title: Medial substantia nigra Parkinson's disease case 09 - A chip

description: Gene expression data from medial substantia nigra (MNPD09A)

value: 86; gender:F


title: WT BMM WT Lm 180 min + CAPE A

status: Public on Jan 01 2008

type: RNA

city: Chicago

first: Jess

last: Leber

state: IL

address: 920 E. 58th Street CLSC 615

department: Microbiology

country: USA

institute: The University of Chicago

description: biological replicate 1 of 2

hyb_protocol: 2 days at 63 °C

scan_protocol: Scanned on Axon 4000B

data_processing: GenePix Pro, SpotReader, Acuity

molecule: total RNA

organism: Mus musculus

source_name: aRNA from WT macrophage, infected with WT Lm for 180 min, treated with CAPE

label_protocol: 5 ug aRNA was labeled, using 100 mM Na bicarbonate (pH 9) and 50% DMSO

growth_protocol: Macrophages grown in DMEM supplemented with 10% CSF from 3T3 cells, 20% FBS, pyruvate, and glutamine.  Bacteria grown in BHI at 30 °C, shaking, to mid-log.

extract_protocol: RNA was isolated using RNAlater and RNAqueous (Ambion), then amplified to aRNA

treatment_protocol: Macrophages were infected for 30 minutes, washed 3X with pre-warmed media, and at 60 minutes treated with gentamicin.  CAPE was added at 60 minutes.

tag: primary macrophage from C57BL/6

source_name: aRNA from reference pool

tag: pooled from all samples used


title: WT BMM WT Lm 180 min + CAPE B

description: biological replicate 2 of 2


title: Gender_Baseline_Difference

status: Public on Jan 04 2008

city: Niskayuna

first: Erik

middle: A

last: Carlson

state: NY

address: 1 Research Circle

institute: General Electric

description: Linear model output for the gender baseline difference reported as the natural log fold difference estimate of the average female rat receiving corn oil over male corn oil control

hyb_protocol: One RNA sample from each rat was hybridized to a single microarray. In addition, technical replicates were generated from re-extracted RNA of randomly chosen rats within selected groups, while in other cases existing extracts were hybridized to two additional chips.

scan_protocol: GeneChips were scanned according to the standard Affymetrix protocol

data_processing: Background corrected  .CEL files were natural logarithm-transformed, then quantile-normalized using the bg.adjust.gcrma and normalize.AffyBatch.quantiles functions of the Bioconductor affy package (Irizarry et al., 2003) as implemented in R (R Development Core Team, 2006).  Each probe set was modeled independently using a linear mixed-effects model (Pinheiro et al., 2000) to account for fixed treatment, gender, probe affinity, and scanner (batch) effects, as well as animal, RNA extraction, and hybridization random effects. A model selection procedure was implemented to choose the most parsimonious model that describes the variability in measured intensities. Starting from a complex model containing all estimable two-way interactions between fixed effects, terms were tested for removal one-by-one using hypothesis tests based on sums of squared residuals. Thus, the model chosen by some probesets may not have had a treatment effect term which is depicted as an "NA" value across all data columns except the X intercept. Furthermore, probesets lacking a gender*treatment interaction term would predict the same response to treatment for both genders and be relected as identical values within exposure groups across genders. The complete model output is given in the supplementary file Linear_model_output.xls (linked to GSE9838).

label: biotin

organism: Rattus norvegicus

source_name: Liver from Female Rats receiving corn oil

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

extract_protocol: Total RNA was isolated from 200 mg of tissue using the RNA-STAT-60 (Tel-Test, Friendswood, TX) procedure. The RNA was dissolved in RNAse-free water and quantified by spectrophotometry. Quality of RNA isolations was determined using the Agilent BioAnalyzer 2100 (Agilent, Palo Alto, CA).

treatment_protocol: Test chemicals were administered by gastric intubation in corn oil (5 ml/kg) at dose levels of 0.6, 6.0, or 60 Aroclor 1254 mg/kg, or 0.3 or 3.0 TCDD ug/kg for 3 consecutive days. Control groups for each gender received corn oil alone. On Day 4 the animals were euthanized by CO2 overdose and the livers were removed and dissected into 10 sections. Each section was wrapped in foil, frozen in liquid nitrogen within two minutes of death, and stored at –70o C until processed for RNA.

tag: Organism

value: Sprague Dawley Rats

tag: Gender

value: Female

tag: Chemical

value: Vehicle Control

tag: Dose

value: NA (Sex difference)


title: Spn_D39vsD39spxR6_CDM_rep1

city: Bloomington

first: Ho-Ching

middle: Tiffany

last: Tsui

state: IN

address: 1001 E. Third St.

department: Biology

institute: Indiana University

description: Independent biological replicate, dye swap

hyb_protocol: Performed as per microarray manufacturer’s recommendations (http://www.ocimumbio.com/web/arrays/assets/downloads/manuals/manual_bacteria.pdf). Fluorescently-labeled cDNAs were resuspended in the manufacturer’s salt-based hybridization buffer. Samples were heated for 3 min at 95C, then chilled on ice for 3 min before application to the microarray slide. Slides were hybridized at 42C overnight (~18 hrs). Slides were washed sequentially for 5 min in the following buffers pre-warmed to 30C: Buffer 1, 2X SSC, 0.1% SDS; Buffer 2, 1X SSC; Buffer 3, 0.1X SSC.

scan_protocol: Microarray slides were scanned on an Axon GenePix 4200A microarray scanner at 532 nm and 635 nm. Slides were scanned at gain settings which balanced the signal acquired in both channels (pixel ratio ~ 1.0). Images were analyzed using GenePix Pro 5.0 software (Molecular Devices).

data_processing: Data were normalized with web-based BASE (BioArray Software Environment, iubase.cgb.indiana.edu/index/phtml) without background subtraction, excluding empty wells and Arabidopsis controls with the plug-in Lowess Normalization.

organism: Streptococcus pneumoniae

source_name: S. pneumoniae D39spxR6

label_protocol: Single strand cDNA synthesis and direct labeling performed using 30 micrograms of total RNA and Superscript II reverse transcriptase (Invitrogen) as per microarray manufacturer’s recommendations (http://www.ocimumbio.com/web/arrays/assets/downloads/manuals/manual_bacteria.pdf)

growth_protocol: Bacterial strains were grown statically in brain heart infusion media (BHI, Oxoid) at 37°C and an atmosphere of 5% CO2 overnight. Overnight cultures were centrifuged at 14,000 g for 2 minutes. Cell pellets were washed with complete defined media (CDM) formulated by JRH Biosciences (Denver, Pa.) and resuspended in CDM.  The starting density of cultures OD620 used for final experiments was 0.01. Cultures were grown at 37°C and an atmosphere of 5% CO2 until an OD620 value of 0.2.

extract_protocol: Total RNA was extracted from exponentially growing cultures (OD620~0.2) using a hot lysis/ acid phenol procedure followed by on-column DNase treatment and purification using the RNAeasy mini kit (Qiagen) as described in Robertson et al, J. Bact (2002) 184:3508-3520.

tag: S. pneumoniae D39spxR6, strain # is IU1976

source_name: S pneumoniae bacterial strain D39 (NCTC)

label_protocol: same as channel 1

extract_protocol: same as channel 1

tag: S. pneumoniae D39(NCTC)(strain IU1690), virulent, type 2 capsule


title: WT BMM Uninfected - CAPE A

description: biological replicate 1 of 2

source_name: aRNA from WT macrophage, uninfected

tag: primary macrophage from C57BL/6 mouse


title: IRF3+ BMM Uninfected B

description: biological replicate 2 of 3

treatment_protocol: Macrophages were infected for 20 minutes, washed 3X with pre-warmed media, and at 30 minutes treated with gentamicin.


title: irf3- BMM WT Lm 180 min B

description: biological replicate 2 of 3

source_name: aRNA from irf3-/- macrophage, infected with WT Lm for 180 min


title: WT BMM Uninfected - CAPE B

description: biological replicate 2 of 2


title: Medial substantia nigra Parkinson's disease case 02 - A chip

city: London

first: Linda

middle: B

last: Moran

address: Fulham Palace Road

department: Neuropathology

country: United Kingdom

institute: Imperial College London

description: Gene expression data from medial substantia nigra  (MNPD02A)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45oC to a Human Genome 133 A array (HG_U133A; Affymetrix). The GeneChips was washed and stained in an Affymetrix Fluidics Station 400.  Standard Affymetrix Protocols were used  (Affymetrix GeneChip Expression Analysis Technical Manual, 2001).

scan_protocol: Standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2001).

data_processing: CEL files were read using ArrayAssist software (version 4.1, Stratagene) and PathwayStudio 5 (Ariadne).  Intensity values were derived applying the (GeneChip) Robust Multi Array (RMA) algorithm.

label: Biotin

organism: Homo sapiens

source_name: Post-mortem medial substantia nigra

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

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol (http://www.qiagen.com). Tissue samples were mechanically disrupted using a rotary homogenizer, lysed in buffer containing guanidine isothiocyanate (GITC) and then further homogenized (Shredder tubes, Qiagen).

tag: age

value: 83; gender:M


title: irf3- BMM Uninfected A

description: biological replicate 1 of 3

source_name: aRNA from irf3-/- macrophage, uninfected


title: WT BMM WT Lm 180 min - CAPE A

description: biological replicate 1 of 2

source_name: aRNA from WT macrophage, infected with WT Lm for 180 min


title: irf3- BMM WT Lm 180 min C

description: biological replicate 3 of 3


title: IRF3+ BMM Uninfected A

description: biological replicate 1 of 3


title: IRF3+ BMM WT Lm 180 min B

description: biological replicate 2 of 3


title: irf3- BMM Uninfected C

description: biological replicate 3 of 3


title: IRF3+ BMM WT Lm 180 min A

description: biological replicate 1 of 3


title: IRF3+ BMM WT Lm 180 min C

description: biological replicate 3 of 3


title: IRF3+ BMM Uninfected C

description: biological replicate 3 of 3


title: Medial substantia nigra control case 9 - A chip

description: Gene expression data from medial substantia nigra (MNCON9A)

value: 57; gender:M


title: myd88- BMM hly- Lm 120 min B

description: biological replicate 2 of 2

source_name: aRNA from myd88-/- macrophage, infected with hly- Lm for 120 min


title: irf3- BMM Uninfected B

description: biological replicate 2 of 3


title: myd88- BMM hly- Lm 180 min A

description: biological replicate 1 of 4

source_name: aRNA from myd88-/- macrophage, infected with hly- Lm for 180 min


title: myd88- BMM hly- Lm 180 min B

description: biological replicate 2 of 4


title: Medial substantia nigra control case 3 - A chip

description: Gene expression data from medial substantia nigra (MNCON3A)

value: 81; gender:M


title: Medial substantia nigra Parkinson's disease case 04 - A chip

description: Gene expression data from medial substantia nigra  (MNPD04A)

value: 68; gender:M


title: Medial substantia nigra disease-control case MS155 - A chip

description: Gene expression data from medial substantia nigra  (MNMS155A)

value: 80; gender:F


title: irf3- BMM WT Lm 180 min A

description: biological replicate 1 of 3


title: myd88- BMM hly- Lm 180 min C

description: biological replicate 3 of 4


title: Medial substantia nigra Parkinson's disease case 01 - A chip

description: Gene expression data from medial substantia nigra (MNPD01A)

value: 87; gender:F


title: Medial substantia nigra control case 2  - A chip

description: Gene expression data from medial substantia nigra  (MNCON2A)

value: 77; gender:M


title: myd88- BMM hly- Lm 180 min D

description: biological replicate 4 of 4


title: Medial substantia nigra control case 4 - A chip

description: Gene expression data from medial substantia nigra  (MNCON4A)

value: 77; gender:F


title: Medial substantia nigra control case 8 - A chip

description: Gene expression data from medial substantia nigra (MNCON8A)

