title: NA12056 growth 2.

description: Probeset expression data from NA12056 growth 2

source_name: CEU NA12056 Biological Growth 2

tag: Coriell cell line repository identifier:GM12056


title: NA12056 growth 3.

status: Public on Jan 13 2008

type: RNA

city: Montreal

first: Tony

last: Kwan

state: Quebec

address: 740 Dr. Penfield

department: Human Genetics

country: Canada

institute: McGill University

description: Probeset expression data from NA12056 growth 3

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16-20 hr at 45C on GeneChip Human Exon 1.0 ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Affymetrix Power Tools package using Affymetrix default analysis settings and sketch quantile as normalization method.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: CEU NA12056 Biological Growth 3

label_protocol: Biotinlabelled target for the microarray experiment were prepared using 1 ug of total RNA. The RNA was subjected to a rRNA removal procedure with the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen) and cDNA was synthesized using the GeneChip® WT (Whole Transcript) Sense Target Labeling and Control Reagents kit as described by the manufacturer (Affymetrix).

growth_protocol: Cells were grown at 37°C and 5% CO2 in RPMI 1640 medium supplemented with 15% heat-inactivated fetal bovine serum, 2 mM L-glutamine and penicillin/streptomycin

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

treatment_protocol: Cells were harvested at a density of 0.8-1.1 x 10e6 cells/mL. Cells were then resuspended and lysed in TRIzol reagent

tag: Gender

value: male, Cell-type:lymphoblasts


title: NA12044 growth 2.

description: Probeset expression data from NA12044 growth 2

source_name: CEU NA12044 Biological Growth 2

value: female, Cell-type:lymphoblasts

tag: Coriell cell line repository identifier:GM12044


title: NA12144 growth 1.

description: Probeset expression data from NA12144 growth 1

source_name: CEU NA12144 Biological Growth 1

tag: Coriell cell line repository identifier:GM12144


title: NA12144 growth 2.

description: Probeset expression data from NA12144 growth 2

source_name: CEU NA12144 Biological Growth 2


title: NA12044 growth 1.

description: Probeset expression data from NA12044 growth 1

source_name: CEU NA12044 Biological Growth 1


title: NA12043 growth 3.

description: Probeset expression data from NA12043 growth 3

source_name: CEU NA12043 Biological Growth 3

tag: Coriell cell line repository identifier:GM12043


title: NA12056 growth 1.

description: Probeset expression data from NA12056 growth 1

source_name: CEU NA12056 Biological Growth 1


title: NA12057 growth 1.

description: Probeset expression data from NA12057 growth 1

source_name: CEU NA12057 Biological Growth 1

tag: Coriell cell line repository identifier:GM12057


title: NA12006 growth 1.

description: Probeset expression data from NA12006 growth 1

source_name: CEU NA12006 Biological Growth 1

tag: Coriell cell line repository identifier:GM12006


title: NA12005 growth 3.

description: Probeset expression data from NA12005 growth 3

source_name: CEU NA12005 Biological Growth 3

tag: Coriell cell line repository identifier:GM12005


title: NA12057 growth 2.

description: Probeset expression data from NA12057 growth 2

source_name: CEU NA12057 Biological Growth 2


title: NA12043 growth 2.

description: Probeset expression data from NA12043 growth 2

source_name: CEU NA12043 Biological Growth 2


title: NA12005 growth 1.

description: Probeset expression data from NA12005 growth 1

source_name: CEU NA12005 Biological Growth 1


title: NA12003 growth 2.

description: Probeset expression data from NA12003 growth 2

source_name: CEU NA12003 Biological Growth 2

tag: Coriell cell line repository identifier:GM12003


title: NA12044 growth 3.

description: Probeset expression data from NA12044 growth 3

source_name: CEU NA12044 Biological Growth 3


title: NA12004 growth 3.

description: Probeset expression data from NA12004 growth 3

source_name: CEU NA12004 Biological Growth 3

tag: Coriell cell line repository identifier:GM12004


title: NA12043 growth 1.

description: Probeset expression data from NA12043 growth 1

source_name: CEU NA12043 Biological Growth 1


title: NA12004 growth 1.

description: Probeset expression data from NA12004 growth 1

source_name: CEU NA12004 Biological Growth 1


title: NA11995 growth 3.

description: Probeset expression data from NA11995 growth 3

source_name: CEU NA11995 Biological Growth 3

tag: Coriell cell line repository identifier:GM11995


title: NA12004 growth 2.

description: Probeset expression data from NA12004 growth 2

source_name: CEU NA12004 Biological Growth 2


title: NA12006 growth 2.

description: Probeset expression data from NA12006 growth 2

source_name: CEU NA12006 Biological Growth 2


title: NA12003 growth 3.

description: Probeset expression data from NA12003 growth 3

source_name: CEU NA12003 Biological Growth 3


title: NA11995 growth 1.

description: Probeset expression data from NA11995 growth 1

source_name: CEU NA11995 Biological Growth 1


title: NA11995 growth 2.

description: Probeset expression data from NA11995 growth 2

source_name: CEU NA11995 Biological Growth 2


title: NA12005 growth 2.

description: Probeset expression data from NA12005 growth 2

source_name: CEU NA12005 Biological Growth 2


title: NA11994 growth 3.

description: Probeset expression data from NA11994 growth 3

source_name: CEU NA11994 Biological Growth 3

tag: Coriell cell line repository identifier:GM11994


title: NA12003 growth 1.

description: Probeset expression data from NA12003 growth 1

source_name: CEU NA12003 Biological Growth 1


title: NA12057 growth 3.

description: Probeset expression data from NA12057 growth 3

source_name: CEU NA12057 Biological Growth 3


title: NA11994 growth 2.

description: Probeset expression data from NA11994 growth 2

source_name: CEU NA11994 Biological Growth 2


title: NA11994 growth 1.

description: Probeset expression data from NA11994 growth 1

source_name: CEU NA11994 Biological Growth 1


title: NA11992 growth 3.

description: Probeset expression data from NA11992 growth 3

source_name: CEU NA11992 Biological Growth 3

tag: Coriell cell line repository identifier:GM11992


title: NA11993 growth 3.

description: Probeset expression data from NA11993 growth 3

source_name: CEU NA11993 Biological Growth 3

tag: Coriell cell line repository identifier:GM11993


title: NA11993 growth 2.

description: Probeset expression data from NA11993 growth 2

source_name: CEU NA11993 Biological Growth 2


title: NA11993 growth 1.

description: Probeset expression data from NA11993 growth 1

source_name: CEU NA11993 Biological Growth 1


title: NA11882 growth 3.

description: Probeset expression data from NA11882 growth 3

source_name: CEU NA11882 Biological Growth 3

tag: Coriell cell line repository identifier:GM11882


title: NA11882 growth 2.

description: Probeset expression data from NA11882 growth 2

source_name: CEU NA11882 Biological Growth 2


title: NA11992 growth 1.

description: Probeset expression data from NA11992 growth 1

source_name: CEU NA11992 Biological Growth 1


title: NA11832 growth 2.

description: Probeset expression data from NA11832 growth 2

source_name: CEU NA11832 Biological Growth 2

tag: Coriell cell line repository identifier:GM11832


title: NA11839 growth 2.

description: Probeset expression data from NA11839 growth 2

source_name: CEU NA11839 Biological Growth 2

tag: Coriell cell line repository identifier:GM11839


title: NA11840 growth 1.

description: Probeset expression data from NA11840 growth 1

source_name: CEU NA11840 Biological Growth 1

tag: Coriell cell line repository identifier:GM11840


title: NA11840 growth 2.

description: Probeset expression data from NA11840 growth 2

source_name: CEU NA11840 Biological Growth 2

tag: Gender


title: NA11831 growth 2.

description: Probeset expression data from NA11831 growth 2

source_name: CEU NA11831 Biological Growth 2

tag: Coriell cell line repository identifier:GM11831


title: NA11882 growth 1.

description: Probeset expression data from NA11882 growth 1

source_name: CEU NA11882 Biological Growth 1


title: NA11840 growth 3.

description: Probeset expression data from NA11840 growth 3

source_name: CEU NA11840 Biological Growth 3


title: NA11830 growth 2.

description: Probeset expression data from NA11830 growth 2

source_name: CEU NA11830 Biological Growth 2

tag: Coriell cell line repository identifier:GM11830


title: NA11831 growth 3.

description: Probeset expression data from NA11831 growth 3

source_name: CEU NA11831 Biological Growth 3


title: NA11831 growth 1.

description: Probeset expression data from NA11831 growth 1

source_name: CEU NA11831 Biological Growth 1


title: NA11832 growth 1.

description: Probeset expression data from NA11832 growth 1

source_name: CEU NA11832 Biological Growth 1


title: NA11839 growth 1.

description: Probeset expression data from NA11839 growth 1

source_name: CEU NA11839 Biological Growth 1


title: NA11881 growth 2.

description: Probeset expression data from NA11881 growth 2

source_name: CEU NA11881 Biological Growth 2

tag: Coriell cell line repository identifier:GM11881


title: NA11832 growth 3.

description: Probeset expression data from NA11832 growth 3

source_name: CEU NA11832 Biological Growth 3


title: NA11881 growth 3.

description: Probeset expression data from NA11881 growth 3

source_name: CEU NA11881 Biological Growth 3


title: NA11830 growth 1.

description: Probeset expression data from NA11830 growth 1

source_name: CEU NA11830 Biological Growth 1


title: NA11839 growth 3.

description: Probeset expression data from NA11839 growth 3

source_name: CEU NA11839 Biological Growth 3


title: NA11829 growth 3.

description: Probeset expression data from NA11829 growth 3

source_name: CEU NA11829 Biological Growth 3

tag: Coriell cell line repository identifier:GM11829


title: NA11992 growth 2.

description: Probeset expression data from NA11992 growth 2

source_name: CEU NA11992 Biological Growth 2


title: NA11881 growth 1.

description: Probeset expression data from NA11881 growth 1

source_name: CEU NA11881 Biological Growth 1


title: NA11830 growth 3.

description: Probeset expression data from NA11830 growth 3

source_name: CEU NA11830 Biological Growth 3


title: NA11829 growth 1.

description: Probeset expression data from NA11829 growth 1

source_name: CEU NA11829 Biological Growth 1


title: NA07357 growth 3.

description: Probeset expression data from NA07357 growth 3

source_name: CEU NA07357 Biological Growth 3

tag: Coriell cell line repository identifier:GM07357


title: NA07357 growth 2.

description: Probeset expression data from NA07357 growth 2

source_name: CEU NA07357 Biological Growth 2


title: NA07345 growth 1.

description: Probeset expression data from NA07345 growth 1

source_name: CEU NA07345 Biological Growth 1

tag: Coriell cell line repository identifier:GM07345


title: NA11829 growth 2.

description: Probeset expression data from NA11829 growth 2

source_name: CEU NA11829 Biological Growth 2


title: NA07357 growth 1.

description: Probeset expression data from NA07357 growth 1

source_name: CEU NA07357 Biological Growth 1


title: NA07056 growth 1.

description: Probeset expression data from NA07056 growth 1

source_name: CEU NA07056 Biological Growth 1

tag: Coriell cell line repository identifier:GM07056


title: NA07055 growth 3.

description: Probeset expression data from NA07055 growth 3

source_name: CEU NA07055 Biological Growth 3

tag: Coriell cell line repository identifier:GM07055


title: NA07345 growth 3.

description: Probeset expression data from NA07345 growth 3

source_name: CEU NA07345 Biological Growth 3


title: Control rat number 11

city: Angers

first: Matthieu

last: Arvier

address: 4 rue larrey

department: UMR 694

country: France

institute: INSERM

hyb_protocol: Samples were applied to microarrays enclosed in Telechem hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Perkinhelmer 4000 Scanner. Images were quantified using Perkin elmer ScanArray® Express Software

data_processing: LOWESS normalized. Genspring GX 7.3 software was used.

organism: Rattus norvegicus

source_name: Total RNA from control rats labelled with Cyanine-5 (red).

label_protocol: tRNA extractions were prepared using the Amino Allyl MessageAmpII aRNA Amplification Kit (Ambion, 1753) and  labeled individually with Cy3 or Cy5 (Amersham).

