title: Adipose Pool vs Adipose_Sample_40


title: Adipose Pool vs Adipose_Sample_30

status: Public on Jun 13 2007

type: RNA

city: Seattle

first: Valur

last: Emilsson

state: WA

address: 401 Terry Avenue N

department: Genetics

country: USA

institute: Merck

description: The genetics of human gene expression from population based tissue sampling

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

molecule: total RNA

organism: Homo sapiens

source_name: Adipose

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: Adipose Pool


title: Adipose Pool vs Adipose_Sample_39


title: Adipose Pool vs Adipose_Sample_28


title: Adipose Pool vs Adipose_Sample_47


title: Adipose Pool vs Adipose_Sample_29


title: Adipose Pool vs Adipose_Sample_33


title: Adipose Pool vs Adipose_Sample_37


title: Adipose Pool vs Adipose_Sample_38


title: Adipose Pool vs Adipose_Sample_32


title: Adipose Pool vs Adipose_Sample_31


title: Adipose Pool vs Adipose_Sample_36


title: Adipose Pool vs Adipose_Sample_26


title: Adipose Pool vs Adipose_Sample_25


title: Adipose Pool vs Adipose_Sample_27


title: Adipose Pool vs Adipose_Sample_24


title: Adipose Pool vs Adipose_Sample_23


title: Adipose Pool vs Adipose_Sample_21


title: Adipose Pool vs Adipose_Sample_12


title: Adipose Pool vs Adipose_Sample_19


title: Adipose Pool vs Adipose_Sample_41


title: Adipose Pool vs Adipose_Sample_17


title: Adipose Pool vs Adipose_Sample_16


title: Adipose Pool vs Adipose_Sample_22


title: Adipose Pool vs Adipose_Sample_18


title: Adipose Pool vs Adipose_Sample_11


title: Adipose Pool vs Adipose_Sample_15


title: Adipose Pool vs Adipose_Sample_20


title: Adipose Pool vs Adipose_Sample_9


title: Adipose Pool vs Adipose_Sample_5


title: Adipose Pool vs Adipose_Sample_13


title: Adipose Pool vs Adipose_Sample_14


title: Adipose Pool vs Adipose_Sample_10


title: Adipose Pool vs Adipose_Sample_8


title: Adipose Pool vs Adipose_Sample_4


title: Adipose Pool vs Adipose_Sample_3


title: Adipose Pool vs Adipose_Sample_7


title: Adipose Pool vs Adipose_Sample_6


title: NO_KIDNEY_11

status: Public on Jun 12 2007

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

description: Gene expression data from human normal kidney tissue and human kidney tumor tissues. Tumor subtypes include Papillary types 1, 1.2A, 2A, and 2B.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with custom CDF environments created by the MBNI - The version 6 entrez gene ID CDF was used.

label: R-Phycoerythrin Streptavidin (SAPE), from Molecular Probes, 1 mg/ml  ( we use 6 ul per reaction )

source_name: subtype: NO

label_protocol: 10 ug of Qiagen-purified total RNA

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

tag: subtype

value: NO


title: NO_KIDNEY_8


title: NO_KIDNEY_7


title: NO_KIDNEY_9


title: NO_KIDNEY_10


title: NO_KIDNEY_4


title: NO_KIDNEY_6


title: Adipose Pool vs Adipose_Sample_1


title: NO_KIDNEY_5


title: P2B_KIDNEY_10

source_name: subtype: P2B


title: P2B_KIDNEY_12


title: P2B_KIDNEY_11


title: NO_KIDNEY_1


title: P2B_KIDNEY_4


title: P2B_KIDNEY_8


title: P2B_KIDNEY_7


title: P2B_KIDNEY_2


title: P2B_KIDNEY_5


title: NO_KIDNEY_2


title: P2A_KIDNEY_4

source_name: subtype: P2A


title: P2B_KIDNEY_1


title: P2B_KIDNEY_9


title: P2B_KIDNEY_3


title: P2B_KIDNEY_6


title: P2A_KIDNEY_3


title: P2A_KIDNEY_2


title: P2A_KIDNEY_1


title: NO_KIDNEY_3


title: P1.2A_KIDNEY_5

source_name: subtype: P1.2A


title: P1.2A_KIDNEY_4


title: P1.2A_KIDNEY_2


title: Adipose Pool vs Adipose_Sample_2


title: P1.2A_KIDNEY_3


title: P1_KIDNEY_14

source_name: subtype: P1


title: P1_KIDNEY_12


title: P1_KIDNEY_13


title: P1_KIDNEY_10


title: P1_KIDNEY_8


title: P1_KIDNEY_5


title: P1_KIDNEY_7


title: P1_KIDNEY_3


title: P1_KIDNEY_11


title: P1_KIDNEY_9


title: P1_KIDNEY_2


title: P1_KIDNEY_4


title: P1.2A_KIDNEY_1


title: P1_KIDNEY_6


title: VDXRHU_1959

status: Public on Jun 11 2007

city: Toronto

first: Benjamin

last: Haibe-Kains

state: Ontario

address: 610 University Avenue

department: Princess Margaret Research

country: Canada

institute: Princess Margaret Cancer Centre

hyb_protocol: standard Affymetrix procedures.

scan_protocol: standard Affymetrix procedures.

data_processing: MAS5 Bioconductor (target value of 600).

label: biotin

label_protocol: Approximately 1 microgram of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Isolation of RNA was performed using the Trizol method (Invitrogen) according to the manufacturers instructions and was purified using RNeasy mini-columns (Qiagen, Valencia, CA). The quality of the RNA obtained from each tumour sample was assessed based on the RNA profile generated by the bioanalyzer (Agilent Inc)olation of RNA was performed using the Trizol method (Invitrogen) according to the manufacturers instructions and was purified using RNeasy mini-columns (Qiagen, Valencia, CA). The quality of the RNA obtained from each tumour sample was assessed based on the RNA profile generated by the bioanalyzer (Agilent Inc).

tag: samplename

tag: id

tag: filename

tag: hospital

value: RH

tag: age

tag: size

tag: Histtype

tag: Angioinv

tag: node

tag: grade

tag: er

tag: risksg

tag: NPI

tag: risknpi

value: Poor


title: VDXKIU_266C51

value: KAR

value: Good


title: VDXOXFU_869

value: JRH


title: P1_KIDNEY_1


title: VDXIGRU_255160

value: IGR


title: VDXIGRU_287897


title: VDXRHU_329


title: Pancreas at e15.5, Chip A, rep 1

status: Public on Jun 09 2007

city: Maaloev

first: Andreas

last: Petri

address: Novo Nordisk Park D6 2.154

department: Molecualr Genetics

country: Denmark

institute: Novo Nordisk A/S

description: Gene expression data from dorsal pancreas at e15.5, MG-U74A version2

hyb_protocol: Standard Affymetrix hybridization protocol was followed.

scan_protocol: Standard Affymetrix scan protocol was followed.

data_processing: The data were analyzed using the R environment and Bioconductor packages and expression summaries were based on the default RMA algorithm.

organism: Mus musculus

source_name: Pancreas at e15.5

label_protocol: Standard Affymetrix labelling protocol was followed.

growth_protocol: Time mated NMRI mice (M&B, Ry, Denmark) were killed by cervical dislocation at embryonic day 12.5, 13.5, 14.5, 15.5, or 16.5. Embryos were placed in ice cold PBS and decapitated, and the dorsal pancreas was removed by dissection with DUMONT #SS Biologie forceps (Fine Science Tools) using an inverted microscope. Only dorsal pancreatic buds were isolated due to the difficulty of isolating ventral pancreas at early stages. Dorsal pancreata from a litter were pooled and stored in RNAlater (Ambion) at 4C until RNA isolation (no more than one week).

extract_protocol: Pancreata stored in RNAlater were collected by centrifugation at 100 x g for 15 minutes followed by removal of RNAlater. The tissue was homogenized in Eppendorf tubes by addition of 500μl TRIzol (GibcoBRL/Life Technologies) and grinding with disposable pistils (Buch & Holm, Denmark). Total RNA isolation was performed as described in the standard TRIzol procedure. Following RNA isolation genomic DNA contamination was eliminated using DNAfree (Ambion) according to manufacturer’s instructions and total RNA was purified on RNeasy columns (Qiagen) following the standard protocol. RNA integrity was assessed by gel electrophoresis using 1% ethidium bromide containing agarose gels. The amount of isolated RNA was quantified spectrophotometrically on an UltroSpec 2100pro (Amersham Bioscience).

tag: Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74A


title: VDXIGRU_280352


title: Pancreas at e15.5, Chip A, rep 2


title: VDXGUYU_4080

value: GUY


title: Pancreas at e16.5, Chip A, rep 2

description: Gene expression data from dorsal pancreas at e16.5, MG-U74A version2

scan_protocol: Standard Affymetrix hybridization protocol was followed.

source_name: Pancreas at e16.5


title: Pancreas at e13.5, Chip A, rep 1

description: Gene expression data from dorsal pancreas at e13.5, MG-U74A version2

source_name: Pancreas at e13.5


title: Pancreas at e14.5, Chip A, rep 1

description: Gene expression data from dorsal pancreas at e14.5, MG-U74A version2

source_name: Pancreas at e14.5


title: Pancreas at e12.5, Chip A, rep 2

description: Gene expression data from dorsal pancreas at e12.5, MG-U74A version2

source_name: Pancreas at e12.5


title: Pancreas at e14.5, Chip A, rep 2


title: Pancreas at e13.5, Chip A, rep 2


title: Pancreas at e16.5, Chip A, rep 1


title: Pancreas at e15.5, Chip B, rep 2

description: Gene expression data from dorsal pancreas at e15.5, MG-U74B version2

tag: Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74B


title: VDXIGRU_254031


title: Pancreas at e12.5, Chip A, rep 1


title: Pancreas at e16.5, Chip B, rep 2

description: Gene expression data from dorsal pancreas at e16.5, MG-U74B version2


title: Pancreas at e15.5, Chip B, rep 1


title: Pancreas at e14.5, Chip B, rep 1

description: Gene expression data from dorsal pancreas at e14.5, MG-U74B version2


title: Pancreas at e16.5, Chip B, rep 1


title: Pancreas at e14.5, Chip B, rep 2


title: Pancreas at e12.5, Chip B, rep 1

description: Gene expression data from dorsal pancreas at e12.5, MG-U74B version2


title: Pancreas at e13.5, Chip B, rep 1

description: Gene expression data from dorsal pancreas at e13.5, MG-U74B version2


title: Pancreas at e12.5, Chip B, rep 2


title: Pancreas at e15.5, Chip C, rep 1

description: Gene expression data from dorsal pancreas at e15.5, MG-U74C version2

tag: Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74C


title: Pancreas at e13.5, Chip B, rep 2


title: Pancreas at e16.5, Chip C, rep 1

description: Gene expression data from dorsal pancreas at e16.5, MG-U74C version2


title: Pancreas at e15.5, Chip C, rep 2


title: Pancreas at e16.5, Chip C, rep 2


title: Pancreas at e12.5, Chip C, rep 2

description: Gene expression data from dorsal pancreas at e12.5, MG-U74C version2


title: Pancreas at e13.5, Chip C, rep 2

description: Gene expression data from dorsal pancreas at e13.5, MG-U74C version2


title: Pancreas at e13.5, Chip C, rep 1


title: Pancreas at e14.5, Chip C, rep 2

description: Gene expression data from dorsal pancreas at e14.5, MG-U74C version2


title: Pancreas at e14.5, Chip C, rep 1


title: Pancreas at e12.5, Chip C, rep 1


title: Scoelicolor_R5_22h_2

status: Public on Jun 08 2007

type: mixed

city: Minneapolis

first: Karthik

middle: P

last: Jayapal

state: MN

address: 421 Washington Ave SE

department: Chemical Engineering and Materials Science

institute: University of Minnesota

description: No additional description

hyb_protocol: The labeled cDNA and gDNA were then mixed and co-hybridized to microarray slides in the presence of 50% formamide.  After 16 hours incubation at 50°C, slides were washed and scanned.

scan_protocol: Arrays were scanned using ScanArray5000 (Perkin Elmer, Wellesley, MA). Images were analyzed using GenePix (Axon Instruments, Union City, CA) to obtain raw intensity data for each spot.  The median fluorescence intensity from each spot was used for all subsequent analysis.

data_processing: A quantile normalization method was employed to normalize these log2 ratios from each hybridization (S Mehra, W Lian, KP Jayapal, SP Charaniya, DH Sherman, WS Hu: A framework to analyze multiple time series data: a case study with Streptomyces coelicolor. J Ind Microbiol Biotechnol 2006, 33:159-72).  The resulting log2 ratios were not only used to compare transcript levels of the same mRNA species in different biological samples, but also used as an estimate of the relative abundance of each mRNA species.