value: 46; gender:M


title: myd88- BMM hly- Lm 120 min A

description: biological replicate 1 of 2


title: myd88- BMM hly- Lm 60 min B

description: biological replicate 2 of 2

source_name: aRNA from myd88-/- macrophage, infected with hly- Lm for 60 min


title: Lateral substantia nigra Parkinson's disease case 10 - A chip

description: Gene expression data from lateral substantia nigra  (LNPD10A)

source_name: Post-mortem lateral substantia nigra

value: 81; gender:F


title: myd88- BMM WT Lm 120 min B

description: biological replicate 2 of 2

source_name: aRNA from myd88-/- macrophage, infected with WT Lm for 120 min


title: myd88- BMM WT Lm 180 min A

description: biological replicate 1 of 4

source_name: aRNA from myd88-/- macrophage, infected with WT Lm for 180 min


title: myd88- BMM WT Lm 180 min D

description: biological replicate 4 of 4


title: Lateral substantia nigra Parkinson's disease case 29 - A chip

description: Gene expression data from lateral substantia nigra (LNPD29A)

value: 76; gender:M


title: Lateral substantia nigra Parkinson's disease case 28 - A chip

description: Gene expression data from lateral substantia nigra (LNPD28A)

value: 82; gender:M


title: myd88- BMM WT Lm 30 min B

description: biological replicate 2 of 2

source_name: aRNA from myd88-/- macrophage, infected with WT Lm for 30 min


title: myd88- BMM WT Lm 120 min A

description: biological replicate 1 of 2


title: myd88- BMM hly- Lm 30 min A

description: biological replicate 1 of 2

source_name: aRNA from myd88-/- macrophage, infected with hly- Lm for 30 min


title: myd88- BMM WT Lm 180 min C

description: biological replicate 3 of 4

source_name: aRNA from reference pool


title: myd88- BMM WT Lm 60 min A

description: biological replicate 1 of 2

source_name: aRNA from myd88-/- macrophage, infected with WT Lm for 60 min


title: Lateral substantia nigra Parkinson's disease case 16 - A chip

description: Gene expression data from lateral substantia nigra (LNPD16A)

value: 85; gender:F


title: Lateral substantia nigra Parkinson's disease case 09 - A chip

description: Gene expression data from Lateral substantia nigra (LNPD09A)

value: 86; gender:F


title: myd88- BMM hly- Lm 30 min B

description: biological replicate 2 of 2


title: Lateral substantia nigra Parkinson's disease case 07 - A chip

description: Gene expression data from lateral substantia nigra  (LNPD07A)

value: 78; gender:M


title: Lateral substantia nigra Parkinson's disease case 02 - A chip

description: Gene expression data from lateral substantia nigra  (LNPD02A)


title: myd88- BMM WT Lm 60 min B

description: biological replicate 2 of 2


title: Lateral substantia nigra Parkinson's disease case 04 - A chip

description: Gene expression data from lateral substantia nigra  (LNPD04A)


title: myd88- BMM Uninfected C

description: biological replicate 3 of 4

source_name: aRNA from myd88-/- macrophage, uninfected


title: Medial substantia nigra control case 10 - A chip

description: Gene expression data from medial substantia nigra (MNCON10A)

value: 71; gender:M


title: myd88- BMM WT Lm 180 min B

description: biological replicate 2 of 4


title: myd88- BMM hly- Lm 60 min A

description: biological replicate 1 of 2


title: myd88- BMM Uninfected A

description: biological replicate 1 of 4


title: myd88- BMM Uninfected D

description: biological replicate 4 of 4


title: WT BMM hly- Lm 180 min D

description: biological replicate 4 of 4

source_name: aRNA from WT macrophage, infected with hly- Lm for 180 min


title: myd88- BMM WT Lm 30 min A

description: biological replicate 1 of 2


title: Lateral substantia nigra control case PDC1 - A chip

description: Gene expression data from lateral substantia nigra  (LNPDC1A)


title: Lateral substantia nigra control case 9 - A chip

description: Gene expression data from lateral substantia nigra  (LNCon9A)


title: Lateral substantia nigra disease-control case MS155 - A chip

description: Gene expression data from lateral substantia nigra (MS155A)


title: Lateral substantia nigra Parkinson's disease case 01 - A chip

description: Gene expression data from lateral substantia nigra  (LNPD01A)


title: WT BMM hly- Lm 120 min C

description: biological replicate 3 of 3

source_name: aRNA from WT macrophage, infected with hly- Lm for 120 min


title: WT BMM hly- Lm 60 min B

description: biological replicate 2 of 3

source_name: aRNA from WT macrophage, infected with hly- Lm for 60 min


title: WT BMM hly- Lm 180 min A

description: biological replicate 1 of 4


title: WT BMM hly- Lm 120 min B

description: biological replicate 2 of 3


title: WT BMM hly- Lm 60 min C

description: biological replicate 3 of 3


title: Lateral substantia nigra control case 8 - A chip

description: Gene expression data from lateral substantia nigra  (LNCon8A)


title: myd88- BMM Uninfected B

description: biological replicate 2 of 4


title: Lateral substantia nigra control case 4 - A chip

description: Gene expression data from lateral substantia nigra (LNCon4A)


title: WT BMM hly- Lm 120 min A

description: biological replicate 1 of 3


title: Lateral substantia nigra control case 2 - A chip

description: Gene expression data from lateral substantia nigra  (LNCon2A)


title: WT BMM WT Lm 180 min B

description: biological replicate 2 of 3


title: WT BMM hly- Lm 180 min B

description: biological replicate 2 of 4


title: WT BMM hly- Lm 30 min A

description: biological replicate 1 of 3

source_name: aRNA from WT macrophage, infected with hly- Lm for 30 min


title: WT BMM hly- Lm 60 min A

description: biological replicate 1 of 3


title: WT BMM hly- Lm 180 min C

description: biological replicate 3 of 4


title: Spn_D39vsD39spxR6_CDM_rep3

description: Independent biological replicate, dye swap

source_name: S. pneumoniae D39spxR6

source_name: S pneumoniae bacterial strain D39 (NCTC)

growth_protocol: same as channel 1

tag: S. pneumoniae D39 (NCTC) (strain IU1690), virulent, type 2 capsule


title: WT BMM hly- Lm 30 min C

description: biological replicate 3 of 3


title: WT BMM WT Lm 180 min C

description: biological replicate 3 of 3

source_name: aRNA from WT macrophage, infected with WT Lm for 180 min


title: Superior frontal gyrus Parkinson's disease case 34 - A chip

description: Gene expression data from superior frontal gyrus (CxPD34A)

source_name: Post mortem superior frontal gyrus

value: 84; gender:F


title: Superior frontal gyrus Parkinson's disease case 36 - A chip

description: Gene expression data from superior frontal gyrus (CxPD36A)


title: WT BMM WT Lm 60 min A

description: biological replicate 1 of 3

source_name: aRNA from WT macrophage, infected with WT Lm for 60 min


title: WT BMM Uninfected D

description: biological replicate 4 of 4

source_name: aRNA from WT macrophage, uninfected


title: Superior frontal gyrus Parkinson's disease case 04 - A chip

description: Gene expression data from superior frontal gyrus (CxPD04A)


title: WT BMM WT Lm 30 min A

description: biological replicate 1 of 3

source_name: aRNA from WT macrophage, infected with WT Lm for 30 min


title: Lateral substantia nigra control case 10 - A chip

description: Gene expression data from lateral substantia nigra  (LNCon10A)

source_name: Post-mortem lateral substantia nigra


title: WT BMM WT Lm 60 min B

description: biological replicate 2 of 3


title: WT BMM WT Lm 120 min C

description: biological replicate 3 of 3

source_name: aRNA from WT macrophage, infected with WT Lm for 120 min


title: WT BMM WT Lm 180 min A

description: biological replicate 1 of 3


title: WT BMM WT Lm 30 min B

description: biological replicate 2 of 3


title: WT BMM Uninfected A

description: biological replicate 1 of 4


title: WT BMM hly- Lm 30 min B

description: biological replicate 2 of 3


title: Superior frontal gyrus control case 2 - A chip

description: Gene expression data from superior frontal gyrus (CxCON2A)


title: WT BMM WT Lm 60 min C

description: biological replicate 3 of 3


title: WT BMM WT Lm 120 min B

description: biological replicate 2 of 3


title: WT BMM WT Lm 120 min A

description: biological replicate 1 of 3


title: Superior frontal gyrus Parkinson's disease case 29 - A chip

description: Gene expression data from superior frontal gyrus (CxPD29A)


title: WT BMM Uninfected B

description: biological replicate 2 of 4


title: Superior frontal gyrus control case 9 - A chip

description: Gene expression data from superior frontal gyrus (CxCON9A)


title: WT BMM WT Lm 30 min C

description: biological replicate 3 of 3


title: WT BMM Uninfected C

description: biological replicate 3 of 4


title: Superior frontal gyrus control case 3 - A chip

description: Gene expression data from superior frontal gyrus (CxCON3A)


title: Transcriptional response of the marine pennate diatom Phaeodactylum tricornutum to Fe limitation_dyeflip_slide5

city: La Jolla

first: Andrew

middle: E

last: Allen

state: CA

address: 11149, North Torrey Pines Road, Suite 220

department: Deptartment of Environmental Genomics

institute: J. Craig Venter Institute

description: Comparison of P. tricornutum cultured under Fe deplete and Fe replete conditions. Culture replicates for each condition - 2. Hybridization replicates for each pair of culture replicates – 3

hyb_protocol: Prior to hybridization 5 µg of labeled aRNA constructed from Fe replete and Fe deplete samples was mixed together, precipitated, re-suspended, and fragmented (Ambion 8740). Each pair of RNA samples from Fe replete and Fe deplete duplicate cultures was competitively hybridized three times for a total of six slides. Sample GSM214819 was a dye-flip hybridization where the Fe deplete sample was labeled with Cy3.

scan_protocol: Microarray slides were scanned using a GenePix4000B (Axon) two-laser scanner and image analysis was performed using GenePix 5.0 (Axon) software.

data_processing: Mean intensities for both RNA populations were processed through minimum and maximum saturation and diameter filters and normalized using global lowess followed by a block mean normalization.

organism: Phaeodactylum tricornutum

source_name: Phaeodactylum tricornutum cultured under Fe limiting conditions. Rep2

label_protocol: Using the Ambion Amino Allyl MessageAmp kit (1752), 500 ng of total RNA was used as a template for first strand cDNA sysnthesis. cDNA was subsequently converted to double-stranded DNA (dsDNA), purified, and subsequently in vitro transcribed with amino allyl modified  UTPs (aaUTP) to generated amplified RNA (aRNA). aRNA was then purified and quantified. 10 ug of amino allyl RNA was vacuum-dried and re-suspended in 9 µls of dye coupling buffer prior to dye coupling reactions.  Dye coupling efficiency was evaluated spectrophotometrically on a ND-1000.  Samples that contained 25-50 incorporated dye molecules per 1000 nt were considered suitable for competitive hybridization experiments.

growth_protocol: Phaeodactylum tricornutum was grown under iron deplete conditions with articficial seawater medium and F/2 macro nutrient concentrations. Iron concentrations were adjusted to a final concentrations of 5 nM with FeCl/EDTA solutions. Cells were grown in 5 nM Fe in small volume (1 liter) cultures for several generations before transfer to 8 L volumes. Cells were grown for 11 days at a light intensity of 70 µE m-2 s-1 at 18ºC, then harvested by centrifugation. Duplicate Fe deplete cultures were prepared. At the time of harvest a small aliquaot was taked to measure cell density, chl a levels, and photosynthetic efficiency (Fv/Fm) using a PAM fluorometer. A small aliquot was also taken to test for bacterial contamination of the cultures (acridine orange staining, and growth on marine broth). All cultures were axenic at the time of harvest.

extract_protocol: RNA was isolated using the TRIZOL reagent (Invitrogen 15596-026). An on-column digestion of DNA was performed (Qiagen 79254) during an RNA cleanup step (Qiagen 74106). Purified RNA was prepared separately for each of the culture replicates. RNA quality and quantity was inspected on an Agilent 2100 Bioanalyzer and NanoDrop (ND-1000) respectively.

