title: Medicago truncatula (DZA315.16)  12 hours after E. pisi infection, rep6

description: Medicago truncatula  12 hours after no pathogen treatment (control)rep6


title: hatching stage (Cy5) vs  mouth opening stage (Cy3)

status: Public on Jan 26 2007

type: RNA

city: Heraklion

first: Elena

middle: Athina

last: Sarropoulou

department: Marine Biology and Genetics

country: Greece

institute: HCMR

description: mouth opening stage(144hpf)(Cy3)  and hatching stage (48hpf) (Cy5) of sea bream.

molecule: total RNA

organism: Sparus aurata

source_name: hatching stage (Cy5)

source_name: mouth opening stage (Cy3)


title: Halobacterium NRC-1, ura3 Knockout, vng1179 Knockout, Set A, 0.85mM Cu, Array 08423

city: Seattle

first: Michael

middle: Hiroshi

last: Johnson

state: WA

address: 1441 North 34th Street

department: Computational Biology

country: USA

institute: Institute for Systems Biology

description: Halobacterium NRC-1, ura3 Knockout, vng1179 Knockout (0.85mM Cu, Set A) vs. control

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35[optional]

scan_protocol: ScanArray 5000, using Packard BioChip ScanArray software. See http://www.systemsbiology.org/Scientists_and_Research/Technology/ISB_Facilities/Microarray for microarray scanning details

data_processing: AnalyzerDG software for spotfinding.  see http://www.systemsbiology.org/Scientists_and_Research/Technology/Data_Management/Microarray_Pipeline for more details

label: Alexa 546

organism: Halobacterium salinarum NRC-1

growth_protocol: Mid-log phase (OD600-0.5 - 0.6) Halobacterium NRC-1 culture grown in standard media

extract_protocol: Total DNA-free RNA prepared using the Absolutely RNA miniprep kit (Stratagene) and analyzed by PCR to rule out DNA contamination, with Agilent Bioanalyzer to verify integrity, and in the spectrophotometer for quantification.

tag: Halobacterium NRC-1, ura3 Knockout, vng1179 Knockout grown in standard growth media with 0.85mM Cu

label: Alexa 647

source_name: Halobacterium NRC-1, control

tag: Halobacterium NRC-1 grown in standard growth media


title: neurula stage (Cy3) vs mouth opening stage (Cy5)

description: neurula stage  (24hpf) (Cy3) vs mouth opening stage (144hpf) (Cy5)

source_name: neurula stage (Cy3)

source_name: mouth opening stage (Cy5)


title: stage hatching (Cy5) vs stage eye pigmentation (Cy3)

description: stage of hatching (Cy5) (48hpf) and stage of eye pigmentation (Cy3) (168hpf) of sea bream.

source_name: stage hatching (Cy5)

source_name: stage eye pigmentation (Cy3)


title: top1, A2S9a.gpr

city: Acton

first: Anthony

last: Millgate

state: ACT

address: PO Box 1600

country: Australia

institute: CSIRO

description:
Thebaine and oripavine accumulating mutant (Norman) verses wildtype.
leaf RNA extracted from preflowering material of the top1 mutant of Papaver somniferum
leaf RNA extracted from preflowering Papaver somniferum cv C052.  Plants were grown in the glasshouse All RNA isolation was accomplished with the NTES method Higgins et al., Vol 260: 166-168 1976. RNA (100 µg) was reverse-transcribed into cDNA and flurescently labeled for microarray hybridization as per the methods in Schenk, P.M. et al. "Coordinated Plant Defense Responses in Arabidopsis Revealed by Microarray Analysis." Proceedings of the National Academy of Sciences of the United States of America 97, 11655-11660 (2000).
Hybridisation protocols are as per Protocols for Corning Gaps II coated slides Refer: http://www.corning.com/Lifesciences/technical_information/techDocs/gaps_ii_manual_protocol_5_02_cls_gaps_005.pdf
Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner (Axon Instruments, Union, CA) and image intensity data were extracted and analyzed with GenePix Pro 3.0 analysis software. After background correction and removal of flagged values, the data was normalised using the spatial-normalisation protocol from the tRMA package Wilson, D.L , Buckley, M.J., Helliwell, C.A., and Wilson, I.W. "New Normalization Methods for cDNA Microarray Data." Bioinformatics 19, 1325-1332 (2003).   Using the relevant function in tRMA the spatially normalised back to ratio differentially-expressed genes were extracted from the complete list of 17,000 clones' median values.  Gaussian distribution outliers were selected.  Log Red dye/log Green dye [log(R/G)] data were compared using GenePix Pro 3 software (after spatial normalisation).  A ratio threshold cut-off of 2 was used.
Biological Replicate: 1, Technical Replicate: 2, Dye Swapped: true
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = Opium Poppy, Secondary Metabolism

organism: Papaver somniferum

source_name: RNA from whole leaf/stem of Wild Type CO52 at running up stage

source_name: RNA from whole leaf/stem of D233 mutant at running up stage


title: Medicago truncatula (DZA315.16)  12 hours after E. pisi infection, rep4

status: Public on Jan 25 2007

city: St Paul

first: Kathryn

middle: A

last: VandenBosch

state: MN

address: Room 250 BioSci 6022 1445 Gortner Ave

department: Plant Biology

institute: University of Minnesota

description: Medicago truncatula  12 hours after no pathogen treatment (control)rep4

hyb_protocol: The hybridization and washing procedures of 3DNA Array 50 Expression Array Detection Kit were followed. Briefly, the hybridization mix consisted of 2.5 ó L of cDNAs from inoculated and uninoculated roots, 2.5 ó L of Cy3 and Cy5 dyes, 2 ó L of LNA dT blocker and 9 ó L of 2X SDS hybridization buffer. Hybridization was carried out at 62.0oC for 20- 23 h. Hybridized slides were washed in 2X SSC, 0.2% SDS for 10 min at 55oC, 2X SSC for 10 min at room temperature, and 0.2X SSC for 10 min at room temperatures with gentle agitation. Each hybridization was repeated a total of 6 times to sample the technical variability, with 3 repeats of each dye combination to control for dye effects.

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

data_processing: Background-subtracted mean intensities for both tissues were log2 transformed and normalized using lowess and ANOVA

organism: Medicago truncatula

label_protocol: 11 ug RNA from each of 3 biological replicates (9 plants total) was pooled to make a total of 33 ug for cDNA synthesis.  cDNA synthesis and fluorescent labeling was performed using the Genisphere Array 50 kit (Hatfield, PA USA) with a modified bulk-synthesis protocol that generated cDNA sufficient for 10 slide hybridizations.  32-40 mg total RNA in a volume of 8  l was mixed with 2  l of the Cy5 capture RT primer, then heated to 80oC for 10 min.  Tubes were immediately transferred to ice and then 1  l Superase-In RNase Inhibitor was added.  In a separate tube, 4  l 5X Superscript II RT buffer, 1  l 10 mM dNTPs, 2  l 0.1 M DTT, 1  l (200 U) Superscript II Reverse Transcriptase enzyme (Invitrogen, Carlsbad, CA USA) and nuclease-free ddH20 were mixed before addition to the RNA/primer combination.  Each tube was incubated for 2 h at 42oC, before the addition of 3.5  l of 0.5M NaOH/50mM EDTA and transfer to 65oC for 10 minutes to stop the reaction.  Finally, 5  l of 1 M Tris-HCL (pH 7.5) was added to neutralize the reaction.  cDNAs were stored at -20oC.  11 ug RNA from each of 3 biological replicates.

growth_protocol: Surface-sterilized Medicago truncatula seeds were vernalized at 40 C for 36 h, and then transferred to water-soaked Jiffy-7 peat pellets (Jiffy Product of America, Norwalk, OH, USA) that were placed inside clay pots containing SB-300 soil mix (Sungrow USA, Pine Bluff, AS, USA).  A pure culture of Erysiphe pisi that was established from a naturally-infected pea plant was obtained from Dr. Tim L.W. Carver, Department of Environmental Biology,  Institute of Grassland and Environmental Research, Plas Gogerddan, Aberystwyth, Ceredigion SY23 3EB, Wales, UK.  Cultures were maintained on Perfection 8771 pea plants grown in isolation at 22°C with a 16 h photoperiod (300 µmol/min/m2) and 8 h of darkness at 16°C.  Four-week-old M. truncatula plants with 2-3 fully expanded compound leaves were inoculated with approximately 300-500 spores/cm2 leaflet area using a 180 cm settling tower.  After 20 min, plants were returned to the growth chamber.  Control plants were grown in parallel in a separate chamber under the same conditions.

extract_protocol: Trifoliate leaf samples from 3 experimental replicates (9 plants total) were collected for the experiment. RNA from frozen leaf samples following the manufacturer's instructions.

tag: Medicago truncatula; lines - DZA315.16; tissue-trifoliate leaves; age - 4 weeks; treatment  12 hours after pathogen inoculation

source_name: Medicago truncatula (DZA315.16)  12 hours after no pathogen treatment (control)

label_protocol: 11 ug RNA from each of 3 biological replicates (9 plants total) was pooled to make a total of 33 ug for cDNA synthesis.  cDNA synthesis and fluorescent labeling was performed using the Genisphere Array 50 kit (Hatfield, PA USA) with a modified bulk-synthesis protocol that generated cDNA sufficient for 10 slide hybridizations.  32-40 mg total RNA in a volume of 8  l was mixed with 2  l of the Cy3 capture RT primer, then heated to 80oC for 10 min.  Tubes were immediately transferred to ice and then 1  l Superase-In RNase Inhibitor was added.  In a separate tube, 4  l 5X Superscript II RT buffer, 1  l 10 mM dNTPs, 2  l 0.1 M DTT, 1  l (200 U) Superscript II Reverse Transcriptase enzyme (Invitrogen, Carlsbad, CA USA) and nuclease-free ddH20 were mixed before addition to the RNA/primer combination.  Each tube was incubated for 2 h at 42oC, before the addition of 3.5  l of 0.5M NaOH/50mM EDTA and transfer to 65oC for 10 minutes to stop the reaction.  Finally, 5  l of 1 M Tris-HCL (pH 7.5) was added to neutralize the reaction.  cDNAs were stored at -20oC.  11 ug RNA from each of 3 biological replicates.