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: Age

value: week 13

source_name: Total RNA from pooled control rats tRNA labeled with Cyanine-3 (green).


title: NA07056 growth 3.

description: Probeset expression data from NA07056 growth 3

source_name: CEU NA07056 Biological Growth 3


title: Control rat number 7


title: NA07034 growth 3.

description: Probeset expression data from NA07034 growth 3

source_name: CEU NA07034 Biological Growth 3

tag: Coriell cell line repository identifier:GM07034


title: NA07034 growth 2.

description: Probeset expression data from NA07034 growth 2

source_name: CEU NA07034 Biological Growth 2


title: NA07055 growth 1.

description: Probeset expression data from NA07055 growth 1

source_name: CEU NA07055 Biological Growth 1


title: NA07055 growth 2.

description: Probeset expression data from NA07055 growth 2

source_name: CEU NA07055 Biological Growth 2


title: NA07056 growth 2.

description: Probeset expression data from NA07056 growth 2

source_name: CEU NA07056 Biological Growth 2


title: NA07034 growth 1.

description: Probeset expression data from NA07034 growth 1

source_name: CEU NA07034 Biological Growth 1


title: Control rat number 3


title: Control rat number 5


title: Control rat number 6


title: Control rat number 12


title: Control rat number 10


title: Control rat number 4


title: Dexamethasone treated rat number 10

source_name: Total RNA from dexamethasone treated rats labelled with Cyanine-5 (red).


title: NA07022 growth 3.

description: Probeset expression data from NA07022 growth 3

source_name: CEU NA07022 Biological Growth 3

tag: Coriell cell line repository identifier:GM07022


title: NA07345 growth 2.

description: Probeset expression data from NA07345 growth 2

source_name: CEU NA07345 Biological Growth 2


title: Control rat number 8


title: NA07022 growth 1.

description: Probeset expression data from NA07022 growth 1

source_name: CEU NA07022 Biological Growth 1


title: NA07000 growth 3.

description: Probeset expression data from NA07000 growth 3

source_name: CEU NA07000 Biological Growth 3

tag: Coriell cell line repository identifier:GM07000


title: Control rat number 9


title: NA07022 growth 2.

description: Probeset expression data from NA07022 growth 2

source_name: CEU NA07022 Biological Growth 2


title: NA07000 growth 2.

description: Probeset expression data from NA07000 growth 2

source_name: CEU NA07000 Biological Growth 2


title: Control rat number 1


title: Dexamethasone treated rat number 8


title: Dexamethasone treated rat number 9


title: Dexamethasone treated rat number 6


title: NA06993 growth 3.

description: Probeset expression data from NA06993 growth 3

source_name: CEU NA06993 Biological Growth 3

tag: Coriell cell line repository identifier:GM06993


title: NA07000 growth 1.

description: Probeset expression data from NA07000 growth 1

source_name: CEU NA07000 Biological Growth 1


title: Dexamethasone treated rat number 5

source_name: Total RNA from pooled control rats tRNA labeled with Cyanine-3 (green).


title: NA06993 growth 2.

description: Probeset expression data from NA06993 growth 2

source_name: CEU NA06993 Biological Growth 2


title: NA06994 growth 2.

description: Probeset expression data from NA06994 growth 2

source_name: CEU NA06994 Biological Growth 2

tag: Coriell cell line repository identifier:GM06994


title: Dexamethasone treated rat number 4


title: Dexamethasone treated rat number 3


title: Dexamethasone treated rat number 1


title: Control rat number 2

source_name: Total RNA from control rats labelled with Cyanine-5 (red).


title: Dexamethasone treated rat number 2


title: NA06985 growth 3.

description: Probeset expression data from NA06985 growth 3

source_name: CEU NA06985 Biological Growth 3

tag: Coriell cell line repository identifier:GM06985


title: NA06994 growth 1.

description: Probeset expression data from NA06994 growth 1

source_name: CEU NA06994 Biological Growth 1


title: NA06994 growth 3.

description: Probeset expression data from NA06994 growth 3

source_name: CEU NA06994 Biological Growth 3


title: NA06985 growth 2.

description: Probeset expression data from NA06985 growth 2

source_name: CEU NA06985 Biological Growth 2


title: NA06993 growth 1.

description: Probeset expression data from NA06993 growth 1

source_name: CEU NA06993 Biological Growth 1


title: NA06985 growth 1.

description: Probeset expression data from NA06985 growth 1

source_name: CEU NA06985 Biological Growth 1


title: 3T3-L1 adipocyte tissue culture, LA treated, T2, biological rep4

status: Public on Jan 11 2008

city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

country: USA

institute: University of Nebraska-Lincoln

description: 3T3-L1 RNA treated with cis-9,trans-11 CLA and control samples at different time points

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C, refer to GeneChip Expression Analysis Technical Manual (www.affymetrix.com). GeneChips were washed and stained with streptavidin-phycoerythrin conjugate on an Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G; Pixel size: 1.56 um; Filter: 570 nm

data_processing: The data was analysed using Rosetta Resolver 6.0, creating ratio-experiments  for each timepoint using control reps as one pool, and treatment reps as the other pool.  Resulting logratios and p-values are calculated using Rosetta's proprietary ratio error model.

organism: Mus musculus

source_name: 3T3-L1 adipocyte tissue culture, LA, 12 hours

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (reaction at 37C for 16h) from 15 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

tag: cell line:3T3-L1


title: BioRep C control 120h

city: Davis

first: Enid

middle: T

last: Gonzalez

state: CA

address: One Shields Drive

department: Crops Pathology and Genetics Research Unit

institute: USDA-Agricultural Research Service

hyb_protocol: see supplementary PDF file on GSE9005

scan_protocol: see supplementary PDF file on GSE9005

data_processing: see supplementary PDF file on GSE9005

organism: Pseudomonas putida KT2440

source_name: Bacterial cells

label_protocol: 10 ug of total DNAse treated RNA was reverse transcribed into double stranded cDNA Invitrogen's Double Stranded cDNA synthesis kit.  All double stranded cDNA  samples were treated with RNAseA and cleaned-up using Qiagen MinElute columns.  cDNA was quantitated on a DU800 spectrophotometer and run on an agarose gel prior to submission. NimbleGen Systems labeled the double stranded cDNA according to their protocols.

growth_protocol: All treatments were grown in a Conviron Growth Chamber set to 22C, 16 hour day/8 hour night, and 70% humidity.  Both plants & bacteria were cultivated on 1/2 M9 medium ammended with 1% glucose.

extract_protocol: The Ambion RiboPure Bacteria kit was used to isolate total RNA from P. putida cells scraped from 1/2 M9 +1% glucose plates with or without plants present.  Total RNA was precipitated with 7.5 M LiCL and treated with DNAse (Ambion TurboDNase).  Care was taken to eliminate all residual DNA.  Traditional PCR was used to detect contaminating DNA.  All RNA samples were anayled using denatuing agaraose gel electrophoresis, and quantified using a DU800 Spectrophotometer.  Also, RNA integrity was assessed used the Agilent Bioanalyzer prior to further processing.

treatment_protocol: Prior to RNA extraction, P. putida KT2440 cells were scraped from either 1/2 M9 + 1% glucose plates with or without plants.  The scraped cell mass was resuspended in 4 ml of Qiagen RNA protect, vortexed, and allowed to incubate at room temperature as per manufacturers instructions.  Cells were spun down in a room temperature centrifuge, supernatant was decanted, and cell pellets were stored at -80C until RNA was extracted.

tag: P. putida KT2440 cells scraped from 1/2 M9 +1% glucose plates at 48 hours post inoculation


title: BioRep B plant 120h

tag: P. putida KT2440 cells scraped from 1/2 M9 +1% glucose + A. thalina platnts plates at 120 hours post inoculation


title: BioRep C control 48h


title: 3T3-L1 adipocyte tissue culture, LA fed, T2, biological rep2

description: mouse 3T3-L1 RNA for each time point was isolated from control (LA) and treatment (CLA) samples

source_name: 3T3-L1 adipocyte tissue culture, LA, 8 hours


title: BioRep B control 48h


title: BioRep C plant 120h


title: BioRep A control 120h


title: 3T3-L1 adipocyte tissue culture, LA treated, T2, biological rep3


title: BioRep A control 48h


title: 3T3-L1 adipocyte tissue culture, LA treated, T1, biological rep1


title: 3T3-L1 adipocyte tissue culture, LA fed, T2, biological rep1


title: BioRep B plant 48h

tag: P. putida KT2440 cells scraped from 1/2 M9 +1% glucose + A. thalina platnts plates at 48 hours post inoculation


title: BioRep C plant 48h


title: BioRep A plant 120h


title: 3T3-L1 adipocyte tissue culture, LA treated, T2, biological rep1


title: BioRep A plant 48h


title: 3T3-L1 adipocyte tissue culture, LA fed, T3, biological rep3


title: BioRep B control 120h


title: T.pseudonana1335_gene-specific-array_Temp_rep4

status: Public on Jan 09 2008

city: Seattle

first: E.

middle: Virginia

last: Armbrust

state: WA

address: Ben Hall IRB, 616 NE Northlake Pl, Room 306

department: Oceanography

institute: University of Washington

description: Biological replicate 4 for temperature limitation

hyb_protocol: Hybridization was performed with 10ug of fragmented cRNA in 300ul in the presence of 100mM MES, 1M Na, 20mM EDTA and 0.01% tween20 for 17 hours at 45C.  After hybridization, arrays were washed with a non stringent wash buffer (NSWB) (6X SSPE and 0.01% Tween 20) followed by incubation with a stringent wash buffer (100mM MES, 0.1M Na+, 0.01% Tween 20) for 30 minutes at 45C. Arrays were stained with streptavidin-cy3 (Amersham) for 25 minutes at room temperature, washed with NSWB, rinsed with Final Wash Buffer (Nimblegen) and dried under argon.

scan_protocol: Arrays were scanned using an Arrayworx scanner (Applied Precision).  Array feature intensity was extracted from images using in-house software.

