title: HKI-117-other


title: HKI-115-other

status: Public on May 10 2011

type: RNA

city: Helsinki

first: Taru

middle: A

last: Muranen

address: Haartmaninkatu

department: Department of Obstetrics and Gynecology

country: Finland

institute: Helsinki University Central Hospital

hyb_protocol: Samples were hybridized and washed as previously described (PMID:17334996).

scan_protocol: Arrays were scanned with Agilent Microarray Scanner (Agilent Technologies) and quality controlled using the GenePix 4.1.1.4 software (Axon instruments)

data_processing: Background correction was done with the normexp method recommended by [PMID: 17720982]. Data was normalized first within arrays with the print-tip loess method and subsequently between arrays with the quantile method. Measurements of replicate reporters were averaged.

molecule: total RNA

organism: Homo sapiens

source_name: breast tumor tissue

label_protocol: Fluorescently labeled cDNA targets for hybridization were prepared according to manufacturers' instructions using the Corning Pronto Plus system 6.

extract_protocol: Sections of frozen tumor tissues (roughly 10 – 100 mg) were submerged in liquid nitrogen and homogenized using a mechanical homogenizer, after which the tissue powder was dissolved in 4 ml of TrizolTM. The RNA was then separated into an aqueous phase by adding 800 ml of chloroform followed by centrifugation at 12,000 g at four degrees centigrade for 15 min. Subsequent RNA extraction and purification was performed using the Qiagen RNeasy RNA purification kit (Qiagen Inc., CA, USA).

tag: chek2 1100delc mutation status

value: other

tag: er status (1=positive, o=negative)

tag: family history of breast cancer (1=familial case, 0=sporadic case)

tag: histological subtype

value: ductal

tag: nqo1 rs1800566 genotype

value: CT

source_name: Universal Human RNA

tag: sample type

value: reference

tag: disease state


title: HKI-121-CHEK2

value: CC


title: HKI-114-other


title: HKI-099-cy3-CHEK2

type: genomic

hyb_protocol: Labeled DNA was resuspended in 50 μl hybridization solution (50% formamide, 10% dextran sulfate, 2×SSC, 2% SDS, 10 μg/μl yeast tRNA) and heated to 70°C for 15 min followed by a 30 min incubation at 37°C for 30 min. Hybridization reactions were applied to arrays and incubated under cover slips for 72 hr at 37°C. Arrays were washed with PN buffer, 50% formamide and finally in PN buffer at room temperature for 15 min.

data_processing: popLOWESS normalization of background subtracted intensity values in BASE data management environment, segmentation and copy number estimation using R package CGHcall

molecule: genomic DNA

label_protocol: All DNAs were labeled using a random primer labeling kit according manufacturers instructions (Invitrogen Life Technologies)

extract_protocol: Genomic DNA was extracted from frozen tissue sections using a proteinase K treatment followed by phenol chloroform purification; 1-4 punches (0.6 mm in diameter) from each paraffin-embedded tissue were combined and then incubated in xylene to remove the paraffin and DNA was subsequently extracted similarly as from the fresh frozen tumors.

source_name: Normal human male genomic DNA


title: HKI-102-cy3-CHEK2


title: HKI-097-cy3-CHEK2


title: HKI-110-other

value: in situ


title: HKI-113-other


title: HKI-111-other


title: HKI-100-cy3-other


title: NTD spina 2

city: Beijing

first: Liuyan

last: Zhang

address: 4A Dutun Rd., Chaoyang District

country: China

institute: Institute of Psychology, Chinese Academy of Sciences

description: A chip was employed for each total RNA sample derived from a pool of spinal cord tissue from fetuses whose mother had been either treated or not treated with RA.

hyb_protocol: Labeled control and test samples were quantitatively adjusted based on the efficiency of Cy-dye incorporation and mixed into 80 mL hybridization solution (3×SSC, 0.2% SDS, 25% formamide, and 5×Denhart’s). DNA was denatured at 95 °C for 3 min prior loading on a microarray, and hybridized 16 h at 42 °C, then washed with 0.2% SDS, 2× SSC at 42 °C for 5 min and 0.2% SSC for 5 min at room temperature.

scan_protocol: A LuxScan 10KA Scanner (Capital Bio) was used to scan arrays, and images were analyzed with LuxScan 3.0 software (Capital Bio).

data_processing: The median average intensity of foreground and background was extracted from the .LSR files. If a spot intensity was zero or negative after background subtraction, it was set at half of the minimum positive corrected intensities in the array. We performed normalization using the spike probes that were previously shown to have a consistent log-ratio. Then, linear model and empirical Bayes smoothing analyses were combined to obtain the statistics value and fold change of each spot. Significant candidates were selected with values of fold change >1.5, which means genes with at least a 1.5-fold change in expression as compared to control samples were considered significant.

organism: Mus musculus

source_name: Spinal cord from day 18 fetuses obtained from mothers treated with RA

label_protocol: An aliquot of 5 ug total RNA was used to produce fluorescent dye-labeled cDNA with the Eberwine’s linear RNA amplification method and subsequent enzymatic reactions according to previously published protocols (Guo et al., 2005; Patterson et al., 2006). The labeled DNA was purified with PCR Clean-up NucleoSpin kits (Macherey Nagel, Duren, Germany), re-suspended in Elution buffer, and quantified by UV spectrophotometry. Two samples (NTD and normal control) were labeled with different fluorophores (Cy3 and Cy5 dyes) and hybridized together on a single microarray.

growth_protocol: Male and female C57BL/6J mice (8 weeks of age) were housed in a temperature-controlled (23 ± 2°C) and humidity-controlled (50 ± 5%) animal facility. The mice were maintained on a 12-h light/dark cycle with access to food and water ad libitum.

extract_protocol: The total RNA was isolated using TRIZOL (Invitrogen, Gaithersburg, MD, USA) and purified with the NucleoSpin RNA clean-up kit (Macherey-negel, Germany), according to the manufacturer’s protocol. The quality and concentration of total RNA was assessed using a 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany) and A260, respectively.

treatment_protocol: The female mice were mated at 8 weeks from 9:00 - 11:00 A.M. and the experimenter checked the plugged females at 2:00 P.M. Animals with vaginal plugs were considered to be at 0 days and 0 h (0 d, 0 h) of pregnancy (0 dpc). Pregnant mice were gavage-fed three successive doses of all-trans retinoic acid (RA, 20 mg/kg/dose) suspended in olive oil on day 8 of gestation at 6, 12 and 18 h. Groups of treated and control mice were allowed to survive to day 18 of pregnancy. At the time their uteri were excised, the number of live fetuses with opened or closed neural tubes, as well as the number of dead fetuses, was determined under a dissecting microscope. Embryos were staged by somite number. For the gene expression studies, the spinal cords of 20 fetuses from 11 litters with spina bifida induced by maternal RA treatment were specifically removed. Tissues from 20 normal fetuses, from 5 vehicle-treated litters, were used as controls.

tag: strain

tag: tissue

value: spinal cord

tag: developmental stage

value: day 18 fetus

tag: treatment

value: maternal retinoic acid (RA) treatment

source_name: Spinal cord from day 18 fetuses obtained from mothers treated with olive oil vehicle

value: maternal olive oil treatment

value: control


title: HKI-096-cy3-other


title: HKI-094-cy3-other


title: HKI-109-other


title: HKI-101-cy3-other


title: HKI-095-cy3-other


title: HKI-108-other


title: HKI-093-cy3-other


title: HKI-090-cy3-other


title: HKI-103-other


title: HKI-107-CHEK2

value: lobular


title: HKI-089-cy3-other


title: HKI-102-CHEK2


title: HKI-087-cy3-other


title: HKI-099-CHEK2


title: HKI-101-other


title: HKI-091-cy3-other


title: HKI-104-CHEK2


title: HKI-106-other


title: BA02_heart_hibernating_N06-030

city: Shanghai

first: Haifang

last: Wang

address: 320 yueyang road

department: CAS-MPG Partner institute for Computational Biology

institute: Shanghai institute for biology science

description: heart tissue from hibernating black bear

hyb_protocol: The hybridization was carried out for 18 hours at 42°C in 4 ml of MicroHyb buffer (Invitrogen). Filters were rinsed at room temperature with 2× SSC/1% SDS to remove residual probe and MicroHyb solution and then transferred to preheated wash solutions in a temperature-controlled shaking water bath. Filters were washed twice for 30 min in 1.5 l of 2× SSC/1% SDS at 50°C and then once for 30 min in 1.5 l of 0.5× SSC/1% SDS at 55°C.

scan_protocol: Filters were then exposed to phosphorimager screens for four days and scanned at 50-µm resolution in a Storm Phosphorimager.

data_processing: Image analysis was performed with the ImaGene program (Biodiscovery). Only nonempty spots with signal median density exceeding double background median in all individuals were included in the analysis. Background corrected signal was obtained by subtracting local background median density from signal median density. Background corrected signals were divided by their median on the array to obtain the normalized median densities representing the normalized expression values.

