title: P4_WT_3

description:
Origin of sample: Sciatic nerve of 4 day old (P4) wild type mice (mixed background), pooled from 4--7 mice.
RNA extracted with RNeasy kits (Qiagen).
Target preparation by two rounds of in vitro transcription (Hoffmann, R., Seidl, T., Neeb, M., Rolink, A. & Melchers, F. Changes in gene expression profiles in developing B cells of murine bone marrow. Genome Res 12, 98-111 (2002)).
Labeling protocol: Standard Affymetrix biotin labeling protocol (Affymetrix, Expression Analysis: Technical manual, 2000) in 2nd round of in vitro transcription.
Hybridization procedure: Standard Affymetrix protocols (Affymetrix, Expression analysis: Technical manual, 2000).
Scanning with Affymetrix scanner and MAS 5.0 software. The original images (.dat files) are available on request (mantei@cell.biol.ethz.ch) The .cel files produced by MAS 5.0 were normalized using the program dChip (smoothing spline normalization; Li, C. & Wong, W.H. Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol. 2, research0032.0031-0032.0011 (2001); http://www.dchip.org). dChip was also used to calculate a probe sensitivity index for each probe on the basis of 27 arrays, and then a "model-based expression index" (MBEI) for each gene on each array (Li, C. & Wong, W.H. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc. Natl. Acad. Sci. U.S.A. 98, 31-36 (2001)).
Keywords = peripheral nervous system
Keywords = PMP22

source_name: sciatic nerve of P4 wild type mice


title: P60_WT_1

status: Public on Nov 10 2004

type: RNA

city: Zurich

first: Ned

last: Mantei

department: Institute for Cell Biology

country: Switzerland

institute: Swiss Federal Institute of Technology

description:
Origin of sample: Sciatic nerve of 60 day old (P60) wild type mice (mixed background), pooled from 4--7 mice.
RNA extracted with RNeasy kits (Qiagen).
Target preparation by two rounds of in vitro transcription (Hoffmann, R., Seidl, T., Neeb, M., Rolink, A. & Melchers, F. Changes in gene expression profiles in developing B cells of murine bone marrow. Genome Res 12, 98-111 (2002)).
Labeling protocol: Standard Affymetrix biotin labeling protocol (Affymetrix, Expression Analysis: Technical manual, 2000) in 2nd round of in vitro transcription.
Hybridization procedure: Standard Affymetrix protocols (Affymetrix, Expression analysis: Technical manual, 2000).
Scanning with Affymetrix scanner and MAS 5.0 software. The original images (.dat files) and .cel files are available on request (mantei@cell.biol.ethz.ch) The .cel files produced by MAS 5.0 were normalized using the program dChip (smoothing spline normalization; Li, C. & Wong, W.H. Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol. 2, research0032.0031-0032.0011 (2001); http://www.dchip.org). dChip was also used to calculate a probe sensitivity index for each probe on the basis of 18 arrays, and then a "model-based expression index" (MBEI) for each gene on each array (Li, C. & Wong, W.H. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc. Natl. Acad. Sci. U.S.A. 98, 31-36 (2001)).
Keywords = peripheral nervous system
Keywords = PMP22

molecule: total RNA

organism: Mus musculus

source_name: sciatic nerve of P60 wild type mice


title: PMI40 deletion strain, 1.5 g/L initial mannose, repeat 1/3

city: Helsinki

first: Anssi

last: Torma

address: Haartmaninkatu 8

department: Department of Bacteriology and Immunology

country: Finland

institute: Haartman Institute

description: A Saccharomyces cerevisiae strain with PMI40 knockout (parent CEN.PK113-7A) was cultivated in an aerated batch with mineral medium initially containing 15 g/L glucose and 1.5 g/L mannose. Samples for gene expression measurement were taken 6 hours after inoculation. Replicate assay 1 of 3.

organism: Saccharomyces cerevisiae

source_name: Total RNA from an aerobic batch culture of a pmi40 deletion strain


title: PMI40 deletion strain, 3 g/L initial mannose, repeat 3/3

description: A Saccharomyces cerevisiae strain with PMI40 knockout (parent CEN.PK113-7A) was cultivated in an aerated batch with mineral medium initially containing 15 g/L glucose and 3 g/L mannose. Samples for gene expression measurement were taken 6 hours after inoculation. Replicate assay 3 of 3.


title: C_Ctrl_2

city: Columbus

first: David

middle: Lawrence

last: Newsom

state: OH

department: Human Cancer Genetics

country: USA

institute: Comprehensive Cancer Center

description:
K562 cell line was mock treated.  RNA was extracted using Trizol plus Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA and included suggested level of Affymetrix RNA spike controls.
Keywords = Human, leukemia, mock treated

organism: Homo sapiens

source_name: K562 cell line


title: PMI40 deletion strain, 3 g/L initial mannose, repeat 2/3

description: A Saccharomyces cerevisiae strain with PMI40 knockout (parent CEN.PK113-7A) was cultivated in an aerated batch with mineral medium initially containing 15 g/L glucose and 3 g/L mannose. Samples for gene expression measurement were taken 6 hours after inoculation. Replicate assay 2 of 3.


title: P60_WT_2

description:
Origin of sample: Sciatic nerve of 60 day old (P60) wild type mice (mixed background), pooled from 4--7 mice.
RNA extracted with RNeasy kits (Qiagen).
Target preparation by two rounds of in vitro transcription (Hoffmann, R., Seidl, T., Neeb, M., Rolink, A. & Melchers, F. Changes in gene expression profiles in developing B cells of murine bone marrow. Genome Res 12, 98-111 (2002)).
Labeling protocol: Standard Affymetrix biotin labeling protocol (Affymetrix, Expression Analysis: Technical manual, 2000) in 2nd round of in vitro transcription.
Hybridization procedure: Standard Affymetrix protocols (Affymetrix, Expression analysis: Technical manual, 2000).
Scanning with Affymetrix scanner and MAS 5.0 software. The original images (.dat files) are available on request (mantei@cell.biol.ethz.ch) The .cel files produced by MAS 5.0 were normalized using the program dChip (smoothing spline normalization; Li, C. & Wong, W.H. Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol. 2, research0032.0031-0032.0011 (2001); http://www.dchip.org). dChip was also used to calculate a probe sensitivity index for each probe on the basis of 27 arrays, and then a "model-based expression index" (MBEI) for each gene on each array (Li, C. & Wong, W.H. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc. Natl. Acad. Sci. U.S.A. 98, 31-36 (2001)).
Keywords = peripheral nervous system
Keywords = PMP22


title: PMI40 deletion strain, 3 g/L initial mannose, repeat 1/3

description: A Saccharomyces cerevisiae strain with PMI40 knockout (parent CEN.PK113-7A) was cultivated in an aerated batch with mineral medium initially containing 15 g/L glucose and 3 g/L mannose. Samples for gene expression measurement were taken 6 hours after inoculation. Replicate assay 1 of 3.


title: P4_WT_1

source_name: sciatic nerve of P4 wild type mouse


title: P4_WT_2

description:
Origin of sample: Sciatic nerve of 4 day old (P4) wild type mice (mixed background), pooled from 4--7 mice.
Target preparation by two rounds of in vitro transcription (Hoffmann, R., Seidl, T., Neeb, M., Rolink, A. & Melchers, F. Changes in gene expression profiles in developing B cells of murine bone marrow. Genome Res 12, 98-111 (2002)).
Labeling protocol: Standard Affymetrix biotin labeling protocol (Affymetrix, Expression Analysis: Technical manual, 2000) in 2nd round of in vitro transcription.
Hybridization procedure: Standard Affymetrix protocols (Affymetrix, Expression analysis: Technical manual, 2000).
RNA extracted with RNeasy kits (Qiagen).
Scanning with Affymetrix scanner and MAS 5.0 software. The original images (.dat files) are available on request (mantei@cell.biol.ethz.ch) The .cel files produced by MAS 5.0 were normalized using the program dChip (smoothing spline normalization; Li, C. & Wong, W.H. Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol. 2, research0032.0031-0032.0011 (2001); http://www.dchip.org). dChip was also used to calculate a probe sensitivity index for each probe on the basis of 27 arrays, and then a "model-based expression index" (MBEI) for each gene on each array (Li, C. & Wong, W.H. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc. Natl. Acad. Sci. U.S.A. 98, 31-36 (2001)).
Keywords = peripheral nervous system
Keywords = PMP22


title: C_Ctrl_1


title: PMI40 deletion strain, 0.75 g/L initial mannose, repeat 2/3

description: A Saccharomyces cerevisiae strain with PMI40 knockout (parent CEN.PK113-7A) was cultivated in an aerated batch with mineral medium initially containing 15 g/L glucose and 0.75 g/L mannose. Samples for gene expression measurement were taken 6 hours after inoculation. Replicate 2 of 3.


title: PMI40 deletion strain, 0.75 g/L initial mannose, repeat 3/3

description: A Saccharomyces cerevisiae strain with PMI40 knockout (parent CEN.PK113-7A) was cultivated in an aerated batch with mineral medium initially containing 15 g/L glucose and 0.75 g/L mannose. Samples for gene expression measurement were taken 6 hours after inoculation. Replicate 3 of 3.


title: PMI40 deletion strain, 0.75 g/L initial mannose, repeat 1/3

description: A Saccharomyces cerevisiae strain with PMI40 knockout (parent CEN.PK113-7A) was cultivated in an aerated batch with mineral medium initially containing 15 g/L glucose and 0.75 g/L mannose. Samples for gene expression measurement were taken 6 hours after inoculation. Replicate 1 of 3.


title: 2DCOL2

status: Public on Nov 09 2004

city: Boston

first: Catherine

last: Klapperich

state: MA

address: 44 Cummington St. 7th Floor

department: Biomedical and Manufacturing Engineering

institute: Boston University

description:
Human IMR-90 Cells grown on Collagen-Chondroitin Sulfate coated Tissue Culture Polystyrene Dish for 8 hours.
Keywords = Collagen Type I
Keywords = Chondroitin sulfate
Keywords = IMR-90

source_name: Human IMR-90 Cells


title: 2DCOL4


title: TCPS2

description:
Human IMR-90 Cells grown on Tissue Culture Polystyrene Dish for 8 hours.
Keywords = TCPS
Keywords = IMR-90


title: 430A (no treatment) 7-24-03

city: Chicago

first: Julia

last: Tao

state: IL

address: 5841 south maryland

department: Medicine

institute: University of Chicago

description: Sample was obtained from no treatment (YAMC cells-young adult mouse colon epithelial cells). RNA was extracted with Trizol and purified with Qiagen kit and was profiled for detection of gene expression without treatment.

source_name: Mouse colon epithelial cells


title: Ifh1, array 1, upper half

first: Joseph

last: Wade

address: 240 Longwood Ave

department: BCMP

institute: Harvard Medical School

description: Ifh1 ChIP-chip

source_name: Ifh1 IP

source_name: IP from untagged strain


title: Ifh1, array 1, lower half

description: Ifh1 ChIP-chip


title: 3DCOL3

description:
Human IMR-90 Cells grown on three dimensional collagen-chondroiting sulfate meshes for 8 hours.
Keywords = Collagen Type I
Keywords = Chondroitin sulfate
Keywords = IMR-90


title: 2DCOL1


title: YSS89, T=30, b

status: Public on Nov 06 2004

city: Geneva

first: Stephan

middle: B.