data_processing:
Raw data (linked below as supplementary file) was background corrected (LESN, exponential parameter -4, (6), and then all data were normalized to the same scale using quantile normalization procedure.
The column headers for the raw data files are:
1) probe-sequence-3'-to-5'
2) probe_label
3) array_coord1
4) array_coord2
5) intensity

organism: Thalassiosira pseudonana CCMP1335

source_name: Total RNA from T. pseudonana CCMP 1335, temperature limitation

label_protocol: The quality of each RNA sample was confirmed on the Agilent 2100BioAnalyzer using the RNA6000 Nano Chip.  Total RNA was converted to double-stranded cDNA using an oligo dT primer containing the T7 RNA polymerase promoter (5" - GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG-T24 - 3").  Briefly, 5 to 7 ug of total RNA was incubated with 100 pmol of T7-d(T) 24 primer (UW-Madison DNA Synthesis Facility), 1x first stand buffer (Invitrogen Life Technologies), 10 mM DTT (Invitrogen Life Technologies), 200 U SuperScript II RT (Invitrogen Life Technologies), and 500 _M dNTPs (GE Healthcare Life Sciences) for one hour at 37C.  Second strand synthesis was accomplished by incubation with 1x second strand buffer, 200 _M dNTPs, 10 U DNA Ligase (Invitrogen Life Technologies), 40 U DNA Polymerase I (Invitrogen Life Technologies), and 2 U RNaseH (Invitrogen Life Technologies) for two hours at 16C  followed by a five minute incubation with 10 U T4 Polymerase (Invitrogen Life Technologies).  Double stranded cDNA was purified using the GeneChip Sample Cleanup Module kit (Affymetrix Inc.). A biotin-labeled in vitro transcription reaction was performed using the cDNA template and the Affymetrix 3"-Amplification IVT Labeling kit.  Briefly, double stranded cDNA was incubated with 1x IVT Labeling buffer, 1x Labeling NTP mix, and 1X T7 Labeling Enzyme mix for 16 hours at 37C. cRNA was purified using the GeneChip Sample Cleanup Module.  cRNA yield was determined by absorbance at 260 nM.  The cRNA was fragmented at 0.5 ug/ul final concentration in 1x fragmentation buffer (40 mM Tris-acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate) for 32 minutes at 94C.  The size range of the cRNA before (0.1 kb and longer) and after (35-200 base fragments) fragmentation was checked by agarose gel electrophoresis.

growth_protocol: Axenic Thalassiosira pseudonana clone CCMP 1335, for which whole genome sequence is available, was used for this study. Temperature limitation entailed a transfer of culture growing exponentially at 20C to 4C and 100 µmol photons m-2s-1 for 24h under nutrient replete growth (middle of exponential growth phase). Carbon dioxide was provided by vigorous bubbling with air. Dissolved nutrients (phosphate, silicate and nitrate) were measured for each treatment according to Whitledge et al.

extract_protocol: Concert Plant RNA Reagent (Invitrogen)

tag: temperature limitation (4C)


title: T.pseudonana1335_gene-specific-array_Temp_rep1

description: Biological replicate 1 for temperature limitation


title: Normal myocardium sold commercially (H)

city: Toyoake

first: Masatsugu

last: Ohtsuki

state: Aichi

address: 1-98 Dengakugakubo, kutsukakecho

department: School of Medicine

country: Japan

institute: Fujita Health University

description: Cardiac muscles from patients with DCM or specific cardiomyopathy as well as non-disease control hearts

hyb_protocol: The microarray experiments were then carried out using competitive hybridization experiments with Cy5-labeled heart RNAs as a test RNA and with Cy3-labeled pooled heart RNA (Sample N) as a template control for normalization.

scan_protocol: The glass slides were scanned using an Agilent G2565BA microarray scanner.

data_processing: Data processed with FeautureExtractin v7.1

source_name: H with Cy5

label_protocol: 200ng of total RNA was used for T7 RNA polymerase-based cRNA labeling.

extract_protocol: Total RNA was extracted from myocardium.

tag: myocardium sold commercially

source_name: normal contorol with Cy3


title: T.pseudonana1335_gene-specific-array_Temp_rep3

description: Biological replicate 3 for temperature limitation


title: Left ventricular myocardium in patients with Dilated cardiomyopathty (16)

source_name: 16 with Cy5


title: Dexamethasone treated rat number 7

source_name: Total RNA from dexamethasone treated rats labelled with Cyanine-5 (red).

source_name: Total RNA from pooled control rats tRNA labeled with Cyanine-3 (green).


title: Non-disease heart (19)

source_name: 19 with Cy5

tag: Non-disease heart


title: T.pseudonana1335_gene-specific-array_Temp_rep2

description: Biological replicate 2 for temperature limitation


title: T.pseudonana1335_gene-specific-array_NO3_rep3

description: Biological replicate 3 for nitrogen (nitrate) deplete growth

source_name: Total RNA from T. pseudonana CCMP 1335, nitrogen (nitrate) deplete growth

growth_protocol: Axenic Thalassiosira pseudonana clone CCMP 1335, for which whole genome sequence is available, was used for this study. Nitrogen (nitrate) limitation experiments were conducted with sea water collected from 100 m (Puget Sound, Washington) that had been amended with 2x f/2 nutrients but without the addition of nitrate. Cells were harvested for RNA when the growth rate began to significantly decrease compared to the control cultures under nitrate replete growth. Carbon dioxide was provided by vigorous bubbling with air. Dissolved nutrients (phosphate, silicate and nitrate) were measured for each treatment according to Whitledge et al.

tag: nitrogen (nitrate) deplete growth


title: T.pseudonana1335_gene-specific-array_NO3_rep4

description: Biological replicate 4 for nitrogen (nitrate) deplete growth


title: T.pseudonana1335_gene-specific-array_NO3_rep1

description: Biological replicate 1 for nitrogen (nitrate) deplete growth


title: T.pseudonana1335_gene-specific-array_Ctl_rep7

description: Biological replicate 7 for control growth

source_name: Total RNA from T. pseudonana CCMP 1335, control growth

growth_protocol: Axenic Thalassiosira pseudonana clone CCMP 1335, for which whole genome sequence is available, was used for this study. Nutrient replete growth (control growth) was achieved in natural seawater autoclaved and supplemented with 2x f/2 nutrients at 20 ± 1C and 100 µmol photons m-2s-1 (24h light). Carbon dioxide was provided by vigorous bubbling with air. Cells were harvested for RNA in the middle of the exponential growth phase. Dissolved nutrients (phosphate, silicate and nitrate) were measured for each treatment according to Whitledge et al.

tag: control growth


title: T.pseudonana1335_gene-specific-array_Si_rep2

description: Biological replicate 2 for silicon deplete growth

source_name: Total RNA from T. pseudonana CCMP 1335, silicon deplete growth

growth_protocol: Axenic Thalassiosira pseudonana clone CCMP 1335, for which whole genome sequence is available, was used for this study. Silicate limitation experiments were conducted with sea water collected from 100 m (Puget Sound, Washington) that had been amended with 2x f/2 nutrients but without the addition of silicate. Cells were harvested for RNA when the growth rate began to significantly decrease compared to the control cultures under silicon replete growth. Carbon dioxide was provided by vigorous bubbling with air. Dissolved nutrients (phosphate, silicate and nitrate) were measured for each treatment according to Whitledge et al.

tag: silicon deplete growth


title: T.pseudonana1335_gene-specific-array_NO3_rep2

description: Biological replicate 2 for nitrogen (nitrate) deplete growth


title: No Ab Spike in DNA sample diluted ENCODE NimbleGen hg17 tiling array (90899)

status: Public on Jan 10 2008

type: genomic

city: La Jolla

first: Bing

last: Ren

address: 9500 Gilman Drive

department: Department of Cellular and Molecular Medicine

institute: Ludwig Institute for Cancer Research

description: Spike in DNA was amplified by LM-PCR, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.

hyb_protocol: NimbleGen hybridization protocol

scan_protocol: NimbleGen scan protocol

data_processing: log2R normalized using the limma R package method=loess

molecule: genomic DNA

source_name: Spike in DNA sample diluted

extract_protocol: Spike in DNA

tag: Spike in DNA sample amplified by LM-PCR

source_name: Control DNA

extract_protocol: Control DNA

tag: Control DNA


title: No Ab Spike in DNA sample diluted ENCODE NimbleGen hg17 tiling array (90951)

source_name: Spike in DNA sample


title: T.pseudonana1335_gene-specific-array_Fe_rep1

description: Biological replicate 1 for iron deplete growth

source_name: Total RNA from T. pseudonana CCMP 1335, iron deplete growth

growth_protocol: Axenic Thalassiosira pseudonana clone CCMP 1335, for which whole genome sequence is available, was used for this study. Iron limitation experiments were conducted with surface water from Puget Sound (from ca. 20m depth) without addition of dissolved iron but with addition of all other trace elements and macronutrients according to 2 x f/2 nutrients (Guillard and Ryther, 1962). Cells were harvested for RNA when the growth rate began to significantly decrease compared to the control culture. Carbon dioxide was provided by vigorous bubbling with air. Dissolved nutrients (phosphate, silicate and nitrate) were measured for each treatment according to Whitledge et al.

tag: iron deplete growth


title: T.pseudonana1335_gene-specific-array_Si_rep1

description: Biological replicate 1 for silicon deplete growth


title: T.pseudonana1335_gene-specific-array_Si_rep4

description: Biological replicate 4 for silicon deplete growth


title: Non-disease heart (23)

source_name: 23 with Cy5


title: No Ab Spike in DNA sample diluted ENCODE NimbleGen hg17 tiling array (92003)


title: T.pseudonana1335_gene-specific-array_Si_rep3

description: Biological replicate 3 for silicon deplete growth


title: Left ventricular myocardium in patients with Dilated cardiomyopathty (30)

source_name: 30 with Cy5


title: T.pseudonana1335_gene-specific-array_Ctl_rep6

description: Biological replicate 6 for control growth


title: T.pseudonana1335_gene-specific-array_Fe_rep3

description: Biological replicate 3 for iron deplete growth


title: T.pseudonana1335_gene-specific-array_Fe_rep4

description: Biological replicate 4 for iron deplete growth


title: No Ab Spike in DNA sample undiluted ENCODE NimbleGen hg17 tiling array (91991)

description: Spike in DNA sample undiluted was fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.