organism: Ursus americanus

source_name: heart, hibernating

label_protocol: Samples of total RNA were linearly amplified with Illumina TotalPrep RNA Amplification Kit (Ambion), and 1.6 μg of the amplified RNA was labeled with 65 μCi of [33P]dCTP. All RNA samples were amplified, labeled and hybridized in the same batch.

extract_protocol: Total RNA was extracted from frozen tissues stored at -80 C by grinding in liquid nitrogen with mortar and pestle and using RNeasy Kit (Qiagen). Skeletal muscle tissue was treated by proteinase K and RNA was extracted by using RNeasy Fibrous Tissue Kit (Qiagen). All RNA samples were processed by DNase I (Qiagen) treatment. For cDNA library construction, mRNA was selected from total RNA with the oligo(dT) cellulose by the use of Poly(A) Purist Kit (Ambion).

tag: tissue type

value: heart

tag: gender

value: male


title: HKI-097-CHEK2


title: HKI-105-other


title: HKI-083-cy3-other


title: HKI-084-cy3-other


title: HKI-100-other


title: HKI-086-cy3-other


title: HKI-095-other


title: HKI-085-cy3-other


title: HKI-098-other


title: HKI-081-cy3-other


title: HKI-078-cy3-other


title: HKI-088-cy3-CHEK2


title: HKI-094-other


title: HKI-082-cy3-other


title: HKI-079-cy3-other


title: HKI-093-other


title: HKI-076-cy3-other


title: HKI-092-other


title: HKI-090-other


title: HKI-091-other


title: HKI-088-CHEK2


title: HKI-082-other


title: HKI-068-cy3-other


title: HKI-062-cy3-other


title: HKI-071-Cy5-CHEK2


title: HKI-070-cy3-CHEK2


title: HKI-089-other


title: HKI-067-cy3-CHEK2


title: HKI-073-other


title: HKI-069-cy5-CHEK2


title: HKI-087-other

value: medullar


title: HKI-083-other


title: HKI-063-cy3-other


title: HKI-065-cy3-other


title: HKI-059-cy3-other


title: HKI-077-cy3-other


title: HKI-057-cy3-other


title: HKI-061-cy5-other


title: HKI-086-other


title: HKI-068-other


title: HKI-072-other


title: HKI-064-cy3-other


title: HKI-078-other


title: HKI-075-cy3-CHEK2


title: HKI-070-CHEK2


title: HKI-056-cy3-other


title: HKI-055-cy3-CHEK2


title: HKI-065-other

value: TT


title: HKI-054-other


title: HKI-057-other


title: HKI-067-CHEK2


title: HKI-051-cy3-other


title: HKI-048-cy3-other


title: HKI-058-other


title: HKI-043-cy3-other


title: HKI-054-cy3-other


title: HKI-046-cy5-CHEK2


title: HKI-049-other


title: HKI-049-cy3-other


title: HKI-040-cy3-other


title: HKI-059-other


title: HKI-052-cy3-other


title: HKI-053-CHEK2


title: HKI-039-cy5-CHEK2


title: HKI-053-cy3-CHEK2


title: HKI-052-other


title: HKI-051-other


title: HKI-050-other


title: HKI-038-cy3-other


title: HKI-045-other


title: HKI-047-other


title: HKI-050-cy3-other


title: HKI-056-other


title: HKI-044-cy3-CHEK2


title: HKI-035-cy3-CHEK2


title: HKI-048-other


title: HKI-044-CHEK2


title: HKI-043-other


title: HKI-037-cy3-CHEK2


title: HKI-034-cy5-other


title: HKI-038-other


title: HKI-032-cy3-CHEK2


title: HKI-040-other


title: HKI-030-cy3-CHEK2


title: HKI-033-cy5-CHEK2


title: HKI-029-cy3-other


title: HKI-037-CHEK2


title: HKI-029-other


title: HKI-027-other


title: HKI-027-cy3-other


title: HKI-022-other


title: HKI-026-cy3-other


title: HKI-023-other


title: HKI-025-other


title: HKI-024-cy5-other


title: HKI-021-other


title: HKI-020-other


title: HKI-021-cy3-other


title: HKI-023-cy3-other


title: HKI-028-cy3-other


title: HKI-019-other


title: HKI-020-cy3-other


title: HKI-018-other


title: HKI-018-cy3-other


title: HKI-002-other


title: HKI-015-cy5-other


title: HKI-013-cy3-other


title: HKI-012-cy3-other


title: HKI-007-cy5-CHEK2


title: HKI-010-cy3-other


title: HKI-009-cy3-other


title: HKI-004-other


title: HKI-016-other


title: HKI-017-other


title: HKI-008-cy5-CHEK2


title: HKI-019-cy3-other


title: Dg vs Control

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: Genomic Services

country: Germany

institute: Miltenyi Biotec GmbH

description: Dg - 100% Ph+ cells in bone marrow; 60-312% of BCR-ABL (IS) in peripheral blood

hyb_protocol: The fluorescently labeled samples were hybridized overnight to miRXplore TM Microarrays using the a-HybTM Hybridization Station (Miltenyi Biotec).

scan_protocol: Image capture and signal quantification of hybridized miRXplore ™ microarrays was done with the Agilent’s Microarray Scanner System (Agilent Technologies, Palo Alto, USA) and ImaGene software Version 8.0.1 (BioDiscovery, Los Angeles, CA, USA).

data_processing: Signal quantification of the scanned miRXplore TM microarrays was done using ImaGene software Version 8.0.1 (BioDiscovery, Los Angeles, CA, USA). Local background was subtracted from the signal to obtain the net signal intensity and the ratio of Hy5/Hy3. Subsequently, the mean of the ratios of 4 corresponding spots representing the same miRNA was computed. The mean ratios were normalised using the calibration oligos.

source_name: Pool of leukocytes from 11 healthy donors

label_protocol: 2 µg of respective total RNA were each mixed with 2.5 fmol of each of 18 RNA oligonucleotides reverse complement to miRControl 3 probes and subsequently fluorescently labelled using a commercial kit (miRCuryTM LNA microRNA Array Power labeling kit, Exiqon) following the instructions of the manufacturer. The corresponding total RNA samples were hybridized in a dual colour approach to microarrays.

growth_protocol: Each patient contributed to the pool by the same amount of leukocytes (107). Total leukocytes were isolated from peripheral blood of all samples by osmotic lysis.

extract_protocol: Total RNA was isolated from guanidine iso- thiocyanate cell lysate homogenates containing 5x106 leukocytes  using miRVana kit (Ambion®, Applied Biosystems, Foster City, CA, USA) method according to the manufacturers' instrcuctions. The concentration and quatity of RNA were measured by UV absorbance at 260 and 280 nm and checked by gel electrophoresis. RNA samples were quality checked via the Agilent 2100 Bioanalyzer (Agilent Technologies). The results of the Bioanalyzer run were visualized in a gel image and electropherogram. The RNA integrity Number (RIN) was between 7.2 and 9.2.

treatment_protocol: Patients were treated with imatinib.

tag: cell type

value: leukocytes

source_name: Pool of leukocytes from 5 patients at diagnosis


title: Dg vs Control (replicate)


title: BC vs Control

description: BC definition - 50 -79% blasts in peripheral blood

source_name: Pool of leukocytes from 4 patients in blast crisis


title: HKI-081-other

value: other


title: Hr vs Control

description: Hr definition - increased number of WBC (range 14-28*109/L); 100% of Ph+ cells in bone marrow

source_name: Pool of leukocytes from 5 patients in hematological relapse


title: HKI-006-cy3-other


title: HKI-005-cy3-other


title: HKI-004-cy3-other


title: TF vs Control

description: TF definition - complete hematological response with failure to achieve complete cytogenetic remission

source_name: Pool of leukocytes from 5 patients with therapy failure


title: MMR vs Control

description: MMR samples are characterized as BCR-ABL <0.1% (IS)

source_name: Pool of leukocytes from 5 patients in major molecular response


title: HKI-012-other


title: H28 HA 24h 4

city: Melbourne

first: Victoria

middle: Mary

last: Perreau

state: Victoria

address: Parkville

department: Center for Neuroscience

country: Australia

institute: University of Melbourne

description: replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Gene expression data was exported from Bead Studio using median shift normalization such that the lowest value is 1 and log2 transformed with the ‘Partek report plug-in’ (Partek® Inc., St. Louis, Missouri, U.S.A.) and analysed in Partek Genomics Suite.  The resultant export file in project file format (.ppj) included log transformed signal intensity data and annotation. This file was then imported into Partek Genomics suite Version 6.3 (Partek® Inc., St. Louis, Missouri, U.S.A.). The normalised expression data was then exported from Partek, signal p values were not available for normalised expression values.

label: biotin

source_name: Mouse forebrain primary cell cultue of astrocytes

label_protocol: RNA was amplified using the Illumina® TotalPrep RNA Amplication Kit. Total RNA sample was reverse transcribed using T7 Oligo(dT) primer to generate first strand second strand cDNA. Biotinylated cRNA was generated from the double-stranded cDNA templates via in vitro transcription.