label: Alexa 647

organism: Streptomyces coelicolor

source_name: S. coelicolor RNA R5- medium 22h

label_protocol: The cDNA was then incubated with Alexa 647 (Invitrogen, Carlsbad, CA) for labeling as per manufacturer's instructions.

growth_protocol: S. coelicolor A3(2) strain M145 was maintained on R5 solid agar (Kieser, T., M. J. Bibb, M. J. Buttner, K. F. Chater, and D. A. Hopwood. 2000. Practical Streptomyces Genetics. The John Innes Foundation, Norwich, UK) for high density spores.  For liquid culture, spores were pre-germinated in 2xYT medium (Kieser, T., M. J. Bibb, M. J. Buttner, K. F. Chater, and D. A. Hopwood. 2000. Practical Streptomyces Genetics. The John Innes Foundation, Norwich, UK) and inoculated into R5- liquid medium (Huang, J., C. J. Lih, K. H. Pan, and S. N. Cohen. 2001. Global analysis of growth phase responsive gene expression and regulation of antibiotic biosynthetic pathways in Streptomyces coelicolor using DNA microarrays. Genes Dev 15:3183-92) at a density of ~107 spores/ml.  Baffled 2L flasks containing stainless steel coils with 350 ml working volume were used for liquid cultures.  Cultures were incubated at 30°C in an orbital shaker at 300 rpm.  For measuring cell growth, samples were collected at regular intervals and mixed with one-eighth volume of 2.5 mM HCl and then subjected to sonication to break mycelial pellets (Brana, A. F., S. Wolfe, and A. L. Demain. 1986. Relationship between nitrogen assimilation and cephalosporin synthesis in Streptomyces clavuligerus. Arch Microbiol 146:46-51).  Absorbance of the resulting solution at 450 nm was then taken as a measure of growth.  Proper dilution was made to ensure an OD450 measurement below 1, which is in the linear range of detection.

extract_protocol: Immediately after culture samples were collected, one-fifth volume of an ice-cold stop solution (5% phenol in ethanol) (Bernstein, J. A., A. B. Khodursky, P. H. Lin, S. Lin-Chao, and S. N. Cohen. 2002. Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc Natl Acad Sci U S A 99:9697-702) was added to the sample volume to prevent RNA degradation.  The sample was quickly centrifuged at 4°C and the supernatant was discarded.  The remaining sample was then stored at -80°C.  To isolate RNA, the frozen pellets were transferred to a mortar and pestle and ground to fine powder in the presence of liquid nitrogen.  RLT solution from RNeasy Mini Kit (Qiagen Inc., Valencia, CA) was added before the ground pellets thawed.  The remaining steps for RNA isolation were carried out as per manufacturer’s instructions.  RNA integrity was determined by gel electrophoresis while its quantity and purity were estimated by UV absorbance at OD260 and OD260/OD280, respectively.Total RNA was reverse transcribed to cDNA by SuperscriptII (Invitrogen, Carlsbad, CA) with random hexamers (IDT, Coralville, IA) incorporating aminoallyl-dUTP (Ambion, Austin, TX).

tag: Strain

tag: Sample

molecule: genomic DNA

source_name: S. coelicolor gDNA

label_protocol: The DNA was labeled with Label IT® Cy3 Labeling Kit (Mirus Bio Corp., Madison, WI) according to suppliers instructions.

growth_protocol: Spores for S. coelicolor M145 were generated on Mannitol-Soy flour or R5 agar  Cultures for genomic DNA preparation were performed in YEME medium with 0.5% glycine supplement at 30°C until early stationary phase (refer to T Kieser, MJ Bibb, MJ Buttner, KF Chater, DA Hopwood: Practical Streptomyces Genetics: The John Innes Foundation, Norwich, UK; 2000).

extract_protocol: Genomic DNA (gDNA) extraction was carried out using Kirby mix procedure as described elsewhere (T Kieser, MJ Bibb, MJ Buttner, KF Chater, DA Hopwood: Practical Streptomyces Genetics: The John Innes Foundation, Norwich, UK; 2000). About 500 µl of 20 µg/µl gDNA was sonicated briefly for 30-40 sec for shearing them to ~500 bp average size (confirmed by gel electrophoresis).


title: Scoelicolor_R5_26h_2

description: No additional description

source_name: S. coelicolor RNA R5- medium 26h


title: Scoelicolor_R5_22h_1

description: No additional description


title: Scoelicolor_R5_38h_1

description: No additional description

source_name: S. coelicolor RNA R5- medium 38h


title: Me3K27 Histone H3 ChIP-ChIP from HeLa S3 Cells applied to the NimbleGen ENCODE Array; [unpublished] Sample 1

type: genomic

city: New Haven

first: Guoneng

last: Zhong

state: CT

address: 300 George St

institute: Yale Med

description: value = log_2(Signal for Cy5 / Signal for Cy3)

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html).

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Red Channel: Me3K27 Histone H3 ChIP DNA purified from HeLa S3 cells with polyclonal antibody; Green Channel: Normal rabbit IgG ChIP DNA purified from HeLa S3 cells.

source_name: Me3K27 Histone H3 ChIP DNA from HeLa S3 cells

label_protocol: ChIP DNA prepared from 1 x 10^8 cells was directly labeled by Klenow (New England Biolabs), random priming with Cy5-coupled nonamers (for Me3K27 Histone H3 ChIP DNA) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: HeLa S3 cells were grown in suspension in Joklik's modified minimal essential medium (MEM), supplemented with 5% FBS at 37C in 5% CO2, to a density of 6 x10^5 cells/ml. Cells were fixed with 1% formaldehyde at room temperature for 20 min. Fixation was terminated with 125 mM glycine (2 M stock made in 1x PBS), and cells were washed twice in cold 1x Dulbeccos PBS (Invitrogen), and then swelled on ice in 10 ml hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, and protease inhibitors). Cell lysates were homogenized with 30 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 10 ml of 1x RIPA buffer per 3 x 10^8 cells (1x RIPA buffer: 10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, and protease inhibitors). Chromatin was sheared with a Branson 250 Sonifier (power setting 2, 100% duty cycle, six 30-second pulses) to an average of 700 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with 20 ug of anti-Me3K27 Histone H3 rabbit polyclonal antibody (Upstate #07-449) per 1x10^8 cells. Following this incubation Protein A agarose (Upstate) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol, 2 volumes of 100% ethanol and 1.5 ul of pellet paint (Novagen).

tag: Polyclonal antibody

source_name: normal rabbit IgG ChIP DNA from HeLa S3 cells

label_protocol: ChIP DNA prepared from 1 x 10^8 cells was directly labeled by Klenow (New England Biolabs), random priming with Cy3-coupled nonamers (for normal rabbit IgG ChIP DNA) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: HeLa S3 cells were grown in suspension in Joklik's modified minimal essential medium (MEM), supplemented with 5% FBS at 37C in 5% CO2, to a density of 6 x10^5 cells/ml. Cells were fixed with 1% formaldehyde at room temperature for 20 min. Fixation was terminated with 125 mM glycine (2 M stock made in 1x PBS), and cells were washed twice in cold 1x Dulbeccos PBS (Invitrogen), and then swelled on ice in 10 ml hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, and protease inhibitors). Cell lysates were homogenized with 30 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 10 ml of 1x RIPA buffer per 3 x 10^8 cells (1x RIPA buffer: 10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, and protease inhibitors). Chromatin was sheared with a Branson 250 Sonifier (power setting 2, 100% duty cycle, six 30-second pulses) to an average of 700 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with 20 ug of normal rabbit IgG per 1x10^8 cells. Following this incubation Protein A agarose (Upstate) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol, 2 volumes of 100% ethanol and 1.5 ul of pellet paint (Novagen).

tag: Normal rabbit IgG


title: Scoelicolor_R5_11h_1

description: No additional description

source_name: S. coelicolor RNA R5- medium 11h


title: Scoelicolor_R5_26h_1

description: No additional description


title: Scoelicolor_R5_38h_2

description: No additional description


title: Scoelicolor_R5_14h_2

description: No additional description

source_name: S. coelicolor RNA R5- medium 14h


title: Scoelicolor_R5_34h_1

description: No additional description

source_name: S. coelicolor RNA R5- medium 34h


title: Scoelicolor_R5_14h_1

description: No additional description


title: Slividans_Scoelicolor_CGH_1

description: No additional description

hyb_protocol: Samples containing ~500 ng each of Cy3 and Cy5 labeled gDNA from S. coelicolor M145 and S. lividans TK21 respectively were hybridized to a whole-genome S. coelicolor microarray as described previously (S Mehra, W Lian, KP Jayapal, SP Charaniya, DH Sherman, WS Hu: A framework to analyze multiple time series data: a case study with Streptomyces coelicolor. J Ind Microbiol Biotechnol 2006, 33:159-72).

scan_protocol: Hybridizations were carried out in triplicate for ~16 hr at 50°C; arrays were washed and scanned using ScanArray5000 (Perkin Elmer, Wellesley, MA). Images were analyzed using GenePix (Axon Instruments, Union City, CA) to obtain raw intensity data for each spot.  The median fluorescence intensity from each spot was used for all subsequent analysis.

data_processing: Raw relative intensity values for each spot were first normalized by scaling one of the gDNA channel signal intensities by a normalization factor to set the total intensity from both channels as equal. Log2 hybridization signal ratios were then calculated from normalized intensities as log2[gDNASliv/gDNAScoe] and values were averaged using the median from triplicate experiments.

organism: Streptomyces lividans

source_name: S. lividans TK21 gDNA

label_protocol: The DNA was labeled with Label IT® Cy5 Labeling Kit (Mirus Bio Corp., Madison, WI) according to suppliers instructions.

growth_protocol: Spores for S. lividans TK21 were generated on Mannitol-Soy flour or R5 agar  Cultures for genomic DNA preparation were performed in YEME medium with 0.5% glycine supplement at 30°C until early stationary phase (refer to T Kieser, MJ Bibb, MJ Buttner, KF Chater, DA Hopwood: Practical Streptomyces Genetics: The John Innes Foundation, Norwich, UK; 2000).

tag: Sheared genomic DNA

source_name: S. coelicolor M145 gDNA


title: Scoelicolor_R5_7h_1

description: No additional description

source_name: S. coelicolor RNA R5- medium 7h


title: Slividans_Scoelicolor_CGH_2

description: No additional description

extract_protocol: Genomic DNA (gDNA) extraction was carried out using Kirby mix procedure as described elsewhere (T Kieser, MJ Bibb, MJ Buttner, KF Chater, DA Hopwood: Practical Streptomyces Genetics: The John Innes Foundation, Norwich, UK; 2000). About 500 µl of 20 µg/µl gDNA was sonicated briefly for 30-40 sec for shearing them to ~500 bp average size (confirmed by gel electrophoresis). The DNA was then labeled with Label IT® Cy3 or Cy5 Labeling Kit (Mirus Bio Corp., Madison, WI) according to suppliers instructions.

growth_protocol: Spores for S. coelicolor M145 were generated on Mannitol-Soy flour or R5 agar  Cultures for genomic DNA preparation were performed in YEME medium with 0.5% lycine supplement at 30°C until early stationary phase (refer to T Kieser, MJ Bibb, MJ Buttner, KF Chater, DA Hopwood: Practical Streptomyces Genetics: The John Innes Foundation, Norwich, UK; 2000).


title: Clostridium_acetobutylicum_Platform_Test_Amount_5_0_microg_PMT_80_40

status: Public on Jun 07 2007

city: Newark

first: Eleftherios

middle: Terry

last: Papoutsakis

state: DE

address: 15 Innovation Way

department: Chemical Engineering

institute: University of Delaware

description: No additional information.

hyb_protocol: Arrays were hybridized following a slightly modified version of the Agilent 60-mer oligo microarray processing protocol v2.0 for 22K arrays protocol. Briefly, oppositely labeled microarray probe pairs (0.75 microg of each) were mixed together, and brought to a final volume of 200 microL using ddH20. The samples were incubated at 98 degrees C for 3 min, spun, and 50 microL of pre-aliquoted 10x control targets and 250 microL of Agilent 2x hybridization buffer was added. 490 microL of the mixture were loaded on the microarray and hybridized for 17 h in a 65 degrees C on a hybridization oven rotating at 4 rpm. Arrays were washed following a slightly modified version of the Two-Color Microarray-Based Gene Expression Analysis Protocol for 22K Agilent oligo microarrays Version 4.0.2 April 2006. Briefly, the slide rack was washed washed twice on 100% acetonitrile for 5 minutes (each wash) and rinsed with copious amounts of ddH2O.  After disassembling the hybridization chamber, the array-gasket sandwiches were submerged into Gene Expression Wash Buffer 1 and opened. The microarray slide was then submerged into fresh Gene Expression Wash Buffer 1 and the liquid was stirred for 1 minute. In the next step, the slides were submerged into Gene Expression Wash Buffer 2 at 37 degrees C stirred for 1 minute and then submerged into and also stirred for 1 minute. Finally, slides were submerged into the Stabilization and Drying Solution and stirred for 30 seconds.