last: Schawalder

address: Quai Ansermet 30

department: Departement of Molecular biology

institute: University of Geneva

description:
Experiment Design:
Keywords = IFH1
Keywords = Transcriptional control of RP genes

source_name: Yeast


title: Ifh1, array 2, lower half

description: Ifh1 ChIP-chip


title: Fhl1, array 2, lower half

description: Fhl1 ChIP-chip

source_name: Fhl1 IP

source_name: Control IP from untagged strain


title: Ifh1, array 2, upper half

description: Ifh1 ChIP-chip


title: 3DCOL4


title: Fhl1, array 1, lower half

description: Fhl1 ChIP-chip


title: TCPS3


title: Fhl1, array 2, upper half

description: Fhl1 ChIP-chip


title: 3DCOL1


title: Fhl1, array 1, upper half

description: Fhl1 ChIP-chip

source_name: IP from control strain


title: 3DCOL2


title: 2DCOL3


title: tomatidine_7.5 uM

city: Bracknell

first: Adam

middle: Alexander

last: Cleaver

country: United Kingdom

institute: Syngenta

description: RNA isolated from Saccharomyces cerevisiae S288c following 5 hours exposure to 7.5 uM tomatidine (dissolved in the carrier solvent DMF)

source_name: Saccharomyces cerevisiae S288c


title: TCPS1


title: YSS37, T=30, b


title: control

description: RNA isolated from Saccharomyces cerevisiae S288c following 5 hours exposure to solvent DMF


title: 430A (LGG treatment) 1-22-2004

description: Sample was obtained from LGG treatment (YAMC cells treated with Lactobacillus GG condition media for 16h). RNA was extracted with Trizol and purified with Qiagen kit and was profiled for detection of gene expression after treatment with Lactobacillus GG condition media for 16h.


title: 430A (no treatment) 1-22-2004


title: TCPS4


title: 430A (LGG treatment) 7-24-03


title: tomatidine_15 uM

description: RNA isolated from Saccharomyces cerevisiae S288c following 5 hours exposure to 15 uM tomatidine (dissolved in the carrier solvent DMF)


title: Postnatal 1-year, mouse 3

status: Public on Nov 05 2004

city: Irvine

first: Kevin

middle: K

last: Lin

state: CA

address: 250 Sprague Hall

department: Biological Chemistry & Medicine

institute: University of California, Irvine

description:
Identification of hair cycle-associated genes from
time-course gene expression profile data by using
replicate variance. Proc. Natl. Acad. Sci. USA (2004)

Lot batch =

source_name: whole RNA from back skin


title: Postnatal 1-year, mouse 4


title: Postnatal 1-year, mouse 1


title: Postnatal 5-month, mouse 2


title: Postnatal 9-week, mouse 1


title: Postnatal 9-week, mouse 3


title: Postnatal 5-month, mouse 3


title: Postnatal 1-year, mouse 2


title: Postnatal 5-month, mouse 1


title: Postnatal day 23, mouse 3


title: Postnatal day 17, mouse 2


title: Postnatal day 17, mouse 3


title: Postnatal day 23, mouse 2


title: Postnatal day 23, mouse 1


title: tub1D_SHI experiment2

city: Baltimore

first: Xuewen

last: Pan

state: MD

address: 733 N. Broadway, Room 331

department: Department of Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

description:
A pool of 5,896 haploid-convertible heterozygous diploid yeast knockout (YKO) strains were transformed with a ura3D::URA3 (as target source1) or a tub1D::URA3 (as target source2) cassette.
The two Pools of diploid YKOs were harvested after incubation at 30 degree for 2 days on SC-Ura medium.
Genomic DNA samples were prepared from these two pools and used as the templates for PCR amplification of the TAGs identifying the YKOs with a pair of primers universal for either Uptags or Downtags.
The PCR products from sample1 were labeled with Cy5 and those from sample2 with Cy3.
The Cy5- and Cy3-labeled Uptags and Downtags were mixed together and hybridized to a Hopkins-TagArray.
Fluorescent array images were collected for both Cy5 and Cy3 with a GenePix4000B microarray scanner.
The image data was annalyzed with a GenePix5.1 program.
Keywords = tub1D, SHI, heterozygotes, YKO

source_name: Pool resulting from ura3D::URA3 transformation

source_name: Pool resulting from tub1D::URA3 transformation


title: tub1D_SHI experiment1


title: Postnatal 9-week, mouse 2


title: sgs1D dSLAM DownTag experiment2

description:
A pool of 5,896 haploid-convertible heterozygous diploid yeast knockout (YKO) strains were transformed with a sgs1D::URA3 cassette.
The resultant diploid double YKO pool was sporulated and the spores were spread on MM with 0.1% 5-FOA (as target source1) and MM-Ura (as target source2).
Pools of haploid YKOs were harvested after incubation at 30 degree for 2 days.
Genomic DNA samples were prepared from these two haploid pools and used as the templates for PCR amplification of the TAGs identifying the YKOs with a pair of primers universal for either Uptags or Downtags.
The PCR products from sample1 were labeled with Cy5 and those from sample2 with Cy3.
The Cy5- and Cy3-labeled Uptags and Downtags were mixed together and hybridized to a Rosetta_DownTag.
Fluorescent array images were collected for both Cy5 and Cy3 with a GenePix4000B microarray scanner.
The image data was annalyzed with the Imagene 5.0 and Genesight 3.1 programs from Biodiscovery.
Keywords = sgs1D, dSLAM, heterozygotes, YKO

source_name: Pool of haploid single YKOs

source_name: Pool of haploid double YKOs


title: sgs1D dSLAM experiment 3

description:
A pool of 5,896 haploid-convertible heterozygous diploid yeast knockout (YKO) strains were transformed with a sgs1D::URA3 cassette.
The resultant diploid double YKO pool was sporulated and the spores were spread on MM with 0.1% 5-FOA (as target source1) and MM-Ura (as target source2).
Pools of haploid YKOs were harvested after incubation at 30 degree for 2 days.
Genomic DNA samples were prepared from these two haploid pools and used as the templates for PCR amplification of the TAGs identifying the YKOs with a pair of primers universal for either Uptags or Downtags.
The PCR products from sample1 were labeled with Cy5 and those from sample2 with Cy3.
The Cy5- and Cy3-labeled Uptags and Downtags were mixed together and hybridized to a Hopkins-TagArray.
Fluorescent array images were collected for both Cy5 and Cy3 with a GenePix4000B microarray scanner.
The image data was annalyzed with a GenePix5.1 program.
Keywords = sgs1D, dSLAM, heterozygotes, YKO


title: sml1D dSLAM

description:
A pool of 5,896 haploid-convertible heterozygous diploid yeast knockout (YKO) strains were transformed with a sml1D::URA3 cassette.
The resultant diploid double YKO pool was sporulated and the spores were spread on MM with 0.1% 5-FOA (as target source1) and MM-Ura (as target source2).
Pools of haploid YKOs were harvested after incubation at 30 degree for 2 days.
Genomic DNA samples were prepared from these two haploid pools and used as the templates for PCR amplification of the TAGs identifying the YKOs with a pair of primers universal for either Uptags or Downtags.
The PCR products from sample1 were labeled with Cy5 and those from sample2 with Cy3.
The Cy5- and Cy3-labeled Uptags and Downtags were mixed together and hybridized to a Hopkins-TagArray.
Fluorescent array images were collected for both Cy5 and Cy3 with a GenePix4000B microarray scanner.
The image data was annalyzed with a GenePix5.1 program.
Keywords = sml1D, dSLAM, heterozygotes, YKO


title: CDC102 wild-type 28 degree

description:
A pool of 5,896 haploid-convertible heterozygous diploid yeast knockout (YKO) strains were transformed with a cdc102D::natMX cassette.
The resultant diploid double mutant pool was again transformed with a CDc102 wild-type gene on a centromere-based plasmid, which also carries a URA3 gene as the selection marker.
This cdc102-1 pool was sporulated and the spores were spread on MM-Ura (as target source 1) and MM-Ura+Nat (as target source 2).
Pools of haploid YKOs were harvested after incubation at 28 degree for 2 days.
Genomic DNA samples were prepared from these two haploid pools and used as the templates for PCR amplification of the TAGs identifying the YKOs with a pair of primers universal for either Uptags or Downtags.
The PCR products from sample1 were labeled with Cy5 and those from sample2 with Cy3.
The Cy5- and Cy3-labeled Uptags and Downtags were mixed together and hybridized to a Hopkins-TagArray.
Fluorescent array images were collected for both Cy5 and Cy3 with a GenePix4000B microarray scanner.
The image data was annalyzed with a GenePix5.1 program.
Keywords = CDC102, wild-type, 28 degree, heterozygotes, YKO

source_name: Pool of haploid single and double YKOs


title: LCD1 overexpression dSLAM experiment2

description:
A pool of 5,896 haploid-convertible heterozygous diploid yeast knockout (YKO) strains were transformed with a control plasmid (as target source1)or a GAL1-LCD1 plasmid (as target source2) with URA3 as the selectable marker.
The resultant diploid double YKO pools were sporulated and the spores were spread on the haploid selection medium with 2% galactose as the sole carbon source.
Pools of haploid YKOs were harvested after incubation at 30 degree for 3 days.
Genomic DNA samples were prepared from these two haploid pools and used as the templates for PCR amplification of the TAGs identifying the YKOs with a pair of primers universal for either Uptags or Downtags.
The PCR products from sample1 were labeled with Cy5 and those from sample2 with Cy3.
The Cy5- and Cy3-labeled Uptags and Downtags were mixed together and hybridized to a Hopkins-TagArray.
Fluorescent array images were collected for both Cy5 and Cy3 with a GenePix4000B microarray scanner.
The image data was annalyzed with a GenePix5.1 program.
Keywords = LCD1, overexpression, dSLAM, heterozygotes, YKO

source_name: Pool of haploid YKOs with control plasmid

source_name: Pool of haploid YKOs with LCD1-overexpression


title: bim1D dSLAM DownTag experiment1

description:
A pool of 5,896 haploid-convertible heterozygous diploid yeast knockout (YKO) strains were transformed with a ura3D::URA3 (as target source1) or a bim1D::URA3 (as target source2) cassette.
The resultant pools of Ura+ transformants were sporulated and spores were spread on MM-Ura.
Pools of Ura+ haploid YKOs were harvested after incubation at 30 degree for 2 days.
Genomic DNA samples were prepared from these two haploid pools and used as the templates for PCR amplification of the TAGs identifying the YKOs with a pair of primers universal for either Uptags or Downtags.
The PCR products from sample1 were labeled with Cy5 and those from sample2 with Cy3.
The Cy5- and Cy3-labeled Uptags and Downtags were mixed together and hybridized to a Rosetta_DownTag.
Fluorescent array images were collected for both Cy5 and Cy3 with a GenePix4000B microarray scanner.
The image data was annalyzed with the Imagene 5.0 and Genesight 3.1 programs from Biodiscovery.
Keywords = bim1D, dSLAM, heterozygotes, YKO

source_name: Pool of haploid single YKOs result from ura3D::URA3 transfromation and sporulation

source_name: Pool of haploid double YKOs result from bim1D::URA3 transformation and sporulation