tag: Phaeodactylum tricornutum; lines - wild type; treatment – Fe deplete cultures

growth_protocol: Phaeodactylum tricornutum was grown under iron replete conditions with articficial seawater medium and F/2 macro nutrient concentrations. Iron concentrations were adjusted to a final concentration of 10,000 nM with FeCl/EDTA solutions. Cells were grown in 5 nM Fe in small volume (1 liter) cultures for several generations before transfer to 8 L volumes. Cells were grown for 11 days at a light intensity of 70 µE m-2 s-1 at 18ºC, then harvested by centrifugation. Duplicate Fe replete cultures were prepared. At the time of harvest a small aliquaot was taken to measure cell density, chl a levels, and photosynthetic efficiency (Fv/Fm) using a PAM fluorometer. A small aliquat was also taken to test for bacterial contamination of the cultures (acridine orange staining, and growth on marine broth). All cultures were axenic at the time of harvest.

tag: Phaeodactylum tricornutum; lines - wild type; treatment – Fe replete cultures. Rep2


title: Superior frontal gyrus Parkinson's disease case 01 - A chip

description: Gene expression data from superior frontal gyrus (CxPD01A)


title: Transcriptional response of the marine pennate diatom Phaeodactylum tricornutum to Fe limitation_slide6

source_name: Phaeodactylum tricornutum cultured under Fe limiting conditions.

label_protocol: Using the Ambion Amino Allyl MessageAmp kit (1752), 500 ng of total RNA was used as a template for first strand cDNA sysnthesis. cDNA was subsequently converted to double-stranded DNA (dsDNA), purified, and subsequently in vitro transcribed with amino allyl modified  UTPs (aaUTP) to generated amplified RNA (aRNA). aRNA was then purified and quantified. 10 ug of amino allyl RNA was vacuum-dried and re-suspended in 9 µls of dye coupling buffer prior to dye coupling reactions.  Dye coupling efficiency was evaluated spectrophotometrically on a ND-1000.  Samples that contained 25-50 incorporated dye molecules per 1000 nt were considered suitable for competitive hybridization experiments


title: Transcriptional response of the marine pennate diatom Phaeodactylum tricornutum to Fe limitation_slide3


title: Transcriptional response of the marine pennate diatom Phaeodactylum tricornutum to Fe limitation_slide4


title: Transcriptional response of the marine pennate diatom Phaeodactylum tricornutum to Fe limitation


title: Transcriptional response of the marine pennate diatom Phaeodactylum tricornutum to Fe limitation_slide2

source_name: Phaeodactylum tricornutum cultured under Fe limiting conditions


title: Gene expression profile of the GidA mutant-7

city: Carbondale

first: KyuHong

last: Cho

address: 1125 Lincoln Dr. Room 131

institute: Southern Illinois University Carbondale

description: An antisense oligonucleotide array based on the published genome of S. pyogenes SF370 (Ferretti et al., 2001) was made at the Microarray Core Facility in the Genome-Sequencing Center at Washington University (GSC). A single 60–80 mer oligonucleotide was designed to hybridize to the putative transcripts from each annotated open reading frame using 'TOP' software that was created at the GSC. To reduce complexity, probes for rRNA, tRNA and prophage-associated genes were not included, which resulted in an array consisting of probes for 1517 genes out of a total of 1752 predicted open reading frames in the SF370 genome. The oligonucleotides were synthesized by Illumina and were deposited onto a MWG epoxy microarray slide by custom Linear Servo Arrayer so that each slide included duplicates spots for each probe. Quality of the array was validated by hybridization with a Cyanine 5-labelled random nonamer (Hybchecker, Sigma) to ensure that the frequency of missed spots were less than 1.0% and by self-self hybridization using a single RNA sample to generate Cyanine 3- and Cyanine 5-labelled cDNAs (see below), which were then co-hybridized on the slide. Slide batches were rejected if the average ratio of hybridization differed significantly from 1.0. The purity and concentration of RNA prepared as described above was analysed by a fluorescent assay involving electrophoretic separation of RNA (Agilent 2100 bioanalyser), and rejected if the electropherogram (a diagram of fluorescence over time) showed the degradation of RNA.

hyb_protocol: Synthesis and labelling of cDNA used a commercial kit (3DNA Array 900, Genisphere). Briefly, cDNA was generated with random hexamers as primers for reverse transcription. The primers (1 pmole) were annealed to total RNA (4 µg) and extended with Superscript II reverse transcriptase (Invitrogen) at 42°C for 2 h. Residual RNA was then removed by alkaline treatment followed by neutralization. The efficiency of cDNA synthesis was monitored by spiking samples with a known RNA complementary to a control DNA probe spotted onto the array (Ambion). A poly T (thymine) tail was synthesized at the 3' end of the cDNA by terminal deoxynucleotidyl transferase and the capture sequence was ligated at the end of the poly T tail. The tagged cDNAs from the appropriate samples were mixed and then allowed to hybridize with the array using a commercial buffer (MWG) at 42°C overnight. Following washing using 2× SSC, 0.2% SDS, at 65°C to remove unhybridized cDNAs, the detection reagents (Cyanine 3 and Cyanine 5 3DNA dendrimers, Genisphere) were added with incubation at 65°C for 3 h. Unbound detection reagents were removed by washing.

scan_protocol: The signal of the bound reagents measured using a laser scanner (ScanArray Express HT, PerkinElmer).

data_processing: The fluorescence values from each array were normalized by the LOWESS (Locally Weighted Scatter plot Smoother) function of the laser scanner. Average values were calculated from a data set consisting of 16 total microarray hybridizations that were derived from RNA samples prepared from two independent experiments, each of which was conducted on a different day. This average value represents the relative amount of cDNA binding to a given probe in competitive hybridization and is presented as a fold difference. VALUES ignored if Ch1 Median - B or Ch2 Median - B is less than 600.

organism: Streptococcus pyogenes

source_name: Log phase TM-GidA2

extract_protocol: Total RNA was isolated by a protocol adapted from the method of Cheung et al. (1994) using glass beads (Lysing Matrix A, Q/BioGene) and a high-speed reciprocating shaking device (FP-120, Savant Instruments). RNA was further purified (RNeasy Mini Kit for RNA clean up, Qiagen) and contaminating DNA was removed by DNase treatments according to the manufacturers instructions (RNase free DNase set, QIAGEN and DNase I, amplification grade, Invitrogen). Representative samples were assessed for RNA integrity by electrophoretic analysis with an Agilent 2100 Bioanalyzer (Agilent Technologies) and measurement of the A260/A280 ratio was used to determine the RNA concentration and purity (accepted if >1.8).

tag: A GidA mutant grown in THY media

source_name: Log phase HSC5

tag: Wild type grown in THY media


title: Gene expression profile of the GidA mutant-8

label_protocol: Synthesis and labelling of cDNA used a commercial kit (3DNA Array 900, Genisphere). Briefly, cDNA was generated with random hexamers as primers for reverse transcription. The primers (1 pmole) were annealed to total RNA (4 µg) and extended with Superscript II reverse transcriptase (Invitrogen) at 42°C for 2 h. Residual RNA was then removed by alkaline treatment followed by neutralization. The efficiency of cDNA synthesis was monitored by spiking samples with a known RNA complementary to a control DNA probe spotted onto the array (Ambion). A poly T (thymine) tail was synthesized at the 3' end of the cDNA by terminal deoxynucleotidyl transferase and the capture sequence was ligated at the end of the poly T tail. The tagged cDNAs from the appropriate samples were mixed and then allowed to hybridize with the array using a commercial buffer (MWG) at 42°C overnight. Following washing using 2× SSC, 0.2% SDS, at 65°C to remove unhybridized cDNAs, the detection reagents (Cyanine 3 and Cyanine 5 3DNA dendrimers, Genisphere) were added with incubation at 65°C for 3 h. Unbound detection reagents were removed by washing.


title: MALT sample # 86

type: genomic

city: Madrid

first: Juan

middle: C

last: Cigudosa

address: C/ Melchor Fernández Almagro, 3

department: Human Cancer Genetics

country: Spain

institute: Centro Nacional de Investigaciones Oncologicas - CNIO

hyb_protocol: Human cot-1 DNA, Agilent 10x blocking agent and Agilent 2x hybridization buffer were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version v:8.1).

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

molecule: genomic DNA

source_name: Genomic DNA from MALT sample # 86 labeled with Cyanine-5 (red)

label_protocol: 2 µg of genomic DNA were primed with 20 µl of 2.5x Random Primers at 95°C for 5 min and then labeled with 5µl of 10x dUTP mix, 3 µl of Cy3 or Cy5 dUTP (1.0mM) and 1 µl of Exp-Klenow at 37ºC for 3 hours.

extract_protocol: Total DNA extracted using Quiagen's Tissue Kit following manufacturer's instructions

tag: MALT

source_name: Genomic DNA from pooled pheripheral blood of ten healthy female donors

tag: no additional information


title: MALT sample # 87

source_name: Genomic DNA from MALT sample # 87labeled with Cyanine-5 (red)


title: Gene expression profile of the GidA mutant-6


title: MALT sample # 82

source_name: Genomic DNA from MALT sample # 82 labeled with Cyanine-5 (red)


title: Gene expression profile of the GidA mutant-5


title: Gene expression profile of the GidA mutant-1

tag: HSC5 grown in THY media

source_name: log phase TM-GidA2


source_name: Genomic DNA from Splenic Marginal Zone Lymphoma sample # 73 labeled with Cyanine-5 (red)

tag: Splenic Marginal Zone Lymphoma


title: MALT sample # 79

source_name: Genomic DNA from MALT sample # 79 labeled with Cyanine-5 (red)


source_name: Genomic DNA from Splenic Marginal Zone Lymphoma sample # 69 labeled with Cyanine-5 (red)


source_name: Genomic DNA from Splenic Marginal Zone Lymphoma sample # 77 labeled with Cyanine-5 (red)


title: Gene expression profile of the GidA mutant-3

source_name: Log phaseTM-GidA2


title: MALT sample # 83

source_name: Genomic DNA from MALT sample # 83 labeled with Cyanine-5 (red)


source_name: Genomic DNA from Splenic Marginal Zone Lymphoma sample # 75 labeled with Cyanine-5 (red)


source_name: Genomic DNA from Splenic Marginal Zone Lymphoma sample # 71 labeled with Cyanine-5 (red)


title: MALT sample # 81

source_name: Genomic DNA from MALT sample # 81 labeled with Cyanine-5 (red)


source_name: Genomic DNA from Splenic Marginal Zone Lymphoma sample # 74 labeled with Cyanine-5 (red)


source_name: Genomic DNA from Splenic Marginal Zone Lymphoma sample # 78 labeled with Cyanine-5 (red)


title: Gene expression profile of the GidA mutant-4

source_name: Log phase TM-GidA2

source_name: Log phase HSC5


source_name: Genomic DNA from Splenic Marginal Zone Lymphoma sample # 70 labeled with Cyanine-5 (red)

source_name: Genomic DNA from pooled pheripheral blood of ten healthy female donors


title: Gene expression profile of the GidA mutant-2


source_name: Genomic DNA from Splenic Marginal Zone Lymphoma sample # 68 labeled with Cyanine-5 (red)


title: MALT sample # 80

source_name: Genomic DNA from MALT sample # 80 labeled with Cyanine-5 (red)


title: MALT sample # 84

source_name: Genomic DNA from MALT sample # 84 labeled with Cyanine-5 (red)


source_name: Genomic DNA from Splenic Marginal Zone Lymphoma sample # 67 labeled with Cyanine-5 (red)


source_name: Genomic DNA from Splenic Marginal Zone Lymphoma sample # 64 labeled with Cyanine-5 (red)


title: MALT sample # 85

source_name: Genomic DNA from MALT sample # 85 labeled with Cyanine-5 (red)


source_name: Genomic DNA from Splenic Marginal Zone Lymphoma sample # 76 labeled with Cyanine-5 (red)