tag: Medicago truncatula; lines - DZA315.16; tissue-trifoliate leaves; age - 4 weeks; treatment  12 hours after no pathogen treatment (control)


title: Medicago truncatula (DZA315.16)  12 hours after E. pisi infection, rep2

description: Medicago truncatula  12 hours after no pathogen treatment (control)2


title: Medicago truncatula (DZA315.16)  12 hours after E. pisi infection, rep1

description: Medicago truncatula  12 hours after no pathogen treatment (control)1


title: Medicago truncatula (DZA315.16)  12 hours after E. pisi infection, rep5

description: Medicago truncatula  12 hours after no pathogen treatment (control)rep5


title: Medicago truncatula (A20)  12 hours after E. pisi infection, rep6

tag: Medicago truncatula; lines - A20; tissue-trifoliate leaves; age - 4 weeks; treatment  12 hours after pathogen inoculation

source_name: Medicago truncatula (A20)  12 hours after no pathogen treatment (control)

tag: Medicago truncatula; lines - A20; tissue-trifoliate leaves; age - 4 weeks; treatment  12 hours after no pathogen treatment (control)


title: Medicago truncatula (A20)  12 hours after E. pisi infection, rep3

description: Medicago truncatula  12 hours after no pathogen treatment (control)3


title: Medicago truncatula (A14)  12 hours after E. pisi infection, rep6

description: Medicago truncatula  12 hours after no pathogen treatment (control)_rep6

tag: Medicago truncatula; lines - A14; tissue-trifoliate leaves; age - 4 weeks; treatment  12 hours after pathogen inoculation

source_name: Medicago truncatula (A14)  12 hours after no pathogen treatment (control)

tag: Medicago truncatula; lines - A14; tissue-trifoliate leaves; age - 4 weeks; treatment  12 hours after no pathogen treatment (control)


title: Medicago truncatula (A20)  12 hours after E. pisi infection, rep2


title: Medicago truncatula (A20)  12 hours after E. pisi infection, rep4


title: Medicago truncatula (A14)  12 hours after E. pisi infection, rep5

description: Medicago truncatula  12 hours after no pathogen treatment (control)_rep5


title: neurula stage (Cy5) vs mouth opening stage (Cy3)

description: neurula stage  (24hpf) (Cy5) vs mouth opening stage (144hpf) (Cy3)

source_name: neurula stage (Cy5)


title: Medicago truncatula (A14)  12 hours after E. pisi infection, rep3


title: Medicago truncatula (A14)  12 hours after E. pisi infection, rep4

description: Medicago truncatula  12 hours after no pathogen treatment (control)_rep4


title: Medicago truncatula (A20)  12 hours after E. pisi infection, rep1


title: Medicago truncatula (A14)  12 hours after E. pisi infection, rep2


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_100_8_43_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014

city: Research Triangle Park

first: James

middle: C

last: Bonner

state: NC

address: 6 Davis Drive

department: Biological Sciences

institute: CIIT Centers for Health Research

description: JCB_100_8_43_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: affylmGUI, The Walter and Eliza Hall Institute of Medical Research

label: biotin

organism: Homo sapiens

source_name: Sample Type: cells, Cell Line: ATCC 16Lu, Cell Type: human lung fibroblasts, Harvest Time Point: 8 hour

growth_protocol: Growth Media: DMEM 10%FBS,  Pen/Strep, Fungizone, Growth Conditions: 5% CO2, 37ïC

extract_protocol: Extraction Method: Qiagen

treatment_protocol: in vitro Treatment: H2O2, Treatment Time: 8, Units of Treatment Time: hour, Dose or Concentration: 100, Units of Dose or Concentration: uM

tag: Array Type

tag: Amount to Core

tag: Units of Amount

value: ul

tag: Ratio

tag: RNA Integrity Number

tag: Sample Preservation

value: snap frozen

tag: Pooled from Multiple Samples

value: Yes


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_100_4_42_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014

description: JCB_100_4_42_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

source_name: Sample Type: cells, Cell Line: ATCC 16Lu, Cell Type: human lung fibroblasts, Harvest Time Point: 4 hour

treatment_protocol: in vitro Treatment: H2O2, Treatment Time: 4, Units of Treatment Time: hour, Dose or Concentration: 100, Units of Dose or Concentration: uM


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_100_8_13_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014

description: JCB_100_8_13_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_100_8_28_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014

description: JCB_100_8_28_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_100_4_27_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014

description: JCB_100_4_27_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts


title: Medicago truncatula (A14)  12 hours after E. pisi infection, rep1


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_100_4_12_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014

description: JCB_100_4_12_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_100_24_45_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014

description: JCB_100_24_45_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

source_name: Sample Type: cells, Cell Line: ATCC 16Lu, Cell Type: human lung fibroblasts, Harvest Time Point: 24 hour

treatment_protocol: in vitro Treatment: H2O2, Treatment Time: 24, Units of Treatment Time: hour, Dose or Concentration: 100, Units of Dose or Concentration: uM


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_100_24_15_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014

description: JCB_100_24_15_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_100_1_41_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014

description: JCB_100_1_41_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

source_name: Sample Type: cells, Cell Line: ATCC 16Lu, Cell Type: human lung fibroblasts, Harvest Time Point: 1 hour

treatment_protocol: in vitro Treatment: H2O2, Treatment Time: 1, Units of Treatment Time: hour, Dose or Concentration: 100, Units of Dose or Concentration: uM


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_100_1_26_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014

description: JCB_100_1_26_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_100_1_11_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014

description: JCB_100_1_11_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts


title: hatching (Cy3) vs eye development (Cy5)

description: eye development and pectoral budding (96hpf) and hatching stage (48hpf) of sea bream.

source_name: hatching (Cy3)

source_name: eye development (Cy5)


title: Medicago truncatula (A20)  12 hours after E. pisi infection, rep5

description: Medicago truncatula  12 hours after no pathogen treatment (control)rep5


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_100_12_44_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014

description: JCB_100_12_44_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

source_name: Sample Type: cells, Cell Line: ATCC 16Lu, Cell Type: human lung fibroblasts, Harvest Time Point: 12 hour

treatment_protocol: in vitro Treatment: H2O2, Treatment Time: 12, Units of Treatment Time: hour, Dose or Concentration: 100, Units of Dose or Concentration: uM


title: Human SW480 cells, ZNF217 Replicate C

type: genomic

city: Columbus

first: Victor

middle: X

last: Jin

state: OH

address: 333 West 10th Ave

department: Biomedical Informatics

institute: OSU Medical Center

description: Human SW480 cells

hyb_protocol: Cy-labeled ChIP Samples

scan_protocol: NimbleScan

data_processing: log base 2 ratios

molecule: genomic DNA

source_name: SW480 cells

label_protocol: Cy dye

extract_protocol: ChIP-chip

tag: ZNF217 antibody

tag: control total input


title: Human SW480 cells, ZNF217 Replicate B

description: Human SW480 cells


title: Human Ntera2 cells, siZNF217 Knockout

description: Human Ntera2 cells

source_name: Ntera2 cells


title: Human Ntera2 cells, siZNF217 Control

description: Human Ntera2 cells


title: Human SW480 cells, ZNF217 Replicate A

description: Human SW480 cells


title: Human Ntera2 cells, ZNF217 Replicate B

description: Human Ntera2 cells


title: Human Ntera2 cells, ZNF217 Replicate C

description: Human Ntera2 cells


title: Human Ntera2 cells, SRY Replicate 1

description: Human Ntera2 cells

hyb_protocol: Cy-labedled ChIP Samples

source_name: Ntera2 cells; SRY antibody

tag: SRY antibody

source_name: Ntera2 cells; control total input

extract_protocol: ChIP-hip


title: Human Ntera2 cells, OCT4 Replicate 2

description: Human Ntera2 cells

source_name: Ntera2 cells; OCT4 antibody

tag: OCT4 antibody


title: Human Ntera2 cells, SRY Replicate 2

description: Human Ntera2 cells


title: Human MCF-7 cells, ZNF217 Replicate B

description: Human MCF-7 cells

source_name: MCF-7 cells


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_100_12_29_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014

description: JCB_100_12_29_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_100_24_30_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014

description: JCB_100_24_30_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts


title: Human Ntera2 cells, IgG Array 2, Replicate A

description: Human Ntera2 cells

tag: IgG antibody


title: Human Ntera2 cells, IgG Array 1, Replicate A

description: Human Ntera2 cells


title: Human Ntera2 cells, OCT4 Replicate 1

description: Human Ntera2 cells


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_100_12_14_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014

description: JCB_100_12_14_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts


title: Wild type retina, 52hpf, pool of ten tissues, biological replicate 3 WR_52hpf_rep3 (WR52_3)

city: West Lafayette

first: Yuk Fai

last: Leung

state: IN

address: 915 W. State Street

institute: Purdue University

hyb_protocol: Hybridization, washing and staining were done according to a standard procedure from Affymetrix.

scan_protocol: Scanning was done according to a standard procedure from Affymetrix.

data_processing: The probe-level data were background adjusted, normalized and summarized by a Robust Multi-array Average (RMA) algorithm implemented in the software package affy of the Bioconductor project release 1.7, running in the R statistical environment version 2.2.0 using default parameters.

label: Biotin

organism: Danio rerio

label_protocol: Thirty-three nanograms of total RNA were labeled by Affymetrix GeneChip Two-Cycle Target Labeling protocol.

growth_protocol: Fish and embryos were maintained according to Westerfield, M. The zebrafish book. A guide for the laboratory use of zebrafish (Danio rerio), 4th edition. University of Oregon Press, Eugene, 2000.

extract_protocol: Total RNA was extracted from the pooled samples according to: Leung YF, Dowling JE. Gene Expression Profiling of Zebrafish Embryonic Retina. Zebrafish 2005:2:269-283.

treatment_protocol: Ten tissues were dissected from developing embryos according to: Leung YF, Dowling JE. Gene Expression Profiling of Zebrafish Embryonic Retina. Zebrafish 2005:2:269-283., and pooled as one biological replicate.

tag: Strain

value: AB

tag: Genotype

value: Wild-type

tag: Age

tag: Tissue

value: Retina


title: Wild type retina, 52hpf, pool of ten tissues, biological replicate 2 WR_52hpf_rep2 (WR52_2)


title: Wild type retina, 52hpf, pool of ten tissues, biological replicate 1 WR_52hpf_rep1 (WR52_1)


title: Human Ntera2 cells, siZNF Array 1, CtBP2 Control B

description: Human Ntera2 cells

tag: CtBP2 antibody


title: Human Ntera2 cells, ZNF217 Replicate A

description: Human Ntera2 cells


title: Human Ntera2 cells, treated Expression C

description: Human Ntera2 cells

scan_protocol: Ilumina

data_processing: The reading is from Illumina software.

source_name: Ntera2 cells treated

extract_protocol: Expression


title: hCD4_rep1

city: st louis

first: kyunghee

last: choi

state: MO

address: 660 s euclid ave

institute: washington university

description:
Generation of Hemangioblast and Blast Colony cell populations:
Scl+/hCD4 ES cells (Chung et al., Development, 2002) were maintained on a layer of mitotically inactivated STO cells in DMEM media in the presence of LIF.  Two days before differentiation, the cells were transferred to gelatinized tissue culture flasks and the media was changed to IMDM-based.  ES cells were differentiated in liquid-differentiation media in the presence of FCS for 2.75 days.  D2.75 EBs were recovered, dissociated in Trypsin/EDTA and stained with antibodies against Flk-1 and human CD4.  Cells were then flow sorted on the basis of Flk-1 and Scl expression and the hemangioblast population was considered to be Flk-1+Scl+.
D2.75 EB cells were replated as described (Chung et al., 2002) and individual Blast colonies were picked and pooled, and RNA was generated with TRIzol according to the manufacturers protocol.  RNA (20 ug) was given to the Washington University Array core were it was reverse transcribed and cRNA synthesized.
Associated paper:  Lugus et al., Development, 2007

hyb_protocol: Hybridized according to Affymetrix standard protocols.