scan_protocol: Scanned using a G2565BA Agilent Microarray Scanner (Agilent, Wilmington, DE, USA) at 10 micrometers resolution and PMTs were set to 60 and 40.

data_processing: Agilent Feature Extraction software (v.8.5) was used to assess spot quality and extract feature intensity statistics; duplicate spots were averaged; background-subtracted data were normalized using SNNLERM (Yang et al., PNAS 2003; 100:1122-1127)

organism: Clostridium acetobutylicum

source_name: Mixture of mRNAs from C. acetobutylicum ATCC824 strain growing in exponential phase.

label_protocol: An indirect labeling approach was followed where cDNA was first made in the presence of nucleotides and aminoallyl dUTP, purified, and then the aminoallyl dUTP groups were coupled to a monoreactive dye (Cy3 or Cy5). Total RNA (25 microg) was mixed with 15 microg random hexamers (Roche, Indianapolis, IN, USA) and the volume brought up to 18.5 microL with RNase-free water. Samples were incubated at 70 degrees C for 10 min and then snap-frozen in a dry ice/ethanol bath for 30 sec. Deoxynucleotide triphosphates (Invitrogen; 0.6 mM dATP, 0.4 mM dCTP, 0.4 mM dGTP, and 0.36 mM dTTP), 0.24 mM aminoallyl dUTP (Sigma), 400 units SuperScript II reverse transcriptase (Invitrogen), First Strand Buffer (Invitrogen), and 6 microM dithiothreitol were added to a final volume of 30 microL. The samples were incubated for 3 h to overnight at 42 degrees C, and the reaction was stopped by addition of 0.5 M EDTA (pH 8.0). The remaining RNA was degraded by addition of NaOH (final concentration 11 mM), incubation at 65oC for 15 min, and neutralization with HCl (final concentration 11 mM). The cDNA was purified by bringing up the volume to 450 microL with sterile water and concentrating three times on a Millipore YM-30 column. The samples were dried in a rotary SpeedVac, redissolved in 4.5 microL of a 0.1 M sodium carbonate buffer (pH 9.0), and combined with 54 nmol NHS-ester Cy3 or Cy5 monofunctional dye (Amersham Biosciences) dissolved in an equal volume of DMSO. The mixture was incubated in the dark for 1 h. To purify the labeled cDNA, 35 microL of a 100 mM sodium acetate solution (pH 5.2) was added before purifying on a Qiagen Qiaquick PCR purification column (Valencia, CA, USA). cDNA quantity, quality, and dye incorporation was measured (A260, A280, A550 [Cy3 probe], and A649 [Cy5 probe]) on a spectrophotometer. Only samples with a dye incorporation of at least 10 dye molecules per 1,000 nucleotides were hybridized on microarrays. Samples were stored at -20 degrees C for up to 3 weeks until microarray hybridization.

growth_protocol: C. acetobutylicum was stored at -85 degrees C in clostridial growth media (CGM) (94) containing 15% glycerol. Solid cultures were carried out on agar-solidified 2xYTG (YTG is 8 g/liter tryptone, 5 g/liter yeast extract, 2 g/liter NaCl, 2.5 g/liter glucose, and 7.5 g/l agar, pH 5.8) plates. Liquid cultures were inoculated with single colonies from plates at least 4 days old and heat shocked at 70 to 80°C for 10 min. Cultures were grown in an anaerobic chamber (Forma Scientific, Marietta, OH) in Clostridial Growth Medium (CGM, Wiesenborn, D. P., et al. 1988. Appl. Environ. Microbiol. 54:2717-2722) supplemented with 80 g/liter glucose.

extract_protocol: Cell pellets were collected by centrifuging 3 to 10 mL of cultures at 5,000xg for 10 min, 4 degrees C. Cells were then lysed by resuspending in 200 microL SET buffer (25% sucrose, 50 mM EDTA [pH 8.0], 50 mM Tris [pH 8.0]) with 20 mg/mL lysozyme (Sigma) and incubation at 37 degrees C for 4 min. One milliliter of ice cold TRIzol (Invitrogen, Carlsbad, CA, USA) was added and the sample was vortexed. Samples were immediately stored at -85 degrees C and used within one month to minimize RNA degradation. To isolate and purify the RNA, samples were thawed at room temperature; 500 microL of sample was diluted with an equal amount of ice cold TRIzol and then purified following manufacturer's instructions. The RNA was resuspended in 20-30 microL RNase-free water and quantitated in a spectrophotometer by measuring absorbance at 260 and 280 nm. Samples were only used if the A260/A280 ratio was greater than 1.8. RNA integrity was also verified by running 0.5 microL of sample on a 1.0% agarose gel. Purified RNA were stored at -85 degree C and used within one week of purification.

treatment_protocol: Samples taken at OD (600 nm) = {1.09, 1.8, 2.6, 2.0} were mixed together.

tag: Clostridium acetobutylicum ATCC 824

source_name: Mixture of mRNAs from C. acetobutylicum M5 strain growing in exponential phase.

label_protocol: Same as channel 1

growth_protocol: Same as channel 1

extract_protocol: Same as channel 1

tag: Clostridium acetobutylicum M5


title: Scoelicolor_R5_16h_1

description: No additional description

source_name: S. coelicolor RNA R5- medium 16h


title: Clostridium_acetobutylicum_Platform_Test_Amount_5_0_microg_PMT_60_10

description: No additional information.

scan_protocol: Scanned using a G2565BA Agilent Microarray Scanner (Agilent, Wilmington, DE, USA) at 10 micrometers resolution and PMTs were set to 60 and 10.


title: Slividans_Scoelicolor_CGH_3

description: No additional description

growth_protocol: Spores for S. lividans TK21 were generated on Mannitol-Soy flour or R5 agar  Cultures for genomic DNA preparation were performed in YEME medium with 0.5% lycine supplement at 30°C until early stationary phase (refer to T Kieser, MJ Bibb, MJ Buttner, KF Chater, DA Hopwood: Practical Streptomyces Genetics: The John Innes Foundation, Norwich, UK; 2000).


title: Clostridium_acetobutylicum_Platform_Test_Amount_5_0_microg_PMT_100_100

description: No additional information.

scan_protocol: Scanned using a G2565BA Agilent Microarray Scanner (Agilent, Wilmington, DE, USA) at 10 micrometers resolution and PMTs were set to 100 and 100.


title: Me3K27 Histone H3 ChIP-ChIP from HeLa S3 Cells applied to the NimbleGen ENCODE Array; [unpublished] Sample 3


title: Clostridium_acetobutylicum_Platform_Test_Amount_5_0_microg_PMT_80_10

description: No additional information.

scan_protocol: Scanned using a G2565BA Agilent Microarray Scanner (Agilent, Wilmington, DE, USA) at 10 micrometers resolution and PMTs were set to 80 and 10.


title: Me3K27 Histone H3 ChIP-ChIP from HeLa S3 Cells applied to the NimbleGen ENCODE Array; [unpublished] Sample 2


title: Clostridium_acetobutylicum_Platform_Test_Amount_3_0_microg_PMT_80_40

description: No additional information.

scan_protocol: Scanned using a G2565BA Agilent Microarray Scanner (Agilent, Wilmington, DE, USA) at 10 micrometers resolution and PMTs were set to 80 and 40.


title: Clostridium_acetobutylicum_Platform_Test_Amount_1_0_microg_PMT_80_40

description: No additional information.


title: Clostridium_acetobutylicum_Platform_Test_Amount_1_0_microg_PMT_80_20

description: No additional information.

scan_protocol: Scanned using a G2565BA Agilent Microarray Scanner (Agilent, Wilmington, DE, USA) at 10 micrometers resolution and PMTs were set to 80 and 20.


title: SAM vs seedling_6H

city: Ames

first: Patrick

middle: S.

last: Schnable

state: IA

address: 2035B Roy J Carver Co-Lab

institute: Iowa State University

description: RNA was isolated from six to ten LCM-collected SAMs using PicoPure RNA Isolation Kit (Arcturus) as per manufacturer’s instructions to generate one biological replication. RNA was also isolated from six above-ground portions of seedlings using “home made Trizol” solution (see full protocol description of extract for details) to generate one biological replication. In total, six biological replications were prepared. Approximately 10 ng of total RNA from each biological replication were used as starting material for T7-based linear RNA amplification, performed as described by Nakazono et al. (2003, Plant Cell 15: 583-596). Each biological replication yielded between 10 and 50 g of amplified RNA (aRNA). Two micrograms of aRNA for each sample was indirectly labeled with Cy dye and hybridized to the GPL2557 platforms.

hyb_protocol: Microarray slides were prehybridized in 5X SSC (1X SSC is 0.15 M NaCl and 0.015 M sodium citrate), 0.1% SDS, and 0.1 mg/ml bovine serum albumin at 42oC for 45 min, then rinsed with autoclaved, Millipore water, dipped in isopropanol, and dried by centrifugation. Each target was resuspended in 30 l hybridization solution (5X SSC, 0.1% SDS, 0.2 g/l of yeast tRNA, 0.2 g/l of polyadenylic acid, 25% super-pure (99.5%) formamide (Fisher Scientific). Targets hybridized to the same slide were mixed, heated at 95oC for 3 min, collected by centrifugation, applied to a prehybridized microarray slide and covered with a 24 x 60 mm LiferSlip (Erie Scientific Company). Ten microliters of 3X SSC were added to each of the two slots of the hybridization chamber (TeleChem).  The array was then sealed, submerged in a 42oC water bath and incubated for 12 to 18 h. Subsequently, each array was washed in 1X SSC and 0.2% SDS for two minutes, 0.1X SSC and 0.2% SDS for two minutes, and 0.1X SSC for two minutes, followed by a quick rinse in autoclaved, Millipore water. Arrays were then dried via centrifugation.  This hybridization procedure is also available at our project website (http://maize-meristems.plantgenomics.iastate.edu/index.html).

scan_protocol: Fluorescence of Cy3 and Cy5 on slides was detected at 10-micron resolution with a ScanArray 5000 (Packard). The following setting was used as initial laser power and PMT gain, respectively: 82 and 63 for Cy3 and 77 and 58 for Cy5. These values were slightly adjusted depending on slides to have enough signals for the lowest scans and to have approximately the same amounts of signals between the two channels for the majority of the spots. For each successive scan, laser power and PMT gain were increased by two to three units and three to four units, respectively. Each slide was scanned seven times. Subsequently, three scans for each slide (“low”, “medium” and “high” laser power and PMT) were selected for statistical analyses.

data_processing: Spots were removed for bad PCR and empty on the microarrays. All data were background corrected and then an R implementation of the lowess normalization method (Dudoit and Fridlyand, 2002, Genome Biol: 3 RESEARCH0036) was used to normalize the two channels for each combination of slide and scan intensity. The data were centered around 0 for each slide. Subsequently, the data from each scan was used to conduct a mixed linear model analysis separately for each of 18,302 spots using a strategy similar to that of Wolfinger et al. (2001, J Comput Biol 8: 625-637). By following the statistical analysis, an additional 3,710 spots were removed from the data set because of concerns regarding the quality of the associated DNA sequences and 192 exogenous spots also were removed. As a result, this study report the gene expression patterns of 14,400 informative spots

organism: Zea mays

source_name: Above ground part of seedlings

label_protocol: Two micrograms of amplified RNA was labeled with Cy3 or Cy5 according to Nakazono et al. (2003, Plant Cell 15: 583-596) with slight modifications. Details of fluorescent target synthesis are available at our project website (http://maize-meristems.plantgenomics.iastate.edu/index.html). To remove dye-specific effects in the statistical analyses, Cy dyes were swapped between the RNA samples with odd and even numbers.

growth_protocol: Maize (Zea mays inbred line B73) kernels were planted ~2 cm deep in plastic pots (8.5 cm x 8.5 cm wide at the top and 7.5 cm deep) filled with SB 300 Universal (Sun Gro Horticulture). Pots were placed in an environmental control room (PGW-40, Percival Scientific). The light intensity at the growth medium surface was kept between 830 to 860 mol/m2s as measured with a quantum meter (Model QMSW, Apogee Instruments). Temperature and light cycles were set at 25C with 15-hour light conditions and at 20C with 9-hour dark conditions. Pots were watered with a solution containing 0.7 mM calcium nitrate. After 14 days SAMs and seedlings were collected from the same batch of plants.