title: Lymphoplasmacytic Lymphoma sample # 63

source_name: Genomic DNA from Lymphoplasmacytic Lymphoma sample # 63 labeled with Cyanine-5 (red)

tag: Lymphoplasmacytic Lymphoma


title: Lymphoplasmacytic Lymphoma sample # 60

source_name: Genomic DNA from Lymphoplasmacytic Lymphoma sample # 60 labeled with Cyanine-5 (red)


title: Lymphoplasmacytic Lymphoma sample # 59

source_name: Genomic DNA from Lymphoplasmacytic Lymphoma sample # 59 labeled with Cyanine-5 (red)


source_name: Genomic DNA from Nodal Marginal Zone Lymphoma sample # 48 labeled with Cyanine-5 (red)

tag: Nodal Marginal Zone Lymphoma


title: Lymphoplasmacytic Lymphoma sample # 58

source_name: Genomic DNA from Lymphoplasmacytic Lymphoma sample # 58 labeled with Cyanine-5 (red)


source_name: Genomic DNA from Nodal Marginal Zone Lymphoma sample # 51 labeled with Cyanine-5 (red)


title: Lymphoplasmacytic Lymphoma sample # 56

source_name: Genomic DNA from Lymphoplasmacytic Lymphoma sample # 56 labeled with Cyanine-5 (red)


source_name: Genomic DNA from Nodal Marginal Zone Lymphoma sample # 49 labeled with Cyanine-5 (red)


source_name: Genomic DNA from Splenic Marginal Zone Lymphoma sample # 66 labeled with Cyanine-5 (red)


title: Lymphoplasmacytic Lymphoma sample # 62

source_name: Genomic DNA from Lymphoplasmacytic Lymphoma sample # 62 labeled with Cyanine-5 (red)

source_name: Genomic DNA from pooled pheripheral blood of ten healthy female donors


source_name: Genomic DNA from Splenic Marginal Zone Lymphoma sample # 65 labeled with Cyanine-5 (red)


source_name: Genomic DNA from Nodal Marginal Zone Lymphoma sample # 53 labeled with Cyanine-5 (red)


source_name: Genomic DNA from Splenic Marginal Zone Lymphoma sample # 72 labeled with Cyanine-5 (red)


title: Lymphoplasmacytic Lymphoma sample # 57

source_name: Genomic DNA from Lymphoplasmacytic Lymphoma sample # 57 labeled with Cyanine-5 (red)


source_name: Genomic DNA from Nodal Marginal Zone Lymphoma sample # 52 labeled with Cyanine-5 (red)


source_name: Genomic DNA from Nodal Marginal Zone Lymphoma sample # 45 labeled with Cyanine-5 (red)


title: Lymphoplasmacytic Lymphoma sample # 54

source_name: Genomic DNA from Lymphoplasmacytic Lymphoma sample # 54 labeled with Cyanine-5 (red)


source_name: Genomic DNA from Nodal Marginal Zone Lymphoma sample # 47 labeled with Cyanine-5 (red)


title: Lymphoplasmacytic Lymphoma sample # 55

source_name: Genomic DNA from Lymphoplasmacytic Lymphoma sample # 55 labeled with Cyanine-5 (red)


title: Lymphoplasmacytic Lymphoma sample # 61

source_name: Genomic DNA from Lymphoplasmacytic Lymphoma sample # 61 labeled with Cyanine-5 (red)


title: Mantle Cell Lymphoma sample # 43

source_name: Genomic DNA from Mantle Cell Lymphoma sample # 43 labeled with Cyanine-5 (red)

tag: Mantle Cell Lymphoma


source_name: Genomic DNA from Nodal Marginal Zone Lymphoma sample # 50 labeled with Cyanine-5 (red)


source_name: Genomic DNA from Nodal Marginal Zone Lymphoma sample # 46 labeled with Cyanine-5 (red)


title: Mantle Cell Lymphoma sample # 41

source_name: Genomic DNA from Mantle Cell Lymphoma sample # 41 labeled with Cyanine-5 (red)


title: Mantle Cell Lymphoma sample # 42

source_name: Genomic DNA from Mantle Cell Lymphoma sample # 42 labeled with Cyanine-5 (red)


title: Mantle Cell Lymphoma sample # 44

source_name: Genomic DNA from Mantle Cell Lymphoma sample # 44 labeled with Cyanine-5 (red)


title: Mantle Cell Lymphoma sample # 40

source_name: Genomic DNA from Mantle Cell Lymphoma sample # 40 labeled with Cyanine-5 (red)

source_name: Genomic DNA from pooled pheripheral blood of ten healthy female donors


title: Mantle Cell Lymphoma sample # 38

source_name: Genomic DNA from Mantle Cell Lymphoma sample # 38 labeled with Cyanine-5 (red)


title: Mantle Cell Lymphoma sample # 39

source_name: Genomic DNA from Mantle Cell Lymphoma sample # 39 labeled with Cyanine-5 (red)


title: Mantle Cell Lymphoma sample # 36

source_name: Genomic DNA from Mantle Cell Lymphoma sample # 36 labeled with Cyanine-5 (red)


title: Mantle Cell Lymphoma sample # 32

source_name: Genomic DNA from Mantle Cell Lymphoma sample # 32 labeled with Cyanine-5 (red)


title: Mantle Cell Lymphoma sample # 35

source_name: Genomic DNA from Mantle Cell Lymphoma sample # 35 labeled with Cyanine-5 (red)


title: Mantle Cell Lymphoma sample # 31

source_name: Genomic DNA from Mantle Cell Lymphoma sample # 31 labeled with Cyanine-5 (red)


source_name: Genomic DNA from Chronic Lymphocytic Leukemia sample # 28 labeled with Cyanine-5 (red)

tag: Chronic Lymphocytic Leukemia


source_name: Genomic DNA from Chronic Lymphocytic Leukemia sample # 27 labeled with Cyanine-5 (red)


title: Mantle Cell Lymphoma sample # 37

source_name: Genomic DNA from Mantle Cell Lymphoma sample # 37 labeled with Cyanine-5 (red)


source_name: Genomic DNA from Chronic Lymphocytic Leukemia sample # 29 labeled with Cyanine-5 (red)


source_name: Genomic DNA from Chronic Lymphocytic Leukemia sample # 30 labeled with Cyanine-5 (red)


title: Mantle Cell Lymphoma sample # 34

source_name: Genomic DNA from Mantle Cell Lymphoma sample # 34 labeled with Cyanine-5 (red)


source_name: Genomic DNA from Chronic Lymphocytic Leukemia sample # 24 labeled with Cyanine-5 (red)


source_name: Genomic DNA from Chronic Lymphocytic Leukemia sample # 23 labeled with Cyanine-5 (red)


source_name: Genomic DNA from Chronic Lymphocytic Leukemia sample # 20 labeled with Cyanine-5 (red)


source_name: Genomic DNA from Chronic Lymphocytic Leukemia sample # 21 labeled with Cyanine-5 (red)


source_name: Genomic DNA from Chronic Lymphocytic Leukemia sample # 26 labeled with Cyanine-5 (red)

source_name: Genomic DNA from pooled pheripheral blood of ten healthy female donors


source_name: Genomic DNA from Chronic Lymphocytic Leukemia sample # 17 labeled with Cyanine-5 (red)


source_name: Genomic DNA from Chronic Lymphocytic Leukemia sample # 25 labeled with Cyanine-5 (red)


title: Follicular Lymphoma sample# 15

source_name: Genomic DNA from Follicular Lymphoma sample # 15 labeled with Cyanine-5 (red).

tag: Follicular Lymphoma


source_name: Genomic DNA from Chronic Lymphocytic Leukemia sample # 22 labeled with Cyanine-5 (red)


source_name: Genomic DNA from Chronic Lymphocytic Leukemia sample # 19 labeled with Cyanine-5 (red)


title: Follicular Lymphoma sample# 14

source_name: Genomic DNA from Follicular Lymphoma sample # 14 labeled with Cyanine-5 (red).


source_name: Genomic DNA from Chronic Lymphocytic Leukemia sample # 18 labeled with Cyanine-5 (red)


title: Follicular Lymphoma sample # 13

source_name: Genomic DNA from Follicular Lymphoma sample # 13 labeled with Cyanine-5 (red).


title: Mantle Cell Lymphoma sample # 33

source_name: Genomic DNA from Mantle Cell Lymphoma sample # 33 labeled with Cyanine-5 (red)


title: Follicular Lymphoma sample# 11

source_name: Genomic DNA from Follicular Lymphoma sample # 11 labeled with Cyanine-5 (red).


title: Follicular Lymphoma sample # 12

source_name: Genomic DNA from Follicular Lymphoma sample # 12 labeled with Cyanine-5 (red).


title: Chronic Lymphocytic Leukemia sample # 16

source_name: Chronic Lymphocytic Leukemia #16


title: Follicular Lymphoma sample# 3

source_name: Genomic DNA from Follicular Lymphoma sample # 3 labeled with Cyanine-5 (red).


title: Follicular Lymphoma sample # 9

source_name: Genomic DNA from Follicular Lymphoma sample # 9 labeled with Cyanine-5 (red).


title: Slide 2 Norepi lower

city: Ames

first: Chris

last: Minion

state: IA

address: 1130 Vet Med

department: VMPM

institute: Iowa State University

description: Slide images were analyzed using the SoftWorx Tracker package (Applied Precision, Inc.), acquiring mean spot intensity and median background intensity for each spot. Spot signals were corrected for background by subtracting the median background intensity from the mean spot intensity. The natural logarithms of these background-corrected signals were adjusted by an additive constant to give a common median to each scan of the same array-dye combination. The data from both dye channels on a given array were normalized by locally weighted scatterplot smoother (LOWESS) normalization. These normalized data sets were then adjusted by an additive constant to make each median the same across all arrays. The triplicate spots were averaged together to produce one normalized measurement for each probe on the array.

hyb_protocol: After the purification of the cDNA targets, they were hybridized to the array using the previously described protocol [Madsen, M. L., D. Nettleton, E. L. Thacker, R. Edwards, and F. C. Minion. 2006. Transcriptional profiling of Mycoplasma hyopneumoniae during heat shock using microarrays. Infect. Immun. 74:160-166.]. Slides were washed using the Corning UltraGAPS slide wash protocol and dried by centrifugation at 1500 x g for two minutes.

scan_protocol: After hybridization and washing, the arrays were scanned using a ScanArray Express laser scanner (Applied Biosystems) three times with varying photomultiplier tube gain settings to encompass the dynamic range of the signal intensities [Dudley, A. M., J. Aach, M. A. Steffen, and G. M. Church. 2002. Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range. Proc. Natl. Acad. Sci. USA 99:7554-7559.].

data_processing:
We fit a mixed linear model with the normalized signal intensity as the response.
intensity = mu + trt + part + dye + slide + slide*part
where part refers to the upper or lower portion of the slide.

organism: Mesomycoplasma hyopneumoniae

source_name: Strain 232 Norepi treated

label_protocol: Fluorescently labeled cDNA targets were generated and purified using a modified protocol as described in [Boyce, J. D., I. Wilkie, M. Harper, M. L. Paustian, V. Kapur, and B. Adler. 2004. Genomic-scale analysis of Pasteurella multocida gene expression during growth within liver tissue of chickens with fowl cholera. Microbes Infect. 6:290-298.] with a 129 hexamer primer set specific for M. hyopneumoniae open reading frames used in previous studies [Madsen, M. L., D. Nettleton, E. L. Thacker, R. Edwards, and F. C. Minion. 2006. Transcriptional profiling of Mycoplasma hyopneumoniae during heat shock using microarrays. Infect. Immun. 74:160-166.].

extract_protocol: RNA was isolated from frozen cell pellets using the Versagene RNA purification System (Qiagen, Valencia, Calif.). The manufacturer’s protocol was followed with the exception of the DNase treatment, which was extended to thirty minutes. The filter cutoff of 150 base pairs prevented small RNA fragments from interfering in subsequent manipulations.

