title: 129/SvIm_LPS_pool2_lung_2


title: C3H/HeJ_saline_pool2_lung_2


title: 129/SvIm_saline_pool1_lung_2


title: 129/SvIm_saline_pool1_lung_1


title: 129/SvIm_LPS_pool1_lung_2


title: AKR/J_saline_pool2_lung_1


title: AKR/J_LPS_pool1_lung_2


title: AKR/J_saline_pool2_lung_2


title: AKR/J_LPS_pool2_lung_2


title: 129/SvIm_LPS_pool2_lung_1


title: AKR/J_saline_pool1_lung_1


title: AKR/J_LPS_pool1_lung_1


title: A/HeJ_saline_pool2_lung_2


title: FVB/NJ_LPS_pool1_lung_1


title: AKR/J_LPS_pool2_lung_1


title: AKR/J_saline_pool1_lung_2


title: A/HeJ_LPS_pool2_lung_2


title: A/HeJ_saline_pool2_lung_1


title: A/HeJ_LPS_pool2_lung_1


title: A/HeJ_saline_pool1_lung_2


title: A/HeJ_saline_pool1_lung_1


title: 129/SvIm_LPS_pool1_lung_1


title: C57/B6_saline_pool2_lung_1


title: C57/B6_saline_pool1_lung_2


title: C57/B6_saline_pool2_lung_2


title: C57/B6_LPS_pool2_lung_1


title: C57/B6_LPS_pool2_lung_2


title: A/HeJ_LPS_pool1_lung_1


title: C57/B6_LPS_pool1_lung_1


title: C57/B6_saline_pool1_lung_1


title: C57(TLR4-/-)_saline_pool2_lung_1


title: C57(TLR4-/-)_saline_pool1_lung_2


title: A/HeJ_LPS_pool1_lung_2


title: C57(TLR4-/-)_saline_pool2_lung_2


title: C57/B6_LPS_pool1_lung_2


title: C57(TLR4-/-)_LPS_pool2_lung_1


title: C57(TLR4-/-)_LPS_pool1_lung_2


title: C57(TLR4-/-)_saline_pool1_lung_1


title: WT_Gap43_Repl3

status: Public on Jun 01 2009

city: Syracuse

first: Frank

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

description: A total of 9 postnatal day 5 C57BL/6 Wildtype (WT), Heterozygous (HZ), or Knockout (KO) mice (n=3/genotype) for the GAP-43 gene were used. See Maier et al. (1999) [PMID: 10430954] for details on the generation of the mouse lines.

hyb_protocol: GeneChip Hybridization, Wash and Stain Kit was used (Affymetrix, P/N 900720).  Hybridization performed in GeneChip Hybridization Oven 640 for 16 hrs at 45C, with 60rpm rotation.  Washing and staining performed in Fluidics Station 450 according to the EukGE-WS2v4 protocol.

scan_protocol: Scanning performed on Agilent G2500A Gene Array Scanner.

data_processing: MAS 5.0 values generated from CEL files images in Expression Console

source_name: Mouse barrel cortex

label_protocol:
Affymetrix Two-Cycle cDNA Synthesis Protocol from the GeneChip
Expression Analysis Technical Manual (P/N 702232, Rev. 2) was used

extract_protocol: Laser microdissection of layer IV from barrel cortex, followed by Qiagen RNeasy

tag: This sample is 1 of 3 wildtype (WT) mouse samples prepared from postnatal day 5 C57BL/6 barrel cortex.


title: KO_Gap43_Repl3

tag: This sample is 1 of 3 knockout (KO) mouse samples prepared from postnatal day 5 C57BL/6 barrel cortex.


title: mn cells sample 2

city: Basel

first: Dragana

last: Jankovic

address: Hebelstrasse 20

department: Dept. of Research

institute: University Hospital Basel

hyb_protocol: The hybridisation coctail (80microliter) containing fragmented biotin-labeled target DNA at a final concentration of 25nanogram/microliter was transfered into Affymetrix GeneChip Mouse Gene 1.0 ST Arrays and incubated at 45 degrees on a rotator in a hybridisation oven 640 (Affymetrix) for 17 hours at 60rpm. The arrays were washed and stained on a Fluidics Station 450 by using Hybridisation Wash and Stain Kit (Affymetrix, cat. nu. 900720) using fluidics procedure FS450_0007.