extract_protocol: Six whole seedlings without roots (14-day old, 30 to 40 g) were ground in liquid nitrogen and mixed thoroughly with 360 mL of a solution consisting of 38% [v/v] phenol in saturated buffer (pH 4.3 + 0.2, Fisher Scientific), 0.8 M guanidine thiocyanate, 0.4 M ammonium thiocyanate, 0.1 M sodium acetate [pH 5], 5% [v/v] glycerol.  Half of the mixture (about 200 mL) was transferred to a 250 mL centrifuging tube and centrifuged at 12,000g at 4oC for 20 min. The cleared homogenate solution was transferred to a new tube and incubated at room temperature for 25 min. Then, 36 mL of chloroform was added and shaken vigorously for 15 sec followed by 10 min incubation at room temperature. The mixture was centrifuged at 12,000g at 4oC for 30 min and the aqueous phase (about 110 mL) was transferred to a new tube. Then, 36 ml of isopropanol and 36 mL of 0.8 M sodium citrate/1.2 M sodium chloride were added, mixed well and incubated at room temperature for 15 min followed by a centrifugation at 12,000g at 4oC for 20 min to have RNA pellet at the bottom of the tube. The RNA pellet was washed with 75% ethanol and the tube was centrifuged again at 7,500g at 4oC for 8 min. After removing the ethanol, the pellet was air-dried for 30 min at room temperature. The RNA was resuspended with 1.8 mL of diethyl pyrocarbonate (DEPC) treated water at 60oC for 15 min. The RNA solution was transferred into two 1.7-mL Eppendorf tubes and centrifuged at 12,000g at 4oC for 5 min. The supernatant was transferred to new tubes. Five to 30 g of the RNA samples were taken and cleaned up according to the RNA purification step in the RNA amplification procedure (see below). Ten nano-gram of the cleaned up RNA samples were then amplified with T7 RNA polymerase-based (T7-based) RNA amplification according to the method of Nakazono et al. (2003, Plant Cell 15: 583-596) except that amplified RNA was purified with the RNeasy Mini Kit and that after the second strand synthesis cDNA was purified with the QIAquick PCR Purification Kit (Qiagen). The procedure is also available at our project website (http://maize-meristems.plantgenomics.iastate.edu/index.html). Seeding1.1 and Seedling1.2, and Seedling4.1 and Seedling4.2, and Seedling6.1 and Seedling6.2 were amplified from the same RNA pools, respectively.

tag: Inbred line

tag: Developmental stage

value: 14-day old seedlings

tag: Sample name

source_name: Shoot apical meristem (SAM) and very young leaf primordia (P0 and P1). A SAM is comprised of pluripotent stem cells, which divide to regenerate themselves as well as to provide cells to form other organs such as leaves and stems.

label_protocol: the same as ch1

growth_protocol: the same as ch1

extract_protocol: The PicoPure RNA Isolation Kit (Arcturus) was used to extract total RNA from the maize SAMs collected with LCM according to the manual. The RNA samples were treated with RNase-free DNase I (Stratagene) on column using the DNase Incubation Buffer provided with PALM RNA ExtractionKit (P.A.L.M. Microlaser Technologies) according to the manual of PicoPure RNA Isolation Kit. About 10 ng of the Dnase I-treated RNA samples were then amplified with T7 RNA polymerase-based (T7-based) RNA amplification according to the method of Nakazono et al. (2003, Plant Cell 15: 583-596) except that amplified RNA was purified with the RNeasy Mini Kit and that after the second strand synthesis cDNA was purified with the QIAquick PCR Purification Kit (Qiagen). The procedure is also available at our project website (http://maize-meristems.plantgenomics.iastate.edu/index.html).

value: Vegetative SAMs from 14-day old seedlings


title: SAM vs seedling_6M


title: Clostridium_acetobutylicum_Platform_Test_Amount_3_0_microg_PMT_60_20

description: No additional information.

scan_protocol: Scanned using a G2565BA Agilent Microarray Scanner (Agilent, Wilmington, DE, USA) at 10 micrometers resolution and PMTs were set to 60 and 20.


title: SAM vs seedling_4H

source_name: Seedling stage above ground tissue


title: Clostridium_acetobutylicum_60-mer_Selection_Test_cDNA_Spotted_Array_S2

description: No additional information.

hyb_protocol: Oppositely labeled microarray probe pairs (5 microg of each) were mixed together, dried in a rotary SpeedVac, and redissolved in Pronto Universal Hybridization Solution. The samples were incubated at 95 degrees C for 5 min and loaded on the microarray under a LifterSlip (Erie Scientific, Portsmouth, NH, USA). The microarrays were placed in a Corning hybridization chamber with 50 microL 10xSSC (1xSSC is 0.15 M NaCl and 0.015 M sodium citrate) to maintain humidity. Microarrays were hybridized for 14-16 h in a 42 degrees C water bath. Following hybridization, microarrays were washed in TeleChem (Sunnyvale, CA, USA) wash buffers A (42 degrees C, 5 min), B (room temperature, 5 min), and C (room temperature, 2 min) and water. Slides were then spun dry at 240xg for 10 min.

scan_protocol: Scanned using a G2565BA Agilent Microarray Scanner (Agilent, Wilmington, DE, USA) at 10 micrometers resolution.

data_processing: GenePix software (Molecular Devices, Union City, CA, USA) (v. 5.x) was used to assess spot quality and extract feature intensity statistics; duplicate spots were averaged; background-subtracted data were normalized using SNNLERM (Yang et al., PNAS 2003; 100:1122-1127). Spots discarded due to scratches or defective printing have been excluded.


title: Clostridium_acetobutylicum_Platform_Test_Amount_0_5_microg_PMT_60_20

description: No additional information.


title: SAM vs seedling_3H


title: SAM vs seedling_4M


title: SAM vs seedling_4L


title: SAM vs seedling_5H


title: SAM vs seedling_2H


title: Clostridium_acetobutylicum_60-mer_Selection_Test_cDNA_Spotted_Array_S3

description: No additional information.


title: Clostridium_acetobutylicum_Platform_Test_Amount_0_5_microg_PMT_80_40

description: No additional information.


title: Clostridium_acetobutylicum_60-mer_Selection_Test_cDNA_Spotted_Array_S1

description: No additional information.


title: SAM vs seedling_5L


title: SAM vs seedling_1H


title: SAM vs seedling_5M


title: SAM vs seedling_3M


title: Clostridium_acetobutylicum_60-mer_Selection_Test_cDNA_Spotted_Array_S4

description: No additional information.

growth_protocol: C. acetobutylicum ATCC 824 (American Type Culture Collection, Manassas, VA) was stored at -85 degrees C in clostridial growth media (CGM) (94) containing 15% glycerol. Solid cultures were carried out on agar-solidified 2xYTG (YTG is 8 g/liter tryptone, 5 g/liter yeast extract, 2 g/liter NaCl, 2.5 g/liter glucose, and 7.5 g/l agar, pH 5.8) plates. Liquid cultures were inoculated with single colonies from plates at least 4 days old and heat shocked at 70 to 80°C for 10 min. Cultures were grown in an anaerobic chamber (Forma Scientific, Marietta, OH) in Clostridial Growth Medium (CGM, Wiesenborn, D. P., et al. 1988. Appl. Environ. Microbiol. 54:2717-2722) supplemented with 80 g/liter glucose.


title: SAM vs seedling_2M

treatment_protocol: Six whole seedlings without roots (14-day old, 30 to 40 g) were ground in liquid nitrogen and mixed thoroughly with 360 mL of a solution consisting of 38% [v/v] phenol in saturated buffer (pH 4.3 + 0.2, Fisher Scientific), 0.8 M guanidine thiocyanate, 0.4 M ammonium thiocyanate, 0.1 M sodium acetate [pH 5], 5% [v/v] glycerol.  Half of the mixture (about 200 mL) was transferred to a 250 mL centrifuging tube and centrifuged at 12,000g at 4oC for 20 min. The cleared homogenate solution was transferred to a new tube and incubated at room temperature for 25 min. Then, 36 mL of chloroform was added and shaken vigorously for 15 sec followed by 10 min incubation at room temperature. The mixture was centrifuged at 12,000g at 4oC for 30 min and the aqueous phase (about 110 mL) was transferred to a new tube. Then, 36 ml of isopropanol and 36 mL of 0.8 M sodium citrate/1.2 M sodium chloride were added, mixed well and incubated at room temperature for 15 min followed by a centrifugation at 12,000g at 4oC for 20 min to have RNA pellet at the bottom of the tube. The RNA pellet was washed with 75% ethanol and the tube was centrifuged again at 7,500g at 4oC for 8 min. After removing the ethanol, the pellet was air-dried for 30 min at room temperature. The RNA was resuspended with 1.8 mL of diethyl pyrocarbonate (DEPC) treated water at 60oC for 15 min. The RNA solution was transferred into two 1.7-mL Eppendorf tubes and centrifuged at 12,000g at 4oC for 5 min. The supernatant was transferred to new tubes. Five to 30 g of the RNA samples were taken and cleaned up according to the RNA purification step in the RNA amplification procedure (see below). Ten nano-gram of the cleaned up RNA samples were then amplified with T7 RNA polymerase-based (T7-based) RNA amplification according to the method of Nakazono et al. (2003, Plant Cell 15: 583-596) except that amplified RNA was purified with the RNeasy Mini Kit and that after the second strand synthesis cDNA was purified with the QIAquick PCR Purification Kit (Qiagen). The procedure is also available at our project website (http://maize-meristems.plantgenomics.iastate.edu/index.html). Seeding1.1 and Seedling1.2, and Seedling4.1 and Seedling4.2, and Seedling6.1 and Seedling6.2 were amplified from the same RNA pools, respectively.


title: SAM vs seedling_6L


title: SAM vs seedling_2L


title: Ap48hrYESTrp vs Ap48hrYES Slide3B

city: Mississippi State

first: Jeff

last: Wilkinson

state: MS

department: Biochemistry and Molecular Biology

institute: Mississippi State University

organism: Aspergillus parasiticus

source_name: Aspergillus parasiticus SU-1 48 hr YES with Trp

label_protocol:
Pre-hybridization was performed according to TIGR’s protocols  and washed according to post-hybridization instructions for the 3DNA Array 900MPXTM Kit (Genisphere Inc., Hatfield, PA). Hybridizations were performed using the 3DNA Array 900MPXTM Kit (Genisphere Inc.), according to the manufacturer’s protocol. Each experiment consisted of one 48 hour YES sample coupled to a 48 hour YES supplemented with 50 mM tryptophan sample for either Aspergillus flavus or Aspergillus parasiticus. Each comparison was repeated with triplicate biological replicates and with duplicate dye-flip. Briefly, 3 µg of total RNA was used to generate cDNA using Genispheres random and MPX dT primers with Supercript II, Dithiotreitol and 5X SuperScript II First Strand Buffer from Invitrogen (Invitrogen corp., Carlsbad, CA) as per Genisphere’s instructions. The generated cDNA’s were purified using Qiagen MiniElute PCR Purification Kit (Qiagen Inc., Valencia, CA) as well as after terminal deoxynucleotidyl transferase tailing reaction and ligation to 3DNA capture sequence reactions. cDNA hybridizations were performed using the 2X Formamide-Based Hybridization Buffer overnight at 49oC in Hybridization Cassette’s (ArrayIt, TeleChem International, Inc., Sunnyvale, CA).
Hybridized slides were scanned using either a ScanArray5000XL (GSI Lumonics, Packard Biochip, Packard BioScience Company, Billerica, MA) or a GenePix 4000B (Axon Instruments, Molecular Devices, Sunnyvale, CA), and the independent TIFF images from each channel were analyzed using TIGR Spotfinder  software program. After background correction log base 2 expression ratios were and the resulting data is reported in the data tables.

extract_protocol: For systematic studies on the effects of Tryptophan on Aspergillus flavus and Aspergillus parasiticus, an Erlenmeyer flask of 100 ml of YES or YES with 50mM Trp were inoculated with 100 µl of 108 spores to obtain a final concentration of 105 spores/ml, and maintained at 30oC with shaking at 150 rpm, for 48 hours. The fungal mycelia were harvested by filtration through filter paper and frozen in liquid nitrogen. The frozen fungal mycelia were ground to a fine powder in liquid nitrogen using mortar and pestle. Ground mycelium was used to confirm levels of aflatoxins (data not shown) and to isolate total RNA. Total RNA was extracted from approximately 100 mg of ground mycelium in 1 ml of TRIZOL® (Molecular Research Center, Inc., Cincinnati, OH) according to manufacturer's instructions. Total RNA was quantified using a ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE) and visualized by gel electrophoresis to ensure quality.