tag: Strain 232 culture grown in friis media to mid-log phase. 250 ml flask containing 150 ml of culture were grown to early exponential phase as determined by color changing units. Norepinephrine was added to a final concentration of 100 micromolar and incubated at 37°C for 4 hours.

source_name: Strain 232 control


title: Slide 3 Norepi upper

source_name: Strain 232 Control

tag: Strain 232 culture grown in friis media to mid-log phase. 250 ml flask containing 150 ml of culture were grown to early exponential phase as determined by color changing units.


title: Follicular Lymphoma sample # 1

source_name: Genomic DNA from Follicular Lymphoma sample # 1 labeled with Cyanine-5 (red).

source_name: Genomic DNA from pooled pheripheral blood of ten healthy female donors


title: BAL slide 2 lower

description: The normalized values for triplicate spots were averaged within each array to produce one normalized measure of expression for each of the 620 probe sequences and each of the 9 RNA samples. [mean log transformed median centered lowess normalized signal intensity]

hyb_protocol: Following purification of the labeled cDNA, samples were dried in a vacuum centrifuge and then resuspended in 10 µl Pronto! cDNA/long oligonucleotide hybridization solution (Corning). Targets were denatured at 95°C for 5 min and centrifuged at 13,000 x g for 2 min at room temperature. Targets from control and heat-shocked cultures were then combined, pipetted to an array, and covered with a 22- by 22-mm HybriSlip (Schleicher & Schuell, Keene, N.H.). Slides were placed in a Corning hybridization chamber and incubated in a 42°C water bath for 12 to 16 h. Slides were washed according to Corning's UltraGAPS protocol and dried by centrifugation.

scan_protocol: Each dye channel of each array was scanned three times under varying laser power and photomultiplier tube gain settings using a ScanArray Express laser scanner (Applied BioSystems, Inc., Foster City, Calif.) to increase the dynamic range of expression measurement [Dudley, A. M., J. Aach, M. A. Steffen, and G. M. Church. 2002. Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range. Proc. Natl. Acad. Sci. USA 99:7554-7559]. The images were quantified using the softWorRx Tracker analysis software package (Applied Precision, Inc., Issaquah, Wash.).

data_processing: Images were quantified, log transformed, background subtracted and normalized as described in [Madsen, M. L., D. Nettleton, E. L. Thacker, R. Edwards, and F. C. Minion. 2006. Transcriptional profiling of Mycoplasma hyopneumoniae during heat shock using microarrays. Infect. Immun. 74:160-166]. Spot-specific mean signals were corrected for local background by subtracting spot-specific median background intensities. The natural logarithm of the background-corrected signals from a single scan was adjusted by an additive constant so that all scans of the same array-by-dye combination would have a common median. The median of these adjusted-log-background-corrected signals across multiple scans was then computed for each spot to obtain one value for each combination of spot, array, and dye channel. These data for the two dye channels on any given array were normalized using LOWESS normalization to adjust for intensity-dependent dye bias [Dudoit, S., Y. H. Yang, M. J. Callow, and T. P. Speed. 2000. Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments.].  The normalized values for triplicate spots were averaged within each array to produce one normalized measure of expression for each of the 620 probe sequences and each of the 9 RNA samples.

source_name: Strain 232 BALF from 28 day infected pigs

label_protocol: Fluorescently labeled cDNA targets were generated, purified, hybridized to arrays, scanned and analyzed as follows. Briefly, 10 μg of M. hyopneumoniae enriched RNA were incubated at 70°C for 10 min with 5 μl of M. hyopneumoniae open reading frame-specific hexamer oligonucleotide primers (750 ng/µl) in a total reaction volume of 15.5 μl. Samples were incubated at 70°C for 10 min, chilled on ice for 10 min, and then combined with 14.5 μl of reverse transcription reaction mix (3 μl Superscript III 200U/ μl (Invitrogen Corp., Carlsbad, Calif.), 6 μl 5 x First Strand Buffer, 0.6 μl 50 x amino allyl-dUTP/dNTP mix, 3 μl RNase-free water). Reactions were incubated at 42°C for at least 2 hrs. RNA hydrolysis was preformed using 3 μl 0.1 M ETDA and 3.5 μl 0.1 M NaOH at 65°C for 10 min. To neutralize pH, 36.5 μl of 500 mM HEPES (pH 7.0) was added. The hydrolyzed reactions were purified using the Mo Bio UltraClean™ PCR Clean-Up Kit (MO BIO Laboratories, Inc., Carlsbad, Calif.). Reactions were quantified using a ND-1000 (Nanodrop, Wilmington, Del.), lyophilized, and resuspended in 6.5 μl RNase-free water. After 10 min, 1.5 μl sodium bicarbonate (pH 8.7) and 2 μl of Alexa 555 or Alexa 647 (Invitrogen, Carlsbad, Calif.) were added. Dyes were prepared by resuspending a single tube of dye in 2 μl of dimethyl sulfoxide. Dye coupled reactions were purified and quantified as above. Frequency of incorporation was determined as described http://Promega.com/applications/arrays/calculator/#ResultsView).

extract_protocol: RNA was isolated using the VersageneTM RNA Purification System (Gentra Systems, Minneapolis, Minn.) according to the manufacturer’s protocol. The optional step of DNase treatment was performed on column according to the manufacturer’s recommendation. Contaminating pig RNA was removed from each sample using the MICROBEnrich kit (Ambion), and the samples were quantified using the Nanodrop® ND-1000 Spectrophotometer (Nanodrop, Wilmington, Del.). The broth-grown control samples were treated in identical fashion. The efficiency of removal of contaminating pig RNAs was verified by PCR using primers specific for pig cyclophilin (cyclo-f, TAACCCCACCGTCTTCTT, cyclo-r, TGCCATCCAACCACTCAG). In addition, to evaluate the possibility of having false signals on the arrays from swine lung RNAs in the BALF fluid preparations, a hybridization was performed with total RNA isolated from whole-lung tissues harvested from mycoplasma-free control pigs using the VersageneTM RNA Purification Tissue kit (Gentra Systems). For theses studies, total pig lung RNA was labeled with M. hyopneumoniae open reading frame-specific hexamer oligonucleotide primers selected to bind only to M. hyopneumoniae mRNA as previously described [Madsen, M. L., D. Nettleton, E. L. Thacker, R. Edwards, and F. C. Minion. 2006. Transcriptional profiling of Mycoplasma hyopneumoniae during heat shock using microarrays. Infect. Immun. 74:160-166].

tag: For in vivo cultures, pigs were infected with M. hyopneumoniae with 10 ml of mid log phase broth culture (105 color changing units/ml) intratracheally at 4 weeks of age [Thacker, E. L., P. G. Halbur, R. F. Ross, R. Thanawongnuwech, and B. J. Thacker. 1999. Mycoplasma hyopneumoniae potentiation of porcine reproductive and respiratory syndrome virus-induced pneumonia. J. Clin. Microbiol. 37:620-627]. Pigs were evaluated daily for respiratory disease (0-6), sneezing (0-3), coughing (0-3), lethargy (0-3), wasting (0-3), and icterus (0-3) and a summary clinical score recorded.

tag: At 28 days post infection, pigs were necropsied and the lungs were lavaged as described [Mengeling, W. L., K. M. Lager, and A. C. Vorwald. 1995. Diagnosis of porcine reproductive and respiratory syndrome. J. Vet. Diagn. Invest. 7:3-16]. Bronchial alveolar lavage fluids (BALF) were quickly cooled to 4°C and centrifuged at 250 x g for 5 min (4°C) to remove the cellular debris and large host cells from the fluid. The mycoplasmas were isolated by high-speed centrifugation (25,000 x g, 15 min, 4°C). Mycoplasma pellets were then resuspended in RNALater (Ambion, Inc. Austin, Tex.) and stored at -70°C until RNA was extracted. The BALF from each pig represented a single experimental value.

source_name: Strain 232 culture, control

tag: Pathogenic M. hyopneumoniae strain 232, a derivative of strain 11, was used in this study. In vitro cultures consisted of 125 ml of Friis media [Friis, N. F. 1975. Some recommendations concerning primary isolation of Mycoplasma hyopneumoniae and Mycoplasma flocculare, a survey. Nord. Veterinaermed. 27:337-339] in 250 ml Erlenmeyer flasks incubated at 37°C with slow agitation until the culture reached mid log phase as indicated by color change and turbidity. Mycoplasmas were pelleted by centrifugation at 24,000 x g, and the cell pellets were stored at -70°C until the total RNA was isolated.


title: Slide 3 Norepi lower


title: BAL slide 5 lower


title: Follicular Lymphoma sample# 10

source_name: Genomic DNA from Follicular Lymphoma sample # 10 labeled with Cyanine-5 (red).


title: BAL slide 1 upper


title: BAL slide 3 upper


title: BAL slide 4 upper


title: Slide 2 Norepi upper


title: BAL slide 5 upper


title: BAL slide 1 lower


title: BAL slide 2 upper


title: Follicular Lymphoma sample # 7

source_name: Genomic DNA from Follicular Lymphoma sample # 7 labeled with Cyanine-5 (red).


title: Follicular Lymphoma sample # 8

source_name: Genomic DNA from Follicular Lymphoma sample # 8 labeled with Cyanine-5 (red).


title: Slide 1 Norepi upper

tag: Strain 232 culture grown in Friis media to mid-log phase. 250 ml flask containing 150 ml of culture were grown to early exponential phase as determined by color changing units.


title: Follicular Lymphoma sample # 2

source_name: Genomic DNA from Follicular Lymphoma sample # 2 labeled with Cyanine-5 (red).


title: Slide 1 Norepi lower


title: Follicular Lymphoma sample# 4

source_name: Genomic DNA from Follicular Lymphoma sample # 4 labeled with Cyanine-5 (red).


title: Follicular Lymphoma sample# 5

source_name: Genomic DNA from Follicular Lymphoma sample # 5 labeled with Cyanine-5 (red).


title: Follicular Lymphoma sample # 6

source_name: Genomic DNA from Follicular Lymphoma sample # 6 labeled with Cyanine-5 (red).


title: 97MP0001-rep1

description: White light scanner. Biological replicate 1 of 4.

hyb_protocol: Following purification of the fluorescently labeled cDNA per manufacturer’s instructions, samples were dried in a vacuum centrifuge and then resuspended in 10 µl Pronto! cDNA/long oligo hybridization solution (Corning). Targets were denatured at 95°C for 5 min and centrifuged at 13,000 x g for 2 min at room temperature. Labeled targets from one 232 control and one field isolate were then combined, pipetted to an array, and covered with a 22 x 22 mm HybriSlip™ (Schleicher & Schuell, Keene, N. H.). Slides were placed in a Corning hybridization chamber and incubated in a 42°C water bath for 12-16 h. Slides were washed according to Corning’s UltraGAPS™ protocol and dried by centrifugation.

scan_protocol: Eight of the fourteen isolate arrays (95MP1504, 95MP1505, 95MP1506, 95MP1507, 95MP1509, 95MP1510, 00MP1301, and 00MP1502) were scanned with each dye channel using a ScanArray Express laser scanner (Applied BioSystems, Inc., Foster City, Calif.) under varying laser power and PMT gain settings to increase the dynamic range of measurement. The other six arrays (95MP1501, 95MP1502, 95MP1503, 95MP1508, 97MP0001, 05MP2301) were scanned with an Applied Precision’s ArrayWoRx® Biochip Reader (Applied Precision, Inc., Issaquah, Wash.).

data_processing:
Images were analyzed for spots and signal intensities quantified using the softWorRx Tracker software package (Applied Precision, Inc.). Spot-specific mean signals were corrected for local background by subtracting spot-specific median background intensities. The natural logarithm of the background-corrected signals from a single scan were adjusted by an additive constant so that all scans of the same array-by-dye combination would have a common median. The median of these adjusted-log-background-corrected signals across multiple scans was then computed for each spot to obtain one value for each combination of spot, array, and dye channel. These data for the two dye channels on any given array were normalized using LOWESS normalization to adjust for intensity-dependent dye bias. Following LOWESS adjustment, the data from each channel were adjusted by an additive constant so that the median for any combination of array and dye would be the same for all array-by-dye combinations.  The difference in normalized values for each spot was calculated as the signal intensity of Alexa 555 dye minus Alexa 647 dye. The differences for the triplicate spots were then averaged within each array to produce one normalized difference value for each of the 627 probe sequences.