scan_protocol: The GeneChips were processed with an Affymetrix GeneChip Scanner 3000 7G. DAT image files of the microarrays were generated using Affymetrix GeneChip Command Console (AGCC, version 0.0.0.676).

data_processing: RMA

source_name: bone marrow

label_protocol: cDNA target was synthesized, fragmented, biotin-labeled using WT target labeling and Control Reagents (Affymetrix, vat. num. 900652) starting from 200ng total RNA, according to the procedure described in the geneChip Whole Transcript Sense Target labeling Assay Manual, Version 4 (Affymetrix, santa Clara, USA). cDNA was fragmented and the resulting fragments of approximately 40-70 nucleoides were monitored with Bioanalyzer using the RNA nano 6000 Chip.

extract_protocol: Quiagen kit

treatment_protocol: 72 hours after transduction with Mn1, gfp positive bone marrow cells were sorted and RNA isolated

tag: FVB 129 mice were used as bone marrow donors


title: mn cells sample 1


title: WT_Gap43_Repl1


title: KO_Gap43_Repl2


title: gfp control sample 2

treatment_protocol: 72 hours after transduction with MSCV-IRES-GFP, gfp positive bone marrow cells were sorted and RNA isolated


title: C57(TLR4-/-)_LPS_pool2_lung_2

tag: Stratagene cat number 740100

tag: strain


title: WT_Gap43_Repl2


title: gfp control sample 3


title: gfp control sample 1


title: mn cells sample 3

tag: FVB 129 mice used as bone marrow donors


title: Het_Gap43_Repl3

tag: This sample is 1 of 3 heterozygous (HZ) mouse samples prepared from postnatal day 5 C57BL/6 barrel cortex.


title: AML_CD8_10

status: Public on May 20 2009

city: London

first: Rifca

last: Le Dieu

address: 3rd Floor, John Vane Science Building, Charterhouse Square

department: Institute of Cancer

country: United Kingdom

institute: Queen Mary University of London

description: AML10 CD8

hyb_protocol: Following fragmentation, 15 micrograms of cRNA were hybridised for 16 hours at 45C on Affymetrix U133Plus2 GeneChips. Chips were then washed and stained with SAPE in an Affymetrix GeneChip 450 Fluidics Station.

scan_protocol: GeneChips were scanned using the Ayymetrix GeneChip 3000 scanner

data_processing: Data were analysed with MicroArray Suite 5.0 (MAS 5.0) using Affymetrix default analysis settings.

source_name: CD8 T cells

label_protocol: Affymetrix Expression GeneChip Protocol one-cycle procedure. Between 2 and 5micrograms of RNA was used as starting material.

extract_protocol: T cells were isolated by immunomagnetic selection. RNA was then extracted using Trizol.

tag: gender

value: Intermediate


title: Het_Gap43_Repl2


title: Oral99


title: Healthy_CD4_3

description: Healthy3 CD4

source_name: CD4 T cells

value: female

tag: age

value: Not applicable


title: KO_Gap43_Repl1


title: Het_Gap43_Repl1


title: AML_CD8_8

description: AML8 CD8

value: male

value: Favourable


title: AML_CD8_7

description: AML7 CD8


title: Healthy_CD4_10

description: Healthy10 CD4


title: AML_CD8_9

description: AML9 CD8


title: AML_CD8_4

description: AML4 CD8


title: AML_CD8_6

description: AML6 CD8


title: AML_CD8_5

description: AML5 CD8


title: AML_CD8_1

description: AML1 CD8


title: AML_CD8_3

description: AML3 CD8


title: Healthy_CD8_5

description: Healthy5 CD8


title: AML_CD4_2

description: AML2 CD4


title: AML_CD4_6

description: AML6 CD4


title: HBE_t0_code2

status: Public on May 19 2009

first: Wanda

middle: K.

last: O'Neal

department: Cystic Fibrosis/Pulmonary Research and Treatment Center

description: Gene expression data from human airway epithelium treated as described.

hyb_protocol: 15 mug of fragmented cRNA were hybridized for 16 hrs on Genechip Fluidics Station using Affymetrix HU133 plus 2.0 arrays (GPL570).

scan_protocol: Genechips were scanned using Hewlett-packard GeneArray scanner.