source_name: Aspergillus parasiticus SU-1 48 hr YES

tag: Aspergillus parasiticus SU-1 48 hr YES


title: SAM vs seedling_3L


title: Ap48hrYES vs Ap48hrYESTrp Slide3A

hyb_protocol: Pre-hybridization was performed according to TIGR’s protocols  and washed according to post-hybridization instructions for the 3DNA Array 900MPXTM Kit (Genisphere Inc., Hatfield, PA). Hybridizations were performed using the 3DNA Array 900MPXTM Kit (Genisphere Inc.), according to the manufacturer’s protocol. Each experiment consisted of one 48 hour YES sample coupled to a 48 hour YES supplemented with 50 mM tryptophan sample for either Aspergillus flavus or Aspergillus parasiticus. Each comparison was repeated with triplicate biological replicates and with duplicate dye-flip. Briefly, 3 µg of total RNA was used to generate cDNA using Genispheres random and MPX dT primers with Supercript II, Dithiotreitol and 5X SuperScript II First Strand Buffer from Invitrogen (Invitrogen corp., Carlsbad, CA) as per Genisphere’s instructions. The generated cDNA’s were purified using Qiagen MiniElute PCR Purification Kit (Qiagen Inc., Valencia, CA) as well as after terminal deoxynucleotidyl transferase tailing reaction and ligation to 3DNA capture sequence reactions. cDNA hybridizations were performed using the 2X Formamide-Based Hybridization Buffer overnight at 49oC in Hybridization Cassette’s (ArrayIt, TeleChem International, Inc., Sunnyvale, CA).

scan_protocol: Hybridized slides were scanned using either a ScanArray5000XL (GSI Lumonics, Packard Biochip, Packard BioScience Company, Billerica, MA) or a GenePix 4000B (Axon Instruments, Molecular Devices, Sunnyvale, CA), and the independent TIFF images from each channel were analyzed using TIGR Spotfinder  software program. After background correction log base 2 expression ratios were and the resulting data is reported in the data tables.

source_name: Aspergillus parasiticus SU-1 49 hr YES

tag: Aspergillus parasiticus SU-1 49 hr YES

source_name: Aspergillus parasiticus SU-1 49 hr YES with Trp


title: Ap48hrYESTrp vs Ap48hrYES Slide1B

data_processing: After background correction log base 2 expression ratios were and the resulting data is reported in the data tables.

tag: Aspergillus parasiticus SU-1 48 hr YES with Trp


title: Ap48hrYESTrp vs Ap48hrYES Slide2B

source_name: Aspergillus parasiticus SU-1 48 YES with Trp

source_name: Aspergillus parasiticus SU-1 48 YES

tag: Aspergillus parasiticus SU-1 48 YES


title: Ap48hrYES vs Ap48hrYESTrp Slide1A


title: SAM vs seedling_1L


title: SAM vs seedling_1M


title: Af48hrYESTrp vs Af48hrYES Slide2B

organism: Aspergillus flavus NRRL3357

source_name: Aspergillus flavus NRRL 3357 48 hr YES with Trp

source_name: Aspergillus flavus NRRL 3357 48 hr YES

tag: Aspergillus flavus NRRL 3357 48 hr YES


title: Ap48hrYES vs Ap48hrYESTrp Slide2A


title: Af48hrYES vs Af48hrYESTrp Slide2A

source_name: Aspergillus flavus NRRL 3357 48hr YES

tag: Aspergillus flavus NRRL 3357

source_name: Aspergillus flavus NRRL 3357 48hr YES with Trp


title: Af48hrYESTrp vs Af48hrYES Slide3B

tag: Aspergillus flavus NRRL 3357 48 hr YES with Trp


title: Af48hrYESTrp vs Af48hrYES Slide1B


title: SAM vs seedling_18H

description: RNA was isolated from six to ten LCM-collected SAMs using PicoPure RNA Isolation Kit (Arcturus) as per manufacturer’s instructions to generate one biological replication. RNA was also isolated from six above-ground portions of seedlings using “home made Trizol” solution (see full protocol description of extract for details) to generate one biological replication. In total, six biological replications were prepared. Approximately 10 ng of total RNA from each biological replication were used as starting material for T7-based linear RNA amplification, performed as described by Nakazono et al. (2003, Plant Cell 15: 583-596). Each biological replication yielded between 10 and 50 g of amplified RNA (aRNA). Two micrograms of aRNA for each sample was indirectly labeled with Cy dye and hybridized to the GPL3538 platforms.

hyb_protocol: Microarray slides were prehybridized in 5X SSC (1X SSC is 0.15 M NaCl and 0.015 M sodium citrate), 0.1% SDS, and 0.1 mg/ml bovine serum albumin at 42oC for 45 min, then rinsed with autoclaved, Millipore water, dipped in isopropanol, and dried by centrifugation. Each target was resuspended in 30 l hybridization solution (5X SSC, 0.1% SDS, 0.2 g/l of yeast tRNA, 0.2 g/l of polyadenylic acid, 25% super-pure (99.5%) formamide (Fisher Scientific). Targets hybridized to the same slide were mixed, heated at 95oC for 3 min, collected by centrifugation, applied to a prehybridized microarray slide and covered with a 24 x 60 mm LiferSlip (Erie Scientific Company). Ten microliters of 3X SSC were added to each of the two slots of the hybridization chamber (TeleChem). The array was then sealed, submerged in a 42oC water bath and incubated for 12 to 18 h. Subsequently, each array was washed in 1X SSC and 0.2% SDS for two minutes, 0.1X SSC and 0.2% SDS for two minutes, and 0.1X SSC for two minutes, followed by a quick rinse in autoclaved, Millipore water. Arrays were then dried via centrifugation. This hybridization procedure is also available at our project website (http://maize-meristems.plantgenomics.iastate.edu/index.html).

scan_protocol: Fluorescence of Cy3 and Cy5 on slides was detected at 10-micron resolution with a Pro Scan Array HT (PerkinElmer). Each slide was scanned nine times with increasing laser power (44 to 100 with seven intervals) and fixed PMT gain (~60 for Cy5 and ~70 for Cy3) settings. PMT gain settings were slightly adjusted depending on slides to have approximately the same amounts of signals between the two channels for the majority of the spots. Subsequently, three scans for each slide (“low”, “medium” and “high”) were selected for statistical analyses.

data_processing: Spots were removed for bad PCR and empty on the microarrays. All data were background corrected and then an R implementation of the lowess normalization method (Dudoit and Fridlyand, 2002, Genome Biol: 3 RESEARCH0036) was used to normalize the two channels for each combination of slide and scan intensity. The data were centered around 0 for each slide. Subsequently, the data from each scan was used to conduct a mixed linear model analysis separately for each of 30,382 spots using a strategy similar to that of Wolfinger et al. (2001, J Comput Biol 8: 625-637).

extract_protocol: Six whole seedlings without roots (14-day old, 30 to 40 g) were ground in liquid nitrogen and mixed thoroughly with 360 mL of a solution consisting of 38% [v/v] phenol in saturated buffer (pH 4.3 + 0.2, Fisher Scientific), 0.8 M guanidine thiocyanate, 0.4 M ammonium thiocyanate, 0.1 M sodium acetate [pH 5], 5% [v/v] glycerol. Half of the mixture (about 200 mL) was transferred to a 250 mL centrifuging tube and centrifuged at 12,000g at 4oC for 20 min. The cleared homogenate solution was transferred to a new tube and incubated at room temperature for 25 min. Then, 36 mL of chloroform was added and shaken vigorously for 15 sec followed by 10 min incubation at room temperature. The mixture was centrifuged at 12,000g at 4oC for 30 min and the aqueous phase (about 110 mL) was transferred to a new tube. Then, 36 ml of isopropanol and 36 mL of 0.8 M sodium citrate/1.2 M sodium chloride were added, mixed well and incubated at room temperature for 15 min followed by a centrifugation at 12,000g at 4oC for 20 min to have RNA pellet at the bottom of the tube. The RNA pellet was washed with 75% ethanol and the tube was centrifuged again at 7,500g at 4oC for 8 min. After removing the ethanol, the pellet was air-dried for 30 min at room temperature. The RNA was resuspended with 1.8 mL of diethyl pyrocarbonate (DEPC) treated water at 60oC for 15 min. The RNA solution was transferred into two 1.7-mL Eppendorf tubes and centrifuged at 12,000g at 4oC for 5 min. The supernatant was transferred to new tubes. Five to 30 g of the RNA samples were taken and cleaned up according to the RNA purification step in the RNA amplification procedure (see below). Ten nano-gram of the cleaned up RNA samples were then amplified with T7 RNA polymerase-based (T7-based) RNA amplification according to the method of Nakazono et al. (2003, Plant Cell 15: 583-596) except that amplified RNA was purified with the RNeasy Mini Kit and that after the second strand synthesis cDNA was purified with the QIAquick PCR Purification Kit (Qiagen). The procedure is also available at our project website (http://maize-meristems.plantgenomics.iastate.edu/index.html). Seeding1.1 and Seedling1.2, and Seedling4.1 and Seedling4.2, and Seedling6.1 and Seedling6.2 were amplified from the same RNA pools, respectively.


title: Af48hrYES vs Af48hrYESTrp Slide1A

label_protocol:
Pre-hybridization was performed according to TIGR’s protocols  and washed according to post-hybridization instructions for the 3DNA Array 900MPXTM Kit (Genisphere Inc., Hatfield, PA). Hybridizations were performed using the 3DNA Array 900MPXTM Kit (Genisphere Inc.), according to the manufacturer’s protocol.  Each experiment consisted of one 48 hour YES sample coupled to a 48 hour YES supplemented with 50 mM tryptophan sample for either Aspergillus flavus or Aspergillus parasiticus.  Each comparison was repeated with triplicate biological replicates and with duplicate dye-flip.   Briefly, 3 µg of total RNA was used to generate cDNA using Genispheres random and MPX dT primers with Supercript II, Dithiotreitol and 5X SuperScript II First Strand Buffer from Invitrogen (Invitrogen corp., Carlsbad, CA) as per Genisphere’s instructions.  The generated cDNA’s were purified using Qiagen MiniElute PCR Purification Kit (Qiagen Inc., Valencia, CA) as well as after terminal deoxynucleotidyl transferase tailing reaction and ligation to 3DNA capture sequence reactions.  cDNA hybridizations were performed using the 2X Formamide-Based Hybridization Buffer overnight at 49oC in Hybridization Cassette’s (ArrayIt, TeleChem International, Inc., Sunnyvale, CA).
Hybridized slides were scanned using either a ScanArray5000XL (GSI Lumonics, Packard Biochip, Packard BioScience Company, Billerica, MA) or a GenePix 4000B (Axon Instruments, Molecular Devices, Sunnyvale, CA), and the independent TIFF images from each channel were analyzed using TIGR Spotfinder  software program. After background correction log base 2 expression ratios were and the resulting data is reported in the data tables.

extract_protocol: For systematic studies on the effects of Tryptophan on Aspergillus flavus and Aspergillus parasiticus, an Erlenmeyer flask of 100 ml of YES or YES with 50mM Trp were inoculated with 100 µl of 108 spores to obtain a final concentration of 105 spores/ml, and maintained at 30oC with shaking at 150 rpm, for 48 hours.  The fungal mycelia were harvested by filtration through filter paper and frozen in liquid nitrogen.  The frozen fungal mycelia were ground to a fine powder in liquid nitrogen using mortar and pestle.  Ground mycelium was used to confirm levels of aflatoxins (data not shown) and to isolate total RNA. Total RNA was extracted from approximately 100 mg of ground mycelium in 1 ml of TRIZOL® (Molecular Research Center, Inc., Cincinnati, OH) according to manufacturer's instructions.  Total RNA was quantified using a ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE) and visualized by gel electrophoresis to ensure quality.

tag: Aspergillus flavus NRRL3357


title: Af48hrYES vs Af48hrYESTrp Slide3A


title: SAM vs seedling_11H

description: RNA was isolated from six to ten LCM-collected SAMs using PicoPure RNA Isolation Kit (Arcturus) as per manufacturer’s instructions to generate one biological replication. RNA was also isolated from six above-ground portions of seedlings using “home made Trizol” solution (see full protocol description of extract for details) to generate one biological replication. In total, six biological replications were prepared. Approximately 10 ng of total RNA from each biological replication were used as starting material for T7-based linear RNA amplification, performed as described by Nakazono et al. (2003, Plant Cell 15: 583-596). Each biological replication yielded between 10 and 50 g of amplified RNA (aRNA). Two micrograms of aRNA for each sample was indirectly labeled with Cy dye and hybridized to the GPL2572 platforms.