title: sgs1D dSLAM DownTag experiment1


title: cdc102-1 28 degree

description:
A pool of 5,896 haploid-convertible heterozygous diploid yeast knockout (YKO) strains were transformed with a cdc102D::natMX cassette.
The resultant diploid double mutant pool was again transformed with a cdc102-1 allele on a centromere-based plasmid, which also carries a URA3 gene as the selection marker.
This cdc102-1 pool was sporulated and the spores were spread on MM-Ura (as target source 1) and MM-Ura+Nat (as target source 2).
Pools of haploid YKOs were harvested after incubation at 28 degree for 2 days.
Genomic DNA samples were prepared from these two haploid pools and used as the templates for PCR amplification of the TAGs identifying the YKOs with a pair of primers universal for either Uptags or Downtags.
The PCR products from sample1 were labeled with Cy5 and those from sample2 with Cy3.
The Cy5- and Cy3-labeled Uptags and Downtags were mixed together and hybridized to a Hopkins-TagArray.
Fluorescent array images were collected for both Cy5 and Cy3 with a GenePix4000B microarray scanner.
The image data was annalyzed with a GenePix5.1 program.
Keywords = cdc102-1, 28 degree, heterozygotes, YKO


title: cdc102-1 30 degree

description:
A pool of 5,896 haploid-convertible heterozygous diploid yeast knockout (YKO) strains were transformed with a cdc102D::natMX cassette.
The resultant diploid double mutant pool was again transformed with a cdc102-1 allele on a centromere-based plasmid, which also carries a URA3 gene as the selection marker.
This cdc102-1 pool was sporulated and the spores were spread on MM-Ura (as target source 1) and MM-Ura+Nat (as target source 2).
Pools of haploid YKOs were harvested after incubation at 30 degree for 2 days.
Genomic DNA samples were prepared from these two haploid pools and used as the templates for PCR amplification of the TAGs identifying the YKOs with a pair of primers universal for either Uptags or Downtags.
The PCR products from sample1 were labeled with Cy5 and those from sample2 with Cy3.
The Cy5- and Cy3-labeled Uptags and Downtags were mixed together and hybridized to a Hopkins-TagArray.
Fluorescent array images were collected for both Cy5 and Cy3 with a GenePix4000B microarray scanner.
The image data was annalyzed with a GenePix5.1 program.
Keywords = cdc102-1, 30 degree, heterozygotes, YKO


title: LCD1 overexpression dSLAM experiment1


title: CDC102 wild-type 30 degree

description:
A pool of 5,896 haploid-convertible heterozygous diploid yeast knockout (YKO) strains were transformed with a cdc102D::natMX cassette.
The resultant diploid double mutant pool was again transformed with a CDc102 wild-type gene on a centromere-based plasmid, which also carries a URA3 gene as the selection marker.
This cdc102-1 pool was sporulated and the spores were spread on MM-Ura (as target source 1) and MM-Ura+Nat (as target source 2).
Pools of haploid YKOs were harvested after incubation at 30 degree for 2 days.
Genomic DNA samples were prepared from these two haploid pools and used as the templates for PCR amplification of the TAGs identifying the YKOs with a pair of primers universal for either Uptags or Downtags.
The PCR products from sample1 were labeled with Cy5 and those from sample2 with Cy3.
The Cy5- and Cy3-labeled Uptags and Downtags were mixed together and hybridized to a Hopkins-TagArray.
Fluorescent array images were collected for both Cy5 and Cy3 with a GenePix4000B microarray scanner.
The image data was annalyzed with a GenePix5.1 program.
Keywords = CDC102, wild-type, 30 degree, heterozygotes, YKO


title: bim1D dSLAM DownTag experiment2

description:
A pool of 5,896 haploid-convertible heterozygous diploid yeast knockout (YKO) strains were transformed with a bim1D::URA3 cassette.
The resultant diploid double YKO pool was sporulated and the spores were spread on MM with 0.1% 5-FOA (as target source1) and MM-Ura (as target source2).
Pools of haploid YKOs were harvested after incubation at 30 degree for 2 days.
Genomic DNA samples were prepared from these two haploid pools and used as the templates for PCR amplification of the TAGs identifying the YKOs with a pair of primers universal for either Uptags or Downtags.
The PCR products from sample1 were labeled with Cy5 and those from sample2 with Cy3.
The Cy5- and Cy3-labeled Uptags and Downtags were mixed together and hybridized to a Rosetta_DownTag.
Fluorescent array images were collected for both Cy5 and Cy3 with a GenePix4000B microarray scanner.
The image data was annalyzed with the Imagene 5.0 and Genesight 3.1 programs from Biodiscovery.
Keywords = bim1D, dSLAM, heterozygotes, YKO


title: cin8D dSLAM experiment2

description:
A pool of 5,896 haploid-convertible heterozygous diploid yeast knockout (YKO) strains were transformed with a cin8D::URA3 cassette.
The resultant diploid double YKO pool was sporulated and the spores were spread on MM with 0.15% 5-FOA (as target source1) and MM-Ura (as target source2).
Pools of haploid YKOs were harvested after incubation at 30 degree for 2 days.
Genomic DNA samples were prepared from these two haploid pools and used as the templates for PCR amplification of the TAGs identifying the YKOs with a pair of primers universal for either Uptags or Downtags.
The PCR products from sample1 were labeled with Cy5 and those from sample2 with Cy3.
The Cy5- and Cy3-labeled Uptags and Downtags were mixed together and hybridized to a Hopkins-TagArray.
Fluorescent array images were collected for both Cy5 and Cy3 with a GenePix4000B microarray scanner.
The image data was annalyzed with a GenePix5.1 program.
Keywords = cin8D, dSLAM, heterozygotes, YKO


title: cin8D dSLAM experiment3

description:
A pool of 5,896 haploid-convertible heterozygous diploid yeast knockout (YKO) strains were transformed with a cin8D::URA3 cassette.
The resultant diploid double YKO pool was sporulated and the spores were spread on MM with 0.2% 5-FOA (as target source1) and MM-Ura (as target source2).
Pools of haploid YKOs were harvested after incubation at 30 degree for 2 days.
Genomic DNA samples were prepared from these two haploid pools and used as the templates for PCR amplification of the TAGs identifying the YKOs with a pair of primers universal for either Uptags or Downtags.
The PCR products from sample1 were labeled with Cy5 and those from sample2 with Cy3.
The Cy5- and Cy3-labeled Uptags and Downtags were mixed together and hybridized to a Hopkins-TagArray.
Fluorescent array images were collected for both Cy5 and Cy3 with a GenePix4000B microarray scanner.
The image data was annalyzed with a GenePix5.1 program.
Keywords = cin8D, dSLAM, heterozygotes, YKO


title: Postnatal day 17, mouse 1


title: cin8D dSLAM experiment1

description:
A pool of 5,896 haploid-convertible heterozygous diploid yeast knockout (YKO) strains were transformed with a cin8D::URA3 cassette.
The resultant diploid double YKO pool was sporulated and the spores were spread on MM with 0.1% 5-FOA (as target source1) and MM-Ura (as target source2).
Pools of haploid YKOs were harvested after incubation at 30 degree for 2 days.
Genomic DNA samples were prepared from these two haploid pools and used as the templates for PCR amplification of the TAGs identifying the YKOs with a pair of primers universal for either Uptags or Downtags.
The PCR products from sample1 were labeled with Cy5 and those from sample2 with Cy3.
The Cy5- and Cy3-labeled Uptags and Downtags were mixed together and hybridized to a Hopkins-TagArray.
Fluorescent array images were collected for both Cy5 and Cy3 with a GenePix4000B microarray scanner.
The image data was annalyzed with a GenePix5.1 program.
Keywords = cin8D, dSLAM, heterozygotes, YKO


title: Postnatal day 6, mouse 3


title: Postnatal day 14, mouse 2


title: Postnatal day 14, mouse 1


title: Postnatal day 14, mouse 3


title: 25 microgram/ml benomyl

description:
A pool of 5,896 haploid-convertible heterozygous diploid yeast knockout (YKO) strains were sporulated.
A pool of isogenic haploid MATa cells were obtained by selection on a magic medium with (sample2) or without (sample1) 25 microgram/ml of benomyl at 30 degree for 4 days.
Genomic DNA samples were prepared from these two pools of freshly generated haploid cells and used as the templates for PCR amplification of the TAGs identifying the YKOs with a pair of primers universal for either Uptags or Downtags.
The PCR products from sample1 were labeled with Cy5 and those from sample2 with Cy3.
The Cy5- and Cy3-labeled Uptags and Downtags were mixed together and hybridized to a Hopkins-TagArray.
Fluorescent array images were collected for both Cy5 and Cy3 with a GenePix4000B microarray scanner.
The image data was annalyzed with a GenePix5.1 program.
Keywords = 25 microgram/ml, benomyl, heterozygotes, YKO

source_name: no benomyl

source_name: 25 microgram/ml benomyl


title: 40 microgram/ml benomyl

description:
A pool of 5,896 haploid-convertible heterozygous diploid yeast knockout (YKO) strains were sporulated
A pool of isogenic haploid MATa cells were obtained by selection on a magic medium with (sample2) or without (sample1) 40 microgram/ml of benomyl at 30 degree for 4 days.
Genomic DNA samples were prepared from these two pools of freshly generated haploid cells and used as the templates for PCR amplification of the TAGs identifying the YKOs with a pair of primers universal for either Uptags or Downtags.
The PCR products from sample1 were labeled with Cy5 and those from sample2 with Cy3.
The Cy5- and Cy3-labeled Uptags and Downtags were mixed together and hybridized to a Hopkins-TagArray.
Fluorescent array images were collected for both Cy5 and Cy3 with a GenePix4000B microarray scanner.
The image data was annalyzed with a GenePix5.1 program.
Keywords = 40 microgram/ml, benomyl, heterozygotes, YKO

source_name: 40 microgram/ml benomyl


title: INS-1 cell line (FLP-In T-REx clone #5-3.14)

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

country: Germany

institute: Institut fuer Zellbiologie

description:
Starting with the rat insulinoma cell line INS-1, clones were generated that contain a FRT site for site specific integration of specific genes (INS-1 Flp-In T-REx). In addition, the clones contain the tetracycline repressor allowing tetracycline (tet) induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factor can be identified. This entry corresponds to the RNA isolated from the INS-1 cell line #5-3.14
Keywords = INS-1
Keywords = b-cell
Keywords = Flp-In T-Rex
Keywords = tetracycline
Keywords = FRT

organism: Rattus norvegicus

source_name: INS-1 cell line, clone #5-3.14


title: INS-1 cell line (FLP-In T-REx clone #1-1.16)

description:
Starting with the rat insulinoma cell line INS-1, clones were generated that contain a FRT site for site specific integration of specific genes (INS-1 Flp-In T-REx). In addition, the clones contain the tetracycline repressor allowing tetracycline (tet) induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factor can be identified. This entry corresponds to the RNA isolated from the INS-1 cell line #1-1.16
Keywords = INS-1
Keywords = b-cell
Keywords = Flp-In T-Rex
Keywords = tetracycline
Keywords = FRT

source_name: INS-1 cell line, clone #1-1.16


title: INS-1 cell line (FLP-In T-REx clone #5-3.19)

description:
Starting with the rat insulinoma cell line INS-1, clones were generated that contain a FRT site for site specific integration of specific genes (INS-1 Flp-In T-REx). In addition, the clones contain the tetracycline repressor allowing tetracycline (tet) induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factor can be identified. This entry corresponds to the RNA isolated from the INS-1 cell line #5-3.19
Keywords = INS-1
Keywords = b-cell
Keywords = Flp-In T-Rex
Keywords = tetracycline
Keywords = FRT

source_name: INS-1 cell line, clone #5-3.19


title: 30 microgram/ml benomyl

description:
A pool of 5,896 haploid-convertible heterozygous diploid yeast knockout (YKO) strains were sporulated
A pool of isogenic haploid MATa cells were obtained by selection on a magic medium with (sample2) or without (sample1) 30 microgram/ml of benomyl at 30 degree for 4 days.
Genomic DNA samples were prepared from these two pools of freshly generated haploid cells and used as the templates for PCR amplification of the TAGs identifying the YKOs with a pair of primers universal for either Uptags or Downtags.
The PCR products from sample1 were labeled with Cy5 and those from sample2 with Cy3.
The Cy5- and Cy3-labeled Uptags and Downtags were mixed together and hybridized to a Hopkins-TagArray.
Fluorescent array images were collected for both Cy5 and Cy3 with a GenePix4000B microarray scanner.
The image data was annalyzed with a GenePix5.1 program.
Keywords = 30 microgram/ml, benomyl, heterozygotes, YKO

source_name: 30 microgram/ml benomyl


title: Postnatal day 6, mouse 1

description:
Identification of hair cycle-associated genes from
time-course gene expression profile data by using
replicate variance. Proc. Natl. Acad. Sci. USA (2004)