scan_protocol: Scanned according to Affymetrix standard protocols.

data_processing: Analyses were performed using dChip software.

organism: Mus musculus

source_name: Cultured hCD4 ES cells

label_protocol: RNA (20 ug) was given to the Washington University Array core were it was reverse transcribed, cRNA synthesized, and labeled.

extract_protocol: RNA generated with TRIzol according to the manufacturers protocol.  There was no amplification.

tag: Scl+/hCD4 ES cells (Chung et al., Development, 2002) cultured


title: Human Ntera2 cells, siZNF Array 2, CtBP2 Control B

description: Human Ntera2 cells


title: Human Ntera2 cells, treated Expression B

description: Human Ntera2 cells


title: Human MCF-7 cells, ZNF217 Replicate A

description: Human MCF-7 cells


title: Human Ntera2 cells, CtBP1 Array 1, Replicate A

description: Human Ntera2 cells

tag: CtBP1 antibody


title: Human Ntera2 cells, control Expression C

description: Human Ntera2 cells

source_name: Ntera2 cells untreated

tag: untreated


title: Human Ntera2 cells, CtBP1 Array 2, Replicate A

description: Human Ntera2 cells


title: Human Ntera2 cells, siZNF Array 1, CtBP2 Knockout B

description: Human Ntera2 cells


title: Hemangioblast_rep2

source_name: Diffferentiated Cultured Hemangioblasts

tag: Scl+/hCD4 ES cells (Chung et al., Development, 2002) cultured and differentiated into hemangioblast cells.


title: Hemangioblast_rep1


title: Human Ntera2 cells, control Expression B

description: Human Ntera2 cells


title: Senescent passage 26 fibroblasts compared to proliferating passage 8 fibroblasts (replicate 3)

status: Public on Jan 24 2007

city: New Haven

first: Kimberly

last: Johung

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University School of Medicine

hyb_protocol: Oligo array hybridization in Gene Machines hybridization chamber

scan_protocol: Axon GenePix 4000A Scanner

data_processing: Data processing VALUE is log2 (CY5/CY3; exp/ref)

source_name: REF

label_protocol: Cy3 and Cy5 amino-allyl labeled cDNA probes

extract_protocol: Total RNA prepared with Qiagen RNeasy Kit

tag: Passage 8 Proliferating Fibroblasts

source_name: EXP

tag: Passage 26 Senescent Fibroblasts


title: Human Ntera2 cells, control Expression A

description: Human Ntera2 cells


title: Senescent passage 26 fibroblasts compared to proliferating passage 8 fibroblasts (replicate 1)


title: Senescent passage 26 fibroblasts compared to proliferating passage 8 fibroblasts (replicate 4)

data_processing: Data processing VALUE is log2 (CY3/CY5; ref/exp)


title: Senescent passage 26 fibroblasts compared to proliferating passage 8 fibroblasts (replicate 2)


title: Human Ntera2 cells, treated Expression A

description: Human Ntera2 cells


title: HeLa/16E6-16E7d21-24 Cells: Wild-type vs. Mutant E2 infection (Replicate 4)

description: HeLa/16E6-16E7d21-24 Cells after expression of wild-type E2 compared to an E2 DNA-binding mutant

tag: HeLa/16E6-16E7d21-24 Cells - Mutant E2 Infected

tag: HeLa/16E6-16E7d21-24 Cells - Wild-type E2 Infected


title: HeLa/16E6-16E7d21-24 Cells: Wild-type vs. Mutant E2 infection (Replicate 3)


title: HeLa/16E6-16E7 Cells: Wild-type vs. Mutant E2 infection (Replicate 4)

description: HeLa/16E6-16E7 Cells after expression of wild-type E2 compared to an E2 DNA-binding mutant

tag: HeLa/16E6-16E7 Cells - Mutant E2 infected

tag: HeLa/16E6-16E7 Cells - Wild-type E2 infected


title: HeLa/16E6-16E7d21-24 Cells: Wild-type vs. Mutant E2 infection (Replicate 1)


title: HeLa/16E6-16E7d21-24 Cells: Wild-type vs. Mutant E2 infection (Replicate 2)


title: HeLa/16E6-16E7 Cells: Wild-type vs. Mutant E2 infection (Replicate 1)


title: HeLa/16E6-16E7 Cells: Wild-type vs. Mutant E2 infection (Replicate 2)


title: HeLa/16E6-16E7 Cells: Wild-type vs. Mutant E2 infection (Replicate 3)


title: HeLa/16E6 Cells: Wild-type vs. Mutant E2 infection (Replicate 4)

description: Senescent HeLa/16E6 Cells compared to proliferating HeLa/16E6 Cells

tag: HeLa/16E6 Cells - Mutant E2 Infected

tag: HeLa/16E6 Cells - Wild-type E2 Infected


title: Human Ntera2 cells, siZNF217 Array 1, Control B

description: Human Ntera2 cells

tag: ZNF217 antibody

tag: control total input


title: Human Ntera2 cells, CtBP2 Array 1, Replicate A

description: Human Ntera2 cells


title: HeLa/16E6 Cells: Wild-type vs. Mutant E2 infection (Replicate 3)


title: hCD4_rep2

tag: Scl+/hCD4 ES cells (Chung et al., Development, 2002) cultured..


title: Human MCF-7 cells, ZNF217 Replicate C

description: Human MCF-7 cells


title: Human Ntera2 cells, siZNF217 Array 1, Knockout B

description: Human Ntera2 cells


title: Human Ntera2 cells, CtBP2 Array 2, Replicate A

description: Human Ntera2 cells


title: Human Ntera2 cells, siZNF217 Array 2, Control A

description: Human Ntera2 cells


title: Human Ntera2 cells, siZNF217 Array 2, Knockout B

description: Human Ntera2 cells


title: HeLa/16E6 Cells: Wild-type E2 vs. Mock-infection (Replicate 3)

tag: Mock Infected HeLa/16E6 Cells

tag: E2 Infected HeLa/16E6 Cells


title: HeLa/16E6 Cells: Wild-type vs. Mutant E2 infection (Replicate 2)


title: HeLa/16E6 Cells: Wild-type E2 vs. Mock-infection (Replicate 4)


title: HeLa/16E6 Cells: Wild-type E2 vs. Mock-infection (Replicate 2)


title: HeLa/16E6 Cells: Wild-type E2 vs. Mock-infection (Replicate 1)


title: Organpipe-Agria_rep4

city: Huntsville

first: Luciano

middle: Matias

last: Matzkin

state: Alabama

address: 301 Sparkman Drive

institute: University of Alabama in Huntsville

description: Larvae were reared at constant densities and third instar larvae were snap frozen.

data_processing: Intensity was quantile transformed.  The

organism: Drosophila mojavensis

source_name: Organpipe Treatment

tag: Third instar larvae from a Baja California population reared in necrotic organpipe.

source_name: Agria Treatment

tag: Third instar larvae from a Baja California population reared in necrotic agria.


title: Human Ntera2 cells, siZNF217 Array 1, Control A

description: Human Ntera2 cells


title: Organpipe-Agria_rep5


title: Human Ntera2 cells, siZNF217 Array 2, Control B

description: Human Ntera2 cells


title: Human MCF-7 cells, ZNF217 Array 2, Replicate A

description: Human MCF-7 cells


title: Organpipe-Agria_rep3


title: Human SW480 cells, ZNF217 Array 2, Replicate A

description: Human SW480 cells


title: Human Ntera2 cells, siZNF217 Array 1, Knockout A

description: Human Ntera2 cells


title: Agria-Organpipe_rep4


title: Organpipe-Agria_rep2


title: Agria-Organpipe_rep3


title: Human Ntera2 cells, ZNF217 Array 1, Replicate B

description: Human Ntera2 cells


title: LPP vs CPP

type: other

city: Eugene

first: Eric

state: OR

address: 1370 Franklin Blvd

department: Institute of Molecular biology

institute: University of Oregon

description: dual RAD tag hybridization

data_processing: normalized (647/555)

label: alexa 555

molecule: other

organism: Gasterosteus aculeatus

source_name: LPP

tag: RAD tag sample

label: alexa 647

source_name: CPP


title: LPP-replicate vs CPP-replicate

description: dual RAD tag hybridization

source_name: LPP-replicate

source_name: CPP-replicate


title: Human Ntera2 cells, siZNF217 Array 2, Knockout A

description: Human Ntera2 cells

source_name: Ntera2 cells


title: Agria-Organpipe_rep2


title: Human SW480 cells, ZNF217 Array 1, Replicate A

description: Human SW480 cells

source_name: SW480 cells


title: SAMR1 Hippocampus Young Sample 1

city: La Jolla

first: Jennifer

last: Greenhall

state: CA

address: 10010 N. Torrey Pines Rd.

department: MNL-H

institute: The Salk Institute

description: Gene expression data from hippocampus of one young SAMR1TA mouse

hyb_protocol: Hybridizations were performed on Affymetrix MG_U74Av2 GeneChips for 16 hr at 50C at a final cRNA concentration of 0.66 ug/ul. GeneChips were washed and stained in the Salk Megawasher.

scan_protocol: GeneChips were scanned using the Affymetrix/Agilent GeneArray Scanner.