growth_protocol: Cells plated in 24-well plates (2.6 × 104 cells/cm2) and incubated in a humidified incubator at 36.5ºC with 5% CO2.

extract_protocol: Total RNA was extracted in one batch using the RNeasy Mini Kit and quality of the extracted RNA was determined using E-gene HAD-GT12 genetic analyser (John Morris Scientific, Melbourne, Australia).

treatment_protocol: Monolayers of astrocytes were treated with Fasudil (diluted in astrocytic medium pre-warmed at 37ºC) and the volume was maintained at 0.5 ml per well. Vehicle-treated cultures were run in parallel to serve as controls.

value: C57 Bk6

tag: age

value: 1.5 day

value: forebrain

value: primary cell culture astrocyte

tag: time

tag: culture batch

tag: bead chip array sentrix code


title: H31 Ctrl 12h 1

description: replicate 1

value: Control


title: H32 HA 12h 4

description: replicate 4


title: H14 HA 6h 4

description: replicate 4


title: Liver biopsy from GBV-C positive subject, 9

hyb_protocol: Affymetrix fluidics station following protocol EukGE-WS2v5_450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner M10.

data_processing: 1-way ANOVA was used to detect genes differentially expressed between GBV-C positive and negative patients using Partek Genomics suite and applying a custom CDF file (Hs133P_Hs_UG_8), available from Molecular and Behavioural Neuroscience Institute, University of Michigan. RMA was used to generate expression values.

source_name: liver, GBV-C positive

label_protocol: 5-15ug of purified total RNA from each patient was labelled with biotin as recommended in the Affymetrix GeneChip Expression Analysis Technical Manual.

extract_protocol: Tissue was collected into RNA later and then extracted using RNAeasy MiniKit (Qiagen, Dusseldorf, Germany).

treatment_protocol: Ultrasound-guided liver biopsy was performed to obtain liver tissue samples from patients.

value: liver

tag: gbv-c virus status

value: positive

tag: hiv virus status

tag: hcv virus status

tag: hcv genotype


title: Liver biopsy from GBV-C negative subject, 10

source_name: liver, GBV-C negative

value: negative


title: H24 Ctrl 24h 4

description: replicate 4


title: Liver biopsy from GBV-C positive subject, 6


title: H4 Ctrl 2h 4

description: replicate 4


title: H30 Ctrl 6h 4

description: replicate 4


title: Liver biopsy from GBV-C negative subject, 8


title: HKI-036-cy5-CHEK2

tag: chek2 1100delc mutation status

value: reference


title: H8 HA 2h 4

description: replicate 4


title: Liver biopsy from GBV-C negative subject, 5


title: H27 HA 24h 3

description: replicate 3


title: Liver biopsy from GBV-C positive subject, 7


title: Liver biopsy from GBV-C negative subject, 4


title: H20 HA 12h 4

description: replicate 4


title: H23 Ctrl 24h 3

description: replicate 3


title: H17 Ctrl 12h 3

description: replicate 3


title: H13 HA 6h 3

description: replicate 3


title: HKI-026-other

tag: er status (1=positive, o=negative)

tag: family history of breast cancer (1=familial case, 0=sporadic case)

tag: histological subtype

value: ductal

tag: nqo1 rs1800566 genotype

value: CT

tag: sample type

tag: disease state


title: Liver biopsy from GBV-C positive subject, 2

tag: tissue

tag: gender


title: H29 Ctrl 6h 3

description: replicate 3

tag: strain

tag: age

tag: cell type

tag: treatment


title: Liver biopsy from GBV-C negative subject, 3

tag: gbv-c virus status


title: Liver biopsy from GBV-C negative subject, 1

tag: hiv virus status


title: H7 HA 2h 3

description: replicate 3

tag: time

tag: culture batch

tag: bead chip array sentrix code


title: Control vs Dicer mutant cerebellum, Replicate 4

city: Los Angeles

first: Yi

last: Sun

state: CA

address: 635, Charles E. Young Dr. South

department: Molecular and Medical Pharmacology

country: USA

institute: UCLA

hyb_protocol: 825 ng Cy3- or Cy5-labelled cRNA were combined and hybridized to the Agilent 4x44K mouse whole genome microarray (G4122F) for 17 h at 65 ˚C (10 r.p.m.). Microarrays were washed according to Agilent's standard procedures.

scan_protocol: Microarry slides were scanned on at 5-micron resolution using an Agilent Technologies Scanner G2505B (US23502366).

data_processing: Agilent Feature Extraction (FE) Software (v9.5) was used for TIFF image processing, background subtraction and Lowess normalization. Normalized signal intensity from FE was used for identifying differentially expressed transcripts between control and Dicer mutant littermates in NIA array analysis tool (http://igsun.grc.nia.nih.gov/ANOVA).

source_name: Dicer mutant

label_protocol: 500 ng of total RNA from cerebella of control or Dicer mutant littermates was reversed transcribed and labeled with Cy3- or Cy5-CTP using the Agilent Low RNA Input Fluorescent Linear Amplification Kit.

extract_protocol: Total RNA was extracted from control and Dicer mutant cerebella of littermate mice using Trizol (Invitrogen) following manufacturer's instructions.

value: mixed background (B6.Cg-Tg (Gfap-cre)73.12Mvs/J (mGfap-cre 73.12) crossbred with Dicer flox/flox mice from Cobb et al., 2005)

value: Cerebellum

value: postnatal day 30

source_name: Control


title: H3 Ctrl 2h 3

description: replicate 3


title: H26 HA 24h 2

description: replicate 2


title: H22 Ctrl 24h 2

description: replicate 2


title: Control vs Dicer mutant cerebellum, Replicate 2


title: Control vs Dicer mutant cerebellum, Replicate 1


title: H19 HA 12h 3

description: replicate 3


title: H16 Ctrl 12h 2

description: replicate 2


title: TGFbeta1

city: München-Neuherberg

first: Dietrich

last: Trümbach

address: Ingolstädter Landstraße 1

department: Institute for Developmental Genetics

institute: German Research Center for Environmental Health

description: Gene expression data from adult rat subventricular zone cells

hyb_protocol: Following fragmentation, cRNA was hybridized on GeneChip Rat Expression Set 230 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.

organism: Rattus norvegicus

source_name: Rattus norvegicus - subventricular zone - stimulated

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

growth_protocol: Adult rat subventricular zone cells were grown under proliferating conditions in the presence of EGF and FGF for 7 days.

extract_protocol: Extraction of total RNA was performed with Rneasy Midi Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: During this time period, cells were treated with either HCl/BSA (control) or 10 ng/ml TGFbeta1 (TGFbeta1) 3 times per week.

value: 3 months

value: subventricular zone


title: H12 HA 6h 2

description: replicate 2


title: APPsa-DM_hippocampus_rep3

city: Heidelberg

first: Ulrike

last: Müller

address: Im Neuenheimer Feld 364

department: Bioinformatics and Functional Genomics

institute: Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg

description: back-crossed to C57BL/6 for 6 generations

hyb_protocol: Following fragmentation, 15µg cRNA were hybridized for 16 hr at 45°C on Affymetrix Mouse Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner3000.

data_processing: The data was processed in R using the RMA algorithm including RMA background correction, quantile normalization, and median polish as summarization method implemented in the affy package and provided by Bioconductor.

source_name: Hippocampus from adult APPsα-DM knock-out mouse

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

growth_protocol: Animals were kept under specific pathogen free housing conditions (SPF unit) and in compliance with the regulations of the German animal protection law.

extract_protocol: Total RNA was prepared using the RNAeasy kit from Qiagen and following the manufacturer's recommendations. RNA quality was assessed with the Bioanalyzer 2100 (Agilent) to ensure high sample quality across all samples.

treatment_protocol: Animals were sacrificed by cervical dislocation. Dissected brains were stored at -20°C in RNAlater (Qiagen). Subsequently, prefrontal cortices and hippocampi were dissected.

value: hippocampus

tag: background strain

value: female

tag: genotype/variation

value: APPsα-DM (APPα/αAPLP2-/-)

value: adult (38 - 40 weeks)


title: Control vs Dicer mutant cerebellum, Replicate 3


title: heart_active_N05-131

description: heart tissue from summer active black bear

source_name: heat, summer active

tag: tissue type

value: heart

value: male


title: control

source_name: Rattus norvegicus - subventricular zone - unstimulated


title: H10 Ctrl 6h 4

description: replicate 4

value: C57 Bk6

value: 1.5 day

value: forebrain

value: primary cell culture astrocyte

value: Control


title: APPsa-DM_hippocampus_rep2


title: D22-D2 whole brain RNA

city: Portland

first: Ted

last: Laderas

state: OR

address: 3181 SW Sam Jackson Rd CR145

department: OHSU Knight Cancer Institute

institute: Oregon Health & Science University

hyb_protocol: Samples containing at least 10 μg of total RNA were sent to the Oregon Health & Science University Gene Microarray Shared Resource facility for further quality assessment using an Agilent 2100 BioAnalyzer and for GeneChip array analysis. Because two samples were scanned by a different scanner , the dataset reported here includes whole brain samples from 22 individual mice (10 B6 and 12 D2).  After ribosomal RNA reduction, amplification and labeling, whole-brain total RNA samples were each hybridized to AffymetrixGeneChip® Mouse Exon 1.0 ST Array (24 arrays total).  The procedures used follow the Affymetrix Whole Transcript Sense Target Labeling Assay, rev3, protocol. Additional details can be found at (https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf).