Lot batch =

source_name: whole RNA from back skin


title: Postnatal day 6, mouse 2


title: 15 microgram/ml benomyl

description:
A pool of 5,896 haploid-convertible heterozygous diploid yeast knockout (YKO) strains were sporulated
A pool of isogenic haploid MATa cells were obtained by selection on a magic medium with (sample2) or without (sample1) 15 microgram/ml of benomyl at 30 degree for 3 days.
Genomic DNA samples were prepared from these two pools of freshly generated haploid cells and used as the templates for PCR amplification of the TAGs identifying the YKOs with a pair of primers universal for either Uptags or Downtags.
The PCR products from sample1 were labeled with Cy5 and those from sample2 with Cy3.
The Cy5- and Cy3-labeled Uptags and Downtags were mixed together and hybridized to a Hopkins-TagArray.
Fluorescent array images were collected for both Cy5 and Cy3 with a GenePix4000B microarray scanner.
The image data was annalyzed with a GenePix5.1 program.
Keywords = 15 microgram/ml, benomyl, heterozygotes, YKO

source_name: 15 microgram/ml benomyl


title: A263insGG_mut4a-

description:
A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factors can be identified. This entry corresponds to the RNA isolated from uninduced INS-1 cell line #4a containing MODY5 mutant A263insGG of hepatocyte nuclear factor-1b (HNF1b).
Keywords = INS-1
Keywords = beta-cell
Keywords = HNF1b
Keywords = A263insGG
Keywords = MODY5
Keywords = tetracycline
Keywords = FRT

source_name: INS-1 cell line #4a with non-induced HNF1b mutant A263insGG


title: Postnatal day 1, mouse 2


title: Postnatal day 1, mouse 3


title: 10 microgram/ml benomyl

description:
A pool of 5,896 haploid-convertible heterozygous diploid yeast knockout (YKO) strains were sporulated
A pool of isogenic haploid MATa cells were obtained by selection on a magic medium with (sample2) or without (sample1) 10 microgram/ml of benomyl at 30 degree for 2 days.
Genomic DNA samples were prepared from these two pools of freshly generated haploid cells and used as the templates for PCR amplification of the TAGs identifying the YKOs with a pair of primers universal for either Uptags or Downtags.
The PCR products from sample1 were labeled with Cy5 and those from sample2 with Cy3.
The Cy5- and Cy3-labeled Uptags and Downtags were mixed together and hybridized to a Hopkins-TagArray.
Fluorescent array images were collected for both Cy5 and Cy3 with a GenePix4000B microarray scanner.
The image data was annalyzed with a GenePix5.1 program.
Keywords = 10 microgram/ml, benomyl, heterozygotes, YKO

source_name: 10 microgram/ml benomyl


title: sgs1D dSLAM UpTag experiment1

description:
A pool of 5,896 haploid-convertible heterozygous diploid yeast knockout (YKO) strains were transformed with a sgs1D::URA3 cassette.
The resultant diploid double YKO pool was sporulated and the spores were spread on MM with 0.1% 5-FOA (as target source1) and MM-Ura (as target source2).
Pools of haploid YKOs were harvested after incubation at 30 degree for 2 days.
Genomic DNA samples were prepared from these two haploid pools and used as the templates for PCR amplification of the TAGs identifying the YKOs with a pair of primers universal for either Uptags or Downtags.
The PCR products from sample1 were labeled with Cy5 and those from sample2 with Cy3.
The Cy5- and Cy3-labeled Uptags and Downtags were mixed together and hybridized to a Rosetta_UpTag.
Fluorescent array images were collected for both Cy5 and Cy3 with a GenePix4000B microarray scanner.
The image data was annalyzed with the Imagene 5.0 and Genesight 3.1 programs from Biodiscovery.
Keywords = sgs1D, dSLAM, heterozygotes, YKO

source_name: Pool of haploid single YKOs

source_name: Pool of haploid double YKOs


title: sgs1D dSLAM UpTag experiment2


title: INS-1 cell line (FLP-In T-REx clone #1-1.2)

description:
Starting with the rat insulinoma cell line INS-1, clones were generated that contain a FRT site for site specific integration of specific genes (INS-1 Flp-In T-REx). In addition, the clones contain the tetracycline repressor allowing tetracycline (tet) induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factor can be identified. This entry corresponds to the RNA isolated from the INS-1 cell line #1-1.2
Keywords = INS-1
Keywords = b-cell
Keywords = Flp-In T-Rex
Keywords = tetracycline
Keywords = FRT

source_name: INS-1 cell line, clone #1-1.2


title: INS-1

description:
Starting with the rat insulinoma cell line INS-1, clones were generated that contain a FRT site for site specific integration of specific genes. In addition, the clones contain the tetracycline repressor allowing tetracycline (tet) induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factor can be identified. This entry corresponds to the RNA isolated from the parental INS-1 cell line.
Keywords = INS-1
Keywords = beta-cell
Keywords = insulinoma

source_name: INS-1 cell line (parental)


title: bim1D dSLAM UpTag experiment2

description:
A pool of 5,896 haploid-convertible heterozygous diploid yeast knockout (YKO) strains were transformed with a bim1D::URA3 cassette.
The resultant diploid double YKO pool was sporulated and the spores were spread on MM with 0.1% 5-FOA (as target source1) and MM-Ura (as target source2).
Pools of haploid YKOs were harvested after incubation at 30 degree for 2 days.
Genomic DNA samples were prepared from these two haploid pools and used as the templates for PCR amplification of the TAGs identifying the YKOs with a pair of primers universal for either Uptags or Downtags.
The PCR products from sample1 were labeled with Cy5 and those from sample2 with Cy3.
The Cy5- and Cy3-labeled Uptags and Downtags were mixed together and hybridized to a Rosetta_UpTag.
Fluorescent array images were collected for both Cy5 and Cy3 with a GenePix4000B microarray scanner.
The image data was annalyzed with the Imagene 5.0 and Genesight 3.1 programs from Biodiscovery.
Keywords = bim1D, dSLAM, heterozygotes, YKO


title: 5 microgram/ml benomyl

description:
A pool of 5,896 haploid-convertible heterozygous diploid yeast knockout (YKO) strains were sporulated
A pool of isogenic haploid MATa cells were obtained by selection on a magic medium with (sample2) or without (sample1) 5 microgram/ml of benomyl at 30 degree for 2 days.
Genomic DNA samples were prepared from these two pools of freshly generated haploid cells and used as the templates for PCR amplification of the TAGs identifying the YKOs with a pair of primers universal for either Uptags or Downtags.
The PCR products from sample1 were labeled with Cy5 and those from sample2 with Cy3.
The Cy5- and Cy3-labeled Uptags and Downtags were mixed together and hybridized to a Hopkins-TagArray.
Fluorescent array images were collected for both Cy5 and Cy3 with a GenePix4000B microarray scanner.
The image data was annalyzed with a GenePix5.1 program.
Keywords = 5 microgram/ml, benomyl, heterozygotes, YKO

source_name: 5 microgram/ml benomyl


title: 35 microgram/ml benomyl

description:
A pool of 5,896 haploid-convertible heterozygous diploid yeast knockout (YKO) strains were sporulated
A pool of isogenic haploid MATa cells were obtained by selection on a magic medium with (sample2) or without (sample1) 35 microgram/ml of benomyl at 30 degree for 4 days.
Genomic DNA samples were prepared from these two pools of freshly generated haploid cells and used as the templates for PCR amplification of the TAGs identifying the YKOs with a pair of primers universal for either Uptags or Downtags.
The PCR products from sample1 were labeled with Cy5 and those from sample2 with Cy3.
The Cy5- and Cy3-labeled Uptags and Downtags were mixed together and hybridized to a Hopkins-TagArray.
Fluorescent array images were collected for both Cy5 and Cy3 with a GenePix4000B microarray scanner.
The image data was annalyzed with a GenePix5.1 program.
Keywords = 35 microgram/ml, benomyl, heterozygotes, YKO

source_name: 35 microgram/ml benomyl


title: 20 microgram/ml benomyl

description:
A pool of 5,896 haploid-convertible heterozygous diploid yeast knockout (YKO) strains were sporulated
A pool of isogenic haploid MATa cells were obtained by selection on a magic medium with (sample2) or without (sample1) 20 microgram/ml of benomyl at 30 degree for 4 days.
Genomic DNA samples were prepared from these two pools of freshly generated haploid cells and used as the templates for PCR amplification of the TAGs identifying the YKOs with a pair of primers universal for either Uptags or Downtags.
The PCR products from sample1 were labeled with Cy5 and those from sample2 with Cy3.
The Cy5- and Cy3-labeled Uptags and Downtags were mixed together and hybridized to a Hopkins-TagArray.
Fluorescent array images were collected for both Cy5 and Cy3 with a GenePix4000B microarray scanner.
The image data was annalyzed with a GenePix5.1 program.
Keywords = 20 microgram/ml, benomyl, heterozygotes, YKO

source_name: no benomyl

source_name: 20 microgram/ml benomyl


title: bim1D dSLAM UpTag experiment1

description:
A pool of 5,896 haploid-convertible heterozygous diploid yeast knockout (YKO) strains were transformed with a ura3D::URA3 (as target source1) or a bim1D::URA3 (as target source2) cassette.
The resultant pools of Ura+ transformants were sporulated and spores were spread on MM-Ura.
Pools of Ura+ haploid YKOs were harvested after incubation at 30 degree for 2 days.
Genomic DNA samples were prepared from these two haploid pools and used as the templates for PCR amplification of the TAGs identifying the YKOs with a pair of primers universal for either Uptags or Downtags.
The PCR products from sample1 were labeled with Cy5 and those from sample2 with Cy3.
The Cy5- and Cy3-labeled Uptags and Downtags were mixed together and hybridized to a Rosetta_UpTag.
Fluorescent array images were collected for both Cy5 and Cy3 with a GenePix4000B microarray scanner.
The image data was annalyzed with the Imagene 5.0 and Genesight 3.1 programs from Biodiscovery.
Keywords = bim1D, dSLAM, heterozygotes, YKO

source_name: Pool of haploid single YKOs result from ura3D::URA3 transfromation and sporulation

source_name: Pool of haploid double YKOs result from bim1D::URA3 transformation and sporulation