data_processing: Data were analyzed using the Teragenomics Relational Database http://www.teragenomics.com/public/prodNServices_absolutePrecis.asp

source_name: SAMR1 Hippocampus Young Sample 1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: SAMR1TA senescence-accelerated mouse line


title: Human Ntera2 cells, ZNF217 Array 2, Replicate A

description: Human Ntera2 cells


title: Organpipe-Agria_rep1


title: SAMR1 Hippocampus Old Sample 2

description: Gene expression data from hippocampus of one old SAMR1TA mouse

source_name: SAMR1 Hippocampus Old Sample 2


title: SAMR1 Hippocampus Old Sample 3

source_name: SAMR1 Hippocampus Old Sample 3


title: Human Ntera2 cells, ZNF217 Array 1, Replicate A

description: Human Ntera2 cells


title: BP-replicate vs RS-replicate

description: dual RAD tag hybridization

source_name: BP-replicate

source_name: RS-replicate


title: Samp8 Hippocampus Young Sample 1

description: Gene expression data from hippocampus of one young SAMP8/Ta mouse

source_name: SAMP8 Hippocampus Young Sample 1

tag: SAMP8/Ta senescence-accelerated mouse line


title: SAMR1 Hippocampus Young Sample 2

source_name: SAMR1 Hippocampus Young Sample 2


title: SAMR1 Hippocampus Old Sample 1

source_name: SAMR1 Hippocampus Old Sample 1


title: BP vs RS

description: dual RAD tag hybridization

source_name: BP

source_name: RS


title: F2(05) vs RS

description: dual RAD tag hybridization


title: HeLa/16E6 Cells: Wild-type vs. Mutant E2 infection (Replicate 1)

source_name: REF

source_name: EXP


title: F2(08) vs RS

description: dual RAD tag hybridization


title: Samp8 Hippocampus Young Sample 2

source_name: SAMP8 Hippocampus Young Sample 2


title: F2(06) vs RS

description: dual RAD tag hybridization


title: F2(03) vs RS

description: dual RAD tag hybridization


title: Human MCF-7 cells, ZNF217 Array 1, Replicate A

description: Human MCF-7 cells

source_name: MCF-7 cells


title: Agria-Organpipe_rep5

source_name: Agria Treatment

source_name: Organpipe Treatment


title: Agria-Organpipe_rep1


title: F2(04) vs RS

description: dual RAD tag hybridization


title: Samp8 Hippocampus Old Sample 3

description: Gene expression data from hippocampus of one old SAMP8/Ta mouse

source_name: SAMP8 Hippocampus Old Sample 3


title: Samp8 Hippocampus Old Sample 2

source_name: SAMP8 Hippocampus Old Sample 2


title: F2(01) vs RS

description: dual RAD tag hybridization


title: Samp10 Hippocampus Young Sample 1

description: Gene expression data from hippocampus of one young SAMP10//Ta mouse

source_name: SAMP10 Hippocampus Young Sample 1

tag: SAMP10//Ta senescence-accelerated mouse line


title: F2(02) vs RS

description: dual RAD tag hybridization


title: Samp10 Hippocampus Young Sample 2

source_name: SAMP10 Hippocampus Young Sample 2


title: Samp8 Hippocampus Old Sample 1

source_name: SAMP8 Hippocampus Old Sample 1


title: BP vs F2(07)

description: dual RAD tag hybridization


title: Samp10 Hippocampus Old Sample 2

description: Gene expression data from hippocampus of one old SAMP10//Ta mouse

source_name: SAMP10 Hippocampus Old Sample 2


title: Samp10 Hippocampus Old Sample 3

source_name: SAMP10 Hippocampus Old Sample 3


title: BP vs F2(05)

description: dual RAD tag hybridization


title: SAMR1 Retina Young Sample 1

description: Gene expression data from retinas of two young SAMR1TA mice

source_name: SAMR1 Retina Young Sample 1 - 2 animals pooled

tag: SAMR1TA senescence-accelerated mouse resistant -- control strain


title: SAMR1 Retina Old Sample 2

description: Gene expression data from retinas of two old SAMR1TA mice

source_name: SAMR1 Retina Old Sample 2 - 2 animals pooled


title: BP vs F2(02)

description: dual RAD tag hybridization

source_name: BP


title: SAMR1 Retina Young Sample 2

source_name: SAMR1 Retina Young Sample 2 - 2 animals pooled


title: BP vs F2(03)

description: dual RAD tag hybridization


title: BP vs F2(04)

description: dual RAD tag hybridization


title: BP vs F2(08)

description: dual RAD tag hybridization


title: Samp10 Hippocampus Old Sample 1

source_name: SAMP10 Hippocampus Old Sample 1


title: Samp8 Retina Young Sample 2

description: Gene expression data from retinas of two young SAMP8/Ta mice

source_name: SAMP8 Retina Young Sample 2 - 2 animals pooled


title: Bone Marrow-Derived Mesenchymal Stem Cells: Fetal_2

city: Los Angeles

first: Joseph

middle: Gerard

last: Hacia

address: 2250 Alcazar Street, IGM 261

department: Biochemistry and Molecular Biology

institute: University of Southern California

description: This sample was derived from a gestation day 120 donor. rhMSC obtained from bone marrow were collected by flushing the long bones at tissue harvest, and grown under standard conditions. Briefly, the mononuclear cell fraction was enriched by gradient centrifugation and plated at 5x10^5 cells/cm2 in DMEM culture media (Invitrogen Corp., Carlsbad, CA), supplemented with 20% fetal bovine serum (FBS) (Invitrogen Corp.). After three days non-adherent cells were discarded. The medium was changed three to four days thereafter, and when the cells achieved approximately 80% confluence. The cells were then plated at a density of 4x10^5 cells/cm2 on tissue culture dishes, cultured to the second passage, collected before confluence was achieved, and stored at ≤-80 oC until processing.

hyb_protocol: We used the Affymetrix Hybridization Oven 640 and GeneChip® Fluidics Station 450 according to the manufacturer's recomended protocols. However, we used two rounds of signal amplification rather than one in order to increase hybridization signals from rhesus targets to the human microarrays.

data_processing: RMA Normalization

organism: Macaca mulatta

source_name: Rhesus monkey cultured mesenchymal stem cells from a gestation day 120 donor.

label_protocol: We used GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recomended protocols.

growth_protocol: Cells were plated and grown as described above.

extract_protocol: The cells were washed three times with phosphate-buffered saline (PBS), after which TRIzol Reagent (Invitrogen Corp.) was added for total RNA extraction. Isolated RNA was cleaned using the QiaAmp isolation RNA kit (Qiagen, Valencia, CA) following the manufacturer’s instructions.


title: BP vs F2(01)

description: dual RAD tag hybridization


title: BP vs F2(06)

description: dual RAD tag hybridization


title: Bone Marrow-Derived Mesenchymal Stem Cells: Fetal_4

description: This sample was derived from a newborn donor. rhMSC obtained from bone marrow were collected by flushing the long bones at tissue harvest, and grown under standard conditions. Briefly, the mononuclear cell fraction was enriched by gradient centrifugation and plated at 5x10^5 cells/cm2 in DMEM culture media (Invitrogen Corp., Carlsbad, CA), supplemented with 20% fetal bovine serum (FBS) (Invitrogen Corp.). After three days non-adherent cells were discarded. The medium was changed three to four days thereafter, and when the cells achieved approximately 80% confluence. The cells were then plated at a density of 4x10^5 cells/cm2 on tissue culture dishes, cultured to the second passage, collected before confluence was achieved, and stored at ≤-80 oC until processing.

scan_protocol: We used the Affymetrix Hybridization Oven 640 and GeneChip® Fluidics Station 450 according to the manufacturer's recomended protocols.

source_name: Rhesus monkey cultured mesenchymal stem cells from a newborn donor.

treatment_protocol: Cells were plated and grown as described above.


title: Human Ntera2 cells, ZNF217 Array 2, Replicate B

description: Human Ntera2 cells

source_name: Ntera2 cells


title: F2(07) vs RS

description: dual RAD tag hybridization

source_name: RS


title: Bone Marrow-Derived Mesenchymal Stem Cells: Fetal_3

tag: This sample was derived from a newborn donor. rhMSC obtained from bone marrow were collected by flushing the long bones at tissue harvest, and grown under standard conditions. Briefly, the mononuclear cell fraction was enriched by gradient centrifugation and plated at 5x10^5 cells/cm2 in DMEM culture media (Invitrogen Corp., Carlsbad, CA), supplemented with 20% fetal bovine serum (FBS) (Invitrogen Corp.). After three days non-adherent cells were discarded. The medium was changed three to four days thereafter, and when the cells achieved approximately 80% confluence. The cells were then plated at a density of 4x10^5 cells/cm2 on tissue culture dishes, cultured to the second passage, collected before confluence was achieved, and stored at ≤-80 oC until processing.


title: Samp8 Retina Young Sample 1

source_name: SAMP8 Retina Young Sample 1 - 2 animals pooled


title: SAMR1 Retina Old Sample 1

source_name: SAMR1 Retina Old Sample 1 - 2 animals pooled


title: Bone Marrow-Derived Mesenchymal Stem Cells: Infant_4

description: This sample was derived from a 5 month old donor. rhMSC obtained from bone marrow were collected by aspiration under ketamine (10 mg/kg) and local lidocaine (~1-3 ml marrow), and grown under standard conditions. Briefly, the mononuclear cell fraction was enriched by gradient centrifugation and plated at 5x10^5 cells/cm2 in DMEM culture media (Invitrogen Corp., Carlsbad, CA), supplemented with 20% fetal bovine serum (FBS) (Invitrogen Corp.). After three days non-adherent cells were discarded. The medium was changed three to four days thereafter, and when the cells achieved approximately 80% confluence. The cells were then plated at a density of 4x10^5 cells/cm2 on tissue culture dishes, cultured to the second passage, collected before confluence was achieved, and stored at ≤-80 oC until processing.

source_name: Rhesus monkey cultured mesenchymal stem cells from a 5 month old donor.


title: Samp8 Retina Old Sample 2

description: Gene expression data from retinas of two old SAMP8/Ta mice

source_name: SAMP8 Retina Old Sample 2 - 2 animals pooled


title: Human Ntera2 cells, siZNF Array 2, CtBP2 Knockout B

description: Human Ntera2 cells

tag: CtBP2 antibody


title: ptc3 vs wt_ Exp_2

city: Cerdanyola

first: Antonio

last: Casamayor

state: Barcelona

address: Edifici IBB, Campus UAB

country: Spain

institute: Universitat Autonoma de Barcelona

description: Spots with either a diameter smaller than 120 um, or fluorescence intensity for Cy3 and Cy5 lower than 150 units, were not considered for further analysis.

hyb_protocol: Prehybridizations of the DNA microarrays were carried out at 42 oC for 1 h in a solution containing 5x SSC, 0.1% SDS, 1% bovine serum albumin. For hybridization, dried Cy3-and Cy5-labelled probes were resuspended in 35 ul of hybridization solution (50% formamide, 5x SSC, 0.1% SDS) each and mixed. Five ug of salmon sperm DNA was added to the mix before denaturation for 3 min at 95 oC.  DNA microarrays were hybridized in an ArrayBooster hybridization station (Sunergia Group) for 14 h at 42 oC.

scan_protocol: The scanner ScanArray 4000 (Packard) was used to obtain the Cy3 and Cy5 images with a resolution of 10 um. The fluorescent intensity of the spots was measured and processed using the GenePix Pro 6.0 software (Molecular Devices)

data_processing: The GEPAS server (http://gepas.bioinfo.cnio.es) was used to preprocess the data: merge replicates and remove inconsistent replicates (Maximum distance to median of replicates=0.5)

organism: Saccharomyces cerevisiae

source_name: ptc3 mutant strain in log phase culture

label_protocol: Fluorescent labeled cDNA was prepared from 8 ug of purified total RNA by the indirect dUTP-labeling method, using the CyScribe post-labeling kit (Amersham Biosciences)

growth_protocol: Grown at 28 oC in YPD rich medium until A660=0.6-0.8. 30 ml of yeast culture was harvested by centrifugation and washed with cold water. Dried cell pellet was kept at -80 oC until RNA purification

extract_protocol: Total RNA purification using the Ambion RiboPure™-Yeast Total RNA Isolation Kit

tag: Strain BY4741 ptc3::kanMX4

source_name: wt strain in log phase culture

tag: Strain BY4741 wt


title: Samp8 Retina Old Sample 1

source_name: SAMP8 Retina Old Sample 1 - 2 animals pooled


title: Bone Marrow-Derived Mesenchymal Stem Cells: Infant_2

description: This sample was derived from a 6 month old donor. rhMSC obtained from bone marrow were collected by aspiration under ketamine (10 mg/kg) and local lidocaine (~1-3 ml marrow), and grown under standard conditions. Briefly, the mononuclear cell fraction was enriched by gradient centrifugation and plated at 5x10^5 cells/cm2 in DMEM culture media (Invitrogen Corp., Carlsbad, CA), supplemented with 20% fetal bovine serum (FBS) (Invitrogen Corp.). After three days non-adherent cells were discarded. The medium was changed three to four days thereafter, and when the cells achieved approximately 80% confluence. The cells were then plated at a density of 4x10^5 cells/cm2 on tissue culture dishes, cultured to the second passage, collected before confluence was achieved, and stored at ≤-80 oC until processing.