scan_protocol: Standard Affymetrix protocol.

data_processing: All CEL files were processed using the Affy package (version 1.12.2) in the statistical programming environment R under the Bioconductor package [R version 2.6.0 (http://www.r-project.org), Bioconductor2.1 (http://www.bioconductor.org)]. All data was RMA [11] background corrected and normalized. Data were summarized at the probeset level using the median polish. The Mouseexonpmcdf package was utilized for summarization at the probeset-level (http://xmap.picr.man.ac.uk/download/). The data were SNP masked at the probe level. Prior to the summarization step at the probeset level described above, individual probes were masked (expression value replaced by 'null') if there was a known SNP within the boundaries of the probe.  The SNP mask was built by comparing the Affymetrix design time annotation files (GFF) files (based on NCBI mouse build 36) for each chromosome to known SNP locations in DBSNP. A total of 12,101 probesets were masked to some degree, representing 5.4% of the core probesets.

label: Biotin

source_name: D2 whole brain RNA

extract_protocol: Naïve, adult, male C57BL/6J (B6) (n=12) and DBA/2J (D2) (n=12) strain mice were euthanized by cervical dislocation, the whole brain was rapidly removed and flash frozen in liquid nitrogen.  Total RNA was isolated using TRIzol® reagent (Invitrogen, Carlsbad, CA) in a one-step guanidine isothiocyanate procedure. For microarray analyses, the extracted RNA was purified using RNeasy (Qiagen, Valencia, CA). RNA samples were evaluated by ultraviolet spectroscopy for purity and concentration.

value: whole brain

value: DBA/2J (D2)

value: Male


title: D14-D2 whole brain RNA

label_protocol: Samples containing at least 10 μg of total RNA were sent to the Oregon Health & Science University Gene Microarray Shared Resource facility for further quality assessment using an Agilent 2100 BioAnalyzer and for GeneChip array analysis. Because two samples were scanned by a different scanner , the dataset reported here includes whole brain samples from 22 individual mice (10 B6 and 12 D2).  After ribosomal RNA reduction, amplification and labeling, whole-brain total RNA samples were each hybridized to AffymetrixGeneChip® Mouse Exon 1.0 ST Array (24 arrays total).  The procedures used follow the Affymetrix Whole Transcript Sense Target Labeling Assay, rev3, protocol. Additional details can be found at (https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf).


title: heart_active_N04-113

source_name: heart, summer active


title: D16-D2 whole brain RNA


title: APPsa-DM_cortex_rep2

source_name: Prefrontal cortex from adult APPsα-DM mouse

value: prefrontal cortex


title: heart_active_N04-104


title: H6 HA 2h 2

description: replicate 2


title: H2 Ctrl 2h 2

description: replicate 2


title: APPsa-DM_cortex_rep3


title: D20-D2 whole brain RNA


title: D15-D2 whole brain RNA


title: D24-D2 whole brain RNA


title: D23-D2 whole brain RNA


title: APPsa-DM_hippocampus_rep1


title: heart_hibernating_N07-027

source_name: heart,hibernating


title: H21 Ctrl 24h 1

description: replicate 1


title: D13-D2 whole brain RNA


title: APPsa-DM_cortex_rep1


title: D19-D2 whole brain RNA


title: H25 HA 24h 1

description: replicate 1


title: B03-B6 whole brain RNA

source_name: B6 whole brain RNA


title: heart_hibernating_N05-035


title: D17-D2 whole brain RNA


title: H15 Ctrl 12h 1

description: replicate 1


title: D21-D2 whole brain RNA


title: heart_hibernating_N05-034


title: H11 HA 6h 1

description: replicate 1


title: heart_hibernating_N04-047

source_name: heart, hibernating


title: APLP2_cortex_rep2

source_name: Prefrontal cortex from adult APLP2 knock-out mouse

value: APLP2-KO (APLP2-/-)


title: H18 HA 12h 1

description: replicate 1


title: control

hyb_protocol: Following fragmentation, cRNA was hybridized on GeneChip Rat Genome 230 2.0  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with Affymetrix Gene Chip Operating Software (GCOS 1.2).

source_name: Rattus norvegicus (subventricular zone) - control

value: 3 months


title: APLP2_hippocampus_rep2

source_name: Hippocampus from adult APLP2 knock-out mouse

value: hippocampus


title: H9 Ctrl 6h 3

description: replicate 3

source_name: Mouse forebrain primary cell cultue of astrocytes


title: heart_active_N03-152


title: heart_hibernating_N06-030


title: H5 HA 2h 1

description: replicate 1


title: APLP2_hippocampus_rep1

value: female


title: heart_hibernating_N03-056


title: APLP2_hippocampus_rep3


title: B05-B6 whole brain RNA


title: H1 Ctrl 2h 1

description: replicate 1


title: TGFbeta1

source_name: Rattus norvegicus (subventricular zone) - TGFbeta1


title: APLP2_cortex_rep3


title: B02-B6 whole brain RNA


title: B01-B6 whole brain RNA


title: D18-D2 whole brain RNA


title: low nitrogen rep 3 and shade removed at V4 rep 3 [Alexa 647]

status: Public on May 09 2011

city: Fargo

first: David

last: Horvath

state: ND

address: 1605 Albrecht Blvd

department: Agr. Research Service

institute: US Dept. Agriculture

description:
080609 308dR 302dB.txt
Alexa 647: Field experiments were conducted in 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls (Clay et al. 2009. The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 kg N ha-1, from residual nitrate and legume credit. No additional nitrogen was added. Herbicides were applied at V2 to control unwanted species and all plots were maintained weed-free by hoeing or hand-pulling if plants survived or if new plants emerged after initial treatment. The experimental design was a randomized complete block design with three replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plants were grown to the V8 stage of growth and harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.

hyb_protocol: 46,000-element microarray chip developed by the University of Arizona was hybridized using their protocol (International Microarray Workshop Handbook, 2009; Gardiner et al. 2005).

scan_protocol: Intensities based on fluorescence for each probe were visualized and quantified with a GenePix scanner9 and GenePix Pro software.

data_processing:
Data from dual channel hybridization was treated as if it were from single channel hybridizations.  Dual channel hybn: low nitrogen rep 3 and shade removed at V4 rep 3

GeneMaths XT software was used to log transform (log 2) the intensity readings and samples from each individual hybridizations were normalize against each other using default parameters in Genemaths XT software (data was treated as if it were from single channel hybridizations). Probes that had hybridization intensity less than 2 times the standard deviation plus the average of the negative controls were deleted (Horvath et al., 2007) and technical replicates for each probe were averaged to reduce any dye bias that existed. GeneMaths XT software was then used to identify P values based on ANOVA and individual t tests between treatments. Probes were considered differentially expressed if P values for any test were ≤0.05.

label: Alexa 647

organism: Zea mays

source_name: top 8 cm of the topmost fully expanded leaf of four plants grown without added nitrogen to V8 were harvested and pooled.

label_protocol: First strand cDNA synthesis was performed using 1900 ng total RNA and second strand cDNA synthesis was performed using the resulting first-strand cDNA sample to make double-stranded cDNA using the Aminoallyl Message Amp II kit7.  aRNA was synthesized using the resulting double-stranded cDNA. Technical replicates from each treatment were labeled with Alexa Fluor 6478 or Alexa Fluor 5558 dye. An Alexa Fluor 647-labeled sample from one treatment was mixed with an Alexa Fluor 555-labeled sample from another treatment.

growth_protocol: Corn was planted on May 10, 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls) (Clay et al. 2009). The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 (2008) and 41 (2009) kg N ha-1, respectively, from residual nitrate and legume credit. The experimental design was a randomized complete block design with four replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008, and April 28, 2009. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plant matrerial was harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.

extract_protocol: Total RNA was extracted using Trizol reagent5 and purified using Qiagen RNeasy MinElute cleanup kit6, following the manufacturer’s protocol.

treatment_protocol: 8 cm of the top most fully expanded leaf was harvested directly into liquid nitrogen and stored at -80 until RNA extraction.