source_name: Spike in DNA sample undiluted

tag: Spike in DNA sample undiluted

source_name: Control DNA sample undiluted cells


title: No Ab Spike in DNA sample undiluted ENCODE NimbleGen hg17 tiling array (90991)


title: T.pseudonana1335_gene-specific-array_Ctl_rep8

description: Biological replicate 8 for control growth


title: T.pseudonana1335_gene-specific-array_Fe_rep2

description: Biological replicate 2 for iron deplete growth


title: Left ventricular myocardium in patients with Dilated cardiomyopathty (32)

description: Cardiac muscles from patients with DCM or specific cardiomyopathy as well as non-disease control hearts

source_name: 32 with Cy5


title: No Ab Spike in DNA sample undiluted ENCODE NimbleGen hg17 tiling array (90899)


title: T.pseudonana1335_gene-specific-array_Ctl_rep4

description: Biological replicate 4 for control growth


title: Left ventricular myocardium in patients with Dilated cardiomyopathty (33)

source_name: 33 with Cy5

source_name: normal contorol with Cy3


title: Left ventricular myocardium in patients with Dilated cardiomyopathty (14)

source_name: 14 with Cy5


title: T.pseudonana1335_gene-specific-array_Ctl_rep3

description: Biological replicate 3 for control growth


title: Left ventricular myocardium in patients with Dilated cardiomyopathty (34)

source_name: 34 with Cy5


title: Left ventricular myocardium in patients with Dilated cardiomyopathty (29)

source_name: 29 with Cy5


title: Left ventricular myocardium in patients with Dilated cardiomyopathty (2)

source_name: 2 with Cy5


title: Left ventricular myocardium in patients with Alcoholic myopathy (10)

source_name: 10 with Cy5


title: Left ventricular myocardium in patients with Ischemic cardiomyopathy (35)

source_name: 35 with Cy5


title: Pooled normal myocardium sold commercially (E)

source_name: E with Cy5


title: Left ventricular myocardium in patients with Peripartal cardiomyopathy (25)

source_name: 25 with Cy5


title: Left ventricular myocardium in patients with Dilated cardiomyopathty (1)

source_name: 1 with Cy5


title: Left ventricular myocardium in patients with Dilated cardiomyopathty (6)

source_name: 6 with Cy5


title: Left ventricular myocardium in patients with Hypertrophic cardiomyopathy (31)

source_name: 31 with Cy5


title: Pooled normal myocardium sold commercially (B)

source_name: B with Cy5


title: Left ventricular myocardium in patients with Ischemic cardiomyopathy (26)

source_name: 26 with Cy5


title: Pooled normal myocardium sold commercially (N)

source_name: N with Cy5


title: Left ventricular myocardium in patients with Dilated cardiomyopathty (13)

source_name: 13 with Cy5


title: Left ventricular myocardium in patients with Cardiac sarcoidosis (28)

source_name: 28 with Cy5


title: T.pseudonana1335_gene-specific-array_CO2_rep2

description: Biological replicate 2 for alkaline pH (carbon dioxide limitation)

source_name: Total RNA from T. pseudonana CCMP 1335, alkaline pH

growth_protocol: Axenic Thalassiosira pseudonana clone CCMP 1335, for which whole genome sequence is available, was used for this study. Alkaline pH / CO2 limitation was obtained by increasing the pH of the sea water to 8.4 by adding NaOH (1M) in the absence of bubbling under nutrient replete conditions. The final pH of 9.4 (harvest of cells for RNA extraction) was reached due to the natural uptake of dissolved inorganic carbon (DIC) by the diatoms.  Dissolved nutrients (phosphate, silicate and nitrate) were measured for each treatment according to Whitledge et al.

tag: alkaline pH (carbon dioxide limitation)


title: Left ventricular myocardium in patients with Dilated cardiomyopathty (8)

source_name: 8 with Cy5

source_name: normal contorol with Cy3


title: T.pseudonana1335_gene-specific-array_CO2_rep3

description: Biological replicate 3 for alkaline pH (carbon dioxide limitation)


title: Left ventricular myocardium in patients with Eosinophilic myocarditis (4)

source_name: 4 with Cy5


title: Normal myocardium sold commercially (C)

source_name: C with Cy5


title: Normal myocardium sold commercially (F)

source_name: F with Cy5


title: Normal myocardium sold commercially (D)

source_name: D with Cy5


title: T.pseudonana1335_gene-specific-array_Ctl_rep1

description: Biological replicate 1 for control growth

source_name: Total RNA from T. pseudonana CCMP 1335, control growth


title: T.pseudonana1335_gene-specific-array_CO2_rep1

description: Biological replicate 1 for alkaline pH (carbon dioxide limitation)


title: T.pseudonana1335_gene-specific-array_Ctl_rep5

description: Biological replicate 5 for control growth


title: Normal myocardium sold commercially (A)

source_name: A with Cy5

tag: Normal myocardium sold commercially


title: Schz Biological Replicate 1 (Cy5) vs. LS40 Biological Replicate 4 (Cy3)

status: Public on Jan 07 2008

first: Stefan

middle: H. I.

last: Kappe

address: 307 Westlake Ave N, Suite 500

institute: Seattle Biomedical Research Institute

description: ooSpz: Sporozoites from P. yoelii (17XLN) infected A. stephensi mosquitoes were isolated from midguts at day 10 after infectious blood meal. sgSpz: Sporozoites from P. yoelii (17XLN) infected A. stephensi mosquitoes were isolated from salivary glands at day 15 after infectious blood meal. LS24: Isolated liver stage infected hepatocytes from PyGFP-infected BALB/c mice 24 hrs after infection. LS40: Isolated liver stage infected hepatocytes from PyGFP-infected BALB/c mice 40 hrs after infection. LS50: Isolated liver stage infected hepatocytes from PyGFP-infected BALB/c mice 50 hrs after infection. Schz: Purified blood stage schizonts were prepared from Nycodenz purification of P. yoelii infected blood cultured for 12 hours. BS: Parasites in the erythrocytic stages harvested from PyGFP-infected swiss-webster mice when parasitemia was at 5-10%

hyb_protocol: For microarray hybridizations, 10 ug of aRNA was fragmented with the RNA fragmentation kit (Ambion), then coupled with Cy3 or Cy5 (Amersham) according to manufacturer's protocol (Amino Allyl Message Amp II aRNA Amplification Kit, Ambion). Each hybridization mixture (60 ml) contained 1-5 mg of the cy3 and cy5 labeled aRNA, 4 ug yeast tRNA (Invitrogen), 8 ug polyA RNA (Invitrogen), 10mg mouse Cot1 DNA (GE Healthcare), 0.2% SDS, 20mM Hepes pH 7.2 in 3xSSC. Samples were applied beneath lifterslips (Erie) onto microarray slides.  Hybridization of the labeled aRNA was done for 16 hrs in a 60C waterbath using hybridization chambers (Corning). Microarrays were removed from the hybridization chambers and washed in 1X SSC with 0. 1% SDS for 2 min at room temperature , 0.2X SSC for 2min, 0.05X SSC for 1min twice and 0.01X SSC for 30 sec. Slides were dried by centrifugation for 5 min at 60g.

scan_protocol: Scanned on an GenePix 4000A laser scanner. Images were quantified using GenePix Pro software (Axon Instruments Inc.).

data_processing: We processed and analyzed the expression data using the limma package for the R programming environment (Smyth GK, 2005), as follows. Background correction was performed using limma's "normexp" method, which ensures that there were no missing or negative corrected intensities. An offset of 50 was used for both channels to damp down the variability of the log-ratios for low-intensity spots. The resulting log-ratios were normalized by using print-tip loess method (Smyth GK and Speed T, 2003). Between-array normalization was achieved using limma's "Aquantile" method, which does quantile normalization of mean probe intensity values.

organism: Plasmodium yoelii

source_name: Total RNA from Schz Biological Replicate 1 (Cy5) labeled with Cyanine-5 (red).

label_protocol: Total RNA from each sample were extracted using Trizol (Invitrogen) and DNase treated using Turbo-DNAfree (Ambion).Total RNA was then subjected to two rounds of linear amplification using the Amino Allyl Message Amp II aRNA Amplification Kit (Ambion) according to manufaturer's directions. The quality of total and amplified RNAs were examined with the Agilent 2100 BioanalyzerTM (Agilent Technologies, Palo Alto, CA) while the quantity of the RNA samples was assessed using a Nanodrop ND-1000 spectrophotometer prior to microarray hybridization.

extract_protocol: TriZol procedure

tag: P. yoelii, BALB/c mice, blood

source_name: Total RNA from LS40 Biological Replicate 4 (Cy3) labeled with Cyanine-3 (green).

tag: P. yoelii, BALB/c mice, isolated liver stage infected hepatocytes


title: BS Biological Replicate 2 (Cy5) vs. LS24 Biological Replicate 3 (Cy3)

source_name: Total RNA from BS Biological Replicate 2 (Cy5) labeled with Cyanine-5 (red).

source_name: Total RNA from LS24 Biological Replicate 3 (Cy3) labeled with Cyanine-3 (green).


title: Schz Biological Replicate 1 (Cy5) vs. LS24 Biological Replicate 3 (Cy3)


title: Schz Biological Replicate 1 (Cy5) vs. LS24 Biological Replicate 2 (Cy3) Repeated Hybridization 2

source_name: Total RNA from LS24 Biological Replicate 2 (Cy3) labeled with Cyanine-3 (green).


title: BS Biological Replicate 1 (Cy5) vs. LS24 Biological Replicate 3 (Cy3)

source_name: Total RNA from BS Biological Replicate 1 (Cy5) labeled with Cyanine-5 (red).


title: Schz Biological Replicate 2 (Cy5) vs. LS24 Biological Replicate 3 (Cy3)

source_name: Total RNA from Schz Biological Replicate 2 (Cy5) labeled with Cyanine-5 (red).


title: sgSpz Biological Replicate 4 (Cy5) vs. LS24 Biological Replicate 3 (Cy3)

source_name: Total RNA from sgSpz Biological Replicate 4 (Cy5) labeled with Cyanine-5 (red).

tag: P. yoelii, A. stephensi mosquitoes, salivary glands


title: BS Biological Replicate 1 (Cy5) vs. LS24 Biological Replicate 1 (Cy3) Repeated Hybridization 2

source_name: Total RNA from LS24 Biological Replicate 1 (Cy3) labeled with Cyanine-3 (green).


title: BS Biological Replicate 1 (Cy5) vs. LS24 Biological Replicate 2 (Cy3) Repeated Hybridization 2


title: Schz Biological Replicate 2 (Cy5) vs. LS24 Biological Replicate 1 (Cy3)


title: Schz Biological Replicate 1 (Cy5) vs. LS24 Biological Replicate 1 (Cy3) Repeated Hybridization 2


title: BS Biological Replicate 2 (Cy5) vs. LS24 Biological Replicate 2 (Cy3)


title: T.pseudonana1335_tiling-array_Si

description: Samples came from cells grown under optimum growth (silicon repletion).

data_processing:
Raw data from all 8 silicon repletion tiling arrays were normalized to the same scale using a quantile normalization procedure.
The raw data files for the individual chips that make up the 8-array set are linked below as supplementary files.
In addition, there is a supplementary file indicating which raw supplementary file(s) is associated with each probe. Note that some probes have more than one chip because probe replicates were made, and in our final normalized data these replicates are averaged.

source_name: Total RNA from T. pseudonana CCMP 1335, silicon deplete growth


title: BS Biological Replicate 1 (Cy5) vs. LS24 Biological Replicate 1 (Cy3) Repeated Hybridization 1


title: BS Biological Replicate 1 (Cy5) vs. LS24 Biological Replicate 2 (Cy3) Repeated Hybridization 1


title: LS40 Biological Replicate 1 (Cy5) vs. BS Biological Replicate 1 (Cy3)

source_name: Total RNA from LS40 Biological Replicate 1 (Cy5) labeled with Cyanine-5 (red).