source_name: Rhesus monkey cultured mesenchymal stem cells from a 6 month old donor.


title: ptc4 vs wt_ Exp_2

source_name: ptc4 mutant strain in log phase culture

tag: Strain BY4741 ptc4::kanMX4


title: Bone Marrow-Derived Mesenchymal Stem Cells: Fetal_1

tag: This sample was derived from a gestation day 120 donor. rhMSC obtained from bone marrow were collected by flushing the long bones at tissue harvest, and grown under standard conditions. Briefly, the mononuclear cell fraction was enriched by gradient centrifugation and plated at 5x10^5 cells/cm2 in DMEM culture media (Invitrogen Corp., Carlsbad, CA), supplemented with 20% fetal bovine serum (FBS) (Invitrogen Corp.). After three days non-adherent cells were discarded. The medium was changed three to four days thereafter, and when the cells achieved approximately 80% confluence. The cells were then plated at a density of 4x10^5 cells/cm2 on tissue culture dishes, cultured to the second passage, collected before confluence was achieved, and stored at ≤-80 oC until processing.


title: ptc5 vs wt_ Exp_1

source_name: ptc5 mutant strain in log phase culture

tag: Strain BY4741 ptc5::kanMX4


title: ptc5 vs wt_ Exp_2

tag: Strain BY4741 ptc51::kanMX4


title: ptc4 vs wt_ Exp_1


title: Bone Marrow-Derived Mesenchymal Stem Cells: Infant_3

description: This sample was derived from a 3 month old donor. rhMSC obtained from bone marrow were collected by aspiration under ketamine (10 mg/kg) and local lidocaine (~1-3 ml marrow), and grown under standard conditions. Briefly, the mononuclear cell fraction was enriched by gradient centrifugation and plated at 5x10^5 cells/cm2 in DMEM culture media (Invitrogen Corp., Carlsbad, CA), supplemented with 20% fetal bovine serum (FBS) (Invitrogen Corp.). After three days non-adherent cells were discarded. The medium was changed three to four days thereafter, and when the cells achieved approximately 80% confluence. The cells were then plated at a density of 4x10^5 cells/cm2 on tissue culture dishes, cultured to the second passage, collected before confluence was achieved, and stored at ≤-80 oC until processing.

source_name: Rhesus monkey cultured mesenchymal stem cells from a 3 month old donor.


title: Samp10 Retina Young Sample 1

description: Gene expression data from retinas of two young SAMP10//Ta mice

source_name: SAMP10 Retina Young Sample 1 - 2 animals pooled


title: ptc2 vs wt_ Exp_1

source_name: ptc2 mutant strain in log phase culture

tag: Strain BY4741 ptc2::kanMX4


title: Samp10 Retina Old Sample 2

description: Gene expression data from retinas of two old SAMP10//Ta mice

source_name: SAMP10 Retina Old Sample 2 - 2 animals pooled


title: ptc1 vs wt_ Exp_1

source_name: ptc1 mutant strain in log phase culture

tag: Strain BY4741 ptc1::nat1


title: ptc2 vs wt_ Exp_2


title: ptc1 vs wt_ Exp_2


title: Cerebellum Control (AD) 10

status: Public on Jan 23 2007

city: New York

first: Erin

middle: L.

last: Heinzen

state: NY

department: Institute for Genomic Medicine

institute: Columbia University

description: labeling, hybridization, and data extraction performed by ExonHit Therapeutics

hyb_protocol: The standard in situ hybridization kit from Agilent (part # 5184-3568) was used to hybridize the samples to the SpliceArray, with the addition of 40 µg herring sperm DNA added directly to the labeled sample.  The arrays were hybridized at 65°C and washed following the standard Agilent protocol, with washes increased to 5 minutes each (for details, see Agilent’s 60-mer Oligo Microarray Processing Protocol - SSPE Wash).  All incubations are performed in an ozone-free atmosphere to prevent any degradation of signal.

scan_protocol: The arrays were scanned using Agilent’s Microarray Scanner.

data_processing: The images were analyzed with the Feature Extraction software, version 8.1 (FE8.1), using all default settings.  The data headings present in the raw data output (.txt) files and the algorithms used to calculate the values are explained in the Feature Extraction manual.

source_name: Cerebellum Human Brain

label_protocol: An indirect labeling protocol was used to label each sample for analysis.  Five (5) ug of total RNA for each sample was used in each labeling reaction, and was reverse transcribed into first strand cDNA using random primers.  Each comparison, or array experiment, requires two independent labeling reactions, one reaction with Cy3 dye and the second reaction with Cy5 dye.  The cDNA product is purified and equal amounts of labeled material are used for the hybridization experiment.

extract_protocol: Brain tissue was ground in liquid nitrogen (mortar and pestle). Total RNA was extracted from brain tissue using the RNeasy Lipid Tissue Purification Kit (Qiagen) according the manufacturer’s instructions.

treatment_protocol: Hulette C, Welsh-Bohmer K, Crain B, Szymanski M, Sinclaire N, Roses A: Rapid brain autopsy: The Brayn Alzheimer's Disease Research Center experience. Arch Pathol Lab Med 1997(121):615-618.

tag: 88 yo M


title: Bone Marrow-Derived Mesenchymal Stem Cells: Adult_2

description: This sample was derived from 7 year old adult donor. rhMSC obtained from bone marrow were collected by aspiration under ketamine (10 mg/kg) and local lidocaine (~1-3 ml marrow), and grown under standard conditions. Briefly, the mononuclear cell fraction was enriched by gradient centrifugation and plated at 5x10^5 cells/cm2 in DMEM culture media (Invitrogen Corp., Carlsbad, CA), supplemented with 20% fetal bovine serum (FBS) (Invitrogen Corp.). After three days non-adherent cells were discarded. The medium was changed three to four days thereafter, and when the cells achieved approximately 80% confluence. The cells were then plated at a density of 4x10^5 cells/cm2 on tissue culture dishes, cultured to the second passage, collected before confluence was achieved, and stored at ≤-80 oC until processing.

source_name: Rhesus monkey cultured mesenchymal stem cells from a 7 year old adult.


title: Cerebellum Control (AD) 7

tag: 90 yo M


title: Bone Marrow-Derived Mesenchymal Stem Cells: Infant_1

tag: This sample was derived from a 6 month old donor. rhMSC obtained from bone marrow were collected by aspiration under ketamine (10 mg/kg) and local lidocaine (~1-3 ml marrow), and grown under standard conditions. Briefly, the mononuclear cell fraction was enriched by gradient centrifugation and plated at 5x10^5 cells/cm2 in DMEM culture media (Invitrogen Corp., Carlsbad, CA), supplemented with 20% fetal bovine serum (FBS) (Invitrogen Corp.). After three days non-adherent cells were discarded. The medium was changed three to four days thereafter, and when the cells achieved approximately 80% confluence. The cells were then plated at a density of 4x10^5 cells/cm2 on tissue culture dishes, cultured to the second passage, collected before confluence was achieved, and stored at ≤-80 oC until processing.


title: ptc3 vs wt_ Exp_1

source_name: ptc3 vs wt_ Exp_1

tag: Strain BY4741 ptc1::kanMX4


title: Bone Marrow-Derived Mesenchymal Stem Cells: Adult_1

tag: This sample was derived from 7 year old adult donor. rhMSC obtained from bone marrow were collected by aspiration under ketamine (10 mg/kg) and local lidocaine (~1-3 ml marrow), and grown under standard conditions. Briefly, the mononuclear cell fraction was enriched by gradient centrifugation and plated at 5x10^5 cells/cm2 in DMEM culture media (Invitrogen Corp., Carlsbad, CA), supplemented with 20% fetal bovine serum (FBS) (Invitrogen Corp.). After three days non-adherent cells were discarded. The medium was changed three to four days thereafter, and when the cells achieved approximately 80% confluence. The cells were then plated at a density of 4x10^5 cells/cm2 on tissue culture dishes, cultured to the second passage, collected before confluence was achieved, and stored at ≤-80 oC until processing.


title: Samp10 Retina Young Sample 2

source_name: SAMP10 Retina Young Sample 2 - 2 animals pooled

tag: SAMP10//Ta senescence-accelerated mouse line


title: Bone Marrow-Derived Mesenchymal Stem Cells: Adult_3

description: This sample was derived from 8 year old adult donor. rhMSC obtained from bone marrow were collected by aspiration under ketamine (10 mg/kg) and local lidocaine (~1-3 ml marrow), and grown under standard conditions. Briefly, the mononuclear cell fraction was enriched by gradient centrifugation and plated at 5x10^5 cells/cm2 in DMEM culture media (Invitrogen Corp., Carlsbad, CA), supplemented with 20% fetal bovine serum (FBS) (Invitrogen Corp.). After three days non-adherent cells were discarded. The medium was changed three to four days thereafter, and when the cells achieved approximately 80% confluence. The cells were then plated at a density of 4x10^5 cells/cm2 on tissue culture dishes, cultured to the second passage, collected before confluence was achieved, and stored at ≤-80 oC until processing.

source_name: Rhesus monkey cultured mesenchymal stem cells from an 8 year old adult.