tag: stress

value: grown without added nitrogen to V8


title: shade removed at V8 rep 2 and shade removed at V4 rep 2 [Alexa 647]

description:
080509 208dB 203dR.txt
Alexa 647: Field experiments were conducted in 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls (Clay et al. 2009. The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 kg N ha-1, from residual nitrate and legume credit. Nitrogen application of 236 kg N ha-1 was applied at the beginning of the season. Herbicides were applied at V2 to control unwanted species and all plots were maintained weed-free by hoeing or hand-pulling if plants survived or if new plants emerged after initial treatment. Shade tents were 3- by 3-m frames covered with commercially available 40% shade cloth that had extending poles to keep the cloth about 25-30 cm above the corn plants. Shade tents, placed during corn emergence (VE, covered four corn rows in the center of designated plots. The experimental design was a randomized complete block design with three replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plants were grown to the V8 stage of growth and harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.

data_processing:
Data from dual channel hybridization was treated as if it were from single channel hybridizations.  Dual channel hybn: shade removed at V8 rep 2 and shade removed at V4 rep 2

GeneMaths XT software was used to log transform (log 2) the intensity readings and samples from each individual hybridizations were normalize against each other using default parameters in Genemaths XT software (data was treated as if it were from single channel hybridizations). Probes that had hybridization intensity less than 2 times the standard deviation plus the average of the negative controls were deleted (Horvath et al., 2007) and technical replicates for each probe were averaged to reduce any dye bias that existed. GeneMaths XT software was then used to identify P values based on ANOVA and individual t tests between treatments. Probes were considered differentially expressed if P values for any test were ≤0.05.

source_name: top 8 cm of the topmost fully expanded leaf of four plants grown in the presence of shade to V8 were harvested and pooled.

value: grown in the presence of shade to V8


title: shade removed at V8 rep 3 and control rep 3 [Alexa 647]

description:
080609 312dR 304dB.txt
Alexa 647: Field experiments were conducted in 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls (Clay et al. 2009. The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 kg N ha-1, from residual nitrate and legume credit. Nitrogen application of 236 kg N ha-1 was applied at the beginning of the season. Herbicides were applied at V2 to control unwanted species and all plots were maintained weed-free by hoeing or hand-pulling if plants survived or if new plants emerged after initial treatment. Shade tents were 3- by 3-m frames covered with commercially available 40% shade cloth that had extending poles to keep the cloth about 25-30 cm above the corn plants. Shade tents, placed during corn emergence (VE, covered four corn rows in the center of designated plots. The experimental design was a randomized complete block design with three replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plants were grown to the V8 stage of growth and harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.

data_processing:
Data from dual channel hybridization was treated as if it were from single channel hybridizations.  Dual channel hybn: shade removed at V8 rep 3 and control rep 3

GeneMaths XT software was used to log transform (log 2) the intensity readings and samples from each individual hybridizations were normalize against each other using default parameters in Genemaths XT software (data was treated as if it were from single channel hybridizations). Probes that had hybridization intensity less than 2 times the standard deviation plus the average of the negative controls were deleted (Horvath et al., 2007) and technical replicates for each probe were averaged to reduce any dye bias that existed. GeneMaths XT software was then used to identify P values based on ANOVA and individual t tests between treatments. Probes were considered differentially expressed if P values for any test were ≤0.05.

value: top 8 cm of the topmost fully expanded leaf of four plants


title: canola removed at V4 rep 3 and low nitrogen rep 3 [Alexa 647]

description:
080709 302dR 313dB.txt
Alexa 647: Field experiments were conducted in 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls (Clay et al. 2009. The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 kg N ha-1, from residual nitrate and legume credit. Nitrogen application of 236 kg N ha-1 was applied at the beginning of the season. Canola was planted at 7 kg ha-1, drilled 10-cm from the corn row at corn planting.  Herbicides were applied at V4 to control unwanted species (canola and all plots were thereafter maintained weed-free by hoeing or hand-pulling if plants survived or if new plants emerged after initial treatment. The experimental design was a randomized complete block design with three replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plants were grown to the V8 stage of growth and harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.

data_processing:
Data from dual channel hybridization was treated as if it were from single channel hybridizations.  Dual channel hybn: canola removed at V4 rep 3 and low nitrogen rep 3

GeneMaths XT software was used to log transform (log 2) the intensity readings and samples from each individual hybridizations were normalize against each other using default parameters in Genemaths XT software (data was treated as if it were from single channel hybridizations). Probes that had hybridization intensity less than 2 times the standard deviation plus the average of the negative controls were deleted (Horvath et al., 2007) and technical replicates for each probe were averaged to reduce any dye bias that existed. GeneMaths XT software was then used to identify P values based on ANOVA and individual t tests between treatments. Probes were considered differentially expressed if P values for any test were ≤0.05.

source_name: top 8 cm of the topmost fully expanded leaf of four plants grown in the presence of canola to V4 were harvested and pooled.

value: grown in the presence of canola to V4


title: canola removed at V8 rep 2 and control rep 2 [Alexa 647]

description:
080409 209dR 212d B.txt
Alexa 647: Field experiments were conducted in 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls (Clay et al. 2009. The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 kg N ha-1, from residual nitrate and legume credit. Nitrogen application of 236 kg N ha-1 was applied at the beginning of the season. Canola was planted at 7 kg ha-1, drilled 10-cm from the corn row at corn planting.  The experimental design was a randomized complete block design with three replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plants were grown to the V8 stage of growth and harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.

data_processing:
Data from dual channel hybridization was treated as if it were from single channel hybridizations.  Dual channel hybn: canola removed at V8 rep 2 and control rep 2

GeneMaths XT software was used to log transform (log 2) the intensity readings and samples from each individual hybridizations were normalize against each other using default parameters in Genemaths XT software (data was treated as if it were from single channel hybridizations). Probes that had hybridization intensity less than 2 times the standard deviation plus the average of the negative controls were deleted (Horvath et al., 2007) and technical replicates for each probe were averaged to reduce any dye bias that existed. GeneMaths XT software was then used to identify P values based on ANOVA and individual t tests between treatments. Probes were considered differentially expressed if P values for any test were ≤0.05.

source_name: top 8 cm of the topmost fully expanded leaf of four plants grown in the presence of canola to V8 were harvested and pooled.

value: grown in the presence of canola to V8


title: canola removed at V8 and canola removed at V4 rep 3 [Alexa 647]

description:
080709 313dR 310dB.txt
Alexa 647: Field experiments were conducted in 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls (Clay et al. 2009. The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 kg N ha-1, from residual nitrate and legume credit. Nitrogen application of 236 kg N ha-1 was applied at the beginning of the season. Canola was planted at 7 kg ha-1, drilled 10-cm from the corn row at corn planting.  The experimental design was a randomized complete block design with three replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plants were grown to the V8 stage of growth and harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.

data_processing:
Data from dual channel hybridization was treated as if it were from single channel hybridizations.  Dual channel hybn: canola removed at V8 and canola removed at V4 rep 3

GeneMaths XT software was used to log transform (log 2) the intensity readings and samples from each individual hybridizations were normalize against each other using default parameters in Genemaths XT software (data was treated as if it were from single channel hybridizations). Probes that had hybridization intensity less than 2 times the standard deviation plus the average of the negative controls were deleted (Horvath et al., 2007) and technical replicates for each probe were averaged to reduce any dye bias that existed. GeneMaths XT software was then used to identify P values based on ANOVA and individual t tests between treatments. Probes were considered differentially expressed if P values for any test were ≤0.05.


title: shade removed at V4 rep 3 and shade removed at V8 rep 3 [Alexa 647]

description:
080609 304dR 308dB.txt
Alexa 647: Field experiments were conducted in 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls (Clay et al. 2009. The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 kg N ha-1, from residual nitrate and legume credit. Nitrogen application of 236 kg N ha-1 was applied at the beginning of the season. Herbicides were applied at V2 to control unwanted species and all plots were maintained weed-free by hoeing or hand-pulling if plants survived or if new plants emerged after initial treatment. Shade tents were 3- by 3-m frames covered with commercially available 40% shade cloth that had extending poles to keep the cloth about 25-30 cm above the corn plants. Shade tents, placed during corn emergence (VE, covered four corn rows in the center of designated plots and removed at V4. The experimental design was a randomized complete block design with three replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plants were grown to the V8 stage of growth and harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.

data_processing:
Data from dual channel hybridization was treated as if it were from single channel hybridizations.  Dual channel hybn: shade removed at V4 rep 3 and shade removed at V8 rep 3

GeneMaths XT software was used to log transform (log 2) the intensity readings and samples from each individual hybridizations were normalize against each other using default parameters in Genemaths XT software (data was treated as if it were from single channel hybridizations). Probes that had hybridization intensity less than 2 times the standard deviation plus the average of the negative controls were deleted (Horvath et al., 2007) and technical replicates for each probe were averaged to reduce any dye bias that existed. GeneMaths XT software was then used to identify P values based on ANOVA and individual t tests between treatments. Probes were considered differentially expressed if P values for any test were ≤0.05.

source_name: top 8 cm of the topmost fully expanded leaf of four plants grown in the presence of shade to V4 were harvested and pooled.