scan_protocol: Fluorescence of Cy3 and Cy5 on slides was detected at 10-micron resolution with a ScanArray 5000 (Packard). The following setting was used as initial laser power and PMT gain, respectively: 82 and 63 for Cy3 and 77 and 58 for Cy5. These values were slightly adjusted depending on slides to have enough signals for the lowest scans and to have approximately the same amounts of signals between the two channels for the majority of the spots. For each successive scan, laser power and PMT gain were increased by two to three units and three to four units, respectively. Each slide was scanned seven times. Subsequently, three scans (“low”, “medium” and “high” laser power and PMT) for each slide were selected for statistical analyses.


title: SAM vs seedling_18L


title: SAM vs seedling_12H


title: SAM vs seedling_12M


title: SAM vs seedling_11M


title: SAM vs seedling_17M


title: SAM vs seedling_18M


title: SAM vs seedling_17H


title: SAM vs seedling_12L


title: SAM vs seedling_17L


title: kidney_KO3_MT

city: Heidelberg

first: Mathias

last: Treier

address: Meyerhofstrasse 1

department: Developmental Biology Unit

country: Germany

institute: EMBL

description: all steps carried out according to manufacturer's protocol

hyb_protocol: CodeLink Gene Expression System: Single-Assay Bioarray Hybridization and Detection according to manufacturer's instructions http://www4.amershambiosciences.com/aptrix/upp01077.nsf/Content/codelink_user_protocols

data_processing: raw values derived from CodeLink Expression Analysis v4.0 software see http://www4.amershambiosciences.com/aptrix/upp01077.nsf/Content/codelink_software

label: biotin-UTP

molecule: polyA RNA

source_name: 1/2 kidney, flash-frozen in liquid nitrogen after perfusion with PBS

label_protocol:
CodeLink Gene Expression System: Manual Labelled cRNA Target Preparation
according to manufacturer's instructions
http://www4.amershambiosciences.com/aptrix/upp01077.nsf/Content/codelink_user_protocols

extract_protocol: QIAGEN RNeasy mini kit, with on-column DNAse treatment, after homogenization with mortar and pestle plus syringe and needle in buffer RLT

tag: C57BL/6 backcross 10, 4 weeks, homozygous mutant, kidney


title: SAM vs seedling_10M


title: SAM vs seedling_10H


title: SAM vs seedling_11L


title: SAM vs seedling_16H

value: Seedling4.1 and Seedling4.2


title: kidney_KO2_MT

scan_protocol: CodeLink Gene Expression System: Single-Assay Bioarray Hybridization and Detection according to manufacturer's instructions http://www4.amershambiosciences.com/aptrix/upp01077.nsf/Content/codelink_user_protocols

treatment_protocol: QIAGEN RNeasy mini kit, with on-column DNAse treatment, after homogenization with mortar and pestle plus syringe and needle in buffer RLT


title: SAM vs seedling_10L


title: kidney_WT2_MT

tag: C57BL/6 backcross 10, 4 weeks, wildtype, kidney


title: Vehicle control (5.25% glucose) for 24 h_5

city: Bangalore

first: priyanka

last: samji

state: Karnataka

address: Malleswaram

department: Molecular Reproduction Development and Genetics

country: India

institute: Indian Institute of Science

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

scan_protocol: Standard Affymetrix protocols (Chip Expression Analysis Technical Manual rev.3, 2001) using scanner 3000 series

data_processing: MAS5.0, data was normalized with standard Affymetrix protocols (Chip Expression Analysis Technical Manual rev.3, 2001)

label: Biotin

organism: Macaca radiata

source_name: CL from female bonnet monkey 24 h post VEH (5.25% glucose)

extract_protocol: Total RNA was isolated using Trizol reagent (Sigma Aldrich Co., St.Louis, MO) followed by clean up step using RNeasy mini purification kit (# 74104, Qiagen).

treatment_protocol: A single s.c. injection of VEH (5.25% glucose) was administered to female monkeys on day 7 of luteal phase and CL collected at 24 h post VEH injection was cut into small quarters and snap frozen in liquid nitrogen.

tag: CL collected from female bonnet monkey 24 h post VEH (5.25% glucose)


title: kidney_KO1_MT


title: SAM vs seedling_16L


title: SAM vs seedling_16M


title: kidney_WT3_MT


title: Vehicle control (5.25% glucose) for 24 h_6

hyb_protocol: Standard Affymetrix protocols (Chip Expression Analysis Technical Manual rev.3, 2001)


title: SAM vs seedling_9L


title: SAM vs seedling_15H


title: SAM vs seedling_15L


title: SAM vs seedling_13H

value: Seedling1.1 and Seedling1.2


title: SAM vs seedling_8H


title: SAM vs seedling_15M


title: SAM vs seedling_9M


title: SAM vs seedling_9H


title: SAM vs seedling_8L


title: CET at 150 µg/kg BW for 24 h_1

source_name: CL from female bonnet monkey 24 h post CET treatment

label_protocol: Standard Affymetrix protocols (Chip Expression Analysis Technical Manual rev.3, 2001)

treatment_protocol: A single s.c. injection of GnRH receptor antagonist, Cetrorelix (CET) was administered at a dose of 150 µg/kg BW to female monkeys on day 7 of luteal phase and CL collected at 24 h post treatment was cut into small quarters and snap frozen in liquid nitrogen.

tag: CL collected from female bonnet monkey 24 h post CET treatment


title: SAM vs seedling_8M


title: Vehicle control (5.25% glucose) for 24 h_4


title: SAM vs seedling_14L


title: SAM vs seedling_13M


title: SAM vs seedling_14H


title: SAM vs seedling_7H

description: Fluorescence of Cy3 and Cy5 on slides was detected at 10-micron resolution with a ScanArray 5000 (Packard). The following setting was used as initial laser power and PMT gain, respectively: 82 and 63 for Cy3 and 77 and 58 for Cy5. These values were slightly adjusted depending on slides to have enough signals for the lowest scans and to have approximately the same amounts of signals between the two channels for the majority of the spots. For each successive scan, laser power and PMT gain were increased by two to three units and three to four units, respectively. Each slide was scanned seven times. Subsequently, three scans (“low”, “medium” and “high” laser power and PMT) for each slide were selected for statistical analyses.

scan_protocol: RNA was isolated from six to ten LCM-collected SAMs using PicoPure RNA Isolation Kit (Arcturus) as per manufacturer’s instructions to generate one biological replication. RNA was also isolated from six above-ground portions of seedlings using “home made Trizol” solution (see full protocol description of extract for details) to generate one biological replication. In total, six biological replications were prepared. Approximately 10 ng of total RNA from each biological replication were used as starting material for T7-based linear RNA amplification, performed as described by Nakazono et al. (2003, Plant Cell 15: 583-596). Each biological replication yielded between 10 and 50 g of amplified RNA (aRNA). Two micrograms of aRNA for each sample was indirectly labeled with Cy dye and hybridized to the GPL2572 platforms.


title: SAM vs seedling_14M


title: kidney_WT1_MT


title: SAM vs seedling_7M


title: CET at 150 µg/kg BW for 24 h_2


title: SAM vs seedling_13L


title: 8075_Lung did not develop PGD

status: Public on Jun 06 2007

city: St. Louis

first: Monika

last: Ray

state: MO

address: 1 Brookings Deive P O Box 1045

institute: Washington University in St. Louis

description: Samples were immediately snap-frozen in liquid nitrogen and then stored in a -70° Celsius freezer until used for analysis.  An area of lung tissue approximately 1 x 1 cm was isolated and excised using 2 staple lines from a 30 mm EndoGIA stapler (US Surgical, Norwalk, CT).

hyb_protocol: Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array (HGU133Av2). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Affymetrix GeneArray scanner 3000. Image analysis was performed with the Affymetrix GeneChip software.

data_processing: The data were normalised using gcRMA.  Log2-transformed data.

source_name: lung biopsies from the anterior right middle lobe or lingula immediately prior to cold-flushing.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 25 micrograms total RNA.

extract_protocol: Single isolates of donor lung samples were homogenised in the presence of RNAzolB and finally dissolved in RNase-free H2O.  25 micro-grams of total RNA was treated with DNase using the Qiagen RNase-free DNase kit and samples were further purified using RNeasy spin columns (Qiagen, Valencia, CA).  Total RNA treated with DNase was dissolved in RNase-free H2O to a final concentration of 0.2 g/l.  RNA quality was assessed by 1% agarose gel electrophoresis in the presence of ethidium bromide.  Samples that did not reveal intact and approximately equal 18S and 28S ribosomal bands were excluded from further study.

tag: P/F ratio at T0:400


title: SAM vs seedling_7L

source_name: Above ground part of seedlings


title: CET at 150 µg/kg BW for 24 h_3


title: 8077_Lung did not develop PGD

tag: P/F ratio at T0:509


title: 8073_Lung did not develop PGD


title: 8078_Lung did not develop PGD

tag: P/F ratio at T0:529


title: 8076_Lung did not develop PGD

tag: P/F ratio at T0:307


title: 8071_Lung did not develop PGD

tag: P/F ratio at T0:431


title: 8072_Lung did not develop PGD

tag: P/F ratio at T0:520


title: 8067_Lung did not develop PGD

tag: P/F ratio at T0:245


title: 8074_Lung developed PGD


title: 8070_Lung did not develop PGD

tag: P/F ratio at T0:362


title: 8064_Lung did not develop PGD

tag: P/F ratio at T0:432


title: 7122_Lung developed PGD

tag: P/F ratio at T0:73


title: 8066_Lung did not develop PGD

tag: P/F ratio at T0:455


title: 7125_Lung did not develop PGD

tag: P/F ratio at T0:370


title: 8063_Lung developed PGD

tag: P/F ratio at T0:120


title: 7124_Lung developed PGD

tag: P/F ratio at T0:85


title: 8065_Lung developed PGD

tag: P/F ratio at T0:181


title: 8069_Lung did not develop PGD

tag: P/F ratio at T0:329


title: 7120_Lung did not develop PGD

tag: P/F ratio at T0:248


title: 7123_Lung developed PGD

tag: P/F ratio at T0:171


title: 7121_Lung did not develop PGD

tag: P/F ratio at T0:268


title: 8068_Lung did not develop PGD

tag: P/F ratio at T0:278


title: 7119_Lung did not develop PGD

tag: P/F ratio at T0:448.75


title: 7115_Lung did not develop PGD

tag: P/F ratio at T0:395


title: 7117_Lung did not develop PGD

tag: P/F ratio at T0:454


title: 7111_Lung did not develop PGD


title: 7118_Lung did not develop PGD


title: 7116_Lung developed PGD

tag: P/F ratio at T0:193


title: 7113_Lung developed PGD

tag: P/F ratio at T0:82


title: 7114_Lung developed PGD

tag: P/F ratio at T0:154


title: 7110_Lung did not develop PGD

tag: P/F ratio at T0:268.75


title: 7112_Lung did not develop PGD

tag: P/F ratio at T0:201


title: 7109_Lung did not develop PGD

tag: P/F ratio at T0:407


title: 7108_Lung did not develop PGD

tag: P/F ratio at T0:640


title: 2.5 microgram total RNA from EPC derived microvescicles s4

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

hyb_protocol: Standard protocol suggested from Illumina

data_processing: Average intensities were obtained by BeadStudio 1.5.1.3 with out normalization and background subtraction. Subsequently data were normalized by cyclic loess as described in Bolstad et al. Bioinformatics 2003, 19:185

source_name: S4, particle RNA: 2.5 microgram

label_protocol: IVT labelling,  Illumina® TotalPrep™ RNA Amplification Kit Ambion

growth_protocol: Cells are grown as described in Biancone et al. J. Immunol. 2004, 173:5268

extract_protocol: Trizol reagent, as described by manufacturer

treatment_protocol: Microvescicles purified as Ratajczak et al. Leukemia 2006, 20:847

tag: Microvescicles from human endothelial progenitor cells.