title: No benomyl

description:
A pool of 5,896 haploid-convertible heterozygous diploid yeast knockout (YKO) strains were sporulated.
A pool of isogenic haploid MATa cells were obtained by selection on a magic medium without the drug benomyl at 30 degree for 2 days.
Genomic DNA was prepared from this pool of freshly generated haploid cells and used as the template for PCR amplification of the TAGs identifying the YKOs with a pair of primers universal for either Uptags or Downtags.
The PCR products from sample1 or sample2 were differentially labeled with Cy5 or Cy3.
The Cy5- and Cy3-labeled Uptags and Downtags were mixed together and hybridized to a Hopkins-TagArray.
Fluorescent array images were collected for both Cy5 and Cy3 with a GenePix4000B microarray scanner.
The image data was annalyzed with a GenePix5.1 program.
Keywords = benomyl, heterozygote, YKO


title: 1 microgram/ml benomyl

description:
A pool of 5,896 haploid-convertible heterozygous diploid yeast knockout (YKO) strains were sporulated
A pool of isogenic haploid MATa cells were obtained by selection on a magic medium with (sample2) or without (sample1) 1 microgram/ml of benomyl at 30 degree for 2 days.
Genomic DNA samples were prepared from these two pools of freshly generated haploid cells and used as the templates for PCR amplification of the TAGs identifying the YKOs with a pair of primers universal for either Uptags or Downtags.
The PCR products from sample1 were labeled with Cy5 and those from sample2 with Cy3.
The Cy5- and Cy3-labeled Uptags and Downtags were mixed together and hybridized to a Hopkins-TagArray.
Fluorescent array images were collected for both Cy5 and Cy3 with a GenePix4000B microarray scanner.
The image data was annalyzed with a GenePix5.1 program.
Keywords = 1 microgram/ml, benomyl, heterozygotes, YKO

source_name: 1 microgram/ml benomyl


title: P328L329_del6a+

description:
A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factors can be identified. This entry corresponds to the RNA isolated from tet-induced INS-1 cell line #6a containing MODY5 mutant P328L329delCCTCT of hepatocyte nuclear factor-1b (HNF1b).
Keywords = INS-1
Keywords = beta-cell
Keywords = HNF1b
Keywords = P328L329
Keywords = MODY5
Keywords = tetracycline
Keywords = FRT

source_name: INS-1 cell line #6a with induced HNF1b mutant P328L329del


title: CO/LPS 60 min

city: Vienna

first: Martin

last: Bilban

country: Austria

institute: Medical University of Vienna

description:
RAW 264.7 cells pre-treated with carbon monoxide (250 ppm) for 3 hrs followed by addition of LPS for 60 min
Keywords = macrophage
Keywords = LPS
Keywords = inflammation

source_name: macrophage


title: CO/LPS 120 min

description:
RAW 264.7 cells pre-treated with carbon monoxide (250 ppm) for 3 hrs followed by addition of LPS for 120 min
Keywords = macrophage
Keywords = LPS
Keywords = inflammation


title: Postnatal day 1, mouse 1

description:
Identification of hair cycle-associated genes from
time-course gene expression profile data by using
replicate variance. Proc. Natl. Acad. Sci. USA (2004)
Lot batch =

source_name: whole RNA from back skin


title: HNF6_2-

description:
A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and induced cells, target genes of introduced transcription factor can be identified. This entry corresponds to the RNA isolated from uninduced INS-1 cell line #2 containing hepatocyte nuclear factor-6 (HNF6; onecut1).
Keywords = INS-1
Keywords = beta-cell
Keywords = HNF6
Keywords = onecut1
Keywords = tetracycline
Keywords = FRT

source_name: INS-1 cell line #2 with non-induced HNF6


title: P328L329_del5a+

description:
A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factors can be identified. This entry corresponds to the RNA isolated from tet-induced INS-1 cell line #5a containing MODY5 mutant P328L329delCCTCT of hepatocyte nuclear factor-1b (HNF1b).
Keywords = INS-1
Keywords = beta-cell
Keywords = HNF1b
Keywords = P328L329
Keywords = MODY5
Keywords = tetracycline
Keywords = FRT

source_name: INS-1 cell line #5a with induced HNF1b mutant P328L329del


title: CO/LPS 30 min

description:
RAW 264.7 cells pre-treated with carbon monoxide (250 ppm) for 3 hrs followed by addition of LPS for 30 min
Keywords = macrophage
Keywords = LPS
Keywords = inflammation


title: A263insGG_mut3b+

description:
A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factors can be identified. This entry corresponds to the RNA isolated from tet-induced INS-1 cell line #3b containing MODY5 mutant A263insGG of hepatocyte nuclear factor-1b (HNF1b).
Keywords = INS-1
Keywords = beta-cell
Keywords = HNF1b
Keywords = A263insGG
Keywords = MODY5
Keywords = tetracycline
Keywords = FRT

source_name: INS-1 cell line #3b with induced HNF1b mutant A263insGG


title: A263insGG_mut4a+

description:
A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factors can be identified. This entry corresponds to the RNA isolated from tet-induced INS-1 cell line #4a containing MODY5 mutant A263insGG of hepatocyte nuclear factor-1b (HNF1b).
Keywords = INS-1
Keywords = beta-cell
Keywords = HNF1b
Keywords = A263insGG
Keywords = MODY5
Keywords = tetracycline
Keywords = FRT

source_name: INS-1 cell line #4a with induced HNF1b mutant A263insGG


title: CO/LPS 240 min

description:
RAW 264.7 cells pre-treated with carbon monoxide (250 ppm) for 3 hrs followed by addition of LPS for 240 min
Keywords = macrophage
Keywords = LPS
Keywords = inflammation


title: pool transformation

description:
A pool of 5,896 original heterozygous diploid yeast knockout (YKO) strains were transformed with a can1D::LEU2-MFA1pr-HIS3 cassette.
The resultant transformants were pooled after growth on SC-Leu medium for 2 days.
Genomic DNA samples were prepared from this transformant pool (as target source2) as well as the starting pool before transformation (as target source1).
These two genomic DNA samples were used as the templates for PCR amplification of the TAGs identifying the YKOs with a pair of primers universal for either Uptags or Downtags.
The PCR products from sample1 were labeled with Cy5 and those from sample2 with Cy3.
The Cy5- and Cy3-labeled Uptags and Downtags were mixed together and hybridized to a Rosetta_UpTag.
Fluorescent array images were collected for both Cy5 and Cy3 with a GenePix4000B microarray scanner.
The image data was annalyzed with the Imagene 5.0 and Genesight 3.1 programs from Biodiscovery.
Keywords = pool, transformation, heterozygotes, YKO

source_name: Pool of heterozygote YKOs before transfromation

source_name: Pool of heterozygote YKOs after transfromation


title: P328L329_del6a-

description:
A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factors can be identified. This entry corresponds to the RNA isolated from uninduced INS-1 cell line #6a containing MODY5 mutant P328L329delCCTCT of hepatocyte nuclear factor-1b (HNF1b).
Keywords = INS-1
Keywords = beta-cell
Keywords = HNF1b
Keywords = P328L329
Keywords = MODY5
Keywords = tetracycline
Keywords = FRT

source_name: INS-1 cell line #6a with non-induced HNF1b mutant P328L329del


title: P328L329_del5a-

description:
A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factor can be identified. This entry corresponds to the RNA isolated from uninduced INS-1 cell line #5a containing MODY5 mutant P328L329delCCTCT of hepatocyte nuclear factor-1b (HNF1b).
Keywords = INS-1
Keywords = beta-cell
Keywords = HNF1b
Keywords = P328L329
Keywords = MODY5
Keywords = tetracycline
Keywords = FRT

source_name: INS-1 cell line #5a with non-induced HNF1b mutant P328L329del


title: A263insGG_mut3b-

description:
A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factors can be identified. This entry corresponds to the RNA isolated from uninduced INS-1 cell line #3b containing MODY5 mutant A263insGG of hepatocyte nuclear factor-1b (HNF1b).
Keywords = INS-1
Keywords = beta-cell
Keywords = HNF1b
Keywords = A263insGG
Keywords = MODY5
Keywords = tetracycline
Keywords = FRT

source_name: INS-1 cell line #3b with non-induced HNF1b mutant A263insGG


title: HNF6_1+

description:
A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and induced cells, target genes of introduced transcription factor can be identified. This entry corresponds to the RNA isolated from tet-induced INS1 cell line #1 containing hepatocyte nuclear factor-6 (HNF6; onecut1).
Keywords = INS-1
Keywords = beta-cell
Keywords = HNF6
Keywords = onecut1
Keywords = tetracycline
Keywords = FRT

source_name: INS-1 cell line #1 with induced HNF6


title: LPS 240 min

description:
RAW 264.7 cells treated in a time series with LPS, 10ng/ml
Keywords = macrophage
Keywords = LPS
Keywords = inflammation


title: HNF4a2_2+

description:
A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and induced cells, target genes of introduced transcription factor can be identified. This entry corresponds to the RNA isolated from tet-induced INS-1 cell line #2 containing hepatocyte nuclear factor-4a2 (HNF4a2).
Keywords = INS-1
Keywords = beta-cell
Keywords = HNF4a
Keywords = tetracycline
Keywords = FRT

source_name: INS-1 cell line #2 with induced HNF4a2


title: CO/LPS 15 min

description:
RAW 264.7 cells pre-treated with carbon monoxide (250 ppm) for 3 hrs followed by addition of LPS for 15 min
Keywords = macrophage
Keywords = LPS
Keywords = inflammation


title: HNF6_2+

description:
A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and induced cells, target genes of introduced transcription factor can be identified. This entry corresponds to the RNA isolated from tet-induced INS-1 cell line #2 containing hepatocyte nuclear factor-6 (HNF6; onecut1).
Keywords = INS-1
Keywords = beta-cell
Keywords = HNF6
Keywords = onecut1
Keywords = tetracycline
Keywords = FRT

source_name: INS-1 cell line #2 with induced HNF6


title: HNF6_1-

description:
A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and induced cells, target genes of introduced transcription factor can be identified. This entry corresponds to the RNA isolated from uninduced INS-1 cell line #1 containing hepatocyte nuclear factor-6 (HNF6; onecut1).
Keywords = INS-1
Keywords = beta-cell
Keywords = HNF6
Keywords = onecut1
Keywords = tetracycline
Keywords = FRT

source_name: INS-1 cell line #1 with non-induced HNF6


title: CO/LPS 0 min

description:
RAW 264.7 cells pre-treated with carbon monoxide (250 ppm) for 3 hrs followed by addition of LPS for 0 min
Keywords = macrophage
Keywords = LPS
Keywords = inflammation


title: T98G ASYN replicate 1

city: New York

first: Brian

last: Dynlacht

state: NY

address: 550 First Avenue

department: Pathology

institute: NYU Cancer Institute

description:
RNA from asynchronously growing T98G cells was extracted using Trizol.
Keywords = T98G
Keywords = asynchronous
Keywords = growing
Keywords = growth arrest

source_name: T98G cells


title: T98G ASYN replicate 2


title: pool sporulation

description:
A pool of 5,896 haploid-convrtible heterozygote diploid yeast knockout (YKO) strains haboring the can1D::LEU2-MFA1pr-HIS3 cassette was sporulated.
The spores were spread on the haploid selection magic medium (MM) and incubated at 30 degree for 2 days.
Genomic DNA samples were prepared from this freshly converted haploid pool (as target source2) as well as the heterozygote diploid pool before sporulation (as target source1).
These two genomic DNA samples were used as the templates for PCR amplification of the TAGs identifying the YKOs with a pair of primers universal for either Uptags or Downtags.
The PCR products from sample1 were labeled with Cy5 and those from sample2 with Cy3.
The Cy5- and Cy3-labeled Uptags and Downtags were mixed together and hybridized to a Rosetta_UpTag.
Fluorescent array images were collected for both Cy5 and Cy3 with a GenePix4000B microarray scanner.
The image data was annalyzed with the Imagene 5.0 and Genesight 3.1 programs from Biodiscovery.
Keywords = pool, sporulation, heterozygotes, YKO

source_name: Pool of haploid-convertible heterozygote diploid YKOs

source_name: Pool of freshly converted haploid YKOs


title: T98G G0 replicate 3

description:
T98G cells arrested by serum deprivation for 3 days, and RNA was extracted using Trizol.
Keywords = T98G
Keywords = G0
Keywords = serum deprivation
Keywords = growth arrest


title: HNF4a2_2-

description:
A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and induced cells, target genes of introduced transcription factor can be identified. This entry corresponds to the RNA isolated from uninduced INS-1 cell line #2 containing hepatocyte nuclear factor-4a2 (HNF4a2).
Keywords = INS-1
Keywords = b-cell
Keywords = HNF4a
Keywords = tetracycline
Keywords = FRT

source_name: INS-1 cell line #2 with non-induced HNF4a2


title: T98G ASYN replicate 3


title: HNF4a2_1+

description:
A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factor can be identified. This entry corresponds to the RNA isolated from tet-induced INS-1 cell line #1 containing hepatocyte nuclear factor-4a2 (HNF4a2).
Keywords = INS-1
Keywords = beta-cell
Keywords = HNF4a
Keywords = tetracycline
Keywords = FRT

source_name: INS-1 cell line #1 with induced HNF4a2


title: JPP 4 dye-swap vs.  j-MLN

city: St. Paul

first: Kendra

middle: A.