value: grown in the presence of shade to V4


title: low nitrogen rep 2 and canola removed at V4 rep 2 [Alexa 647]

description:
080509 207dR 213dB.txt
Alexa 647: Field experiments were conducted in 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls (Clay et al. 2009. The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 kg N ha-1, from residual nitrate and legume credit. No additional nitrogen was added. Herbicides were applied at V2 to control unwanted species and all plots were maintained weed-free by hoeing or hand-pulling if plants survived or if new plants emerged after initial treatment. The experimental design was a randomized complete block design with three replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plants were grown to the V8 stage of growth and harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.

data_processing:
Data from dual channel hybridization was treated as if it were from single channel hybridizations.  Dual channel hybn: low nitrogen rep 2 and canola removed at V4 rep 2

GeneMaths XT software was used to log transform (log 2) the intensity readings and samples from each individual hybridizations were normalize against each other using default parameters in Genemaths XT software (data was treated as if it were from single channel hybridizations). Probes that had hybridization intensity less than 2 times the standard deviation plus the average of the negative controls were deleted (Horvath et al., 2007) and technical replicates for each probe were averaged to reduce any dye bias that existed. GeneMaths XT software was then used to identify P values based on ANOVA and individual t tests between treatments. Probes were considered differentially expressed if P values for any test were ≤0.05.


title: APLP2_cortex_rep1

value: adult (38 - 40 weeks)


title: control rep 1 and canola removed at V8 rep 3 [Alexa 647]

description:
080709 310dR 101dB.txt
Alexa 647: Field experiments were conducted in 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls (Clay et al. 2009. The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 kg N ha-1, from residual nitrate and legume credit. Nitrogen application of 236 kg N ha-1 was applied at the beginning of the season. Herbicides were applied at V2 to control unwanted species and all plots were maintained weed-free by hoeing or hand-pulling if plants survived or if new plants emerged after initial treatment. The experimental design was a randomized complete block design with three replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plants were grown to the V8 stage of growth and harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.

data_processing:
Data from dual channel hybridization was treated as if it were from single channel hybridizations.  Dual channel hybn: control rep 1 and canola removed at V8 rep 3

GeneMaths XT software was used to log transform (log 2) the intensity readings and samples from each individual hybridizations were normalize against each other using default parameters in Genemaths XT software (data was treated as if it were from single channel hybridizations). Probes that had hybridization intensity less than 2 times the standard deviation plus the average of the negative controls were deleted (Horvath et al., 2007) and technical replicates for each probe were averaged to reduce any dye bias that existed. GeneMaths XT software was then used to identify P values based on ANOVA and individual t tests between treatments. Probes were considered differentially expressed if P values for any test were ≤0.05.

source_name: top 8 cm of the topmost fully expanded leaf of four control plants were harvested and pooled.

value: control


title: canola removed at V4 rep 2 and canola removed at V8 rep 2 [Alexa 647]

description:
073009 212dR 207dB.txt
Alexa 647: Field experiments were conducted in 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls (Clay et al. 2009. The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 kg N ha-1, from residual nitrate and legume credit. Nitrogen application of 236 kg N ha-1 was applied at the beginning of the season. Canola was planted at 7 kg ha-1, drilled 10-cm from the corn row at corn planting.  Herbicides were applied at V4 to control unwanted species (canola and all plots were thereafter maintained weed-free by hoeing or hand-pulling if plants survived or if new plants emerged after initial treatment. The experimental design was a randomized complete block design with three replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plants were grown to the V8 stage of growth and harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.

data_processing:
Data from dual channel hybridization was treated as if it were from single channel hybridizations.  Dual channel hybn: canola removed at V4 rep 2 and canola removed at V8 rep 2

GeneMaths XT software was used to log transform (log 2) the intensity readings and samples from each individual hybridizations were normalize against each other using default parameters in Genemaths XT software (data was treated as if it were from single channel hybridizations). Probes that had hybridization intensity less than 2 times the standard deviation plus the average of the negative controls were deleted (Horvath et al., 2007) and technical replicates for each probe were averaged to reduce any dye bias that existed. GeneMaths XT software was then used to identify P values based on ANOVA and individual t tests between treatments. Probes were considered differentially expressed if P values for any test were ≤0.05.


title: low nitrogen rep 1 and shade removed at V4 rep 1 [Alexa 647]

description:
080409 109dR 108d B.txt
Alexa 647: Field experiments were conducted in 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls (Clay et al. 2009. The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 kg N ha-1, from residual nitrate and legume credit. No additional nitrogen was added. Herbicides were applied at V2 to control unwanted species and all plots were maintained weed-free by hoeing or hand-pulling if plants survived or if new plants emerged after initial treatment. The experimental design was a randomized complete block design with three replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plants were grown to the V8 stage of growth and harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.

data_processing:
Data from dual channel hybridization was treated as if it were from single channel hybridizations.  Dual channel hybn: low nitrogen rep 1 and shade removed at V4 rep 1

GeneMaths XT software was used to log transform (log 2) the intensity readings and samples from each individual hybridizations were normalize against each other using default parameters in Genemaths XT software (data was treated as if it were from single channel hybridizations). Probes that had hybridization intensity less than 2 times the standard deviation plus the average of the negative controls were deleted (Horvath et al., 2007) and technical replicates for each probe were averaged to reduce any dye bias that existed. GeneMaths XT software was then used to identify P values based on ANOVA and individual t tests between treatments. Probes were considered differentially expressed if P values for any test were ≤0.05.


title: IGF-treated cells (24hr), biological rep_3

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description:
H21.24hrIGF
MCF-7 cells were plated in 10cm dishes and then switched to SFM on the next day.  Following overnight starvation, cells were treated in triplicate with IGF-I (100ng/mL)  for 24hr.
Reanalysis of GSM183431.

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized on U133A GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-2v4.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner (Agilent).

data_processing: log2 expression values estimated using GC RMA with Array analyzer software

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

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

tag: cell line

value: MCF-7 breast cancer cell line

tag: agent

value: IGF


title: IGF-treated cells (24hr), biological rep_2

description:
H20.24hrIGF
MCF-7 cells were plated in 10cm dishes and then switched to SFM on the next day.  Following overnight starvation, cells were treated in triplicate with IGF-I (100ng/mL)  for 24hr.
Reanalysis of GSM183430.


title: control rep 2 and canola removed at V8 rep 1  [Alexa 647]

description:
071009 107dR 209dB.txt
Alexa 647: Field experiments were conducted in 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls (Clay et al. 2009. The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 kg N ha-1, from residual nitrate and legume credit. Nitrogen application of 236 kg N ha-1 was applied at the beginning of the season. Herbicides were applied at V2 to control unwanted species and all plots were maintained weed-free by hoeing or hand-pulling if plants survived or if new plants emerged after initial treatment. The experimental design was a randomized complete block design with three replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plants were grown to the V8 stage of growth and harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.

data_processing:
Data from dual channel hybridization was treated as if it were from single channel hybridizations.  Dual channel hybn: control rep 2 and canola removed at V8 rep 1

GeneMaths XT software was used to log transform (log 2) the intensity readings and samples from each individual hybridizations were normalize against each other using default parameters in Genemaths XT software (data was treated as if it were from single channel hybridizations). Probes that had hybridization intensity less than 2 times the standard deviation plus the average of the negative controls were deleted (Horvath et al., 2007) and technical replicates for each probe were averaged to reduce any dye bias that existed. GeneMaths XT software was then used to identify P values based on ANOVA and individual t tests between treatments. Probes were considered differentially expressed if P values for any test were ≤0.05.

tag: tissue

value: top 8 cm of the topmost fully expanded leaf of four control plants


title: control rep 3 and shade removed at V8 rep 2 [Alexa 647]

description:
072309 208dR 312dB.txt
Alexa 647: Field experiments were conducted in 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls (Clay et al. 2009. The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 kg N ha-1, from residual nitrate and legume credit. Nitrogen application of 236 kg N ha-1 was applied at the beginning of the season. Herbicides were applied at V2 to control unwanted species and all plots were maintained weed-free by hoeing or hand-pulling if plants survived or if new plants emerged after initial treatment. The experimental design was a randomized complete block design with three replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plants were grown to the V8 stage of growth and harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.

data_processing:
Data from dual channel hybridization was treated as if it were from single channel hybridizations.  Dual channel hybn: control rep 3 and shade removed at V8 rep 2

GeneMaths XT software was used to log transform (log 2) the intensity readings and samples from each individual hybridizations were normalize against each other using default parameters in Genemaths XT software (data was treated as if it were from single channel hybridizations). Probes that had hybridization intensity less than 2 times the standard deviation plus the average of the negative controls were deleted (Horvath et al., 2007) and technical replicates for each probe were averaged to reduce any dye bias that existed. GeneMaths XT software was then used to identify P values based on ANOVA and individual t tests between treatments. Probes were considered differentially expressed if P values for any test were ≤0.05.