title: Cerebellum Control (AD) 9

tag: 88 yo F


title: Cerebellum Control (AD) 5

tag: 75 yo M


title: Cerebellum Control (AD) 6

tag: 85 yo F


title: Cerebellum Control (AD) 3

tag: 82 yo F


title: Samp10 Retina Old Sample 1

source_name: SAMP10 Retina Old Sample 1 - 2 animals pooled


title: Cerebellum Control (AD) 4

tag: 85 yo M


title: Cerebellum Control (AD) 2

tag: 83 yo M


title: Cerebellum Alzheimer's disease 10

tag: Braak stage VI


title: Cerebellum Control (AD) 8

tag: 72 yo F


title: Cerebellum Alzheimer's disease 8

tag: Braak stage V


title: Cerebellum Control (AD) 1

tag: 80 yo F


title: Cerebellum Alzheimer's disease 9


title: Cerebellum Alzheimer's disease 5

tag: 81 yo F


title: Cerebellum Alzheimer's disease 6


title: Cerebellum Alzheimer's disease 4

tag: Braak stage IV


title: Cerebellum Alzheimer's disease 3


title: Cerebellum Alzheimer's disease 7

tag: 79 yo F


title: Cerebellum Alzheimer's disease 1

tag: 84 yo M


title: Temporal Cortex Alzheimer's disease 9

source_name: Temporal Cortex Human Brain


title: Temporal Cortex Alzheimer's disease 10


title: Temporal Cortex Alzheimer's disease 5


title: Temporal Cortex Alzheimer's disease 3


title: Temporal Cortex Alzheimer's disease 4


title: Temporal Cortex Control (AD) 8

extract_protocol: Brain tissue was ground in liquid nitrogen (mortar and pestle).  Total RNA was extracted from brain tissue using the RNeasy Lipid Tissue Purification Kit (Qiagen) according the manufacturer’s instructions.


title: Temporal Cortex Alzheimer's disease 8


title: Temporal Cortex Control (AD) 9


title: Temporal Cortex Alzheimer's disease 7


title: Temporal Cortex Control (AD) 10

tag: 88 yo M


title: Temporal Cortex Alzheimer's disease 1


title: Cerebellum Alzheimer's disease 2

tag: 82 yo M


title: Temporal Cortex Control (AD) 7

tag: 90 yo M


title: Temporal Cortex Alzheimer's disease 2


title: Temporal Cortex Alzheimer's disease 6


title: Temporal Cortex Control (AD) 5

tag: 33 yo M


title: Temporal Cortex Control (AD) 4


title: Temporal Cortex Control (AD) 6


title: Temporal Cortex Control (AD) 3


title: Temporal Cortex Control (AD) 1


title: Temporal neocortex mTLE 9

source_name: Temporal Neocortex Human Brain

treatment_protocol: Temporal neocortical tissue samples were obtained from material resected from patients undergoing therapeutic surgery for drug-resistant mesial temporal lobe epilepsy (mTLE) according to routine clinical protocols. All tissue used for research was surplus to diagnostic requirements. Samples were flash frozen and store at -80 until use.

tag: 38 yo M

tag: freshly resected tissue sample


title: Temporal neocortex mTLE 7

tag: 33 yo F

tag: freshly resected tissue samples


title: Temporal neocortex mTLE 8

tag: 38 yo F


title: Temporal neocortex mTLE 10

tag: 47 yo female


title: 3T3L1_adipocyte_differentiation_day28_post_induction_ChipA

first: Kevin

middle: Jon

last: Cheung

address: 1230 York Avenue

department: Molecular Genetics

institute: The Rockefeller University

description: all steps as per Expression Analysis Technical Manual, 2001, Affymetrix.

hyb_protocol: Following fragmentation, cRNA were hybridized on the Mu11K GeneChip Murine Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using a Hewlett Packard confocal laser scanner

data_processing: The data were analyzed with GeneChip 3.3 using Affymetrix default analysis settings and global scaling as normalization method.

source_name: 3T3-L1 fibroblast;MDI differentiation; day 28 post induction

tag: 3T3-L1 fibroblast


title: Temporal neocortex mTLE 6

tag: 36 yo F


title: Temporal neocortex mTLE 5

tag: 23 yo F


title: 3T3L1_adipocyte_differentiation_day4_post_induction_ChipA

source_name: 3T3-L1 fibroblast;MDI differentiation; day 4 post induction


title: 3T3L1_adipocyte_differentiation_day7_post_induction_ChipB

source_name: 3T3-L1 fibroblast;MDI differentiation; day 7 post induction


title: 3T3L1_adipocyte_differentiation_day3_post_induction_ChipA

source_name: 3T3-L1 fibroblast;MDI differentiation; day 3 post induction


title: 3T3L1_adipocyte_differentiation_day7_post_induction_ChipA


title: Temporal neocortex mTLE 3

tag: 47 yo F

tag: freshly resected brain tissue sample


title: 3T3L1_adipocyte_differentiation_24hours_post_induction_ChipA

source_name: 3T3-L1 fibroblast;MDI differentiation; 24 hours post induction


title: 3T3L1_adipocyte_differentiation_confluent_ChipA

source_name: 3T3-L1 fibroblast;MDI differentiation; confluent


title: 3T3L1_adipocyte_differentiation_day4_post_induction_ChipB


title: Temporal neocortex mTLE 1

treatment_protocol: Temporal neocortical  tissue samples were obtained from material resected from patients undergoing therapeutic surgery for drug-resistant mesial temporal lobe epilepsy (mTLE) according to routine clinical protocols.  All tissue used for research was surplus to diagnostic requirements.  Samples were flash frozen and store at -80 until use.

tag: 47 yo male


title: Temporal Cortex Control (mTLE) 9

tag: 72 yo F


title: 3T3L1_adipocyte_differentiation_day3_post_induction_ChipB


title: 3T3L1_adipocyte_differentiation_preconfluent_ChipA

source_name: 3T3-L1 fibroblast;MDI differentiation; preconfluent


title: 3T3L1_adipocyte_differentiation_day2_post_induction_ChipB

source_name: 3T3-L1 fibroblast;MDI differentiation; day 2 post induction


title: Temporal Cortex Control (mTLE) 7

tag: 75 yo M


title: 3T3L1_adipocyte_differentiation_24hours_post_induction_ChipB


title: 3T3L1_adipocyte_differentiation_12hours_post_induction_ChipB

source_name: 3T3-L1 fibroblast;MDI differentiation; 12 hours post induction


title: Temporal Cortex Control (mTLE) 5

tag: 63 yo M

tag: PMD


title: 3T3L1_adipocyte_differentiation_6hours_post_induction_ChipB

source_name: 3T3-L1 fibroblast;MDI differentiation; 6 hours post induction


title: 3T3L1_adipocyte_differentiation_day2_post_induction_ChipA


title: 3T3L1_adipocyte_differentiation_6hours_post_induction_ChipA


title: Adult mouse preconfluent_CHIPA

source_name: C57BL/6 adult female mice; White adipose Tissue

tag: C57BL/6 adult female mice; WAT


title: 3T3L1_adipocyte_differentiation_confluent_ChipB


title: Adult mouse hypothalamus_CHIPA

source_name: C57BL/6 adult female mice; Hypothalamus

tag: C57BL/6 adult female mice; Hypothalamus


title: 3T3L1_adipocyte_differentiation_day28_post_induction_ChipB


title: Adult mouse preconfluent_ChipB


title: Temporal Cortex Control (mTLE) 8

extract_protocol: Brain tissue was ground in liquid nitrogen (mortar and pestle).   Total RNA was extracted from brain tissue using the RNeasy Lipid Tissue Purification Kit (Qiagen) according the manufacturer’s instructions.

tag: 88 yo M


title: 3T3L1_adipocyte_differentiation_preconfluent_ChipB


title: Adult mouse hypothalamus_ChipB


title: Temporal neocortex mTLE 2

tag: 43 yo F

tag: freshly resected tissue


title: Temporal Cortex Control (mTLE) 2

tag: 82 yo M


title: Temporal Cortex Control (mTLE) 3

tag: 80 yo F


title: Adult mouse liver_ChipB

source_name: C57BL/6 adult female mice; Liver

tag: C57BL/6 adult female mice; Liver


title: Temporal Cortex Control (mTLE) 10

tag: 85 yo M


title: Temporal Cortex Control (mTLE) 4

tag: 60 yo M


title: Temporal Cortex Control (mTLE) 6

tag: 56 yo F


title: Adult mouse muscle_ChipB

source_name: C57BL/6 adult female mice; Muscle

tag: C57BL/6 adult female mice; Muscle


title: Adult mouse pancreas_ChipB

source_name: C57BL/6 adult female mice; Pancreas

tag: C57BL/6 adult female mice; Pancreas


title: Adult mouse liver_CHIPA


title: 3T3L1_adipocyte_differentiation_12hours_post_induction_ChipA

tag: 3T3-L1 fibroblast


title: Adult mouse muscle_CHIPA


title: Temporal Cortex Control (mTLE) 1

source_name: Temporal Cortex Human Brain

tag: 75 yo male


title: Adult mouse pancreas_ChipA


title: Temporal neocortex mTLE 4

source_name: Temporal Neocortex Human Brain

tag: 24 yo F

tag: freshly resected sample


title: Temporal Cortex Control (AD) 2

tag: 83 yo M


title: ik_H2_T6_r1

status: Public on Jan 22 2007

city: Boston

first: Timothy

middle: S

last: Gardner

state: MA

address: 44 Cummington St.

department: Biomedical Engineering

institute: Boston University

description: GeneChips were washed and stained with an FS450 fluidics machine and scanned using a GeneChip Scanner 3000

hyb_protocol: Following fragmentation, cDNA was hybridized for 16 hr at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

organism: Escherichia coli

source_name: Escherichia coli

label_protocol: Biotinylated cDNA was prepared according to the standard Affymetrix E. coli protocol

extract_protocol: RNAEasy with RNAProtect(Qiagen)

tag: K12 EMG2 on LB with 0.4 percent glucose, 6 hours post-incubation


title: ik_H2_T4_r1

scan_protocol: GeneChips were washed and stained with an FS450 fluidics machine and scanned using a GeneChip Scanner 3000

tag: K12 EMG2 on LB with 0.4 percent glucose, 4 hours post-incubation


title: JP001_ATH1_A4-Pritc-API

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 85.34
Background Stdev (float) = 1.85
Background Max (float) = 90.8
Background Min (float) = 80.4
Noise Avg (float) = 5.23
Noise Stdev (float) = 0.17
Noise Max (float) = 5.6
Noise Min (float) = 4.6
RawQ (float) = 3.09
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 485
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: JP001_ATH1_A4-Pritc-API.DAT

hyb_protocol: EukGE-WS2v4; Protocol Type = Hybridization; Parameter Wash A1 Recovery Mixes = 0 (type integer); Parameter Wash A1 Temperature (C) = 25 (type integer); Parameter Number of Wash A1 Cycles = 10 (type integer); Parameter Mixes per Wash A1 Cycle = 2 (type integer); Parameter Wash B Recovery Mixes = 0 (type integer); Parameter Wash B Temperature (C) = 50 (type integer); Parameter Number of Wash B Cycles = 4 (type integer); Parameter Mixes per Wash B Cycle = 15 (type integer); Parameter Stain Temperature (C) = 25 (type integer); Parameter First Stain Time (seconds) = 600 (type integer); Parameter Wash A2 Recovery Mixes = 0 (type integer); Parameter Wash A2 Temperature (C) = 25 (type integer); Parameter Number of Wash A2 Cycles = 10 (type integer); Parameter Mixes per Wash A2 Cycle = 4 (type integer); Parameter Second Stain Time (seconds) = 600 (type integer); Parameter Third Stain Time (seconds) = 600 (type integer); Parameter Wash A3 Recovery Mixes = 0 (type integer); Parameter Wash A3 Temperature (C) = 30 (type integer); Parameter Number of Wash A3 Cycles = 15 (type integer); Parameter Mixes per Wash A3 Cycle = 4 (type integer); Parameter Holding Temperature (C) = 25 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Fluidics Station, Parameter: Parameter Station Number = 1 (type integer), Parameter: Parameter Position = 3 (type integer); Performers: John,Y,Okyere, , Janet,,Higgins