source_name: Total RNA from BS Biological Replicate 1 (Cy3) labeled with Cyanine-3 (green).


title: Schz Biological Replicate 1 (Cy5) vs. LS24 Biological Replicate 1 (Cy3) Repeated Hybridization 1


title: T.pseudonana1335_tiling-array_Control

description: Samples came from cells grown under optimum growth (silicon depletion).

data_processing:
Raw data from all 8 silicon depletion tiling arrays were normalized to the same scale using a quantile normalization procedure.
The raw data files for the individual chips that make up the 8-array set are linked below as supplementary files.
In addition, there is a supplementary file indicating which raw supplementary file(s) is associated with each probe. Note that some probes have more than one chip because probe replicates were made, and in our final normalized data these replicates are averaged.

source_name: Total RNA from T. pseudonana CCMP 1335, silicon replete growth (control growth)

label_protocol: The quality of each RNA sample was confirmed on the Agilent 2100BioAnalyzer using the RNA6000 Nano Chip.  Total RNA was converted to double-stranded cDNA using an oligo dT primer containing the T7 RNA polymerase promoter (5" - GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG-T24 - 3").  Briefly, 5 to 7 ug of total RNA was incubated with 100 pmol of T7-d(T) 24 primer (UW-Madison DNA Synthesis Facility), 1x first stand buffer (Invitrogen Life Technologies), 10 mM DTT (Invitrogen Life Technologies), 200 U SuperScript II RT (Invitrogen Life Technologies), and 500 _M dNTPs (GE Healthcare Life Sciences) for one hour at 37C.  Second strand synthesis was accomplished by incubation with 1x second strand buffer, 200 _M dNTPs, 10 U DNA Ligase (Invitrogen Life Technologies), 40 U DNA Polymerase I (Invitrogen Life Technologies), and 2 U RNaseH (Invitrogen Life Technologies) for two hours at 16C  followed by a five minute incubation with 10 U T4 Polymerase (Invitrogen Life Technologies).  Double stranded cDNA was purified using the GeneChip Sample Cleanup Module kit (Affymetrix Inc.). A biotin-labeled in vitro transcription reaction was performed using the cDNA template and the Affymetrix 3Õ-Amplification IVT Labeling kit.  Briefly, double stranded cDNA was incubated with 1x IVT Labeling buffer, 1x Labeling NTP mix, and 1X T7 Labeling Enzyme mix for 16 hours at 37C. cRNA was purified using the GeneChip Sample Cleanup Module.  cRNA yield was determined by absorbance at 260 nM.  The cRNA was fragmented at 0.5 ug/ul final concentration in 1x fragmentation buffer (40 mM Tris-acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate) for 32 minutes at 94C.  The size range of the cRNA before (0.1 kb and longer) and after (35-200 base fragments) fragmentation was checked by agarose gel electrophoresis.

growth_protocol: Axenic Thalassiosira pseudonana clone CCMP 1335, for which whole genome sequence is available, was used for this study. Silicon replete growth was achieved in natural seawater autoclaved and supplemented with 2x f/2 nutrients at 20 ± 1C and 100 µmol photons m-2s-1 (24h light). Carbon dioxide was provided by vigorous bubbling with air. Cells were harvested for RNA in the middle of the exponential growth phase. Dissolved nutrients (phosphate, silicate and nitrate) were measured for each treatment according to Whitledge et al.

tag: silicon replete growth (control growth)


title: Schz Biological Replicate 1 (Cy5) vs. LS24 Biological Replicate 2 (Cy3) Repeated Hybridization 1


title: T.pseudonana1335_gene-specific-array_CO2_rep4

description: Biological replicate 4 for alkaline pH (carbon dioxide limitation)

source_name: Total RNA from T. pseudonana CCMP 1335, alkaline pH


title: BS Biological Replicate 1 (Cy5) vs. LS50 Biological Replicate 1 (Cy3)

source_name: Total RNA from LS50 Biological Replicate 1 (Cy3) labeled with Cyanine-3 (green).


title: BS Biological Replicate 2 (Cy5) vs. LS50 Biological Replicate 3 (Cy3)

source_name: Total RNA from LS50 Biological Replicate 3 (Cy3) labeled with Cyanine-3 (green).


title: BS Biological Replicate 1 (Cy5) vs. LS50 Biological Replicate 2 (Cy3)

source_name: Total RNA from LS50 Biological Replicate 2 (Cy3) labeled with Cyanine-3 (green).


title: BS Biological Replicate 2 (Cy5) vs. LS50 Biological Replicate 4 (Cy3)

source_name: Total RNA from LS50 Biological Replicate 4 (Cy3) labeled with Cyanine-3 (green).


title: BS Biological Replicate 1 (Cy5) vs. LS40 Biological Replicate 2 (Cy3)

source_name: Total RNA from LS40 Biological Replicate 2 (Cy3) labeled with Cyanine-3 (green).


title: BS Biological Replicate 2 (Cy5) vs. LS40 Biological Replicate 4 (Cy3)

source_name: Total RNA from BS Biological Replicate 2 (Cy5) labeled with Cyanine-5 (red).

source_name: Total RNA from LS40 Biological Replicate 4 (Cy3) labeled with Cyanine-3 (green).


title: Schz Biological Replicate 2 (Cy5) vs. LS50 Biological Replicate 4 (Cy3)


title: Schz Biological Replicate 2 (Cy5) vs. LS40 Biological Replicate 4 (Cy3)


title: Schz Biological Replicate 1 (Cy5) vs. LS40 Biological Replicate 2 (Cy3)

source_name: Total RNA from Schz Biological Replicate 1 (Cy5) labeled with Cyanine-5 (red).


title: sgSpz Biological Replicate 3 (Cy5) vs. ooSpz Biological Replicate 3 (Cy3)

source_name: Total RNA from sgSpz Biological Replicate 3 (Cy5) labeled with Cyanine-5 (red).

source_name: Total RNA from ooSpz Biological Replicate 3 (Cy3) labeled with Cyanine-3 (green).

tag: P. yoelii, A. stephensi mosquitoes, midguts


title: LS40 Biological Replicate 2 (Cy5) vs. BS Biological Replicate 1 (Cy3)

source_name: Total RNA from LS40 Biological Replicate 2 (Cy5) labeled with Cyanine-5 (red).


title: Schz Biological Replicate 2 (Cy5) vs. LS50 Biological Replicate 3 (Cy3)

source_name: Total RNA from Schz Biological Replicate 2 (Cy5) labeled with Cyanine-5 (red).


title: BS Biological Replicate 1 (Cy5) vs. LS40 Biological Replicate 3 (Cy3)

source_name: Total RNA from BS Biological Replicate 1 (Cy5) labeled with Cyanine-5 (red).

source_name: Total RNA from LS40 Biological Replicate 3 (Cy3) labeled with Cyanine-3 (green).


title: Schz Biological Replicate 1 (Cy5) vs. LS50 Biological Replicate 2 (Cy3)


title: BS Biological Replicate 1 (Cy5) vs. LS40 Biological Replicate 1 (Cy3)

source_name: Total RNA from LS40 Biological Replicate 1 (Cy3) labeled with Cyanine-3 (green).


title: Schz Biological Replicate 1 (Cy5) vs. LS40 Biological Replicate 3 (Cy3)


title: Schz Biological Replicate 1 (Cy5) vs. LS50 Biological Replicate 1 (Cy3)


title: sgSpz Biological Replicate 4 (Cy5) vs. LS24 Biological Replicate 1 (Cy3)

source_name: Total RNA from sgSpz Biological Replicate 4 (Cy5) labeled with Cyanine-5 (red).

source_name: Total RNA from LS24 Biological Replicate 1 (Cy3) labeled with Cyanine-3 (green).


title: Normal myocardium sold commercially (G)

data_processing: Data processed with FeautureExtraction v7.1

source_name: G with Cy5

source_name: normal control with Cy3


title: sorbate_t_50min_combined_2_replicates

city: Leiden

first: Anna

middle: Magdalena

last: Zakrzewska

address: Wassenaarseweg 64

department: IBL

country: Netherlands

institute: University of Leiden

description: B.subtilis_sorbate_t_50min_combined_2_replicates

hyb_protocol: Automated slide processor (ASP), GE Healthcare

scan_protocol: Microarrays were scanned in an Agilent DNA MicroArray Scanner (Agilent Technologies, Palo Alto, CA,USA) at 100 % PMT and 100% laser power

data_processing:
Data supplied is log2 ratio of normalized and filtered 2 biological replicates, each containing 2 technical replicates (duplicate spots on the microarray and duplicate hybridization). Raw data and required information is supplied as supplementary file.
The data was normalized in J-Express Pro 2.6 software (MolMine AS) using a global LOWESS (locally weighted scatterspot smoothing) algorithm. To avoid extreme intensity ratios, low intensity fluorescence data was floored at a value corresponding to a signal-to-noise ratio of 2.0. The data was averaged, log2 transformed and missing values were replaced by the average of the closest values. Genes with more than two missing values in the time-series were omitted. Since the variation in differential expression measurements depends on the fluorescent signal intensity (smaller variation at higher- and larger variation at lower fluorescence intensity levels), we applied an intensity-dependent method to identify differentially expressed genes. A sliding window of 50 genes was selected to calculate a Z-score from the local mean and standard deviation using the data in the R-I plot (log10(Cy5*Cy3) vs. log10(Cy5/Cy3). Genes more than 1.96 standard deviations away from the local average (|Z| > 1.96) were considered differentially expressed. This corresponds to a confidence level of 95 %. Genes that showed significant expression at t = 0 min were excluded from further analysis, unless the gene showed opposite significant expression in at least one of the other time-points. After the processing of the microarray data 3909 genes remained for each time-point, of which 459 were found to be significantly expressed.