title: B08-B6 whole brain RNA

value: whole brain

tag: gender

value: Male


title: shade removed at V4 rep 2 and low nitrogen  rep 2 [Alexa 647]

description:
073009 203dB 213dR.txt
Alexa 647: Field experiments were conducted in 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls (Clay et al. 2009. The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 kg N ha-1, from residual nitrate and legume credit. Nitrogen application of 236 kg N ha-1 was applied at the beginning of the season. Herbicides were applied at V2 to control unwanted species and all plots were maintained weed-free by hoeing or hand-pulling if plants survived or if new plants emerged after initial treatment. Shade tents were 3- by 3-m frames covered with commercially available 40% shade cloth that had extending poles to keep the cloth about 25-30 cm above the corn plants. Shade tents, placed during corn emergence (VE, covered four corn rows in the center of designated plots and removed at V4. The experimental design was a randomized complete block design with three replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plants were grown to the V8 stage of growth and harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.

data_processing:
Data from dual channel hybridization was treated as if it were from single channel hybridizations.  Dual channel hybn: shade removed at V4 rep 2 and low nitrogen  rep 2

GeneMaths XT software was used to log transform (log 2) the intensity readings and samples from each individual hybridizations were normalize against each other using default parameters in Genemaths XT software (data was treated as if it were from single channel hybridizations). Probes that had hybridization intensity less than 2 times the standard deviation plus the average of the negative controls were deleted (Horvath et al., 2007) and technical replicates for each probe were averaged to reduce any dye bias that existed. GeneMaths XT software was then used to identify P values based on ANOVA and individual t tests between treatments. Probes were considered differentially expressed if P values for any test were ≤0.05.


title: E2-treated cells (24hr), biological rep_3

description:
H18.24hrE2
MCF-7 cells were plated in 10cm dishes and then switched to SFM on the next day.  Following overnight starvation, cells were treated in triplicate with E2 (10nM) for 24hr.

value: estradiol (E2)


title: B04-B6 whole brain RNA

data_processing: All CEL files were processed using the Affy package (version 1.12.2) in the statistical programming environment R under the Bioconductor package [R version 2.6.0 (http://www.r-project.org), Bioconductor2.1 (http://www.bioconductor.org)]. All data was RMA [11] background corrected and normalized. Data were summarized at the probeset level using the median polish. The Mouseexonpmcdf package was utilized for summarization at the probeset-level (http://xmap.picr.man.ac.uk/download/). The data were SNP masked at the probe level. Prior to the summarization step at the probeset level described above, individual probes were masked (expression value replaced by 'null') if there was a known SNP within the boundaries of the probe.  The SNP mask was built by comparing the Affymetrix design time annotation files (GFF) files (based on NCBI mouse build 36) for each chromosome to known SNP locations in DBSNP. A total of 12,101 probesets were masked to some degree, representing 5.4% of the core probesets.

tag: strain


title: E2-treated cells (24hr), biological rep_2

description:
H17.24hrE2
MCF-7 cells were plated in 10cm dishes and then switched to SFM on the next day.  Following overnight starvation, cells were treated in triplicate with E2 (10nM) for 24hr.


title: IGF-treated cells (24hr), biological rep_1

description:
H19.24hrIGF
MCF-7 cells were plated in 10cm dishes and then switched to SFM on the next day.  Following overnight starvation, cells were treated in triplicate with IGF-I (100ng/mL)  for 24hr.
Reanalysis of GSM183429.


title: B09-B6 whole brain RNA


title: B06-B6 whole brain RNA


title: canola removed at V8 rep 1 and Canola removed at V4 rep 1 [Alexa 647]

description:
070909 107dB 105dR.txt
Alexa 647: Field experiments were conducted in 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls (Clay et al. 2009. The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 kg N ha-1, from residual nitrate and legume credit. Nitrogen application of 236 kg N ha-1 was applied at the beginning of the season. Canola was planted at 7 kg ha-1, drilled 10-cm from the corn row at corn planting.  The experimental design was a randomized complete block design with three replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plants were grown to the V8 stage of growth and harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.

data_processing:
Data from dual channel hybridization was treated as if it were from single channel hybridizations.  Dual channel hybn: canola removed at V8 rep 1 and Canola removed at V4 rep 1

GeneMaths XT software was used to log transform (log 2) the intensity readings and samples from each individual hybridizations were normalize against each other using default parameters in Genemaths XT software (data was treated as if it were from single channel hybridizations). Probes that had hybridization intensity less than 2 times the standard deviation plus the average of the negative controls were deleted (Horvath et al., 2007) and technical replicates for each probe were averaged to reduce any dye bias that existed. GeneMaths XT software was then used to identify P values based on ANOVA and individual t tests between treatments. Probes were considered differentially expressed if P values for any test were ≤0.05.


title: IGF-treated cells (3hr), biological rep_3

description:
H9.3hrIGF
MCF-7 cells were plated in 10cm dishes and then switched to SFM on the next day.  Following overnight starvation, cells were treated in triplicate with IGF-I (100ng/mL)  for 3hr.
Reanalysis of GSM183428.


title: E2-treated cells (24hr), biological rep_1

description:
H16.24hrE2
MCF-7 cells were plated in 10cm dishes and then switched to SFM on the next day.  Following overnight starvation, cells were treated in triplicate with E2 (10nM) for 24hr.


title: canola removed at V4 rep 1 and low nitrogen rep 1 [Alexa 647]

description:
070909 105d B 108dR.txt
Alexa 647: Field experiments were conducted in 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls (Clay et al. 2009. The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 kg N ha-1, from residual nitrate and legume credit. Nitrogen application of 236 kg N ha-1 was applied at the beginning of the season. Canola was planted at 7 kg ha-1, drilled 10-cm from the corn row at corn planting.  Herbicides were applied at V4 to control unwanted species (canola and all plots were thereafter maintained weed-free by hoeing or hand-pulling if plants survived or if new plants emerged after initial treatment. The experimental design was a randomized complete block design with three replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plants were grown to the V8 stage of growth and harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.

data_processing:
Data from dual channel hybridization was treated as if it were from single channel hybridizations.  Dual channel hybn: canola removed at V4 rep 1 and low nitrogen rep 1

GeneMaths XT software was used to log transform (log 2) the intensity readings and samples from each individual hybridizations were normalize against each other using default parameters in Genemaths XT software (data was treated as if it were from single channel hybridizations). Probes that had hybridization intensity less than 2 times the standard deviation plus the average of the negative controls were deleted (Horvath et al., 2007) and technical replicates for each probe were averaged to reduce any dye bias that existed. GeneMaths XT software was then used to identify P values based on ANOVA and individual t tests between treatments. Probes were considered differentially expressed if P values for any test were ≤0.05.


title: shade removed at V8 rep 3 and control rep 3 [Alexa 555]

description:
080609 312dR 304dB.txt
Alexa 555: Field experiments were conducted in 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls (Clay et al. 2009. The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 kg N ha-1, from residual nitrate and legume credit. Nitrogen application of 236 kg N ha-1 was applied at the beginning of the season. Herbicides were applied at V2 to control unwanted species and all plots were maintained weed-free by hoeing or hand-pulling if plants survived or if new plants emerged after initial treatment. The experimental design was a randomized complete block design with three replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plants were grown to the V8 stage of growth and harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.

label: Alexa 555


title: canola removed at V8 and canola removed at V4 rep 3 [Alexa 555]

description:
080709 313dR 310dB.txt
Alexa 555: Field experiments were conducted in 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls (Clay et al. 2009. The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 kg N ha-1, from residual nitrate and legume credit. Nitrogen application of 236 kg N ha-1 was applied at the beginning of the season. Canola was planted at 7 kg ha-1, drilled 10-cm from the corn row at corn planting.  Herbicides were applied at V4 to control unwanted species (canola and all plots were thereafter maintained weed-free by hoeing or hand-pulling if plants survived or if new plants emerged after initial treatment. The experimental design was a randomized complete block design with three replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plants were grown to the V8 stage of growth and harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.


title: IGF-treated cells (3hr), biological rep_2

description:
H8.3hrIGF
MCF-7 cells were plated in 10cm dishes and then switched to SFM on the next day.  Following overnight starvation, cells were treated in triplicate with IGF-I (100ng/mL)  for 3hr.
Reanalysis of GSM183427.


title: SFM control cells (24hr), biological rep_1

description:
H13.24hrSFM
MCF-7 cells were plated in 10cm dishes and then switched to SFM on the next day.
Reanalysis of GSM183423.

value: SFM (control)


title: shade removed at V4 rep 1 and shade removed at V8 rep 1 [Alexa 647]

description:
071009 109dB 111dR.txt
Alexa 647: Field experiments were conducted in 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls (Clay et al. 2009. The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 kg N ha-1, from residual nitrate and legume credit. Nitrogen application of 236 kg N ha-1 was applied at the beginning of the season. Herbicides were applied at V2 to control unwanted species and all plots were maintained weed-free by hoeing or hand-pulling if plants survived or if new plants emerged after initial treatment. Shade tents were 3- by 3-m frames covered with commercially available 40% shade cloth that had extending poles to keep the cloth about 25-30 cm above the corn plants. Shade tents, placed during corn emergence (VE, covered four corn rows in the center of designated plots and removed at V4. The experimental design was a randomized complete block design with three replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plants were grown to the V8 stage of growth and harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.