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 228 (type integer); Parameter Upper left corner y coordinate = 232 (type integer); Parameter Upper right corner x coordinate = 4498 (type integer); Parameter Upper right corner y coordinate = 275 (type integer); Parameter Lower right corner x coordinate = 4456 (type integer); Parameter Lower right corner y coordinate = 4545 (type integer); Parameter Lower left corner x coordinate = 187 (type integer); Parameter Lower left corner y coordinate = 4502 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.384767 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

organism: Arabidopsis thaliana

label_protocol: Preparation of biotin-labeled cRNA; RNA samples were quality controlled using the Agilent 2100 Bioanalyzer. 100 pmol T7-(dT)24 primer (5'-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG-(dT)24-3')  was hybridized with the Total RNA ( 8 - 12ug) at 70°C for 10 minutes. First strand cDNA was synthesized by reverse transcription using 400 units SuperScript II Reverse Transcriptase in a reaction containing 50 mM Tris-HCl (pH 8.3), 75 mM KCl, 3 mM MgCl2, 10 mM dithiothreitol (DTT) and 0.5 mM dNTPs at 42C for 1 hour.  The reaction was then put on ice for 2 mins, followed by second strand cDNA synthesis.  130ul of the second strand reaction mix was added to the 20ul  first strand synthesis reaction. The second strand reaction mix  contained 40 units E. coli DNA polymerase I, 10 units E. coli DNA ligase, 2 units  E. coli RNase H and 0.2 mM dNTPs in a buffer containing 20 mMTris-HCl (pH 6.9), 90 mM KCl, 4.6 mM MgCl2, 10mM (NH4)SO4 and 0.15 mM ß-NAD+. The reaction was incubated at 16 C for 2 hours.  10 units T4 DNA Polymerase was added and the reaction incubated for a further 5 minutes at 16 C, then the reaction was terminated using EDTA.  The double-stranded cDNA was cleaned up using the cDNA Cleanup Spin Column supplied in the Affymetrix GeneChip Sample Cleanup Module.  The double-stranded cDNA was used as a template for in Vitro transcription of biotin-labeled cRNA using the ENZO BioArray RNA Transcript Labeling Kit supplied by Affymetrix.  The Transcript Labeling kit produces large amounts of hybridizable biotin-labeled RNA targets by in Vitro transcription from bacteriophage T7 RNA polymerase promoters.  The reaction mixture containing Biotin-Labeled ribonucleotides (ATP, GTP, CTP, UTP with Bio-UTP and Bio-CTP), DTT, RNase inhibitor mix and T7 RNA polymerase was incubated at 37 C for 5 hrs, gently mixing every 30 minutes during the incubation. This produced an average of 40ug biotin-labeled cRNA . The biotin-labeled cRNA  was cleaned up using the cRNA Cleanup Spin Column supplied in the Affymetrix GeneChip Sample Cleanup Module.  The quantity and quality of the cRNA was measured using the Agilent 2100 Bioanalyzer. The total amount of cRNA was calculated, the starting quantity of RNA subtracted to give the quantity of adjusted cRNA.  The cRNA was fragmented by metal-induced hydrolysis to break down full-length cRNA to 35-200 base fragments.  15ug of adjusted cRNA was used to prepare 300ul of hybridization cocktail of which 200ul was hybridized with the GeneChip.   ; Protocol Type = labeling; Performers: John,Y,Okyere, Janet,,Higgins

growth_protocol: unknown; Parameter location = Growth Room; Parameter Humidity = 70%; Parameter Temperature = 22oC; Parameter Lighting = 18 hour days; Parameter Medium = compost; Parameter Nutrients = osmocote slow release fertiliser mixed in compost; Parameter Water = 3 x per week; Performer: Jeremy,,Pritchard

extract_protocol: Qiagen / Trizol; Protocol: Qiagen RNAeasy kit protocol ; Protocol Type = nucleic_acid_extraction; Performer: Jeremy,,Pritchard

treatment_protocol: 10 aphids caged on 2 rosette leaves for 8 hours ; Performer: Jeremy,,Pritchard

tag: OrganismPart

value: 2 mature rosette leaves

tag: Ecotype

tag: NASC:Growth Stage


title: ik_H2_T4.5_r1

data_processing: GeneChips were washed and stained with an FS450 fluidics machine and scanned using a GeneChip Scanner 3000

tag: K12 EMG2 on LB with 0.4 percent glucose, 4.5 hours post-incubation


title: JPritchard_A-4_API_Rep1_ATH1

institute: Nottingham Arabidopsis Stock Centre (NASC)

description:
location: Growth Room
Humidity: 70%
Temperature: 22oC
Lighting: 18 hour days
Medium: compost
Nutrients: osmocote slow release fertiliser mixed in compost
Water: 3 x per week
treatment: 10 aphids caged on 2 rosette leaves for 8 hours

hyb_protocol: standard NASC hybridization protocol

scan_protocol: standard NASC scanning protocol

data_processing: The data were analysed using Affymetrix Microarray Suite 5.0 (MAS5)

label_protocol: standard NASC labeling protocol

extract_protocol: standard NASC extraction protocol

tag: Stock Code

tag: Developmental stage

tag: Tissue


title: ik_H2_T8_r1

tag: K12 EMG2 on LB with 0.4 percent glucose, 8 hours post-incubation


title: Birnbaum_1-27_J0571-3_Rep3_ATH1

description:
Media: MS + 4.5% sucrose
Light: 16h light 8h dark

value: Marks ground tissue (endodermis and cortex) and the QC

tag: Genetic background

value: Columbia


title: ik_H2_T5_r1

tag: K12 EMG2 on LB with 0.4 percent glucose, 5 hours post-incubation


title: JP001_ATH1_A6-Pritc-API

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 71.61
Background Stdev (float) = 1.35
Background Max (float) = 76.3
Background Min (float) = 69.3
Noise Avg (float) = 4.42
Noise Stdev (float) = 0.28
Noise Max (float) = 5.1
Noise Min (float) = 3.9
RawQ (float) = 2.81
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 294
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: JP001_ATH1_A6-Pritc-API.DAT

hyb_protocol: EukGE-WS2v4; Protocol Type = Hybridization; Parameter Wash A1 Recovery Mixes = 0 (type integer); Parameter Wash A1 Temperature (C) = 25 (type integer); Parameter Number of Wash A1 Cycles = 10 (type integer); Parameter Mixes per Wash A1 Cycle = 2 (type integer); Parameter Wash B Recovery Mixes = 0 (type integer); Parameter Wash B Temperature (C) = 50 (type integer); Parameter Number of Wash B Cycles = 4 (type integer); Parameter Mixes per Wash B Cycle = 15 (type integer); Parameter Stain Temperature (C) = 25 (type integer); Parameter First Stain Time (seconds) = 600 (type integer); Parameter Wash A2 Recovery Mixes = 0 (type integer); Parameter Wash A2 Temperature (C) = 25 (type integer); Parameter Number of Wash A2 Cycles = 10 (type integer); Parameter Mixes per Wash A2 Cycle = 4 (type integer); Parameter Second Stain Time (seconds) = 600 (type integer); Parameter Third Stain Time (seconds) = 600 (type integer); Parameter Wash A3 Recovery Mixes = 0 (type integer); Parameter Wash A3 Temperature (C) = 30 (type integer); Parameter Number of Wash A3 Cycles = 15 (type integer); Parameter Mixes per Wash A3 Cycle = 4 (type integer); Parameter Holding Temperature (C) = 25 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Fluidics Station, Parameter: Parameter Station Number = 1 (type integer), Parameter: Parameter Position = 1 (type integer); Performers: John,Y,Okyere, , Janet,,Higgins

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 229 (type integer); Parameter Upper left corner y coordinate = 232 (type integer); Parameter Upper right corner x coordinate = 4499 (type integer); Parameter Upper right corner y coordinate = 262 (type integer); Parameter Lower right corner x coordinate = 4471 (type integer); Parameter Lower right corner y coordinate = 4532 (type integer); Parameter Lower left corner x coordinate = 201 (type integer); Parameter Lower left corner y coordinate = 4502 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.456933 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;


title: DV001_ATH1_A5-degra-Cg3

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 84.05
Background Stdev (float) = 1.88
Background Max (float) = 88.6
Background Min (float) = 79.3
Noise Avg (float) = 6.00
Noise Stdev (float) = 0.27
Noise Max (float) = 6.7
Noise Min (float) = 5.2
RawQ (float) = 3.28
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 362
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: DV001_ATH1_A5-degra-Cg3.DAT

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 232 (type integer); Parameter Upper left corner y coordinate = 230 (type integer); Parameter Upper right corner x coordinate = 4499 (type integer); Parameter Upper right corner y coordinate = 220 (type integer); Parameter Lower right corner x coordinate = 4511 (type integer); Parameter Lower right corner y coordinate = 4490 (type integer); Parameter Lower left corner x coordinate = 244 (type integer); Parameter Lower left corner y coordinate = 4500 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.259005 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

source_name: De Grauwe_1-5_GA4-Col0-3hr_Rep1_ATH1

growth_protocol: unknown; Parameter location = Growth Room; Parameter Atmosphere = Normal; Parameter Humidity = 70% RH; Parameter Temperature = 22 C; Parameter Lighting = 16/8; Parameter Medium = MS/2; Parameter Nutrients = 1%sucrose; Performer: Liesbeth,,De Grauwe

extract_protocol: Qiagen / Trizol; Protocol: Qiagen RNAeasy kit protocol ; Protocol Type = nucleic_acid_extraction; Performer: Liesbeth,,De Grauwe

treatment_protocol: This plant was sprayed GA4, which was dissolved in water, and harvested 3hours after treatment. ; Performer: Liesbeth,,De Grauwe

value: Whole plant


title: MW001_ATH1_A1-Wheel-w14

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 100.89
Background Stdev (float) = 1.98
Background Max (float) = 106.5
Background Min (float) = 97.4
Noise Avg (float) = 6.70
Noise Stdev (float) = 0.39
Noise Max (float) = 7.7
Noise Min (float) = 5.6
RawQ (float) = 3.78
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 723
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: MW001_ATH1_A1-Wheel-w14.DAT

hyb_protocol: EukGE-WS2v4; Protocol Type = Hybridization; Parameter Wash A1 Recovery Mixes = 0 (type integer); Parameter Wash A1 Temperature (C) = 25 (type integer); Parameter Number of Wash A1 Cycles = 10 (type integer); Parameter Mixes per Wash A1 Cycle = 2 (type integer); Parameter Wash B Recovery Mixes = 0 (type integer); Parameter Wash B Temperature (C) = 50 (type integer); Parameter Number of Wash B Cycles = 4 (type integer); Parameter Mixes per Wash B Cycle = 15 (type integer); Parameter Stain Temperature (C) = 25 (type integer); Parameter First Stain Time (seconds) = 600 (type integer); Parameter Wash A2 Recovery Mixes = 0 (type integer); Parameter Wash A2 Temperature (C) = 25 (type integer); Parameter Number of Wash A2 Cycles = 10 (type integer); Parameter Mixes per Wash A2 Cycle = 4 (type integer); Parameter Second Stain Time (seconds) = 600 (type integer); Parameter Third Stain Time (seconds) = 600 (type integer); Parameter Wash A3 Recovery Mixes = 0 (type integer); Parameter Wash A3 Temperature (C) = 30 (type integer); Parameter Number of Wash A3 Cycles = 15 (type integer); Parameter Mixes per Wash A3 Cycle = 4 (type integer); Parameter Holding Temperature (C) = 25 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Fluidics Station, Parameter: Parameter Station Number = 1 (type integer), Parameter: Parameter Position = 2 (type integer); Performers: John,Y,Okyere, , Janet,,Higgins