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: B.subtilis t_50min control

label_protocol: Direct incorporation: Random priming of SSII RT to incorporate cy3-labeled dUTP, followed by NaOH hydrolysis of RNA

extract_protocol: Fast RNA pro Blue - Qbiogene

treatment_protocol: A sample of 20 ml was withdrawn from the culture at 50 min after t_0min. The cells were collected using a vacuum-filtering set-up, immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. The whole procedure took no longer than 50 s.

tag: Time

value: 50 minutes of exponential growth in minimal defined medium; sample is part of time series

source_name: B.subtilis t_50min sorbate treatment

label_protocol: Direct incorporation: Random priming of SSII RT to incorporate cy5-labeled dUTP, followed by NaOH hydrolysis of RNA

growth_protocol: An exponentially growing culture of B. subtilis WT strain 168 was inoculated in well-controlled batch-fermentor (500 ml working volume) to an OD600 of 0.05. The culture was grown at 37 °C in defined medium at pH 6.4 with an aeration rate of 0.5 liters/min and vigorous stirring (200 rpm). At an OD600 of 0.2, the culture was stressed with 3 mM KS.

treatment_protocol: A sample of 20 ml was withdrawn from the culture at 50 min after addition of 3mM potassium sorbate. The cells were collected using a vacuum-filtering set-up, immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. The whole procedure took no longer than 50 s.

value: 50 minutes of growth in minimal defined medium after addition of 3 mM potassium sorbate; sample is part of time series


title: sgSpz Biological Replicate 4 (Cy5) vs. LS24 Biological Replicate 2 (Cy3)

source_name: Total RNA from LS24 Biological Replicate 2 (Cy3) labeled with Cyanine-3 (green).


title: sorbate_t_30min_combined_2_replicates

description: B.subtilis_sorbate_t_30min_combined_2_replicates

source_name: B.subtilis t_30min control

growth_protocol: An exponentially growing culture of B. subtilis WT strain 168 was inoculated in well-controlled batch-fermentor (500 ml working volume) to an OD600 of 0.05. The culture was grown at 37 °C in defined medium at pH 6.4 with an aeration rate of 0.5 liters/min and vigorous stirring (200 rpm).

treatment_protocol: A sample of 20 ml was withdrawn from the culture at 30 min after t_0min. The cells were collected using a vacuum-filtering set-up, immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. The whole procedure took no longer than 50 s.

value: 30 minutes of exponential growth in minimal defined medium; sample is part of time series

source_name: B.subtilis t_30min sorbate treatment

treatment_protocol: A sample of 20 ml was withdrawn from the culture at 30 min after addition of 3mM potassium sorbate. The cells were collected using a vacuum-filtering set-up, immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. The whole procedure took no longer than 50 s.

value: 30 minutes of growth in minimal defined medium after addition of 3 mM potassium sorbate; sample is part of time series


title: sorbate_t_10min_combined_2_replicates

description: B.subtilis_sorbate_t_10min_combined_2_replicates

source_name: B.subtilis t_10min control

treatment_protocol: A sample of 20 ml was withdrawn from the culture at 10 min after t_0min. The cells were collected using a vacuum-filtering set-up, immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. The whole procedure took no longer than 50 s.

value: 10 minutes of exponential growth in minimal defined medium; sample is part of time series

source_name: B.subtilis t_10min sorbate treatment

treatment_protocol: A sample of 20 ml was withdrawn from the culture at 10 min after addition of 3mM potassium sorbate. The cells were collected using a vacuum-filtering set-up, immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. The whole procedure took no longer than 50 s.

value: 10 minutes of growth in minimal defined medium after addition of 3 mM potassium sorbate; sample is part of time series


title: sorbate_t_20min_combined_2_replicates

description: B.subtilis_sorbate_t_20min_combined_2_replicates

source_name: B.subtilis t_20min control

treatment_protocol: A sample of 20 ml was withdrawn from the culture at 20 min after t_0min. The cells were collected using a vacuum-filtering set-up, immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. The whole procedure took no longer than 50 s.

value: 20 minutes of exponential growth in minimal defined medium; sample is part of time series

source_name: B.subtilis t_20min sorbate treatment

treatment_protocol: A sample of 20 ml was withdrawn from the culture at 20 min after addition of 3mM potassium sorbate. The cells were collected using a vacuum-filtering set-up, immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. The whole procedure took no longer than 50 s.

value: 20 minutes of growth in minimal defined medium after addition of 3 mM potassium sorbate; sample is part of time series


title: Schz Biological Replicate 1 (Cy5) vs. LS40 Biological Replicate 1 (Cy3)

source_name: Total RNA from Schz Biological Replicate 1 (Cy5) labeled with Cyanine-5 (red).


title: sorbate_t_0min_combined_2_replicates

description: B.subtilis_sorbate_t_0min_combined_2_replicates

source_name: B.subtilis t_0min control

treatment_protocol: A sample of 20 ml was withdrawn from the culture at 0 min. The cells were collected using a vacuum-filtering set-up, immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. The whole procedure took no longer than 50 s.

value: 0 minutes of exponential growth in minimal defined medium; sample is part of time series

source_name: B.subtilis t_0min sorbate treatment


title: sorbate_t_40min_combined_2_replicates

description: B.subtilis_sorbate_t_40min_combined_2_replicates

source_name: B.subtilis t_40min control

treatment_protocol: A sample of 20 ml was withdrawn from the culture at 40 min after t_0min. The cells were collected using a vacuum-filtering set-up, immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. The whole procedure took no longer than 50 s.

value: 40 minutes of exponential growth in minimal defined medium; sample is part of time series

source_name: B.subtilis t_40min sorbate treatment

treatment_protocol: A sample of 20 ml was withdrawn from the culture at 40 min after addition of 3mM potassium sorbate. The cells were collected using a vacuum-filtering set-up, immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. The whole procedure took no longer than 50 s.

value: 40 minutes of growth in minimal defined medium after addition of 3 mM potassium sorbate; sample is part of time series


title: ooSpz Biological Replicate 3 (Cy5) vs. sgSpz Biological Replicate 3 (Cy3)

source_name: Total RNA from ooSpz Biological Replicate 3 (Cy5) labeled with Cyanine-5 (red).

source_name: Total RNA from sgSpz Biological Replicate 3 (Cy3) labeled with Cyanine-3 (green).


title: sgSpz Biological Replicate 2 (Cy5) vs. BS Biological Replicate 4 (Cy3)

source_name: Total RNA from sgSpz Biological Replicate 2 (Cy5) labeled with Cyanine-5 (red).

source_name: Total RNA from BS Biological Replicate 4 (Cy3) labeled with Cyanine-3 (green).


title: ooSpz Biological Replicate 2 (Cy5) vs. BS Biological Replicate 4 (Cy3)

source_name: Total RNA from ooSpz Biological Replicate 2 (Cy5) labeled with Cyanine-5 (red).


title: sgSpz Biological Replicate 2 (Cy5) vs. ooSpz Biological Replicate 2 (Cy3)

source_name: Total RNA from ooSpz Biological Replicate 2 (Cy3) labeled with Cyanine-3 (green).


title: BS Biological Replicate 4 (Cy5) vs. ooSpz Biological Replicate 2 (Cy3)

source_name: Total RNA from BS Biological Replicate 4 (Cy5) labeled with Cyanine-5 (red).


title: ooSpz Biological Replicate 1 (Cy5) vs. BS Biological Replicate 3 (Cy3)

source_name: Total RNA from ooSpz Biological Replicate 1 (Cy5) labeled with Cyanine-5 (red).

source_name: Total RNA from BS Biological Replicate 3 (Cy3) labeled with Cyanine-3 (green).


title: BS Biological Replicate 4 (Cy5) vs. sgSpz Biological Replicate 2 (Cy3)

source_name: Total RNA from sgSpz Biological Replicate 2 (Cy3) labeled with Cyanine-3 (green).


title: 2221DELTACEP_THY_exponential phase_rep4

status: Public on Jan 05 2008

city: Reno

first: Paul

last: Sumby

state: NV

address: 1554 N. Virginia St.

department: Microbiology & Immunology

institute: University of Nevada

hyb_protocol: As per the Affymetrix protocol, with overnight hyb at 42 degC.

scan_protocol: As per the Affymetrix protocol using the GeneChip scanner 3000.

data_processing: Data was analyzed in GCOS.  Data was normalized to ensure overall signal intensities were identical between samples.

label: Biotin

organism: Streptococcus pyogenes

source_name: Strain 2221DELTACEP is a derivative of strain MGAS2221

label_protocol: The Affymetrix labeling reagent was used as per the manufacturers protocol.

growth_protocol: Grown in THY broth to an O.D. 600 reading of 0.6, corresponding to exponential phase.

extract_protocol: 4.5ml culture was added to 9ml RNA protect (Qiagen), and GAS collected by centrifugation.  RNA was extracted from bacterial cell pellets through mechanical disruption using a FastPrep machine and tubes containing fine glass beads.  Following mechanical disruption RNA was purified on Qiagen miRNeasy columns using the miRNease protocol.  Four treatments with DNA-free (Ambion) was performed on RNA eluted from the Qiagen columns to remove contaminating DNA.  RNA quality was assessed by bioanalyzer and O.D. measurements.

tag: 2221DELTACEP is an isogenic spyCEP mutant of strain MGAS2221.


title: ooSpz Biological Replicate 2 (Cy5) vs. sgSpz Biological Replicate 2 (Cy3)


title: 2221DELTACEP_THY_exponential phase_rep1

tag: Isogenic spyCEP mutant of MGAS2221.


title: MGAS2221_THY_exponential phase_rep1

source_name: GAS strain MGAS2221 during THY exponential phase growth

tag: MGAS2221 is an M1T1 GAS isolate.


title: MGAS2221_THY_exponential phase_rep3

source_name: Strain MGAS2221 grown in THY broth to exponential phase.

tag: MGAS2221 is an M1T1 GAS.


title: MGAS2221_THY_exponential phase_rep4

source_name: Strain MGAS2221 grown in THY broth to exponential phase


title: 2221DELTACEP_THY_exponential phase_rep3


title: ooSpz Biological Replicate 1 (Cy5) vs. sgSpz Biological Replicate 1 (Cy3)

source_name: Total RNA from sgSpz Biological Replicate 1 (Cy3) labeled with Cyanine-3 (green).


title: 2221DELTACEP_THY_exponential phase_rep2

tag: 2221DELTACEP is an isogenic spyCEP mutant of MGAS2221.


title: T.pseudonana1335_gene-specific-array_Ctl_rep2

description: Biological replicate 2 for control growth

source_name: Total RNA from T. pseudonana CCMP 1335, control growth

tag: control growth


title: sgSpz Biological Replicate 1 (Cy5) vs. BS Biological Replicate 3 (Cy3)

source_name: Total RNA from sgSpz Biological Replicate 1 (Cy5) labeled with Cyanine-5 (red).


title: BS Biological Replicate 3 (Cy5) vs. ooSpz Biological Replicate 1 (Cy3)

source_name: Total RNA from BS Biological Replicate 3 (Cy5) labeled with Cyanine-5 (red).

source_name: Total RNA from ooSpz Biological Replicate 1 (Cy3) labeled with Cyanine-3 (green).


title: Low Capacity Runner - Exercise Trained Number 4 - Left Ventricle

status: Public on Jan 04 2008

city: TRONDHEIM

first: Anja

last: Bye

address: Olav Kyrres gt 9

country: Norway

institute: NTNU

description: Commercial method by Affymetrix

hyb_protocol: Commercial method by Affymetrix

scan_protocol: Commercial method by Affymetrix

data_processing:
Gene expression were analyzed on whole-genome RAE 230 2.0 chip from Affymetrix GeneChip (Affymetrix, Santa Clara, US) comprised of 31,042 probe sets, analyzing over 30,000 transcripts and variants from over 28,000 substantiated rat genes. On the Affymetrix GeneChip arrays, each gene is represented by a set of 11-20 probe pairs consisting of a perfect match (PM) and a mismatch (MM) probe. The statistical analysis is based on summary expression measures for each probe set, RMA.
The arrays also include a set of rat maintenance genes to facilitate the normalization and scaling of array experiments. These probe sets serve as a tool to normalize or scale your data prior to performing data comparison. All normalization genes show consistent levels of expression over defined sample sets.
Statistical analysis for finding differential expressed genes
For each gene (probeset), a linear regression model, including parameters representing the effect of aerobe capacity is specified. Based on the estimated effects, tests for significant differential expression are performed using T-tests. However, to improve the power of the tests, the T-tests are modified by replacing the gene-specific variance estimates by estimates found by borrowing strength from data on the remaining genes. The software package Limma implementing the method is available as part of the Bioconductor project.