last: Hyland

state: MN

address: 1971 Commonwealth Ave.

department: Veterinary and Biomedical Sciences

institute: University of Minneosta

description:
Four juvenile Yorkshire-Landrace outbred pigs, 6 to 7 weeks of age (approximately 15 kg), were obtained from a farm negative for swine influenza virus (H1N1 and H3N3), porcine reproductive and respiratory syndrome virus (PRRSV), Mycoplasma hyopneumoniae, psuedorabies virus, transmissible gastroenteritis virus, and parvovirus. The pigs were anesthetized by intramuscular injection of tiletamine hydrochloride-zolazepam (Telazol, 8 mg/kg; Fort Dodge Laboratories, Inc., Fort Dodge, IA) and were sacrificed with intravenous Beuthanasia-D Special (0.5 ml/kg; Schering-Plough Animal Health, Union, NJ) in accordance with approved University of Minnesota IACUC protocols.  Segments of jejunum containing Peyer's patches were removed and placed in ice-cold PBS.  Intestinal segments were incised longitudinally along the mesenteric border and stripped of circular and longitudinal muscle layers by blunt dissection.  Tissues were stored in RNAlater (Ambion, Austin, TX, USA) at -20 C.
Three different JPPs were pooled from each animal during total RNA isolation, using a Qiagen RNeasy kit (Qiagen Inc., Valencia, CA).. RNA quality was verified on an Agilent Bioanalyzer (Agilent Technologies, Carmel, IN) and examination of the 28S/18S rRNA ratio.  RNA with a ratio less than 1.0 was excluded, and high quality RNA was quantified by spectrophotometry.  RNA from juvenile pig jejunal mesenteric lymph node (j-MLN) was pooled from all animals in the study for a standard reference sample.
Pobes were prepared using the SuperScript Indirect cDNA Labeling System kit (Invitrogen Corporation, Carlsbad, CA, USA).  Seven to ten ?g of total RNA was reversed-transcribed along with positive mRNA controls in fixed ratios (ArrayControl System, Ambion, Austin, TX).  Purified cDNA was coupled separately to monoreactive fluorescent dyes Cy3 and Cy5 (Amersham Biosciences, Piscataway, NJ).  Purified dye-labeled cDNA was mixed with a hybridization buffer to a final concentration of 3.3X SSC, 1.6 mg/ml PolyA and 0.3% SDS in 70 microliter, boiled for 2 min and cooled briefly at room temperature.  A LifterSlip (Erie Scientific, Portsmouth, NH, USA) was placed over the DNA targets, and the dye-labeled probe was hybridized for 5 to 16 h in a sealed hybridization cassette at 63 C.  After hybridization, the slides were washed in solutions at 42 C, first in 0.6x SSC and 0.03% SDS, and then in 0.06x SSC, each for 5 min.
Slides were scanned by a ScanArray 5000 laser scanner (PerkinElmer, Boston, MA, USA) with ScanArray software at 10 ?m resolution.  Images were quantified with QuantArray software version 3 (PerkinElmer, Boston, MA) using the adaptive method to calculate the mean spot intensity and mean background intensity.
External controls: These exogenous mRNAs were added to the probes (Ambion, Austin, TX, USA).  Cy5 labeled probe: ArrayControl1 (30 pg), ArrayControl2 (500 pg), ArrayControl3 (200 pg), ArrayControl4 (80 pg), ArrayControl5 (50 pg), ArrayControl6 (90 pg), ArrayControl7 (200 pg), ArrayControl8 (50 pg). Cy3 labeled probe: ArrayControl1 (300 pg), ArrayControl2 (50 pg), ArrayControl3 (40 pg), ArrayControl4 (400 pg), ArrayControl5 (150 pg), ArrayControl6 (30 pg), ArrayControl7 (200 pg), ArrayControl8 (50 pg).
Sample_age: 4-6 weeks
Sample_dye_swap: JPP (Cy3)/ j-MLN (Cy5)
Sample_health_status: healthy, untreated
Sample_sex: female
Keywords = JPP, pig, small intestine
Lot batch =

organism: Sus scrofa

source_name: JPP Pig4

source_name: pool of jejunal MLN


title: LPS 60 min

source_name: macrophage


title: HNF1b_2b+

description:
A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factors can be identified. This entry corresponds to the RNA isolated from tet-induced INS-1 cell line #2b containing hepatocyte nuclear factor-1b (HNF1b).
Keywords = INS-1
Keywords = beta-cell
Keywords = HNF1b
Keywords = tetracycline
Keywords = FRT

source_name: INS-1 cell line #2b with induced HNF1b


title: LPS 120 min


title: T98G CI replicate 3

description:
T98G cells arrested by contact inhibition for 3 days, and RNA was extracted using Trizol.
Keywords = T98G
Keywords = CI
Keywords = contact inhibition
Keywords = growth arrest


title: HNF4a2_1-

description:
A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factor can be identified. This entry corresponds to the RNA isolated from uninduced INS-1 cell line #1 containing hepatocyte nuclear factor-4a2 (HNF4a2).
Keywords = INS-1
Keywords = beta-cell
Keywords = HNF4a
Keywords = tetracycline
Keywords = FRT

source_name: INS-1 cell line #1 with non-induced HNF4a2


title: JPP 2 dye-swap vs.  j-MLN

source_name: JPP Pig2


title: T98G CI replicate 2


title: JPP 4 vs.  j-MLN

description:
Four juvenile Yorkshire-Landrace outbred pigs, 6 to 7 weeks of age (approximately 15 kg), were obtained from a farm negative for swine influenza virus (H1N1 and H3N3), porcine reproductive and respiratory syndrome virus (PRRSV), Mycoplasma hyopneumoniae, psuedorabies virus, transmissible gastroenteritis virus, and parvovirus. The pigs were anesthetized by intramuscular injection of tiletamine hydrochloride-zolazepam (Telazol, 8 mg/kg; Fort Dodge Laboratories, Inc., Fort Dodge, IA) and were sacrificed with intravenous Beuthanasia-D Special (0.5 ml/kg; Schering-Plough Animal Health, Union, NJ) in accordance with approved University of Minnesota IACUC protocols.  Segments of jejunum containing Peyer's patches were removed and placed in ice-cold PBS.  Intestinal segments were incised longitudinally along the mesenteric border and stripped of circular and longitudinal muscle layers by blunt dissection.  Tissues were stored in RNAlater (Ambion, Austin, TX, USA) at -20 C.
Three different JPPs were pooled from each animal during total RNA isolation, using a Qiagen RNeasy kit (Qiagen Inc., Valencia, CA).. RNA quality was verified on an Agilent Bioanalyzer (Agilent Technologies, Carmel, IN) and examination of the 28S/18S rRNA ratio.  RNA with a ratio less than 1.0 was excluded, and high quality RNA was quantified by spectrophotometry.  RNA from juvenile pig jejunal mesenteric lymph node (j-MLN) was pooled from all animals in the study for a standard reference sample.
Pobes were prepared using the SuperScript Indirect cDNA Labeling System kit (Invitrogen Corporation, Carlsbad, CA, USA).  Seven to ten ?g of total RNA was reversed-transcribed along with positive mRNA controls in fixed ratios (ArrayControl System, Ambion, Austin, TX).  Purified cDNA was coupled separately to monoreactive fluorescent dyes Cy3 and Cy5 (Amersham Biosciences, Piscataway, NJ).  Purified dye-labeled cDNA was mixed with a hybridization buffer to a final concentration of 3.3X SSC, 1.6 mg/ml PolyA and 0.3% SDS in 70 microliter, boiled for 2 min and cooled briefly at room temperature.  A LifterSlip (Erie Scientific, Portsmouth, NH, USA) was placed over the DNA targets, and the dye-labeled probe was hybridized for 5 to 16 h in a sealed hybridization cassette at 63 C.  After hybridization, the slides were washed in solutions at 42 C, first in 0.6x SSC and 0.03% SDS, and then in 0.06x SSC, each for 5 min.
Slides were scanned by a ScanArray 5000 laser scanner (PerkinElmer, Boston, MA, USA) with ScanArray software at 10 ?m resolution.  Images were quantified with QuantArray software version 3 (PerkinElmer, Boston, MA) using the adaptive method to calculate the mean spot intensity and mean background intensity.
External controls: These exogenous mRNAs were added to the probes (Ambion, Austin, TX, USA).  Cy5 labeled probe: ArrayControl1 (395 pg), ArrayControl2 (100 pg), ArrayControl3 (150 pg), ArrayControl4 (100 pg), ArrayControl5 (465 pg), ArrayControl6 (100 pg), ArrayControl7 (135 pg), ArrayControl8 (20 pg). Cy3 labeled probe: ArrayControl1 (50 pg), ArrayControl2 (10 pg), ArrayControl3 (50 pg), ArrayControl4 (20 pg), ArrayControl5 (20 pg), ArrayControl6 (40 pg), ArrayControl7 (20 pg), ArrayControl8 (20
Sample_age: 4-6 weeks
Sample_dye_swap: JPP (Cy5)/ j-MLN (Cy3)
Sample_health_status: healthy, untreated
Sample_sex: female
Keywords = JPP, pig, small intestine
Lot batch =