data_processing:
Data from dual channel hybridization was treated as if it were from single channel hybridizations.  Dual channel hybn: shade removed at V4 rep 1 and shade removed at V8 rep 1

GeneMaths XT software was used to log transform (log 2) the intensity readings and samples from each individual hybridizations were normalize against each other using default parameters in Genemaths XT software (data was treated as if it were from single channel hybridizations). Probes that had hybridization intensity less than 2 times the standard deviation plus the average of the negative controls were deleted (Horvath et al., 2007) and technical replicates for each probe were averaged to reduce any dye bias that existed. GeneMaths XT software was then used to identify P values based on ANOVA and individual t tests between treatments. Probes were considered differentially expressed if P values for any test were ≤0.05.


title: control rep 1 and canola removed at V8 rep 3 [Alexa 555]

description:
080709 310dR 101dB.txt
Alexa 555: Field experiments were conducted in 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls (Clay et al. 2009. The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 kg N ha-1, from residual nitrate and legume credit. Nitrogen application of 236 kg N ha-1 was applied at the beginning of the season. Canola was planted at 7 kg ha-1, drilled 10-cm from the corn row at corn planting.  The experimental design was a randomized complete block design with three replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plants were grown to the V8 stage of growth and harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.


title: IGF-treated cells (3hr), biological rep_1

description:
H7.3hrIGF
MCF-7 cells were plated in 10cm dishes and then switched to SFM on the next day.  Following overnight starvation, cells were treated in triplicate with IGF-I (100ng/mL)  for 3hr.
Reanalysis of GSM183426.


title: low nitrogen rep 2 and canola removed at V4 rep 2 [Alexa 555]

description:
080509 207dR 213dB.txt
Alexa 555: Field experiments were conducted in 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls (Clay et al. 2009. The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 kg N ha-1, from residual nitrate and legume credit. Nitrogen application of 236 kg N ha-1 was applied at the beginning of the season. Canola was planted at 7 kg ha-1, drilled 10-cm from the corn row at corn planting.  Herbicides were applied at V4 to control unwanted species (canola and all plots were thereafter maintained weed-free by hoeing or hand-pulling if plants survived or if new plants emerged after initial treatment. The experimental design was a randomized complete block design with three replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plants were grown to the V8 stage of growth and harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.


title: B11-B6 whole brain RNA


title: shade removed at V4 rep 3 and shade removed at V8 rep 3 [Alexa 555]

description:
080609 304dR 308dB.txt
Alexa 555: Field experiments were conducted in 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls (Clay et al. 2009. The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 kg N ha-1, from residual nitrate and legume credit. Nitrogen application of 236 kg N ha-1 was applied at the beginning of the season. Herbicides were applied at V2 to control unwanted species and all plots were maintained weed-free by hoeing or hand-pulling if plants survived or if new plants emerged after initial treatment. Shade tents were 3- by 3-m frames covered with commercially available 40% shade cloth that had extending poles to keep the cloth about 25-30 cm above the corn plants. Shade tents, placed during corn emergence (VE, covered four corn rows in the center of designated plots. The experimental design was a randomized complete block design with three replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plants were grown to the V8 stage of growth and harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.


title: canola removed at V4 rep 3 and low nitrogen rep 3 [Alexa 555]

description:
080709 302dR 313dB.txt
Alexa 555: Field experiments were conducted in 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls (Clay et al. 2009. The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 kg N ha-1, from residual nitrate and legume credit. No additional nitrogen was added. Herbicides were applied at V2 to control unwanted species and all plots were maintained weed-free by hoeing or hand-pulling if plants survived or if new plants emerged after initial treatment. The experimental design was a randomized complete block design with three replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plants were grown to the V8 stage of growth and harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.


title: SFM control cells (24hr), biological rep_3

description:
H15.24hrSFM
MCF-7 cells were plated in 10cm dishes and then switched to SFM on the next day.
Reanalysis of GSM183425.


title: shade removed at V8 rep 2 and shade removed at V4 rep 2 [Alexa 555]

description:
080509 208dB 203dR.txt
Alexa 555: Field experiments were conducted in 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls (Clay et al. 2009. The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 kg N ha-1, from residual nitrate and legume credit. Nitrogen application of 236 kg N ha-1 was applied at the beginning of the season. Herbicides were applied at V2 to control unwanted species and all plots were maintained weed-free by hoeing or hand-pulling if plants survived or if new plants emerged after initial treatment. Shade tents were 3- by 3-m frames covered with commercially available 40% shade cloth that had extending poles to keep the cloth about 25-30 cm above the corn plants. Shade tents, placed during corn emergence (VE, covered four corn rows in the center of designated plots and removed at V4. The experimental design was a randomized complete block design with three replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plants were grown to the V8 stage of growth and harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.

data_processing:
Data from dual channel hybridization was treated as if it were from single channel hybridizations.  Dual channel hybn: shade removed at V8 rep 2 and shade removed at V4 rep 2

GeneMaths XT software was used to log transform (log 2) the intensity readings and samples from each individual hybridizations were normalize against each other using default parameters in Genemaths XT software (data was treated as if it were from single channel hybridizations). Probes that had hybridization intensity less than 2 times the standard deviation plus the average of the negative controls were deleted (Horvath et al., 2007) and technical replicates for each probe were averaged to reduce any dye bias that existed. GeneMaths XT software was then used to identify P values based on ANOVA and individual t tests between treatments. Probes were considered differentially expressed if P values for any test were ≤0.05.


title: SFM control cells (3hr), biological rep_2

description:
H2.3hrSFM
MCF-7 cells were plated in 10cm dishes and then switched to SFM on the next day.
Reanalysis of GSM183422.


title: E2-treated cells (3hr), biological rep_3

description:
H6.3hrE2
MCF-7 cells were plated in 10cm dishes and then switched to SFM on the next day.  Following overnight starvation, cells were treated in triplicate with E2 (10nM) for 3hr.


title: E2-treated cells (3hr), biological rep_2

description:
H5.3hrE2
MCF-7 cells were plated in 10cm dishes and then switched to SFM on the next day.  Following overnight starvation, cells were treated in triplicate with E2 (10nM) for 3hr.


title: low nitrogen rep 1 and shade removed at V4 rep 1 [Alexa 555]

description:
080409 109dR 108d B.txt
Alexa 555: Field experiments were conducted in 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls (Clay et al. 2009. The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 kg N ha-1, from residual nitrate and legume credit. Nitrogen application of 236 kg N ha-1 was applied at the beginning of the season. Herbicides were applied at V2 to control unwanted species and all plots were maintained weed-free by hoeing or hand-pulling if plants survived or if new plants emerged after initial treatment. Shade tents were 3- by 3-m frames covered with commercially available 40% shade cloth that had extending poles to keep the cloth about 25-30 cm above the corn plants. Shade tents, placed during corn emergence (VE, covered four corn rows in the center of designated plots and removed at V4. The experimental design was a randomized complete block design with three replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plants were grown to the V8 stage of growth and harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.


title: SFM control cells (24hr), biological rep_2

description:
H14.24hrSFM
MCF-7 cells were plated in 10cm dishes and then switched to SFM on the next day.
Reanalysis of GSM183424.


title: low nitrogen rep 3 and shade removed at V4 rep 3 [Alexa 555]

description:
080609 308dR 302dB.txt
Alexa 555: Field experiments were conducted in 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls (Clay et al. 2009. The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 kg N ha-1, from residual nitrate and legume credit. Nitrogen application of 236 kg N ha-1 was applied at the beginning of the season. Herbicides were applied at V2 to control unwanted species and all plots were maintained weed-free by hoeing or hand-pulling if plants survived or if new plants emerged after initial treatment. Shade tents were 3- by 3-m frames covered with commercially available 40% shade cloth that had extending poles to keep the cloth about 25-30 cm above the corn plants. Shade tents, placed during corn emergence (VE, covered four corn rows in the center of designated plots and removed at V4. The experimental design was a randomized complete block design with three replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plants were grown to the V8 stage of growth and harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.

data_processing:
Data from dual channel hybridization was treated as if it were from single channel hybridizations.  Dual channel hybn: low nitrogen rep 3 and shade removed at V4 rep 3

GeneMaths XT software was used to log transform (log 2) the intensity readings and samples from each individual hybridizations were normalize against each other using default parameters in Genemaths XT software (data was treated as if it were from single channel hybridizations). Probes that had hybridization intensity less than 2 times the standard deviation plus the average of the negative controls were deleted (Horvath et al., 2007) and technical replicates for each probe were averaged to reduce any dye bias that existed. GeneMaths XT software was then used to identify P values based on ANOVA and individual t tests between treatments. Probes were considered differentially expressed if P values for any test were ≤0.05.