To account for multiple testing, we calculate adjusted p-values controlling the False Discovery Rate (FDR). Consequently, selecting differentially expressed genes based on a threshold of 0.05 on the adjusted FDR p-values means that the expected proportion of genes falsely classified as differential expressed should be below 0.01 or 0.05. The model is fitted using the R statistical package (R Development Core Team, 2004).
RMA using the Bioconduction libraries
The summary measures are computed based on a linear statistical model for background-corrected, normalized and log-transformed PM values for each probe pair denoted the robust multiarray average (RMA) method. The PM values are normalized using the quantile normalization method, normalizing the arrays such that the empirical distribution of the expression measures is equal across arrays.

source_name: Left Ventricle

label_protocol: Commercial method by Affymetrix

extract_protocol:
Tissue samples (20 mg) were homogenized in 100 µL TRIzol (Life Technologies, Gaithersburg, US) using a Mixer Mill MM301 at 20-25 Hz. RNA clean-up was performed using RNA Mini kit (Qiagen, Germantown, US). Total RNA was isolated and RNA clean-up was performed according to the manufacturer's instructions.
RNA integrity, purity and quantity were assessed by Bioanalyzer (Agilent Technologies, Santa Clara, US) and Nanodrop (NanoDrop Technologies, Baltimore, US). The concentration of total RNA was measured by Nanodrop with ultraviolet spectrophotometry at 260/280 nm. RNA quality was assessed by electrophoresis on Bioanalyzer chips (Agilent Technologies, Santa Clara, US).

High quality RNA was classified as a 260/280 ratio above 1.8. Only samples with a 260/280 ratio of more than 1.8 and no signs of degradation based on Bioanalyzer results were used for analysis.

tag: Gender

value: Female Age:7 months Tissue:Left Ventricle


title: Low Capacity Runner - Exercise Trained Number 3 - Left Ventricle

description: Commercial method by Affymetrix


title: MGAS2221_THY_exponential phase_rep2

tag: Strain MGAS2221 is an M1T1 GAS.


title: High Capacity Runner - Exercise Trained Number 3 - Left Ventricle

description: Commercial method by Affymetrix

hyb_protocol: Commercial method by AffymetrixCommercial method by Affymetrix

data_processing:
Gene expression were analyzed on whole-genome RAE 230 2.0 chip from Affymetrix GeneChip (Affymetrix, Santa Clara, US) comprised of 31,042 probe sets, analyzing over 30,000 transcripts and variants from over 28,000 substantiated rat genes. On the Affymetrix GeneChip arrays, each gene is represented by a set of 11-20 probe pairs consisting of a perfect match (PM) and a mismatch (MM) probe. The statistical analysis is based on summary expression measures for each probe set, RMA.
The arrays also include a set of rat maintenance genes to facilitate the normalization and scaling of array experiments. These probe sets serve as a tool to normalize or scale your data prior to performing data comparison. All normalization genes show consistent levels of expression over defined sample sets.
Statistical analysis for finding differential expressed genes
For each gene (probeset), a linear regression model, including parameters representing the effect of aerobe capacity is specified. Based on the estimated effects, tests for significant differential expression are performed using T-tests (22). However, to improve the power of the tests, the T-tests are modified by replacing the gene-specific variance estimates by estimates found by borrowing strength from data on the remaining genes (35). The software package Limma implementing the method is available as part of the Bioconductor project (11).

To account for multiple testing, we calculate adjusted p-values controlling the False Discovery Rate (FDR) (5). Consequently, selecting differentially expressed genes based on a threshold of 0.05 on the adjusted FDR p-values means that the expected proportion of genes falsely classified as differential expressed should be below 0.01 or 0.05. The model is fitted using the R statistical package (R Development Core Team, 2004).
RMA using the Bioconduction libraries
The summary measures are computed based on a linear statistical model for background-corrected, normalized and log-transformed PM values for each probe pair denoted the robust multiarray average (RMA) method (17). The PM values are normalized using the quantile normalization method (7), normalizing the arrays such that the empirical distribution of the expression measures is equal across arrays.


title: sgSpz Biological Replicate 1 (Cy5) vs. ooSpz Biological Replicate 1 (Cy3)


title: Low Capacity Runner - Sedentary Number 5 - Left Ventricle

description: Commercial method by Affymetrix


title: Low Capacity Runner - Sedentary Number 2 - Left Ventricle

description: Commercial method by Affymetrix


title: BS Biological Replicate 3 (Cy5) vs. sgSpz Biological Replicate 1 (Cy3)


title: High Capacity Runner - Sedentary Number 5 - Left Ventricle

description: Commercial method by Affymetrix

data_processing:
Processing of Affymetrix data
Gene expression were analyzed on whole-genome RAE 230 2.0 chip from Affymetrix GeneChip (Affymetrix, Santa Clara, US) comprised of 31,042 probe sets, analyzing over 30,000 transcripts and variants from over 28,000 substantiated rat genes. On the Affymetrix GeneChip arrays, each gene is represented by a set of 11-20 probe pairs consisting of a perfect match (PM) and a mismatch (MM) probe. The statistical analysis is based on summary expression measures for each probe set, RMA.
The arrays also include a set of rat maintenance genes to facilitate the normalization and scaling of array experiments. These probe sets serve as a tool to normalize or scale your data prior to performing data comparison. All normalization genes show consistent levels of expression over defined sample sets.
Statistical analysis for finding differential expressed genes
For each gene (probeset), a linear regression model, including parameters representing the effect of aerobe capacity is specified. Based on the estimated effects, tests for significant differential expression are performed using T-tests (22). However, to improve the power of the tests, the T-tests are modified by replacing the gene-specific variance estimates by estimates found by borrowing strength from data on the remaining genes (35). The software package Limma implementing the method is available as part of the Bioconductor project (11).

To account for multiple testing, we calculate adjusted p-values controlling the False Discovery Rate (FDR) (5). Consequently, selecting differentially expressed genes based on a threshold of 0.05 on the adjusted FDR p-values means that the expected proportion of genes falsely classified as differential expressed should be below 0.01 or 0.05. The model is fitted using the R statistical package (R Development Core Team, 2004).
RMA using the Bioconduction libraries
The summary measures are computed based on a linear statistical model for background-corrected, normalized and log-transformed PM values for each probe pair denoted the robust multiarray average (RMA) method (17). The PM values are normalized using the quantile normalization method (7), normalizing the arrays such that the empirical distribution of the expression measures is equal across arrays.


title: High Capacity Runner - Exercise Trained Number 6 - Left Ventricle

description: Commercial method by Affymetrix


title: High Capacity Runner - Exercise Trained Number 4 - Left Ventricle

description: Commercial method by Affymetrix


title: Low Capacity Runner - Sedentary Number 3 - Left Ventricle

description: Commercial method by Affymetrix


title: High Capacity Runner - Exercise Trained Number 5 - Left Ventricle

description: Commercial method by Affymetrix


title: Low Capacity Runner - Exercise Trained Number 1 - Left Ventricle

description: Commercial method by Affymetrix


title: Female_Aroclor_High

city: Niskayuna

first: Erik

middle: A

last: Carlson

state: NY

address: 1 Research Circle

institute: General Electric

description: Recontrast of model output to generate natural log fold change estimate of the average female rat receiving 60mg/kg/d Aroclor 1254 over female 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).

source_name: Liver from Female Rats receiving 60mg/kg/d Aroclor and female corn oil controls

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

value: Female

tag: Chemical

value: Aroclor 1254

tag: Dose


title: Female_Aroclor_Low

description: Recontrast of model output to generate natural log fold change estimate of the average female rat receiving 0.6mg/kg/d Aroclor 1254 over female corn oil control

source_name: Liver from Female Rats receiving 0.6mg/kg/d Aroclor and female corn oil controls


title: Low Capacity Runner - Exercise Trained Number 2 - Left Ventricle

description: Commercial method by Affymetrix


title: High Capacity Runner - Sedentary Number 4 - Left Ventricle

description: Commercial method by Affymetrix


title: Low Capacity Runner - Sedentary Number 6 - Left Ventricle

description: Commercial method by Affymetrix


title: High Capacity Runner - Sedentary Number 3 - Left Ventricle

description: Commercial method by Affymetrix

value: Female, Age:7 months, Tissue:Left Ventricle


title: Female_TCDD_High

description: Recontrast of model output to generate natural log fold change estimate of the average female rat receiving 3ug/kg/d TCDD over female corn oil control

source_name: Liver from Female Rats receiving 3ug/kg/d TCDD and female corn oil controls

value: TCDD


title: High Capacity Runner - Sedentary Number 6 - Left Ventricle

description: Commercial method by Affymetrix


title: Male_Aroclor_Medium

description: Natural log fold change estimate of the average male rat receiving 6mg/kg/d Aroclor 1254 over male corn oil control

source_name: Liver from Male Rats receiving 6mg/kg/d Aroclor and male corn oil controls

value: Male


title: Male_Aroclor_High

description: Natural log fold change estimate of the average male rat receiving 60mg/kg/d Aroclor 1254 over male corn oil control

source_name: Liver from Male Rats receiving 60mg/kg/d Aroclor and male corn oil controls


title: Male_Aroclor_Low

description: Natural log fold change estimate of the average male rat receiving 0.6mg/kg/d Aroclor 1254 over male corn oil control

source_name: Liver from Male Rats receiving 0.6mg/kg/d Aroclor and male corn oil controls


title: Male_TCDD_High

description: Natural log fold change estimate of the average male rat receiving 3ug/kg/d TCDD over male corn oil control

source_name: Liver from Male Rats receiving 3ug/kg/d TCDD and male corn oil controls


title: X_intercept

description: Linear model output for the X intercept in natural log scale. Equivalent to the natural log of the baseline expression level of the average male rat receiving corn oil

source_name: Liver from Male rats receiving corn oil

value: Vehicle Control

value: NA (Baseline)


title: Male_TCDD_Medium

description: Natural log fold change estimate of the average male rat receiving 0.3ug/kg/d TCDD over male corn oil control

source_name: Liver from Male Rats receiving 0.3ug/kg/d TCDD and male corn oil controls


title: Female_Aroclor_Medium

description: Recontrast of model output to generate natural log fold change estimate of the average female rat receiving 6mg/kg/d Aroclor 1254 over female corn oil control

source_name: Liver from Female Rats receiving 6mg/kg/d Aroclor and female corn oil controls


title: Saccharopolyspora RNA at 60h biological rep.B

status: Public on Jan 02 2008

city: Segrate - Milan

first: Giorgio

last: Corti

address: via Fratelli Cervi 93

department: Institute of Biomedical Technologies

country: Italy

institute: National Research Council

description: Gene expression data from Saccharopolyspora erythraea after 60h of growth

hyb_protocol: The labelled cDNAs were then hybridised for 16h at 50°C on individual GeneChips

scan_protocol: GeneChips were washed and stained with streptavidin-conjugated phycoerythrin by using the Fluidic Station FS450 (Affymetrix) following the ProkGE-WS2v3_450 Protocol. Fluorescent images of the microarrays were acquired using a GeneChip Scanner 3000 (Affymetrix).