title: JPP 3 vs.  j-MLN

description:
Four juvenile Yorkshire-Landrace outbred pigs, 6 to 7 weeks of age (approximately 15 kg), were obtained from a farm negative for swine influenza virus (H1N1 and H3N3), porcine reproductive and respiratory syndrome virus (PRRSV), Mycoplasma hyopneumoniae, psuedorabies virus, transmissible gastroenteritis virus, and parvovirus. The pigs were anesthetized by intramuscular injection of tiletamine hydrochloride-zolazepam (Telazol, 8 mg/kg; Fort Dodge Laboratories, Inc., Fort Dodge, IA) and were sacrificed with intravenous Beuthanasia-D Special (0.5 ml/kg; Schering-Plough Animal Health, Union, NJ) in accordance with approved University of Minnesota IACUC protocols.  Segments of jejunum containing Peyer's patches were removed and placed in ice-cold PBS.  Intestinal segments were incised longitudinally along the mesenteric border and stripped of circular and longitudinal muscle layers by blunt dissection.  Tissues were stored in RNAlater (Ambion, Austin, TX, USA) at -20 C.
Three different JPPs were pooled from each animal during total RNA isolation, using a Qiagen RNeasy kit (Qiagen Inc., Valencia, CA).. RNA quality was verified on an Agilent Bioanalyzer (Agilent Technologies, Carmel, IN) and examination of the 28S/18S rRNA ratio.  RNA with a ratio less than 1.0 was excluded, and high quality RNA was quantified by spectrophotometry.  RNA from juvenile pig jejunal mesenteric lymph node (j-MLN) was pooled from all animals in the study for a standard reference sample.
Pobes were prepared using the SuperScript Indirect cDNA Labeling System kit (Invitrogen Corporation, Carlsbad, CA, USA).  Seven to ten ?g of total RNA was reversed-transcribed along with positive mRNA controls in fixed ratios (ArrayControl System, Ambion, Austin, TX).  Purified cDNA was coupled separately to monoreactive fluorescent dyes Cy3 and Cy5 (Amersham Biosciences, Piscataway, NJ).  Purified dye-labeled cDNA was mixed with a hybridization buffer to a final concentration of 3.3X SSC, 1.6 mg/ml PolyA and 0.3% SDS in 70 microliter, boiled for 2 min and cooled briefly at room temperature.  A LifterSlip (Erie Scientific, Portsmouth, NH, USA) was placed over the DNA targets, and the dye-labeled probe was hybridized for 5 to 16 h in a sealed hybridization cassette at 63 C.  After hybridization, the slides were washed in solutions at 42 C, first in 0.6x SSC and 0.03% SDS, and then in 0.06x SSC, each for 5 min.
Slides were scanned by a ScanArray 5000 laser scanner (PerkinElmer, Boston, MA, USA) with ScanArray software at 10 ?m resolution.  Images were quantified with QuantArray software version 3 (PerkinElmer, Boston, MA) using the adaptive method to calculate the mean spot intensity and mean background intensity.
External controls: These exogenous mRNAs were added to the probes (Ambion, Austin, TX, USA).  Cy5 labeled probe: ArrayControl1 (395 pg), ArrayControl2 (100 pg), ArrayControl3 (150 pg), ArrayControl4 (100 pg), ArrayControl5 (465 pg), ArrayControl6 (100 pg), ArrayControl7 (135 pg), ArrayControl8 (20 pg). Cy3 labeled probe: ArrayControl1 (50 pg), ArrayControl2 (10 pg), ArrayControl3 (50 pg), ArrayControl4 (20 pg), ArrayControl5 (20 pg), ArrayControl6 (40 pg), ArrayControl7 (20 pg), ArrayControl8 (20 pg).
Sample_age: 4-6 weeks
Sample_dye_swap: JPP (Cy5)/ j-MLN (Cy3)
Sample_health_status: healthy, untreated
Sample_sex: male
Keywords = JPP, pig, small intestine
Lot batch =

source_name: JPP Pig3


title: T98G G0 replicate 2


title: LPS 30 min

description:
RAW 264.7 cells treated in a time series with LPS, 10ng/ml
Keywords = macrophage
Keywords = LPS
Keywords = inflammation


title: T98G CI replicate 1


title: LPS 15 min


title: LPS 0 min


title: HNF1b_1a+

description:
A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factors can be identified. This entry corresponds to the RNA isolated from tet-induced INS-1 cell line #1a containing hepatocyte nuclear factor-1b (HNF1b).
Keywords = INS-1
Keywords = beta-cell
Keywords = HNF1b
Keywords = tetracycline
Keywords = FRT

source_name: INS-1 cell line #1a with induced HNF1b


title: T98G G0 replicate 1

description:
T98G cells arrested by serum deprivation for 3 days, and RNA was extracted using Trizol.
Keywords = T98G
Keywords = G0
Keywords = growth arrest


title: HNF1b_2b-

description:
A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factors can be identified. This entry corresponds to the RNA isolated from uninduced INS-1 cell line #2b containing hepatocyte nuclear factor-1b (HNF1b).
Keywords = INS-1
Keywords = beta-cell
Keywords = HNF1b
Keywords = tetracycline
Keywords = FRT

source_name: INS-1 cell line #2b with non-induced HNF1b


title: JPP vs.  j-MLN

description:
Four juvenile Yorkshire-Landrace outbred pigs, 6 to 7 weeks of age (approximately 15 kg), were obtained from a farm negative for swine influenza virus (H1N1 and H3N3), porcine reproductive and respiratory syndrome virus (PRRSV), Mycoplasma hyopneumoniae, psuedorabies virus, transmissible gastroenteritis virus, and parvovirus. The pigs were anesthetized by intramuscular injection of tiletamine hydrochloride-zolazepam (Telazol, 8 mg/kg; Fort Dodge Laboratories, Inc., Fort Dodge, IA) and were sacrificed with intravenous Beuthanasia-D Special (0.5 ml/kg; Schering-Plough Animal Health, Union, NJ) in accordance with approved University of Minnesota IACUC protocols.  Segments of jejunum containing Peyer's patches were removed and placed in ice-cold PBS.  Intestinal segments were incised longitudinally along the mesenteric border and stripped of circular and longitudinal muscle layers by blunt dissection.  Tissues were stored in RNAlater (Ambion, Austin, TX, USA) at -20 C.
Three different JPPs were pooled from each animal during total RNA isolation, using a Qiagen RNeasy kit (Qiagen Inc., Valencia, CA).. RNA quality was verified on an Agilent Bioanalyzer (Agilent Technologies, Carmel, IN) and examination of the 28S/18S rRNA ratio.  RNA with a ratio less than 1.0 was excluded, and high quality RNA was quantified by spectrophotometry.  RNA from juvenile pig jejunal mesenteric lymph node (j-MLN) was pooled from all animals in the study for a standard reference sample.
Pobes were prepared using the SuperScript Indirect cDNA Labeling System kit (Invitrogen Corporation, Carlsbad, CA, USA).  Seven to ten ?g of total RNA was reversed-transcribed along with positive mRNA controls in fixed ratios (ArrayControl System, Ambion, Austin, TX).  Purified cDNA was coupled separately to monoreactive fluorescent dyes Cy3 and Cy5 (Amersham Biosciences, Piscataway, NJ).  Purified dye-labeled cDNA was mixed with a hybridization buffer to a final concentration of 3.3X SSC, 1.6 mg/ml PolyA and 0.3% SDS in 70 microliter, boiled for 2 min and cooled briefly at room temperature.  A LifterSlip (Erie Scientific, Portsmouth, NH, USA) was placed over the DNA targets, and the dye-labeled probe was hybridized for 5 to 16 h in a sealed hybridization cassette at 63 C.  After hybridization, the slides were washed in solutions at 42 C, first in 0.6x SSC and 0.03% SDS, and then in 0.06x SSC, each for 5 min.
Slides were scanned by a ScanArray 5000 laser scanner (PerkinElmer, Boston, MA, USA) with ScanArray software at 10 ?m resolution.  Images were quantified with QuantArray software version 3 (PerkinElmer, Boston, MA) using the adaptive method to calculate the mean spot intensity and mean background intensity.
External controls: These exogenous mRNAs were added to the probes (Ambion, Austin, TX, USA).  Cy5 labeled probe: ArrayControl1 (395 pg), ArrayControl2 (100 pg), ArrayControl3 (150 pg), ArrayControl4 (100 pg), ArrayControl5 (465 pg), ArrayControl6 (100 pg), ArrayControl7 (135 pg), ArrayControl8 (20 pg). Cy3 labeled probe: ArrayControl1 (50 pg), ArrayControl2 (10 pg), ArrayControl3 (50 pg), ArrayControl4 (20 pg), ArrayControl5 (20 pg), ArrayControl6 (40 pg), ArrayControl7 (20 pg), ArrayControl8 (20 pg)
Sample_age: 4-6 weeks
Sample_dye_swap: JPP (Cy5)/ j-MLN (Cy3)
Sample_health_status: healthy, untreated
Sample_sex: male
Keywords = JPP, pig, small intestine
Lot batch =

source_name: JPP Pig1


title: Human bladder smooth muscle cells - non-stretched replicate 1

status: Public on Nov 04 2004

first: Rosalyn

last: Adam

address: 300 Longwood Avenue

department: Urology

institute: Children's Hospital Boston

description: Primary culture smooth muscle cells are explanted from human bladder biopsies obtained from children during open surgery for ureteral reimplantation. Cells are propagated in DMEM/10% FBS and are used between passages 3 and 5. Cells are seeded on silicone elastomer bottomed culture dishes coated with type I collagen. Non-stretched cells are maintained under identical culture conditions to cells subjected to cyclic-stretch relaxation but do not receive  the stretch stimulus. Total RNA is extracted from control and stretched cells using Trizol reagent and reverse-transcribed using Superscript II reverse transcriptase and T7-oligo dT as first-strand primer. Following clean-up cDNA was used as template for synthesis of biotin-labeled cRNA. Labeled cRNA was fragmented prior to hybridization to HG-U133A

source_name: Human bladder smooth muscle cells


title: Human bladder smooth muscle cells - stretched cells replicate 2

description: Primary culture smooth muscle cells are explanted from human bladder biopsies obtained from children during open surgery for ureteral reimplantation. Cells are propagated in DMEM/10% FBS and are used between passages 3 and 5. Cells are seeded on silicone elastomer bottomed culture dishes coated with type I collagen. Non-stretched cells are maintained under identical culture conditions to cells subjected to cyclic-stretch relaxation but do not receive  the stretch stimulus. Total RNA is extracted from control and stretched cells using Trizol reagent and reverse-transcribed using Superscript II reverse transcriptase and T7-oligo dT as first-strand primer. Following clean-up cDNA was used as template for synthesis of biotin-labeled cRNA. Labeled cRNA was fragmented prior to hybridization to HG-U133A.

source_name: Human bladder smooth muscle cells subjected to cyclic stretch-relaxation (20% elongation, 4h)


title: Human bladder smooth muscle cells - stretched cells replicate 1

source_name: Human bladder smooth muscle cells subjected to cyclic-stretch relaxation (20% elongation, 4h).