data_processing: Expressions were computed using the Bioconductor GCRMA package with default parameters.

source_name: well-differentiated primary airway bronchial culture

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7 mug total RNA (Expression analysis technical manual, Affymetrix).

growth_protocol: Human bronchial epithelium harvested from normal lung donors. primary cells are placed on T-col membranes approximately 30 days until well-differentiated. Cells are grown at air-liquid interface which is established in 10-14 days.

extract_protocol: RNAzol followed by Qiagen RNeasy columns with DNAase treatment according to publisher and manufacturers protocols.

treatment_protocol: Well-differentiated human airway epithelium grown at air-liquid interface exposed to nothing. Samples were placed in RNAlater until RNA harvest.


title: AML_CD8_2

description: AML2 CD8


title: AML_CD4_8

description: AML8 CD4


title: AML_CD4_4

description: AML4 CD4


title: AML_CD4_9

description: AML9 CD4


title: AML_CD4_10

description: AML10 CD4


title: AML_CD4_5

description: AML5 CD4


title: AML_CD4_3

description: AML3 CD4


title: HBE_t0_code3


title: AML_CD4_7

description: AML7 CD4


title: HBE_t0_code1


title: AML_CD4_1

description: AML1 CD4


title: HBE_AZIT72SMM24-code2

treatment_protocol: Well-differentiated human airway epithelium grown at air-liquid interface exposed to 30mug/ml serosal Azithromycin for 72 hours + 30mul mucosal SMM during last 24 hrs before harvested. Samples were placed in RNAlater until RNA harvest.


title: HBE_AZIT72SMM24-code3


title: HBE_AZIT48SMM6-code4

treatment_protocol: Well-differentiated human airway epithelium grown at air-liquid interface exposed to 30mug/ml serosal Azithromycin for 48 hours + 30mul mucosal SMM during last 6 hrs before harvested. Samples were placed in RNAlater until RNA harvest.


title: HBE_AZIT48SMM6-code3


title: HBE_AZIT72SMM24-code1


title: HBE_AZIT48_code4

treatment_protocol: Well-differentiated human airway epithelium grown at air-liquid interface exposed to 30mug/ml serosal Azithromycin for 48 hours. Samples were placed in RNAlater until RNA harvest.


title: HBE_AZIT6_code2

treatment_protocol: Well-differentiated human airway epithelium grown at air-liquid interface exposed to 30mug/ml serosal Azithromycin for 6 hours. Samples were placed in RNAlater until RNA harvest.


title: HBE_AZIT48SMM6-code2


title: HBE_AZIT24_code2

treatment_protocol: Well-differentiated human airway epithelium grown at air-liquid interface exposed to 30mug/ml serosal Azithromycin for 24 hours. Samples were placed in RNAlater until RNA harvest.


title: HBE_AZIT6_code1


title: HBE_SMM6_code1

treatment_protocol: Well-differentiated human airway epithelium grown at air-liquid interface exposed to 30mul mucosal SMM for 6 hours. Samples were placed in RNAlater until RNA harvest.


title: HBE_AZIT48_code3


title: HBE_AZIT48_code2


title: HBE_SMM6_code2


title: HBE_SMM24_code1

treatment_protocol: Well-differentiated human airway epithelium grown at air-liquid interface exposed to 30mul mucosal SMM for 24 hours. Samples were placed in RNAlater until RNA harvest.


title: HBE_AZIT24_code4


title: HBE_AZIT6_code4


title: HBE_AZIT48_code1


title: HBE_AZIT24_code1


title: HBE_SMM6_code4


title: HBE_SMM24_code2


title: HBE_AZIT24_code3


title: HBE_SMM24_code3


title: HBE_PBS6_code4

treatment_protocol: Well-differentiated human airway epithelium grown at air-liquid interface exposed to 30mul mucosal PBS for 6 hours. Samples were placed in RNAlater until RNA harvest.


title: HBE_PBS24_code4

treatment_protocol: Well-differentiated human airway epithelium grown at air-liquid interface exposed to 30mul mucosal PBS for 24 hours. Samples were placed in RNAlater until RNA harvest.


title: HBE_PBS6_code2


title: HBE_PBS24_code3


title: HBE_PBS24_code1


title: HBE_PBS6_code1