data_processing: Raw data quality was assessed considering MAS5.0 control parameters after a global scaling at a target intensity of 100. Quality and control parameters as well as boxplot of raw intensities indicated the overall high quality of the data set and the absence of any outlying sample. Probe level data was converted to expression values using both Robust Multi-array Average procedure  and MAS5.0 algorithms. In the former case, PM values have been background adjusted, normalized using invariant set normalization, and log transformed. In the latter case, intensity levels have been normalized using the Global Scaling option to target value (i.e., TGT=100).

organism: Saccharopolyspora erythraea

source_name: RNA extracted from Saccharopolyspora erythraea after 60h of growth

label_protocol: The RNAs were processed following the Affymetrix Protocol Target Labeling for Prokaryotic GeneChip® Antisense Arrays (Affymetrix Procaryotic gene Expression Manual). The protocol consists in cDNA synthesis by reverse transcription (starting with 10 µg RNA), followed by cDNA fragmentation with DNase I and labelling with Terminal Deoxynucleotidyl Transferase.

growth_protocol: A dense culture of Sac. erythraea grown in oat meal agar was  inoculated into SCM liquid medium (20 g soytone, 15 g soluble starch, 10.5 g morpholinepropanesulfonic acid, 1.5 g yeast extract and 0.1 g CaCl2 per liter of distilled H2O) and grown for 48 h at 33ºC at 200 rpm. The culture was then stored as 1-ml frozen aliquots, which were individually used to inoculate three independent 500 ml buffled flasks each containing 100 ml SCM medium. After 12 h at 33ºC and 200 rpm, 1 ml samples, from each flask, were withdrawn, separating the mycelium from the broth by centrifugation.

extract_protocol: For each time point, RNA was extracted from mycelium pellets deriving fron 1 ml culture samples using the GeneElute™ total RNA Purification Kit (SIGMA), recovering it in 50 µl of Elution Solution.

treatment_protocol: No treatment.

tag: strain

value: NRRL 2338


title: Saccharopolyspora RNA at 32h biological rep.B

description: Gene expression data from Saccharopolyspora erythraea after 32h of growth

source_name: RNA extracted from Saccharopolyspora erythraea after 32h of growth


title: Saccharopolyspora RNA at 72h biological rep.A

description: Gene expression data from Saccharopolyspora erythraea after 72h of growth

source_name: RNA extracted from Saccharopolyspora erythraea after 72h of growth


title: Saccharopolyspora RNA at 52h biological rep.B

description: Gene expression data from Saccharopolyspora erythraea after 52h of growth

source_name: RNA extracted from Saccharopolyspora erythraea after 52h of growth


title: Saccharopolyspora RNA at 56h biological rep.B

description: Gene expression data from Saccharopolyspora erythraea after 56h of growth

source_name: RNA extracted from Saccharopolyspora erythraea after 56h of growth


title: Saccharopolyspora RNA at 60h biological rep.A


title: Spn_D39vsD39spxR6_CDM_rep2

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

growth_protocol: same as channel 1

extract_protocol: same as channel 1

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


title: Saccharopolyspora RNA at 72h biological rep.B


title: Saccharopolyspora RNA at 40h biological rep.A

description: Gene expression data from Saccharopolyspora erythraea after 40h of growth

source_name: RNA extracted from Saccharopolyspora erythraea after 40h of growth


title: Saccharopolyspora RNA at 20h biological rep.A

description: Gene expression data from Saccharopolyspora erythraea after 20h of growth

source_name: RNA extracted from Saccharopolyspora erythraea after 20h of growth


title: Saccharopolyspora RNA at 40h biological rep.B


title: Saccharopolyspora RNA at 52h biological rep.A


title: Saccharopolyspora RNA at 16h biological rep.B

description: Gene expression data from Saccharopolyspora erythraea after 16h of growth

source_name: RNA extracted from Saccharopolyspora erythraea after 16h of growth


title: Female_TCDD_Medium

description: Recontrast of model output to generate natural log fold change estimate of the average female rat receiving 0.3ug/kg/d TCDD over female corn oil control

source_name: Liver from Female Rats receiving 0.3ug/kg/d TCDD and female corn oil controls


title: Saccharopolyspora RNA at 36h biological rep.A

description: Gene expression data from Saccharopolyspora erythraea after 36h of growth

source_name: RNA extracted from Saccharopolyspora erythraea after 36h of growth


title: Saccharopolyspora RNA at 16h biological rep.A


title: Saccharopolyspora RNA at 12h biological rep.B

description: Gene expression data from Saccharopolyspora erythraea after 12h of growth

source_name: RNA extracted from Saccharopolyspora erythraea after 12h of growth


title: Saccharopolyspora RNA at 56h biological rep.A


title: Saccharopolyspora RNA at 20h biological rep.B


title: Saccharopolyspora RNA at 32h biological rep.A


title: Saccharopolyspora RNA at 36h biological rep.B


title: Saccharopolyspora RNA at 12h biological rep.A


title: Soleus36_control

status: Public on Jan 01 2008

city: Buffalo

first: Kathleen

middle: M

last: McCormick

address: 3435 Main Street

institute: University at Buffalo

hyb_protocol: Each array was prehybridized in 3 ml GEAhyb Hybridization solution (SuperArray) containing denatured salmon sperm DNA (100 µg/ml) for at least 4 hours at 60°C and then hybridized for at least 18 hours at 60°C with the denatured probe.

scan_protocol: After washing, hybridized arrays were blocked with GEAblocking solution Q, incubated with alkaline phosphatase-conjugated streptavidin (1:8000), and then incubated with CPD-Star chemiluminescent substrate (SuperArray) for signal detection by CCD camera (Kodak 2000MM Multimodal Imaging System).

data_processing: Spot intensity was analyzed with Kodak Digital Science Image Analysis Software (version 4.0) using local background-corrected mean intensity values for each spot.  All data were normalized to GAPDH after calculation of a gene stability measure for four different housekeeping genes revealed that GAPDH had the most stable expression.

source_name: soleus muscle, control

label_protocol: Equivalent amounts of total RNA were reverse transcribed and subsequently amplifed in the presence of biotin-16-dUTP with the AmpoLabeling-LPR Kit (SuperArray) according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted with the Rneasy Mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Muscles were frozen in liquid nitrogen and stored at -80°C prior to RNA extraction.

tag: Strain:Fisher 344


title: Soleus5_control


title: Soleus52_exercise

source_name: soleus muscle, exercise


title: Soleus57_control


title: Soleus16_exercise


title: Soleus27_control


title: Soleus58_control


title: Soleus61_control


title: Soleus13_exercise


title: Soleus11_exercise


title: comparison of HL60 cell and HL60-RG cell

city: Shanghai

first: Luan

last: Yang

address: 555 Zu Chong Zhi Road , Zhang Jiang Hi-Tech Park, Pudong,

country: China

institute: Shanghai Institute of Materia Medica , Chinese Academy of Sciences

hyb_protocol: according to the standard GeneChip Mapping 10K (V2.0) Xba Assay protocol (Affymetrix Inc., Santa Clara, CA).Hybridized arrays were processed with an Affymetrix Fluidics Station 450.

scan_protocol: fluorescence signals were detected using the Affymetrix GeneChip Scanner 3000.

data_processing: Alleles (AA, AB, or BB) at each SNP were called using the algorithm of Affymetrix software package GDAS. The generated CEL. file and TXT. file were imported into a dChip software for copy number analysis. Regional LOH was identified whenever an uninterrupted contiguous stretch of >50 homozygous (AA or BB) genotypes was encountered, with the segments of DNA greater than ~15Mb.

source_name: cell line

growth_protocol: cell were cultured in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum and kanaMYCin (50 µg/ml). The cultures were incubated at 37 °C in a 5% CO2 atmosphere with 100% humidity.

extract_protocol: Total genomic DNA was extracted from cells using a DNA Extractor WB Kit (Wako Pure Chemical Industries, Osaka, Japan). Total RNA was isolated and purified from cells by RNeasy columns (Qiagen, Valencia, CA).

tag: HL60 cell line，derived from the human acute promyelotic leukemia, can be induced to differentiate to morphologically and functionally mature granulocyutes.HL60-RG is the sub-line of the HL60, was isolated after a long-term continuous culture of HL60, having faster growth rate with doubling time around 20hr, about half the HL60’s.


title: Soleus19_exercise


title: Medial substantia nigra Parkinson's disease case 36 -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 (MNPD36A)

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.

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: 76; gender:M


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

description: Gene expression data from medial substantia nigra (MNPD34A)

value: 84; gender:F


title: mock transfected A

city: Chicago

first: Jess

last: Leber

state: IL

address: 920 E. 58th Street CLSC 615

department: Microbiology

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

source_name: aRNA from WT macrophage, mock transfected

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.

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

treatment_protocol: Macrophages were transfected with ligands using FuGene 6, and all RNA was harvested after 6 hours.

tag: primary macrophage from C57BL/6 mouse

source_name: aRNA from reference pool

tag: pooled from all samples used


title: MDP A

description: biological replicate 1 of 2

source_name: aRNA from WT macrophage, transfected with MDP

tag: primary macrophage from C57BL/6


title: DNA + MDP A

description: biological replicate 1 of 2

source_name: aRNA from WT macrophage, transfected with DNA and MDP


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

description: Gene expression data from medial substantia nigra  (MNPD20A)

value: 75; gender:M


title: DNA + MDP B

description: biological replicate 2 of 2


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

description: Gene expression data from medial substantia nigra  (MNPD21A)


title: MDP B

description: biological replicate 2 of 2


title: DNA A

description: biological replicate 1 of 2

source_name: aRNA from WT macrophage, transfected with Lm genomic DNA


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

description: Gene expression data from medial substantia nigra (MNPD29A)


title: Medial substantia nigra control case PDC1 - A chip

description: Gene expression data from medial substantia nigra (MNPDC1A)


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

description: Gene expression data from medial substantia nigra (MNPD28A)

value: 82; gender:M


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

description: Gene expression data from medial substantia nigra (MNPD22A)

value: 76; gender:F


title: mock transfected B

description: biological replicate 2 of 2


title: DNA B

description: biological replicate 2 of 2


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

description: Gene expression data from medial substantia nigra (MNPD32A)

value: 89; gender:M


title: Soleus63_control


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

description: Gene expression data from medial substantia nigra (MNPD16A)

value: 85; gender:F


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

description: Gene expression data from medial substantia nigra (MNPD10A)

value: 81; gender:F


title: WT BMM WT Lm 180 min - CAPE B

description: biological replicate 2 of 2

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

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.

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.


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

description: Gene expression data from medial substantia nigra (MNPD07A)

value: 78; gender:M


title: WT BMM Uninfected + CAPE B

description: biological replicate 2 of 2

source_name: aRNA from WT macrophage, uninfected, treated with CAPE


title: WT BMM Uninfected + CAPE A

description: biological replicate 1 of 2