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 232 (type integer); Parameter Upper left corner y coordinate = 231 (type integer); Parameter Upper right corner x coordinate = 4499 (type integer); Parameter Upper right corner y coordinate = 231 (type integer); Parameter Lower right corner x coordinate = 4501 (type integer); Parameter Lower right corner y coordinate = 4501 (type integer); Parameter Lower left corner x coordinate = 233 (type integer); Parameter Lower left corner y coordinate = 4501 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.263045 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

growth_protocol: unknown; Parameter location = Greenhouse; Parameter Atmosphere = Normal; Parameter Humidity = 80%; Parameter Temperature = 20C; Parameter Lighting = 16h photoperiod; Parameter Medium = compost; Parameter Treatment = Intersept; Parameter Nutrients = John Innes compost and perlite; Parameter Water = daily from below; Parameter Stratification = 4 days at 4C; Performer: Mike,,Wheeler

extract_protocol: Wheeler Trizol Protocol; Protocol:  Centrifuged at 12000g for 10 min at 4C, SN transferred to fresh 50ml tube. 3ml chloroform added, vortex 15s. RT for 2 min. Centrifuged at 10000g 15min at 4C. Aq. phase collected and placed in new 50ml tube. RNA precipitated using 0.5 vol isopropanol and 0.5 vol 0.8M Na citate/1.2M NaCl. Mixed and set at Rt for 10 min. Centrifuged at 10,000g for 10 min at 4C. SN discarded, pellet washed with 20ml 75% ethanol. Vortexed 10s. Centrifuged at 10000g, 10 min at 4C. Pellet dried in air for 10 min. 300 microlitres of DEPC-water added + 1 microlitre of RNase Inhibitor. Concentration checked by spec and by gel electrophoresis. Cleaned up using QIAgen RNA minikits. Frozen on dry ice. ; Protocol Type = nucleic_acid_extraction; Performer: Mike,,Wheeler

value: rosette leaves


title: DB001_ATH1_A5-Brown-cal

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 105.48
Background Stdev (float) = 2.28
Background Max (float) = 112.6
Background Min (float) = 101.3
Noise Avg (float) = 8.07
Noise Stdev (float) = 0.24
Noise Max (float) = 8.6
Noise Min (float) = 7.3
RawQ (float) = 3.86
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 499
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: DB001_ATH1_A5-Brown-cal.DAT

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 231 (type integer); Parameter Upper left corner y coordinate = 232 (type integer); Parameter Upper right corner x coordinate = 4499 (type integer); Parameter Upper right corner y coordinate = 250 (type integer); Parameter Lower right corner x coordinate = 4482 (type integer); Parameter Lower right corner y coordinate = 4520 (type integer); Parameter Lower left corner x coordinate = 214 (type integer); Parameter Lower left corner y coordinate = 4502 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.398152 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

growth_protocol: unknown; Parameter location = Growth Room; Parameter Temperature = 22oC; Parameter Medium = Murahige and Skoog; Parameter Treatment = 0.2mgl-1 auxin( 2,4-D NA IAA) 1.0mgl-1 BA; Parameter Nutrients = 0.2% sucrose 4% mannitol; Performer: David,,Brown

extract_protocol: Qiagen Plant RNAeasy kit; Protocol: Seedlings harvested and snap-frozen in liquid nitrogen and RNA extracted as described in the Qiagen RNAeasy kit. ; Protocol Type = nucleic_acid_extraction; Performer: David,,Brown

treatment_protocol: Leaves from seedlings, grown aseptically (14-17 days)on MS agar, excised and transferred to callus induction medium (Gamborg's B5 Basil Medium with minimal organics, 2.0% glucose, 0.5mgl-1 MES, 0.5mgl-1 2,4-D, 0.05mgl-1 Kinetin. pH 5.7). Incubated in darkness, at 22oC for 2 weeks. Callus transferred to low differentiating liquid media (MS 0.2% sucrose, 4% mannitol, 0.5mgl-1 2,4-D, 1.5ugl-1 Kinetin, pH5.7). Incubated at 22oC on a rotary shaker (105rpm). Sample taken at day =5 ; Performer: David,,Brown

value: Cell culture

tag: Age time point

value: 5 day timepoint

value: Ler


title: Gan_1-4_mutant-nitrate-minus(ANM)_Rep2_ATH1

description:
Humidity: 55 to 75%
Temperature: 20oC
Lighting: 8h light/16h dark
Medium: hydropony
Nutrients: holgand medium

value: Whole root system

tag: Genetic variation

value: knock-out mutant


title: ik_H2_T3_r1

tag: K12 EMG2 on LB with 0.4 percent glucose, 3 hours post-incubation


title: ik_H2_T2.5_r1

tag: K12 EMG2 on LB with 0.4 percent glucose, 2.5 hours post-incubation


title: ik_H2_T3.5_r1

tag: K12 EMG2 on LB with 0.4 percent glucose, 3.5 hours post-incubation


title: JP001_ATH1_A5-Pritc-API

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 81.45
Background Stdev (float) = 2.06
Background Max (float) = 87.1
Background Min (float) = 76.5
Noise Avg (float) = 4.71
Noise Stdev (float) = 0.16
Noise Max (float) = 5.3
Noise Min (float) = 4.2
RawQ (float) = 3.04
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 368
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: JP001_ATH1_A5-Pritc-API.DAT

hyb_protocol: EukGE-WS2v4; Protocol Type = Hybridization; Parameter Wash A1 Recovery Mixes = 0 (type integer); Parameter Wash A1 Temperature (C) = 25 (type integer); Parameter Number of Wash A1 Cycles = 10 (type integer); Parameter Mixes per Wash A1 Cycle = 2 (type integer); Parameter Wash B Recovery Mixes = 0 (type integer); Parameter Wash B Temperature (C) = 50 (type integer); Parameter Number of Wash B Cycles = 4 (type integer); Parameter Mixes per Wash B Cycle = 15 (type integer); Parameter Stain Temperature (C) = 25 (type integer); Parameter First Stain Time (seconds) = 600 (type integer); Parameter Wash A2 Recovery Mixes = 0 (type integer); Parameter Wash A2 Temperature (C) = 25 (type integer); Parameter Number of Wash A2 Cycles = 10 (type integer); Parameter Mixes per Wash A2 Cycle = 4 (type integer); Parameter Second Stain Time (seconds) = 600 (type integer); Parameter Third Stain Time (seconds) = 600 (type integer); Parameter Wash A3 Recovery Mixes = 0 (type integer); Parameter Wash A3 Temperature (C) = 30 (type integer); Parameter Number of Wash A3 Cycles = 15 (type integer); Parameter Mixes per Wash A3 Cycle = 4 (type integer); Parameter Holding Temperature (C) = 25 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Fluidics Station, Parameter: Parameter Station Number = 1 (type integer), Parameter: Parameter Position = 4 (type integer); Performers: John,Y,Okyere, , Janet,,Higgins

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 230 (type integer); Parameter Upper left corner y coordinate = 231 (type integer); Parameter Upper right corner x coordinate = 4501 (type integer); Parameter Upper right corner y coordinate = 246 (type integer); Parameter Lower right corner x coordinate = 4488 (type integer); Parameter Lower right corner y coordinate = 4516 (type integer); Parameter Lower left corner x coordinate = 217 (type integer); Parameter Lower left corner y coordinate = 4501 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.461692 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;


title: Birnbaum_1-2_src5-2_Rep2_ATH1

value: Marks the QC and the endodermis at least past the mature hair zone

value: Landsberg


title: DV001_ATH1_A2-degra-Cc1_repeat2

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 88.66
Background Stdev (float) = 4.06
Background Max (float) = 96.4
Background Min (float) = 78.6
Noise Avg (float) = 4.99
Noise Stdev (float) = 0.22
Noise Max (float) = 5.8
Noise Min (float) = 4.4
RawQ (float) = 3.33
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 270
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: DV001_ATH1_A2-degra-Cc1_repeat2.DAT

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 230 (type integer); Parameter Upper left corner y coordinate = 231 (type integer); Parameter Upper right corner x coordinate = 4497 (type integer); Parameter Upper right corner y coordinate = 245 (type integer); Parameter Lower right corner x coordinate = 4484 (type integer); Parameter Lower right corner y coordinate = 4516 (type integer); Parameter Lower left corner x coordinate = 217 (type integer); Parameter Lower left corner y coordinate = 4502 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.392133 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

source_name: De Grauwe_1-2_water-Col0-1hr_Rep3_ATH1

treatment_protocol: This plant was sprayed with water and harvested 1hour after treatment ; Performer: Liesbeth,,De Grauwe


title: JP001_ATH1_A1-Pritc-CTR

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 87.12
Background Stdev (float) = 1.56
Background Max (float) = 92.0
Background Min (float) = 83.3
Noise Avg (float) = 5.21
Noise Stdev (float) = 0.25
Noise Max (float) = 6.0
Noise Min (float) = 4.5
RawQ (float) = 3.04
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 463
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: JP001_ATH1_A1-Pritc-CTR.DAT

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 230 (type integer); Parameter Upper left corner y coordinate = 231 (type integer); Parameter Upper right corner x coordinate = 4498 (type integer); Parameter Upper right corner y coordinate = 256 (type integer); Parameter Lower right corner x coordinate = 4474 (type integer); Parameter Lower right corner y coordinate = 4526 (type integer); Parameter Lower left corner x coordinate = 206 (type integer); Parameter Lower left corner y coordinate = 4502 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.477230 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

treatment_protocol: Aphid cages attached to leaves- no aphids ; Performer: Jeremy,,Pritchard


title: ik_H2_T5.5_r1

tag: K12 EMG2 on LB with 0.4 percent glucose, 5.5 hours post-incubation