title: PB_Donor 2_rep2

description: Study of mature PB neutrophil

hyb_protocol: Followed Agilent 60-mer oligo microarray processing protocol v 4.1, using SSC wash protocol and forced nitrogen drying

scan_protocol: Scanned using Agilent Microarray Scanner (G2565BA) at 10um resolution

data_processing: Agilent Feature Extraction software (v.7.2) was used to assess spot quality and extract feature intensity statistics; duplicate spots were averaged; background-subtracted data were normalized using SNNLERM (Yang et al., PNAS 2003; 100:1122-1127)

source_name: PB_Donor 2

label_protocol: Agilent Low RNA Input Fluorescent Linear Amplification kit (v2.0) (reverse transcription with oligo-dT primers, in vitro transcription with direct incorporation of fluorescently labeled CTP analogs)

extract_protocol: Extracted by AllCells

tag: PB neutrophil RNA

source_name: Universal Reference RNA

extract_protocol: Extracted by Stratagene

tag: Pooled RNA from 10 human cell lines


title: 0.25 microgram total RNA from EPC derived microvescicles s5

scan_protocol: Standard protocol suggested from Illumina

source_name: S5, particle RNA: 0.25 microgram


title: 1 microgram toal RNA from EPC derived microvescicles s2

source_name: S2, particle RNA: 1 microgram

tag: Total RNA from EPC derived microvescicles sample s2


title: 6632_Lung did not develop PGD

tag: P/F ratio at T0:411


title: 2.5 microgram total RNA from EPC derived microvescicles s3

source_name: S3, particle RNA: 2.5 microgram

tag: Microvescicles from human endothelial progenitor cells


title: PB_Donor 1_rep2

description: Study of mature PB neutrophil

source_name: PB_Donor 1


title: 6630_Lung did not develop PGD


title: PB_Donor 3_rep1

description: Study of mature PB neutrophil

source_name: PB_Donor 3


title: PB_Donor 1_rep1

description: Study of mature PB neutrophil


title: 0.25 microgram total RNA from EPC derived microvescicles s6

source_name: S6, particle RNA: 0.25 microgram


title: PB_Donor 2_rep1

description: Study of mature PB neutrophil


title: 6628_Lung did not develop PGD

tag: P/F ratio at T0:287


title: 6629_Lung did not develop PGD

tag: P/F ratio at T0:442.5


title: PriG_20%O2_Expt3_Day21_rep1

description: Study of in vitro granulocyte differentiation

growth_protocol: Cultured as described (Hevehan et al., Experimental Hematology 2000;28:267-75) with IL-3, IL-6, SCF and G-CSF in serum-containing McCoy's 5A media at pH 7.2 and 20% O2

extract_protocol: Agilent RNA isolation mini-kit

treatment_protocol: Cultured for 21 days

tag: Culture initiated from G-CSF mobilized peripheral blood CD34-positive hematopoietic stem and progenitor cell donation, female donor, age 21, Caucasian, nonsmoker


title: 1 microgram total RNA from EPC derived microvescicles s1

source_name: Total RNA from EPC derived microvescicles sample s1, 1 microgram


title: 6627_Lung did not develop PGD

tag: P/F ratio at T0:406.25


title: 6631_Lung did not develop PGD


title: PriG_20%O2_Expt3_Day17_rep1

treatment_protocol: Cultured for 17 days


title: 6626_Lung developed PGD

tag: P/F ratio at T0:121


title: PriG_20%O2_Expt3_Day14_rep1

treatment_protocol: Cultured for 14 days


title: PriG_20%O2_Expt3_Day9_rep1

treatment_protocol: Cultured for 9 days


title: PriG_20%O2_Expt3_Day11_rep1

treatment_protocol: Cultured for 11 days


title: PriG_20%O2_Expt3_Day7_rep2

treatment_protocol: Cultured for 7 days


title: PriG_20%O2_Expt3_Day5_rep1

treatment_protocol: Cultured for 5 days


title: PriG_5%O2_Expt3_Day21_rep1

growth_protocol: Cultured as described (Hevehan et al., Experimental Hematology 2000;28:267-75) with IL-3, IL-6, SCF and G-CSF in serum-containing McCoy's 5A media at pH 7.2 and 5% O2


title: 6424_Lung did not develop PGD

tag: P/F ratio at T0:309


title: PriG_5%O2_Expt3_Day21_rep2


title: PriG_20%O2_Expt3_Day3_rep1

treatment_protocol: Cultured for 3 days


title: PriG_20%O2_Expt3_Day7_rep1


title: 6624_Lung did not develop PGD

tag: P/F ratio at T0:318


title: 6422_Lung developed PGD

tag: P/F ratio at T0:169


title: PriG_5%O2_Expt3_Day14_rep1


title: 6423_Lung developed PGD

tag: P/F ratio at T0:124


title: 6625_Lung developed PGD


title: 6421_Lung developed PGD

tag: P/F ratio at T0:151


title: PriG_5%O2_Expt3_Day11_rep2


title: PriG_5%O2_Expt3_Day7_rep1


title: 6420_Lung did not develop PGD

tag: P/F ratio at T0:627


title: PriG_5%O2_Expt3_Day3_rep1


title: PriG_5%O2_Expt3_Day5_rep1


title: PriG_5%O2_Expt3_Day11_rep1


title: PriG_5%O2_Expt3_Day17_rep1


title: PriG_5%O2_Expt3_Day9_rep1


title: PriG_5%O2_Expt3_Day4_rep1

treatment_protocol: Cultured for 4 days


title: Homotypic [WT] control chIP replicate B

city: University Park

first: Melissa

last: Durant

state: PA

address: 452 N Frear

institute: Penn State University

description: no additional information needed

hyb_protocol: see above

scan_protocol: Chitikila et al.  2002. Mol Cell. 10:871-82

data_processing: MeanFRG- MedianBCK>S.D. BCK, <26% saturation.  Ratio of Test/Ref.

organism: Saccharomyces cerevisiae

source_name: TAF1-TAP chIP DNA

growth_protocol: Cells were grown in CSM-HIS to OD600 of ~0.8.  Cultures were then rapidly shifted to 37?C by adding warm media and placing in a 37?C shaker incubator for 45 minutes.  After HS, cells were crosslinked with 1% formaldehyde for 120minutes at RT and subsequently quenched with 0.125M glycine and harvested.

treatment_protocol: Heat shock (37C) of WT and mutant strains, see below.

tag: strain TAF1-TAP

growth_protocol: see above

extract_protocol: see above

treatment_protocol: see above


title: PriG_5%O2_Expt3_Day2_rep1

treatment_protocol: Cultured for 2 days


title: BDF1-TAP taf1-ts2 chIP replicate B

description: no additional information needed

source_name: BDF1-TAP taf1-ts2 [yMD59] chIP DNA

label_protocol: Chitikila et al.  2002. Mol Cell. 10:871-82

tag: strain yMD59 [BDF1-TAP taf1-ts2]

source_name: BDF1-TAP [yMD52] chIP DNA

tag: strain yMD52 [BDF1-TAP]


title: BDF1-TAP taf1-ts2 chIP replicate A

description: no additional information needed


title: PriG_Expt3_Day0_rep1

treatment_protocol: Uncultured

tag: Pooled RNA from 10 human cell lines


title: PriG_5%O2_Expt3_Day1_rep1

treatment_protocol: Cultured for 1 days


title: PriG_Expt3_Day0_rep2


title: Homotypic [WT] control chIP replicate A

description: no additional information needed


title: PriG_20%O2_Expt2_Day11_rep1

tag: Culture initiated from G-CSF mobilized peripheral blood CD34-positive hematopoietic stem and progenitor cell donation, male donor, age 24, Caucasian


title: Untagged [Null] chIP replicate B

description: no additional information needed

source_name: bdf1 delete chIP DNA

tag: strain bdf1 delete

source_name: SWR1-TAP [yMD55] chIP DNA

tag: strain yMD55 [SWR1-TAP]


title: 6416_Lung developed PGD

source_name: lung biopsies from the anterior right middle lobe or lingula immediately prior to cold-flushing.

tag: P/F ratio at T0:180


title: PriG_20%O2_Expt2_Day9_rep1


title: PriG_20%O2_Expt2_Day17_rep1


title: PriG_20%O2_Expt2_Day7_rep1


title: 6419_Lung developed PGD

tag: P/F ratio at T0:71


title: Untagged [Null] chIP replicate A

description: no additional information needed


title: PriG_20%O2_Expt2_Day14_rep1


title: TAF1-TAP esa1-414 chIP replicate B

description: no additional information needed

source_name: TAF1-TAP esa1-414 [yMD69] chIP DNA

tag: strain yMD69 [TAF1-TAP esa1-414]


title: PriG_20%O2_Expt2_Day5_rep1


title: PriG_20%O2_Expt2_Day7_rep2


title: TAF1-TAP esa1-414 chIP replicate A

description: no additional information needed


title: PriG_5%O2_Expt2_Day17_rep1


title: PriG_5%O2_Expt2_Day11_rep2


title: PriG_5%O2_Expt2_Day14_rep1


title: PriG_5%O2_Expt2_Day9_rep1


title: PriG_5%O2_Expt2_Day11_rep1


title: PriG_20%O2_Expt2_Day3_rep1


title: PriG_5%O2_Expt2_Day7_rep1


title: SWR1-TAP esa1-414 chIP replicate B

description: no additional information needed

source_name: SWR1-TAP esa1-414 [yMD70] chIP DNA

tag: strain yMD70 [SWR1-TAP esa1-414]


title: HTZ1-TAP esa1-414 chIP replicate B

description: no additional information needed

source_name: HTZ1-TAP esa1-414 [yMD73] chIP DNA

growth_protocol: Cells were grown in CSM-HIS to OD600 of ~0.8.  Cultures were then rapidly shifted to 37?C by adding warm media and placing in a 37?C shaker incubator for 45 minutes.  After HS, cells were crosslinked with 1% formaldehyde for 15minutes at RT and subsequently quenched with 0.125M glycine and harvested.

tag: strain yMD73 [HTZ1-TAP esa1-414]

source_name: HTZ1-TAP [yMD58] chIP DNA

tag: strain yMD58 [HTZ1-TAP]


title: SWR1-TAP esa1-414 chIP replicate A

description: no additional information needed


title: PriG_5%O2_Expt2_Day5_rep1

source_name: Universal Reference RNA


title: HTZ1-TAP esa1-414 chIP replicate A

description: no additional information needed


title: PriG_5%O2_Expt2_Day2_rep1


title: PriG_5%O2_Expt2_Day4_rep1


title: PriG_5%O2_Expt2_Day1_rep1


title: PriG_5%O2_Expt2_Day3_rep1


title: PriG_Expt2_Day0_rep1


title: BDF1-TAP esa1-414 chIP replicate B

description: no additional information needed

source_name: BDF1-TAP esa1-414 [yMD67] chIP DNA

tag: strain yMD67 [BDF1-TAP esa1-414]


title: PriG_20%O2_Expt1_Day9_rep1

tag: Culture initiated from G-CSF mobilized peripheral blood CD34-positive hematopoietic stem and progenitor cell donation, male donor, age 24, Caucasian, smoker


title: BDF1-TAP esa1-414 chIP replicate A

description: no additional information needed


title: PriG_Expt2_Day0_rep2


title: PriG_20%O2_Expt1_Day7_rep1


title: TAF1-TAP bdf1 delete chIP replicate B

description: no additional information needed

source_name: TAF1-TAP bdf1 delete [yMD75] chIP DNA

tag: strain yMD75 [TAF1-TAP bdf1 delete]


title: PriG_20%O2_Expt1_Day9_rep2


title: TAF1-TAP bdf1 delete chIP replicate A

description: no additional information needed


title: PriG_20%O2_Expt1_Day3_rep1


title: SWR1-TAP bdf1 delete chIP replicate B

description: no additional information needed

source_name: SWR1-TAP bdf1 delete [yMD76] chIP DNA

tag: strain yMD76 [SWR1-TAP bdf1 delete]


title: PriG_20%O2_Expt1_Day11_rep1


title: PriG_20%O2_Expt1_Day3_rep2


title: Colon Specific Pathogen Free rep3

city: Shinjuku

first: Masahiro

last: Yamamoto

state: Tokyo

address: 35 Shinano-machi

department: Department of Kampo Medicine

country: Japan

institute: Keio University School of Medicine

description: Gene expression data from colon of specific pathogen free mice

hyb_protocol: The labeled cRNA was fragmented, hybridized to MG-U74Av2 array (Affymetrix, Santa Clara, CA) using an Affymetrix fluidics station according to the Affymetrix protocols.

scan_protocol: GeneChips were scanned with an Affymetrix scanner, according to the Affymetrix protocols.