Intensity diff = (Cy3-Cy5) + x1(FI1 - strain 232) + x2(FI2 - strain 232) + ... + x14(FI14 - strain 232) + error

where x1 - x14 are 1 or -1 depending on labeling of the FI and strain 232.

source_name: Genomic DNA from strain 232

label_protocol: Targets were generated and purified from mechanically sheared DNA samples using the BioPrime® Plus Array CGH Indirect Genomic Labeling System (Invitrogen Corp., Carlsbad, Calif.). A set of 129 open reading frame-specific hexamer oligonucleotide primers was used to generate amino-allyl modified DNA targets. These targets were then labeled with either Alexa Fluor™ 555 Reactive Dye or Alexa Fluor™ 647 Reactive Dye (Molecular Probes, Inc.) according to the experimental design.

growth_protocol: All M. hyopneumoniae strains were grown in Friis media as previously described in [Friis, N. F. 1975. Some recommendations concerning primary isolation of Mycoplasma hyopneumoniae and Mycoplasma flocculare, a survey. Nord. Veterinaermed. 27:337-339] and are from in vitro passage less than 15. Cultures consisted of 125 ml of Friis media in 250 ml Erlenmeyer flasks incubated at 37°C with slow agitation until the culture reached mid log phase as indicated by color change and turbidity. Mycoplasmas were pelleted by centrifugation at 24,000 x g, and the cell pellets were stored at 70°C until the chromosomal DNA was isolated.

extract_protocol: DNA isolation. DNA was isolated from frozen cell pellets as follows. The cells were first resuspended in 1 ml of TNE buffer (10 mM Tris, 140 mM sodium chloride, 1 mM ethylenediamine tetraacetic acid, pH 8.0), and Proteinase K was added to a final concentration of 70 µg/ml. The suspension was incubated at 50°C for 5 min, and then sodium dodecyl sulfate was added to a final concentration of 0.1% and incubation was continued at 50°C for 4 h. The suspension was then extracted with an equal volume of 25:24:1 phenol:chloroform:isoamyl alcohol three times, and the DNA was precipitated by the addition of one tenth volume of 3 M sodium acetate and bringing the solution to 70% ethanol as described in [Sambrook, J., and W. R. David. 2001. Purification of nucleic acids, p. A8.9-A8.15. In J. Argentine (ed.), Molecular Cloning: a laboratory manual, Third ed, vol. 3. Cold Spring Harbor Laboratory Press, Cold Spring Harbor.]. The DNA pellets were dissolved in nuclease-free water, and samples were quantified and checked for purity using the Nanodrop® ND-1000 Spectrophotometer (Nanodrop, Wilmington, Del.).  TempliPhi™ reactions. Field isolate samples yielded low amounts of genomic DNA compared to strain 232 due to their fastidious growth and lack of adaptation to growth media. To overcome the issue of limited quantities of DNA, genomic samples were amplified using the TempliPhi™ 100 Reaction Kit (Amersham, Biosciences, Piscataway, N.J.) according to the manufacturer’s protocol. A total of five reactions were combined for each field isolate and strain 232, yielding approximately 5-8 µg total DNA in each preparation which was subjected to mechanical shearing.  Nebulization. The DNA was mechanically sheared prior to labeling to ensure an optimized fragment size for efficient labeling and hybridization. Each amplified sample was added to the modified nebulizer (product # 4100, MEDEX, Carlsbad, Calif.) containing 2 ml of sterile 50% glycerol. The nebulizer was modified by removing the plastic cuff, trimming the edge and inverting it during reassembly. The samples were sheared using a 10 psi nitrogen stream for 15 min. The fragment size of less than 1,000 base pairs was optimal for efficient labeling and signal strength. This was confirmed by gel electrophoresis on 1.5% agarose gel.

treatment_protocol: TempliPhi™ amplified DNA samples from field isolates were compared to control strain 232 using a two-color experimental microarray design. Independent samples from one isolate labeled with one dye were paired with control samples labeled with the alternate dye; the samples were mixed and hybridized to the microarray.

tag: Strain 232

source_name: Genomic DNA from strain 97MP0001

tag: Strain 97MP0001


title: 97MP0001-rep2

description: White light scanner. Biological replicate 2 of 4.


title: 97MP0001-rep3

description: White light scanner. Biological replicate 3 of 4.


title: 97MP0001-rep4

description: White light scanner. Biological replicate 4 of 4.


title: 95MP1510-rep3

description: Laser scanner. Biological replicate 3 of 4.

source_name: Genomic DNA from strain 95MP1510

tag: Strain 95MP1510


title: 95MP1510-rep1

description: Laser scanner. Biological replicate 1 of 4.


title: 95MP1510-rep2

description: Laser scanner. Biological replicate 2 of 4.


title: 95MP1510-rep4

description: Laser scanner. Biological replicate 4 of 4.


title: 95MP1509-rep3

source_name: Genomic DNA from strain 95MP1509

tag: Strain 95MP1509


title: 95MP1509-rep1


title: 95MP1508-rep4

source_name: Genomic DNA from strain 95MP1508

tag: Strain 95MP1508


title: 95MP1509-rep4


title: 95MP1507-rep5

description: Laser scanner. Biological replicate 5 of 5.

source_name: Genomic DNA from strain 95MP1507

tag: Strain 95MP1507


title: 95MP1506-rep3

description: Laser scanner. Biological replicate 3 of 5.

source_name: Genomic DNA from strain 95MP1506

tag: Strain 95MP1506


title: BAL slide 3 lower


title: 95MP1507-rep4

description: Laser scanner. Biological replicate 4 of 5.


title: 95MP1506-rep1

description: Laser scanner. Biological replicate 1 of 5.


title: 95MP1508-rep2


title: 95MP1506-rep2

description: Laser scanner. Biological replicate 2 of 5.


title: 95MP1505-rep5

source_name: Genomic DNA from strain 95MP1505

tag: Strain 95MP1505


title: 95MP1506-rep4


title: 95MP1507-rep3


title: 95MP1507-rep1


title: 95MP1505-rep3


title: 95MP1508-rep3


title: 95MP1506-rep5


title: 95MP1508-rep1


title: 95MP1505-rep4


title: 95MP1509-rep2


title: 95MP1505-rep1


title: 95MP1505-rep2


title: 95MP1504-rep3

source_name: Genomic DNA from strain 95MP1504

tag: Strain 95MP1504


title: 95MP1504-rep4


title: 95MP1504-rep1


title: 95MP1504-rep2


title: 95MP1503-rep3

source_name: Genomic DNA from strain 95MP1503

tag: Strain 95MP1503


title: 95MP1503-rep4


title: 95MP1502-rep4

source_name: Genomic DNA from strain 95MP1502

tag: Strain 95MP1502


title: 95MP1503-rep2


title: 95MP1503-rep1


title: 95MP1501-rep4

source_name: Genomic DNA from strain 95MP1501

tag: Strain 95MP1501


title: 95MP1502-rep1


title: 95MP1502-rep3


title: 95MP1501-rep1


title: 95MP1501-rep2


title: 95MP1502-rep2


title: 95MP1501-rep3


title: 05MP2301-rep4

source_name: Genomic DNA from strain 05MP2301

tag: Strain 05MP2301


title: 05MP2301-rep3


title: 05MP2301-rep1


title: 00MP1502-rep4

description: Laser scanner. Biological replicate 4 of 6.

source_name: Genomic DNA from strain 00MP1502

tag: Strain 00MP1502


title: 00MP1502-rep5

description: Laser scanner. Biological replicate 5 of 6.


title: 05MP2301-rep2


title: 00MP1502-rep6

description: Laser scanner. Biological replicate 6 of 6.


title: 00MP1502-rep2

description: Laser scanner. Biological replicate 2 of 6.


title: 00MP1502-rep3

description: Laser scanner. Biological replicate 3 of 6.


title: methylated DNA Immunoprecipitation/INPUT HCT116 DNMT1/3b doubleknockout (DKO) - array 2 of 2

first: Filipe

middle: Vicente

last: Jacinto

state: Madrid

address: C/ Melchor Fernández Almagro, 3,

department: Molecular Pathology

institute: CNIO

data_processing: LINEAR normalized, background subtracted data obtained from log10 of processed Red signal/processed Green signal. Agilent feature extraction software (version v8.1) was used.

source_name: methylated DNA immunoprecipitated

extract_protocol: DNA from the Methylated DNA Immunoprecipitation (MeDIP) as previously described (Weber et al. Nat Genet 2005)

tag: methyalted DNA immunoprecipitated from HCT116 DNMT1/3b doubleknockout (DKO)

source_name: Total Genomic DNA (INPUT)

tag: Total genomic from HCT116 DNMT1/3b doubleknockout (DKO)


title: methylated DNA Immunoprecipitation/INPUT HCT116 wild type- array 2 of 2

tag: methylated DNA immunoprecipitated from the HCT116 wild type

tag: Total genomic DNA from HCT116 wild type


title: 00MP1502-rep1

description: Laser scanner. Biological replicate 1 of 6.

tag: Strain 232


title: 00MP1301-rep2

source_name: Genomic DNA from strain 00MP1301

tag: Strain 00MP1301


title: 00MP1301-rep3

source_name: Genomic DNA from strain 232


title: 00MP1301-rep1


title: 00MP1301-rep4


title: Medial substantia nigra control case PDC1 - B chip

description: Gene expression data from medial substantia nigra (MNPDC1B)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45oC to a Human Genome 133 B array (HG_U133B; Affymetrix). The GeneChips was washed and stained in an Affymetrix Fluidics Station 400.  Standard Affymetrix Protocols were used  (Affymetrix GeneChip Expression Analysis Technical Manual, 2001).

source_name: Post-mortem medial substantia nigra

tag: age


title: Medial substantia nigra Parkinson's disease case 22 - B chip

description: Gene expression data from medial substantia nigra (MNPD22B)

value: 76; gender:F


title: Medial substantia nigra Parkinson's disease case 21 - B chip

description: Gene expression data from medial substantia nigra  (MNPD21B)

value: 75; gender:M


title: Medial substantia nigra Parkinson's disease case 07 - B chip

description: Gene expression data from medial substantia nigra (MNPD07B)


title: Medial substantia nigra Parkinson's disease case 04 - B chip

description: Gene expression data from medial substantia nigra  (MNPD04B)


title: LM2 lung metastatic cell + short hairpin control replicate A

city: new york

first: sohail

middle: f.

last: tavazoie

address: 1275 york avenue

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Institute

description: LM2 cells

hyb_protocol: 10 ug cRNA were hybridized to the affymetrix HG-U133 plus chips

scan_protocol: genechips were scanned using the Hewlett-packard genearray scanner

data_processing: median-normalized across chips

source_name: Breast Cancer cell line MDA-MB-231 derivative LM2

label_protocol: biotinylated cRNA were prepared from 10 ug of total RNA using the standard labeling techniques for affymetrix chips

extract_protocol: miRVANA total RNA isolation kit

tag: LM2 cell line is a highly lung metastatic derivative of the breast cancer cell line MDA-MB-231.  this line has been transduced with a control short hairpin vector


title: Medial substantia nigra Parkinson's disease case 32 - B chip

description: Gene expression data from medial substantia nigra (MNPD32B)

value: 89; gender:M


title: LM2 lung metastatic cell + short hairpin control replicate B

description: LM2 cell line is an in vivo derived lung metastatic derivative of the MDA-MB-231 cell line.  this LM2 cell line was transduced with a short hairpin control vector.

hyb_protocol: cRNA were hybridized to affymetrix HG-u133 plus array.

scan_protocol: Gene chips were scanned using HP Genearray scanner.