title: JPP 2 vs.  j-MLN

description:
Four juvenile Yorkshire-Landrace outbred pigs, 6 to 7 weeks of age (approximately 15 kg), were obtained from a farm negative for swine influenza virus (H1N1 and H3N3), porcine reproductive and respiratory syndrome virus (PRRSV), Mycoplasma hyopneumoniae, psuedorabies virus, transmissible gastroenteritis virus, and parvovirus. The pigs were anesthetized by intramuscular injection of tiletamine hydrochloride-zolazepam (Telazol, 8 mg/kg; Fort Dodge Laboratories, Inc., Fort Dodge, IA) and were sacrificed with intravenous Beuthanasia-D Special (0.5 ml/kg; Schering-Plough Animal Health, Union, NJ) in accordance with approved University of Minnesota IACUC protocols.  Segments of jejunum containing Peyer's patches were removed and placed in ice-cold PBS.  Intestinal segments were incised longitudinally along the mesenteric border and stripped of circular and longitudinal muscle layers by blunt dissection.  Tissues were stored in RNAlater (Ambion, Austin, TX, USA) at -20 C.
Three different JPPs were pooled from each animal during total RNA isolation, using a Qiagen RNeasy kit (Qiagen Inc., Valencia, CA).. RNA quality was verified on an Agilent Bioanalyzer (Agilent Technologies, Carmel, IN) and examination of the 28S/18S rRNA ratio.  RNA with a ratio less than 1.0 was excluded, and high quality RNA was quantified by spectrophotometry.  RNA from juvenile pig jejunal mesenteric lymph node (j-MLN) was pooled from all animals in the study for a standard reference sample.
Pobes were prepared using the SuperScript Indirect cDNA Labeling System kit (Invitrogen Corporation, Carlsbad, CA, USA).  Seven to ten ?g of total RNA was reversed-transcribed along with positive mRNA controls in fixed ratios (ArrayControl System, Ambion, Austin, TX).  Purified cDNA was coupled separately to monoreactive fluorescent dyes Cy3 and Cy5 (Amersham Biosciences, Piscataway, NJ).  Purified dye-labeled cDNA was mixed with a hybridization buffer to a final concentration of 3.3X SSC, 1.6 mg/ml PolyA and 0.3% SDS in 70 microliter, boiled for 2 min and cooled briefly at room temperature.  A LifterSlip (Erie Scientific, Portsmouth, NH, USA) was placed over the DNA targets, and the dye-labeled probe was hybridized for 5 to 16 h in a sealed hybridization cassette at 63 C.  After hybridization, the slides were washed in solutions at 42 C, first in 0.6x SSC and 0.03% SDS, and then in 0.06x SSC, each for 5 min.
Slides were scanned by a ScanArray 5000 laser scanner (PerkinElmer, Boston, MA, USA) with ScanArray software at 10 ?m resolution.  Images were quantified with QuantArray software version 3 (PerkinElmer, Boston, MA) using the adaptive method to calculate the mean spot intensity and mean background intensity.
ample_type: dual channel
External controls: These exogenous mRNAs were added to the probes (Ambion, Austin, TX, USA).  Cy5 labeled probe: ArrayControl1 (395 pg), ArrayControl2 (100 pg), ArrayControl3 (150 pg), ArrayControl4 (100 pg), ArrayControl5 (465 pg), ArrayControl6 (100 pg), ArrayControl7 (135 pg), ArrayControl8 (20 pg). Cy3 labeled probe: ArrayControl1 (50 pg), ArrayControl2 (10 pg), ArrayControl3 (50 pg), ArrayControl4 (20 pg), ArrayControl5 (20 pg), ArrayControl6 (40 pg), ArrayControl7 (20 pg), ArrayControl8 (20 pg).
Sample_age: 4-6 weeks
Sample_dye_swap: JPP (Cy5)/ j-MLN (Cy3)
Sample_health_status: healthy, untreated
Sample_sex: female
Keywords = JPP, pig, small intestine
Lot batch =

source_name: JPP Pig 2


title: Human bladder smooth muscle cells - stretched cells replicate 4


title: Human bladder smooth muscle cells - non-stretched replicate 3


title: Human bladder smooth muscle cells - stretched cells replicate 3


title: Human bladder smooth muscle cells - non-stretched replicate 2


title: chip#12274300

status: Public on Nov 03 2004

city: Toronto

first: Steven

middle: Edward

last: Bosinger

state: Ontario

address: 200 Elizabeth St.

department: Division of Experimental Therapeutics

country: Canada

institute: Toronto General Research Institute, University Health Network

description:
Experiment Design 1) Experiment Type normal vs diseased comparison, time course 2) Experimental Factor response to viral infection - SHIV89.6P 3) Number of hybridizations 60 4) Common Reference No 5) Quality Control Steps 4 technical replicate hybridizations per animal (3 replicate hybridizations for C89115M, C95067F) dual spotting of gene per array multiple spotting of select genes per array 2 biological replicates (2 different animals) per time point dye swaps 6) Experiment Description 4 cynomolgus monkeys (Macaca fascicularis) were infected with TCID50 of SHIV89.6P. Whole blood RNA was collected at 0, 1, 2, 4 and 5 weeks post-infection. Post-infection samples were competitively hybridized with pre-infected samples for each individual animal. Unpublished Data 7) Qualifier, value, source 2.2. Samples: samples used, extract preparation and labeling 2.2.1. Biosource properties 1) Organism (NCBI taxonomy) Macaca fascicularis 2) Contact details for sample Dr Erling W Rud Animal Resources Division, Health Canada. Sir Frederick Banting Research Centre Building 22, Room C308, postal locator 2203E Tunneys' Pasture Ottawa,Ontario, Canada K1A 0L2 Tel:(613) 957-8049 FAX:(613) 941-6625 erling_rud@hc-sc.gc.ca 3) Cell Type not applicable 4) Sex C88015F - female C89115M - male C94071M - male C95067F - female 5) Age C88015F - 13 years C89115M - 12 years C94071M - 7 years C95067F - 6 years 6) Developmental Stage adult 7) Organism Part peripheral whole blood 8) Strain or line not applicable 9) Genetic variation not applicable 10) Individual number C88015F, C89115M, C94071M & C95067F 11) Individual genetic characteristics not applicable 12) Disease state normal, AIDS 13) Targeted cell type blood 14) Cell line not applicable 2.2.2. Biomaterial manipulation 1) Growth conditions not applicable 2) In vivo treatments description - 4 cynomolgus monkeys (Macaca fascicularis) were infected intravenously with TCID50 of SHIV89.6P. 10 ml of peripheral blood was drawn at -2, 0, 1, 2, 4 and 5 weeks post-infection. 3) In vitro treatment not applicable 4) Treatment type infection 5) Compound not applicable 6) Separation technique not applicable 2.2.3. Hybridization extract preparation 1) Extraction method PAXgene peripheral blood RNA preparation 10 ml of peripheral blood was drawn from each animal directly into 4 PAXgene Blood RNA Tubes (QIAGEN #762125) according to manufacturer's protocol (http://www.qiagen.com/literature/Handbooks/PDF/DNA_RNA_isolation_clinical/INT/PAXgene_Blood_RNA/PaxgeneBloodRNAtube.pdf) Total RNA was purified using PAXgene Blood RNA kit (QIAGEN # 762134) according to manufacturer's protocol http://www.qiagen.com/literature/Handbooks/PDF/DNA_RNA_isolation_clinical/INT/PAXgene_Blood_RNA/1017455PAXgeneBloodRNA_prot.pdf) 2) Nucleic acid type total RNA 3) Amplification Method Total RNA was amplified using the Ambion MessageAmp aRNA kit (#1750), an Eberwine based method, with slight modifications to the manufacturer's protocol (http://www.transnet.ca/Amplification%20Protocol.htm). 2.2.3. Sample labeling 1) Amount of nucleic acid labeled 6 micrograms of aRNA was labeled with Cy3/Cy5 for hybridization 2) Label used Cy5 & Cy3 3) Label incorporation method aRNA was labelled by reverse transcription using the standard protocol of the Ontario Cancer Institute with slight modifications (http://www.transnet.ca/Hybridization%20Protocol_2.htm) 2.2.5. Spiking controls 1) Spiking control feature OCI Human 19k3-part1 OCI Human 19k3-part2 2) Spike type and qualifier not applicable 3) Qualifier, value, source not applicable 2.3. Hybridization procedure and parameters 2) Hybridization Protocol Protocol - (http://www.transnet.ca/Hybridization%20Protocol_2.htm) Solution Hybridization buffer: DIG solution (Roche cat.#1603558) supplemented with 0.45 ug/ul yeast tRNA, 0.45 ug/ul salmon sperm DNA Blocking agent not applicable Slide blocking not applicable Probe blocking: 0.45 ug/ul yeast tRNA, 0.45 ug/ul salmon sperm DNA during hybridization Wash procedure 3x15 min with 1xSSC, 0.1% SDS at 50 degrees Celsius, 3 fast washes in 1xSSC at 50 degrees Celsius Quantity of labelled target used all material generated from 6 ug amplified RNA per sample Time 18 hr (overnight) hybridization Concentration 0.2 ug/ul of aRNA per hybridization Volume 60 ul Temperature 30 degrees Celsius Description of the hybridization chamber hybridizations were incubated in a microscope slide box stored within a tissue culture incubator Qualifier, value, source not applicable 2.4. Measurements 2.4.1. Raw data Scanning protocol Scanning hardware: Scanarray Express Microarray Scanner, Packard Biosciences Scanning software: Scanarray Express Microarray Analysis System v1.1 Build #9 Scan Parameters Laser power: see individual image files in section 2.4.1 Spatial resolution:10 microns PMT gain: 60% 2.4.2. Image analysis and quantitation Image analysis software: Quantarray v.3.0, Packard BioSciences Availability: No longer commercially available Quantitation Parameters: Array Pattern: Spot rows: 25 Spot columns: 24 Spot spacing (vertical): 170 microns Spot spacing (horizontal): 170 microns Interstitial spacing: Off Array rows: 8 Array columns: 4 Array spacing (vertical): 4500 microns Array spacing (horizontal): 4500 microns Auto-adjustable Grid: Grid elasticity: 50/100 Spot elasticity: 50/100 Quantitation: Method: Fixed Circle Crosstalk correction: No Normalized to brightest: No Background subtraction: No Gene database file: for OCI Human 19k3-part1- H19k3a.qa (attached) for OCI Human 19k3-part2- H19k3b.qa (attached) Fixed circle quantitation parameters: Spot diameter: 60 microns Inner background diameter: 180 microns Outer background diameter: 200 microns Signal low percentile: 45 Signal high percentile: 95 Background low percentile: 5 Background high percentile: 55 Quantification output: Mean Intensity Quality Criteria Confidence calculation: Minimum Tolerance and weight: None selected Replicates: Combine replicates: no 2.4.3. Normalized and summarized data Data processing protocol Background subtraction and normalization Background subtraction and normalization was performed using the Quantarray Normalization Excel macro on individual quantitation output files. Each channel was background subtracted using the equation: ch Bkg. Subtr. Intensity = ch intensity - ch Bkg. Normalization strategy: total array Normalization algorithm: log ratio median centering Median log ratio = median(log2(ch1 Bkg. Subtr. Intensity) - log2(ch2 Bkg. Subtr. Intensity)) Normalization factor = 2^ median log ratio Normalized ch2 intensity = ch2 intensity*Normalization factor Statistical Analysis The background subtracted normalized intensities were used for statistical analysis. All spot intensities for within-chip, repeat hybridization, fluor-flip hybridization and biological replicates for each time point post-infection were compiled and tested for significance testing using the software package ArrayStat v.1.0, Imaging Research. ArrayStat parameters: Model selection: Manual Model selected: Proportional model with offsets Outlier detection: yes Threshold detection: Manual Threshold detected: p<0.01 Minimum No. of replicates: 12 (for 1 & 5 wks PI), 11 (for 2 & 4 wks PI) Conditions: Dependent Random Error Estimation Method: Small Sample Test: t-test Normalization: By median Nominal alpha: 0.05 Multiple Test correction: False Discovery Rate
Keywords = SHIV89.6P
Keywords = HIV
Keywords = nonhuman primate
Keywords = cDNA microarray
Keywords = time course
Lot batch = lot #467

organism: Macaca fascicularis

source_name: monkey C95067F pre-infected

source_name: monkey C95067F 2 wks post SHIV89.6P infection


title: chip#12321903

source_name: monkey C95067F 5 wks post SHIV89.6P infection