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

source_name: Colon, SPF IQI male mice, 9 week old

label_protocol: The labeled cRNA was prepared from by in vitro transcription (Enzo Biochem, New York, NY)

growth_protocol: GF mice were housed in a Trexler-type flexible film isolator in a standard germ free state and screened on a weekly basis for germ-free status by sampling feces sterilely and culturing on MRS-agar plates under aerobic and anaerobic conditions. All the GF, SPF, ex-GF mice were kept in a 12: 12-h light/dark cycle and at a temperature of 22+-2 ºC.

extract_protocol: Total RNA was extracted from mice (n = 3 per each group) using TRIzol (Life Technologies, Rockville, TX) and re-purified by RNeasy spin columns (Quiagen, Valencia, CA), according to the manufacturer’s instructions.

treatment_protocol: Nine week old mice (n=3) were sacrificed by cervical dislocation and the colon was dissected (the colon was not divided into proximal and distal sections and was treated as a single intestinal section). Tissue destined for RNA extraction were flash-flozen in liquid nitrogen after washing with ice-cold PBS.

tag: Strain:colon, Gender:male, Age:9-week, Tissue:Colon, Enteric flora status:specific pathogen free


title: PriG_20%O2_Expt1_Day5_rep1


title: PriG_5%O2_Expt1_Day9_rep1


title: PriG_5%O2_Expt1_Day14_rep1


title: SWR1-TAP bdf1 delete chIP replicate A

description: no additional information needed


title: HTZ1-TAP bdf1 delete chIP replicate B

description: no additional information needed

source_name: HTZ1-TAP bdf1 delete [yMD79] chIP DNA

tag: strain yMD79 [HTZ1-TAP bdf1 delete]

source_name: HTZ1-TAP chIP DNA


title: PriG_5%O2_Expt1_Day7_rep1


title: Colon Specific Pathogen Free rep2


title: PriG_5%O2_Expt1_Day5_rep1


title: Colon Germ Free rep2

description: Gene expression data from colon of germfree mice

source_name: Colon, GF IQI male mice, 9 week old

tag: Strain:colon, Gender:male, Age:9-week, Tissue:Colon, Enteric flora status:germfree


title: Colon Germ Free rep3


title: Colon Specific Pathogen Free rep1


title: BDF2-TAP bdf1 delete chIP replicate A

description: no additional information needed

source_name: BDF2-TAP chIP DNA

tag: strain BDF2-TAP

source_name: BDF2-TAP bdf1 delete [yMD87] chIP DNA

tag: strain yMD87 [BDF2-TAP bdf1 delete]


title: Wild type fetal liver 1, embryo at 12.5 days of development

status: Public on Jun 05 2007

city: Chicago

first: Kay

middle: F

last: Macleod

state: IL

address: 927 E 57th St

institute: Ben May Institute/University of Chicago

description: Gene expression data from e12.5 mouse fetal liver

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Rb heterozygous 129sv matings

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

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

treatment_protocol:
untreated embryos
fetal liver dissected and disaggregated in PBS

tag: genotype:Rb null

tag: Age


title: PriG_5%O2_Expt1_Day3_rep1

tag: Pooled RNA from 10 human cell lines


title: Rb null fetal liver 2, embryo at 12.5 days of development


title: HTZ1-TAP bdf1 delete chIP replicate A

description: no additional information needed


title: Wild type fetal liver 2, embryo at 12.5 days of development


title: endogenous small RNAs from Chlamydomonas reinhardtii strain J3(mt-) vegetative cells

status: Public on Jun 04 2007

city: Norwich

first: Frank

last: Schwach

state: Norfolk

address: Colney Lane

country: United Kingdom

institute: Sainsbury Laboratory

description: Total endogenuous small RNAs from Chlamydomonas reinhardtii

data_processing: Small RNA sequences that did not match tRNA or rRNA sequences (obtained from RFAM; www.sanger.ac.uk/Software/Rfam) were mapped to version 3.0 of the Chlamydomonas reinhardtii draft genome assembly (scaffolds and bonus scaffolds) obtained from www.jgi.doe.gov. Only full-length complete matches were allowed. Only sequences that had at least one match to the draft genome are contained in the table.

organism: Chlamydomonas reinhardtii

growth_protocol: Vegetative cells were grown in TAP medium at 20 deg C under continuous illumination.

extract_protocol: Total RNA was extracted with Tri®Reagent according to the manufacturer's instructions and further purifed on polyacrylamide gels.

tag: vegetative cells grown under continuous illumination


title: BDF2-TAP bdf1 delete chIP replicate B

description: no additional information needed


title: PriG_Expt1_Day0_rep1


title: 0.5 mg/kg/ml Isoproterenol treatment, 72 hour time point,  biological rep 5

status: Public on Jun 02 2007

city: Nutley

first: Charu

last: Kanwal

state: NJ

address: 340 Kingsland Street

department: RIGG

institute: Hoffman-La Roche

description:
CHIPEXP_NAME: 230_2_050531tpj_62h
LIMS_SITE: Nutley_3
CHIP_TYPE: RAT230_2
TREATMENT: Isoproterenol
TREAT_TOX_MECHANISM1: Heart_Cardiotoxic
TISSUE_OR_CELL_TYPE: Heart
DOSE_AMOUNT: 0.5
SAMPLING_TIME: 72
PROJECT: ISO_TG
STUDY_NO: 9143

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

scan_protocol: GeneChips were scanned using the Gene Chip scanner 3000

data_processing: Chips were pre-processed using robust multichip analysis. Normalized data were fit to a linear model with dose and time contrasts using the GLM procedure of SAS 9.1 (SAS Institute, Carey NC)

organism: Rattus norvegicus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

extract_protocol: Extraction of total RNA was performed from the heart tissues using RNAeasy Mini kit (Qiagen) according to the manufacturer's protocol

treatment_protocol: The tissues from the necropsy were stored in RNA later (Ambion)

tag: Wistar Han

tag: Crl:Wi(Han), Male, tissue

value: Heart


title: Rb null fetal liver 3, embryo at 12.5 days of development


title: Wild type fetal liver 3, embryo at 12.5 days of development


title: Rb null fetal liver 1, embryo at 12.5 days of development


title: 0.5 mg/kg/ml Isoproterenol treatment, 72 hour time point,  biological rep 3

description:
CHIPEXP_NAME: 230_2_050531tpj_60h
LIMS_SITE: Nutley_3
CHIP_TYPE: RAT230_2
TREATMENT: Isoproterenol
TREAT_TOX_MECHANISM1: Heart_Cardiotoxic
TISSUE_OR_CELL_TYPE: Heart
DOSE_AMOUNT: 0.5
SAMPLING_TIME: 72
PROJECT: ISO_TG
STUDY_NO: 9143


title: 0.5 mg/kg/ml Isoproterenol treatment, 72 hour time point,  biological rep 2

description:
CHIPEXP_NAME: 230_2_050531tpj_59h
LIMS_SITE: Nutley_3
CHIP_TYPE: RAT230_2
TREATMENT: Isoproterenol
TREAT_TOX_MECHANISM1: Heart_Cardiotoxic
TISSUE_OR_CELL_TYPE: Heart
DOSE_AMOUNT: 0.5
SAMPLING_TIME: 72
PROJECT: ISO_TG
STUDY_NO: 9143


title: 0.5 mg/kg/ml Isoproterenol treatment, 72 hour time point,  biological rep 1

description:
CHIPEXP_NAME: 230_2_050531tpj_58h
LIMS_SITE: Nutley_3
CHIP_TYPE: RAT230_2
TREATMENT: Isoproterenol
TREAT_TOX_MECHANISM1: Heart_Cardiotoxic
TISSUE_OR_CELL_TYPE: Heart
DOSE_AMOUNT: 0.5
SAMPLING_TIME: 72
PROJECT: ISO_TG
STUDY_NO: 9143


title: Colon Germ Free rep1


title: 0.5 mg/kg/ml Isoproterenol treatment, 24 hour time point,  biological rep 3

description:
CHIPEXP_NAME: 230_2_050531tpj_55h
LIMS_SITE: Nutley_3
CHIP_TYPE: RAT230_2
TREATMENT: Isoproterenol
TREAT_TOX_MECHANISM1: Heart_Cardiotoxic
TISSUE_OR_CELL_TYPE: Heart
DOSE_AMOUNT: 0.5
SAMPLING_TIME: 24
PROJECT: ISO_TG
STUDY_NO: 9143


title: 0.5 mg/kg/ml Isoproterenol treatment, 72 hour time point,  biological rep 4

description:
CHIPEXP_NAME: 230_2_050531tpj_61h
LIMS_SITE: Nutley_3
CHIP_TYPE: RAT230_2
TREATMENT: Isoproterenol
TREAT_TOX_MECHANISM1: Heart_Cardiotoxic
TISSUE_OR_CELL_TYPE: Heart
DOSE_AMOUNT: 0.5
SAMPLING_TIME: 72
PROJECT: ISO_TG
STUDY_NO: 9143


title: 0.5 mg/kg/ml Isoproterenol treatment, 24 hour time point,  biological rep 4

description:
CHIPEXP_NAME: 230_2_050531tpj_57h
LIMS_SITE: Nutley_3
CHIP_TYPE: RAT230_2
TREATMENT: Isoproterenol
TREAT_TOX_MECHANISM1: Heart_Cardiotoxic
TISSUE_OR_CELL_TYPE: Heart
DOSE_AMOUNT: 0.5
SAMPLING_TIME: 24
PROJECT: ISO_TG
STUDY_NO: 9143


title: vehicle treatment, 72 hour time point, biological replicate 3

description:
CHIPEXP_NAME: 230_2_050531tpj_21h
LIMS_SITE: Nutley_3
CHIP_TYPE: RAT230_2
TREATMENT: Vehicle_Control
TREAT_TOX_MECHANISM1: Liver_Non_Toxic
TISSUE_OR_CELL_TYPE: Heart
DOSE_AMOUNT: 0
SAMPLING_TIME: 72
PROJECT: ISO_TG
STUDY_NO: 9143


title: vehicle treatment, 72 hour time point, biological replicate 2

description:
CHIPEXP_NAME: 230_2_050531tpj_20h
LIMS_SITE: Nutley_3
CHIP_TYPE: RAT230_2
TREATMENT: Vehicle_Control
TREAT_TOX_MECHANISM1: Liver_Non_Toxic
TISSUE_OR_CELL_TYPE: Heart
DOSE_AMOUNT: 0
SAMPLING_TIME: 72
PROJECT: ISO_TG
STUDY_NO: 9143


title: vehicle treatment, 72 hour time point, biological replicate 1

description:
CHIPEXP_NAME: 230_2_050531tpj_19h
LIMS_SITE: Nutley_3
CHIP_TYPE: RAT230_2
TREATMENT: Vehicle_Control
TREAT_TOX_MECHANISM1: Liver_Non_Toxic
TISSUE_OR_CELL_TYPE: Heart
DOSE_AMOUNT: 0
SAMPLING_TIME: 72
PROJECT: ISO_TG
STUDY_NO: 9143


title: 0.5 mg/kg/ml Isoproterenol treatment, 24 hour time point,  biological rep 2

description:
CHIPEXP_NAME: 230_2_050531tpj_54h
LIMS_SITE: Nutley_3
CHIP_TYPE: RAT230_2
TREATMENT: Isoproterenol
TREAT_TOX_MECHANISM1: Heart_Cardiotoxic
TISSUE_OR_CELL_TYPE: Heart
DOSE_AMOUNT: 0.5
SAMPLING_TIME: 24
PROJECT: ISO_TG
STUDY_NO: 9143


title: vehicle treatment, 24 hour time point, biological replicate 3

description:
CHIPEXP_NAME: 230_2_050531tpj_18h
LIMS_SITE: Nutley_3
CHIP_TYPE: RAT230_2
TREATMENT: Vehicle_Control
TREAT_TOX_MECHANISM1: Liver_Non_Toxic
TISSUE_OR_CELL_TYPE: Heart
DOSE_AMOUNT: 0
SAMPLING_TIME: 24
PROJECT: ISO_TG
STUDY_NO: 9143


title: vehicle treatment, 24 hour time point, biological replicate 1

description:
CHIPEXP_NAME: 230_2_050531tpj_16h
LIMS_SITE: Nutley_3
CHIP_TYPE: RAT230_2
TREATMENT: Vehicle_Control
TREAT_TOX_MECHANISM1: Liver_Non_Toxic
TISSUE_OR_CELL_TYPE: Heart
DOSE_AMOUNT: 0
SAMPLING_TIME: 24
PROJECT: ISO_TG
STUDY_NO: 9143


title: vehicle treatment, 24 hour time point, biological replicate 2

description:
CHIPEXP_NAME: 230_2_050531tpj_17h
LIMS_SITE: Nutley_3
CHIP_TYPE: RAT230_2
TREATMENT: Vehicle_Control
TREAT_TOX_MECHANISM1: Liver_Non_Toxic
TISSUE_OR_CELL_TYPE: Heart
DOSE_AMOUNT: 0
SAMPLING_TIME: 24
PROJECT: ISO_TG
STUDY_NO: 9143