data_processing: median-normalized

source_name: breast cancer cell line MDA-MB-231 derivative LM2 line with short hairpin control

label_protocol: biotinylated cRNA were prepared from 10ug of total RNA using standard bioarray high yield RNA labeling kit.

extract_protocol: miRVANA total RNA extraction kit.

tag: breast cancer cell line


title: Medial substantia nigra Parkinson's disease case 09 - B chip

description: Gene expression data from medial substantia nigra (MNPD09B)


title: Medial substantia nigra Parkinson's disease case 10 - B chip

description: Gene expression data from medial substantia nigra (MNPD10B)


title: Medial substantia nigra disease-control case MS155 - B chip

description: Gene expression data from medial substantia nigra  (MNMS155B)


title: Medial substantia nigra Parkinson's disease case 16 - B chip

description: Gene expression data from medial substantia nigra (MNPD16B)


title: Medial substantia nigra Parkinson's disease case 34 - B chip

description: Gene expression data from medial substantia nigra (MNPD34B)


title: Medial substantia nigra Parkinson's disease case 29 - B chip

description: Gene expression data from medial substantia nigra (MNPD29B)


title: Medial substantia nigra control case 9 - B chip

description: Gene expression data from medial substantia nigra (MNCON9B)

value: 57; gender:M


title: Medial substantia nigra Parkinson's disease case 02 - B chip

description: Gene expression data from medial substantia nigra  (MNPD02B)

value: 83; gender:M


title: Medial substantia nigra Parkinson's disease case 28 - B chip

description: Gene expression data from medial substantia nigra (MNPD28B)


title: LM2 lung metastatic cell + mir335 replicate B

description: LM2 cell line is an in vivo derived lung metastatic derivative of the MDA-MB-231 cell line.  this LM2 cell line was transduced with miR-335 expression vector.

source_name: breast cancer derivative LM2 line expressing miR-335

tag: breast cancer cell line MDA-MB-231 derivative LM2 line transduced with miR-335 expression vector.


title: Medial substantia nigra control case 4 - B chip

description: Gene expression data from medial substantia nigra  (MNCON4B)


title: Medial substantia nigra Parkinson's disease case 36 - B chip

description: Gene expression data from medial substantia nigra (MNPD36B)


title: Medial substantia nigra control case 8 - B chip

description: Gene expression data from medial substantia nigra (MNCON8B)


title: Mesenchymal clone 15.6

type: mixed

city: Madison

first: Victor

last: Ruotti

state: WI

address: 425 Henry Mall

department: Biotechnology

institute: UW Madison

description: Total RNA from iPS clone was extracted using RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer's recommendations.

hyb_protocol: Hybridizations were performed in 3.6X SSC buffer with 35% formamide and 0.07% SDS at 42% C overnight.

scan_protocol: Arrays were washed, dried and scanned with the GenePix 4000B Scanner

data_processing: Gene Expression data was extracted using NimbleScan Software v2.3

source_name: Genomic DNA extracted from H1 Human Embryonic Stem Cells

label_protocol: Sonicated genomic DNA was primed with random octamers and labeled using Klenow in the present of 5-(3-aminoallyl)-dUTP

extract_protocol: Phenol/Chloroform Extraction

tag: Genomic DNA extracted from H1 ES cells

source_name: Mesenchymal clone 15.6

label_protocol: Total RNA was enriched for the polyA fraction using Oligotex mRNA Mini Kit (Qiagen). Enriched mRNA (250 ng) was primed using random hexamers and reversed transcribed using Superscript III (Invitrogen) in the presence of 5-(3-aminoallyl)-dUTP (Ambion).

extract_protocol: Qiagen on column kit

tag: Mesenchymal clone 15.5 derived from human Oct4 knock-in ES cell lines


title: Medial substantia nigra Parkinson's disease case 20 - B chip

description: Gene expression data from medial substantia nigra (MNPD20B)


title: LM2 lung metastatic cell + mir335 replicate A


title: Reprogramming human somatic cells to a pluripotent state 6.20SF Clone

source_name: iPS Clone 6.20 derived from mesenchymal clone 15.6

tag: Induced pluripotent stem cells from mesenchymal clone 15.6


title: Mesenchymal clone 15.11

tag: Genomic DNA extracted from H1 Human Embryonic Stem Cells

source_name: Mesenchymal clone 15.11


title: Mesenchymal clone 15.5

source_name: Mesenchymal clone 15.5


title: Mesenchymal clone 15.4

source_name: Mesenchymal clone 15.4

tag: Mesenchymal clone 15.4 derived from human Oct4 knock-in ES cell lines


title: Medial substantia nigra Parkinson's disease case 01 - B chip

description: Gene expression data from medial substantia nigra (MNPD01B)

value: 87; gender:F


title: Medial substantia nigra control case 10 - B chip

description: Gene expression data from medial substantia nigra (MNCON10B)


title: Reprogramming human somatic cells to a pluripotent state 6.19 SF Clone

source_name: iPS Clone 6.19 derived from mesenchymal clone 15.6


title: 95MP1507-rep2

description: Laser scanner. Biological replicate 2 of 5.

source_name: Genomic DNA from strain 95MP1507

tag: Strain 95MP1507


title: Medial substantia nigra control case 2  - B chip

description: Gene expression data from medial substantia nigra  (MNCON2B)

value: 77; gender:M


title: Lateral substantia nigra Parkinson's disease case 16 - B chip

description: Gene expression data from lateral substantia nigra (LNPD16B)

source_name: Post-mortem lateral substantia nigra


title: Lateral substantia nigra control case PDC1 - B chip

description: Gene expression data from lateral substantia nigra  (LNPDC1B)


title: Reprogramming human somatic cells to a pluripotent state 4.8SF Clone

source_name: iPS Clone 4.8 derived from mesenchymal clone 15.4

tag: Induced pluripotent stem cells from mesenchymal clone 15.4


title: Lateral substantia nigra Parkinson's disease case 29 - B chip

description: Gene expression data from lateral substantia nigra (LNPD29B)


title: Lateral substantia nigra Parkinson's disease case 10 - B chip

description: Gene expression data from lateral substantia nigra  (LNPD10B)


title: Lateral substantia nigra Parkinson's disease case 28 - B chip

description: Gene expression data from lateral substantia nigra (LNPD28B)


title: Medial substantia nigra control case 3 - B chip

description: Gene expression data from medial substantia nigra (MNCON3B)

value: 81; gender:M


title: Reprogramming human somatic cells to a pluripotent state 4.4SF Clone

source_name: iPS Clone 4.4 derived from mesenchymal clone 15.4


title: Lateral substantia nigra Parkinson's disease case 09 - B chip

description: Gene expression data from Lateral substantia nigra (LNPD09B)


title: Reprogramming human somatic cells to a pluripotent state 4.1SF Clone

source_name: iPS Clone 4.1 derived from mesenchymal clone 15.4


title: Reprogramming human somatic cells to a pluripotent state 114SF Clone

source_name: iPS Clone 11.4 derived from mesenchymal clone 15.11

tag: Induced pluripotent stem cells from mesenchymal clone 15.11


title: Reprogramming human somatic cells to a pluripotent state 1110SF Clone

source_name: iPS Clone 11.10 derived from mesenchymal clone 15.11


title: Lateral substantia nigra Parkinson's disease case 01 - B chip

description: Gene expression data from lateral substantia nigra  (LNPD01B)


title: Lateral substantia nigra disease-control case MS155 - B chip

description: Gene expression data from lateral substantia nigra (MS155B)

value: 80; gender:F


title: Lateral substantia nigra Parkinson's disease case 04 - B chip

description: Gene expression data from lateral substantia nigra  (LNPD04B)

value: 68; gender:M


title: Reprogramming human somatic cells to a pluripotent state (5.7SF Clone)

source_name: iPS Clone 5.7 derived from mesenchymal clone 15.5

tag: Induced pluripotent stem cells from mesenchymal clone 15.5


title: Lateral substantia nigra Parkinson's disease case 02 - B chip

description: Gene expression data from lateral substantia nigra  (LNPD02B)


title: Reprogramming human somatic cells to a pluripotent state  5.11SF Clone

description: Total RNA from iPS clone was extracted using RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer's recommendations.

source_name: iPS Clone 5.11 derived from mesenchymal clone 15.5


title: Reprogramming human somatic cells to a pluripotent state 111SF Clone

source_name: iPS Clone 11.1 derived from mesenchymal clone 15.11


title: UC colon repl2

city: Cincinnati

first: Lee

last: Denson

state: OH

address: 3333 Burnet Avenue

institute: CCHMC

description: gene expression data from human colon

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

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000.

data_processing: The data were analyzed with GeneSpring version 7.3 using RMA normalization with a custom CDF file(Hs133P_Hs_REFSEQ_8), then normalized to the batch-specific '107' internal control (see Series record for the '107' CEL files)

source_name: human colon

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA  amplified with TargetAmp 1-round Aminoallyl-aRNA Amplication Kit 101 (Epicentre, WI) (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNeasy Plus Mini kit (QIAGEN, Hilden, Germany)

tag: UC replicate sample

tag: batch 4


title: UC colon repl3

description: gene expression data from human colon


title: Reprogramming human somatic cells to a pluripotent state (5.5 SF Clone)

source_name: Genomic DNA extracted from H1 Human Embryonic Stem Cells

source_name: iPS Clone 5.5 derived from mesenchymal clone 15.5


title: Lateral substantia nigra Parkinson's disease case 07 - B chip

description: Gene expression data from lateral substantia nigra  (LNPD07B)


title: Reprogramming human somatic cells to a pluripotent state 6.8SF Clone

source_name: iPS Clone 6.8 derived from mesenchymal clone 15.6


title: Lateral substantia nigra control case 2 - B chip

description: Gene expression data from lateral substantia nigra  (LNCon2B)


title: Lateral substantia nigra control case 4 - B chip

description: Gene expression data from lateral substantia nigra (LNCon4B)

value: 77; gender:F


title: Treated CD colon repl8

description: gene expression data from human colon

tag: treated CD replicate sample

tag: batch 3


title: Lateral substantia nigra control case 10 - B chip

description: Gene expression data from lateral substantia nigra  (LNCon10B)

tag: age


title: Superior frontal gyrus Parkinson's disease case 34 - B chip

description: Gene expression data from superior frontal gyrus (CxPD34B)

source_name: Post mortem superior frontal gyrus


title: Treated CD colon repl6

description: gene expression data from human colon


title: Treated CD colon repl7

description: gene expression data from human colon


title: Treated CD colon repl4

description: gene expression data from human colon


title: Superior frontal gyrus Parkinson's disease case 04 - B chip

description: Gene expression data from superior frontal gyrus (CxPD04B)


title: UC colon repl5

description: gene expression data from human colon


title: Lateral substantia nigra control case 9 - B chip

description: Gene expression data from lateral substantia nigra  (LNCon9B)


title: UC colon repl1

description: gene expression data from human colon


title: Superior frontal gyrus Parkinson's disease case 36 - B chip

description: Gene expression data from superior frontal gyrus (CxPD36B)

value: 76; gender:M


title: Superior frontal gyrus Parkinson's disease case 29 - B chip

description: Gene expression data from superior frontal gyrus (CxPD29B)


title: Superior frontal gyrus Parkinson's disease case 01 - B chip

description: Gene expression data from superior frontal gyrus (CxPD01B)


title: Treated CD colon repl3

description: gene expression data from human colon


title: Lateral substantia nigra control case 8 - B chip

description: Gene expression data from lateral substantia nigra  (LNCon8B)

value: 46; gender:M


title: Superior frontal gyrus control case 9 - B chip

description: Gene expression data from superior frontal gyrus (CxCON9B)


title: Treated CD colon repl2

description: gene expression data from human colon


title: Treated CD colon repl5

description: gene expression data from human colon


title: Treated CD colon repl1

description: gene expression data from human colon


title: Superior frontal gyrus control case 2 - B chip

description: Gene expression data from superior frontal gyrus (CxCON2B)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45oC to a Human Genome 133 B array (HG_U133B; Affymetrix). The GeneChips was washed and stained in an Affymetrix Fluidics Station 400.  Standard Affymetrix protocols were used  (Affymetrix GeneChip Expression Analysis Technical Manual, 2001).


title: CD colon repl11

description: gene expression data from human colon

tag: CD replicate sample

tag: batch 1


title: CD colon repl10

description: gene expression data from human colon


title: CD colon repl8

description: gene expression data from human colon


title: CD colon repl6

description: gene expression data from human colon


title: CD colon repl9

description: gene expression data from human colon


title: CD colon repl3

description: gene expression data from human colon


title: Superior frontal gyrus control case 3 - B chip

description: Gene expression data from superior frontal gyrus (CxCON3B)


title: CD colon repl5

description: gene expression data from human colon


title: REF colon repl8

description: gene expression data from human colon

tag: healthy control reference sample


title: CD colon repl7

description: gene expression data from human colon

tag: batch 2


title: CD colon repl4

description: gene expression data from human colon


title: CD colon repl1

description: gene expression data from human colon


title: REF colon repl4

description: gene expression data from human colon


title: CD colon repl2

description: gene expression data from human colon


title: REF colon repl6

description: gene expression data from human colon


title: REF colon repl5

description: gene expression data from human colon


title: REF colon repl7

description: gene expression data from human colon


title: REF colon repl3

description: gene expression data from human colon


title: Wild-type_Mm-infected_rep2_10748

city: Chapel Hill

first: John

middle: F

last: Rawls

state: NC

address: 111 Mason Farm Rd.

department: Department of Cell and Molecular Physiology

institute: University of North Carolina at Chapel Hill

description: Whole 6dpf zebrafish larvae infected with Mycobacterium marinum wild-type strain at 1dpf

hyb_protocol: Hybridization performed using standard Affymetrix protocol available at http://www.affymetrix.com/support/technical/manuals.affx

scan_protocol: Scanning performed using standard Affymetrix protocol available at http://www.affymetrix.com/support/technical/manuals.affx

data_processing: Raw expression values were normalized (Invariant set method) and modelled (PM-MM model), and present/absent calls were generated using dChip software (build date Dec.11, 2005).

organism: Danio rerio

label_protocol: Total RNA from each replicate pool (12ug RNA/replicate) was used as template for independent cDNA synthesis and in vitro transcription reactions (BioArray HighYield RNA Transcript Labeling Kit; Enzo Life Sciences) to generate biotinylated cRNA targets. cRNA targets (30ug/replicate) were fragmented using standard methods. For detailed protocols, see http://pathimm.wustl.edu/~mgacore/protocols.htm

extract_protocol: Total RNA was purified from pooled intact zebrafish larvae (31-82 larvae/pool, 3 biological replicate pools/condition) using Trizol reagent (Invitrogen) followed by DNase I digestion (DNA-Free, Ambion) according to manufacturers' protocols.

tag: Strain

value: AB, Age:6 days post-fertilization (6dpf), Tissue:whole larvae, Rearing conditions:conventional, Microbial status:infected with Mycobacterium marinum wild-type strain, Days post-infection:5, Replicate:2 of 3


title: REF colon repl1

description: gene expression data from human colon

data_processing: The data were analyzed with GeneSpring version 7.3 using RMA normalization with a custom CDF file(Hs133P_Hs_REFSEQ_8), then normalized to the batch-specific '107' internal control (see Series record for the '107' CEL files).


title: Uninfected_rep3_10755

description: Whole 6dpf uninfected zebrafish larvae

source_name: Whole 6dpf uninfected zebrafish larvae

value: AB, Age:6 days post-fertilization (6dpf), Tissue:whole larvae, Rearing conditions:conventional, Microbial status:uninfected, Replicate:3 of 3


title: Mock-infected_rep2_10757

description: Whole 6dpf zebrafish larvae mock-infected at 1dpf

value: AB, Age:6 days post-fertilization (6dpf), Tissue:whole larvae, Rearing conditions:conventional, Microbial status:mock-infected, Days post-infection:5, Replicate:2 of 3


title: Uninfected_rep1_10753

description: Whole 6dpf uninfected zebrafish larvae

value: AB, Age:6 days post-fertilization (6dpf), Tissue:whole larvae, Rearing conditions:conventional, Microbial status:uninfected, Replicate:1 of 3


title: Wild-type_Mm-infected_rep3_10749

source_name: Whole 6dpf zebrafish larvae infected with Mycobacterium marinum wild-type strain at 1dpf

value: AB, Age:6 days post-fertilization (6dpf), Tissue:whole larvae, Rearing conditions:conventional, Microbial status:infected with Mycobacterium marinum wild-type strain, Days post-infection:5, Replicate:3 of 3


title: Wild-type_Mm-infected_rep1_10747

value: AB, Age:6 days post-fertilization (6dpf), Tissue:whole larvae, Rearing conditions:conventional, Microbial status:infected with Mycobacterium marinum wild-type strain, Days post-infection:5, Replicate:1 of 3


title: Mock-infected_rep1_10756

source_name: Whole 6dpf zebrafish larvae mock-infected at 1dpf

value: AB, Age:6 days post-fertilization (6dpf), Tissue:whole larvae, Rearing conditions:conventional, Microbial status:mock-infected, Days post-infection:5, Replicate:1 of 3


title: methylated DNA Immunoprecipitation/INPUT HCT116 DNMT1/3b doubleknockout (DKO) - array 1of 2

source_name: methylated DNA immunoprecipitated

tag: methyalted DNA immunoprecipitated from HCT116 DNMT1/3b doubleknockout (DKO)

source_name: Total Genomic DNA (INPUT)

tag: Total genomic from HCT116 DNMT1/3b doubleknockout (DKO)


title: Uninfected_rep2_10754

description: Whole 6dpf uninfected zebrafish larvae

value: AB, Age:6 days post-fertilization (6dpf), Tissue:whole larvae, Rearing conditions:conventional, Microbial status:uninfected, Replicate:2 of 3


title: Mock-infected_rep3_10758

value: AB, Age:6 days post-fertilization (6dpf), Tissue:whole larvae, Rearing conditions:conventional, Microbial status:mock-infected, Days post-infection:5, Replicate:3 of 3


title: REF colon repl2

description: gene expression data from human colon


title: methylated DNA Immunoprecipitation/INPUT HCT116 wild type - array 1 of 2

tag: methylated DNA immunoprecipitated from the HCT116 wild type

tag: Total genomic DNA from HCT116 wild type


title: stage13_control_Rep3

status: Public on Dec 31 2007

city: Cardiff

first: Michael

middle: Victor

last: Taylor

state: S. Glam

address: Main Building, Park Place

department: School of Biosciences

institute: Cardiff University

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45ºC on Affymetrix GeneChip Drosophila Genome 1 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data were processed and normalised using MAS5.0 algorithm

organism: Drosophila melanogaster

source_name: Whole embryo Stage 13 control Dp cn a px sp

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

growth_protocol: Flies were raised in standard conditions.  Embryo collections were as follows.  Following 2 x 1 hour prelays, 30 minute embryo collections were aged at 25ºC for 6.5 hours prior to sorting.  Mutant embryos were individually selected by absence of the GFP fluorescent balancer chromosome (CyO P(Gal4-twi)P(UAS-2eGFP)).  Both mutant and control embryos were accurately staged at mid 12 using autofluorescence to visualise the germ band to ensure that all were within a 30-minute window.  Pools of 150 embryos were allowed to develop until mid stage 13, dechorionated, inspected to ensure normal development had continued.

extract_protocol: Total RNA was extracted using TriZol (Invitrogen) and cleaned up by RNeasy mini-kit (Qiagen) according to the manufacturer's instructions

treatment_protocol: The staged, dechorionated stage 13 embryos were immediately homogenised in TriZol prior to storage at –80ºC.

tag: Age

value: Stage 13, Tissue:Whole embryo


title: stage13_mef2(Null)_Rep2

description: Drosophila_embryo_stage13_mef2(Null)_Rep2

source_name: Whole embryo Stage 13 mef2(22.21) Allele


title: stage13_control_Rep1


title: stage13_mef2(Null)_Rep4

description: Drosophila_embryo_stage13_mef2(Null)_Rep4


title: stage13_mef2(424)_Rep3

description: Drosophila_embryo_stage13_mef2(424)_Rep3

source_name: Whole embryo Stage 13 mef2(424) Allele


title: stage13_mef2(113)_Rep2

description: Drosophila_embryo_stage13_mef2(113)_Rep2

source_name: Whole embryo Stage 13 mef2(113) Allele


title: stage13_mef2(113)_Rep4

description: Drosophila_embryo_stage13_mef2(113)_Rep4


title: stage13_mef2(Null)_Rep1

description: Drosophila_embryo_stage13_mef2(Null)_Rep1


title: stage13_control_Rep4


title: stage13_mef2(113)_Rep1

description: Drosophila_embryo_stage13_mef2(113)_Rep1


title: stage13_mef2(424)_Rep2

description: Drosophila_embryo_stage13_mef2(424)_Rep2


title: stage13_mef2(113)_Rep3

description: Drosophila_embryo_stage13_mef2(113)_Rep3


title: stage13_mef2(Null)_Rep3

description: Drosophila_embryo_stage13_mef2(Null)_Rep3


title: Y/W_Female_Drosophila melanogaster_Acetone_topical_Replicate2

city: Guelph

first: Andreas

last: Heyland

state: ON

address: 50 Stone Rd East

department: Integrative Biology

country: Canada

institute: University of Guelph

description: A study to look at the antagonistic effects of JH and 20E on the expression of antimicrobial peptides (AMPs) in Drosophila.

hyb_protocol: Standard Affymetrix Protocol

scan_protocol: Standard Affymetrix Protocol

data_processing: Expression data were analyzed for significant over- or underrepresentation of gene ontology (GO) terms with the web application FatiGO (Al-Shahrour et al., 2004), using a two-fold change criterion. To test whether JH treatment significantly suppresses expression of AMPs we used t-tests implemented in JMP IN 5.1. (SAS Institute; Sall et al., 2004).

label_protocol: Standard Affymetrix Protocol

growth_protocol: Flies were grown on regular yeast diet, switched to no-yeast food within one hour of eclosion, and yeast-starved for 5 days posteclosion to lower their endogenous JH titer and to synchronize their physiology (cf. Tu and Tatar, 2003; Gershman et al., 2007).

extract_protocol: Trizole/Chloroform extraction

treatment_protocol: We anesthetized flies on ice and topically treated them with 0.1 microliter of 187 mM JH III in acetone or with 0.1? microliter 100% acetone (control) using a 1 ul Hamilton syringe with a repeating dispenser. 12 hours after hormone administration, samples were snap-frozen in liquid nitrogen and stored at -80°C. RNA was isolated from samples (2 JH samples, 2 control samples, each with 30 females) by lysis, as described in Gershman et al. (2007). cDNA products were hybridized at the Brown University Genomics Core Facility to Affymetrix GeneChip Drosophila_1 Genome Arrays (2 replicate chips per treatment). The dataset consisted of 14,009 probe sets, with 6,142 probe sets annotated. Expression data were analyzed for significant over- or underrepresentation of gene ontology (GO) terms with the web application FatiGO (Al-Shahrour et al., 2004), using a two-fold change criterion

value: y,w Sex:females Stage:Adult Other:Flies were grown on regular yeast diet, switched to no-yeast food within one hour of eclosion, and yeast-starved for 5 days posteclosion


title: stage13_mef2(424)_Rep4

description: Drosophila_embryo_stage13_mef2(424)_Rep4


title: Y/W_Female_Drosophila melanogaster_JHIII_topical_Replicate2


title: stage13_mef2(65)_Rep4

source_name: Whole embryo Stage 13 mef2(65) Allele


title: stage13_control_Rep2


title: stage13_mef2(65)_Rep3


title: Y/W_Female_Drosophila melanogaster_JHIII_topical_Replicate1


title: stage13_mef2(65)_Rep2


title: stage13_mef2(65)_Rep1


title: UC colon repl4

description: gene expression data from human colon