title: Series 1; young; 2 weeks

description:
Study of rat femur fracture healing in young rats (6 weeks old at fracture) at 2 weeks after fracture.  RNA from 2 rats were pooled for each array
Keywords = rat
Keywords = fracture
Keywords = age
Keywords = time
Keywords = femur


title: Series 1; Young; 4 weeks

status: Public on Jan 09 2004

type: RNA

city: Charlotte

first: Ralph

middle: A.

last: Meyer

state: NC

department: Orthopaedic Research Laboratory

country: USA

institute: Carolinas Medical Center

description:
Study of rat femur fracture healing in young rats (6 weeks old at fracture) at 4 weeks after fracture.  RNA from two rats were pooled for each array.
Keywords = rat
Keywords = fracture
Keywords = age
Keywords = time
Keywords = femur

molecule: total RNA

organism: Rattus norvegicus

source_name: SD rat femur


title: Series 1; young; 3 days

description:
Study of rat femur fracture healing in young rats (6 weeks old at fracture).  RNA from 2 rats were pooled for each microarray
Keywords = rat
Keywords = fracture
Keywords = age
Keywords = time
Keywords = femur


title: 2-cell embryo replication 4

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

description:
2-cell embryo replication 4
Keywords = preimplantation
Keywords = development

organism: Mus musculus

source_name: 2-cell embryo

source_name: Universal Control


title: Blastocyst replication 2

description:
Blastocyst replication 2
Keywords = preimplantation
Keywords = development

source_name: Blastocyst


title: ref_v_18

status: Public on Jan 08 2004

city: Rockville

first: David

last: Rasko

address: 9712 Medical Center Drive

department: Microbial Genomics

institute: The Institute for Genomic Research

description:
Potetnial coding regions predicted by Glimmer 30 were arrayed onto glass microscope slides (Telechem, Inc).
RNA samples were reverse transcribedovernight using Random Hexamer Primers (Invitrogen, Rockville MD), Superscript II and dNTP mixture containing aminoallyl-dUTP (Sigma).
Arrays were scanned with a GenePix 4000B scanner (Axon Inc.).
Hybridization signals were quantitated using TIGR SPOTFINDER (software available at http://www.tigr.org/softlab).
Hybridization experiments were competitive usingprobes derived from B. anthracis Stern 34F2 pooled sample and B. anthracis Stern 34F2. Normalized signal intensities were used to generate relative hybridization ratio.
Samp_description: TIFF images were analyzed using the TIGR Spotfinder program (all TIGR software used in this study can be found at http://www.tigr.org/software/tm4/), which uses a dynamic thresholding algorithm to identify spots and calculate local background and integrated fluorescence intensity for each of the Cy3 and Cy5 channels.  This software was also useful in eliminating questionable spots (those for which shape deviates significantly from that of a true circle, or those with a low signal-to-noise ratio).  Each array was normalized globally using a mean-log2-centering approach to adjust the data to an average Cy5/Cy3 log2(ratio) of zero, then locally using a lowess (locally weighted linear regression) algorithm.  Finally, spots with very low intensity in one channel (and thus aberrantly high or low expression ratios) were removed and eliminated from future analyses.  All normalization was carried out using the TIGR MIDAS program.
Samp_description: Following normalization, the log2 ratios for each gene's in-slide replicates were averaged (median variance <0.01), and corresponding flip-dye replicates were averaged to compensate for dye-specific effects.  The data were then filtered in Microsoft Excel to remove those genes that were not present in at least 80% (16/20) of the data sets in order to ensure that subsequent clustering analyses were not confounded by genes with a high percentage of missing data.  All clustering analyses were performed using the TIGR MEV (MultiExperiment Viewer) program, and further statistical analysis was done using MEV or Excel plus the SAM (Significance Analysis for Microarrays) module available at http://www-stat.stanford.edu/~tibs/SAM/index.html .

organism: Bacillus anthracis

source_name: Bacillus anthracis Sterne 34F2 pooled RNA

source_name: Bacillus anthracis Sterne 34F2 from timepoint 18


title: 4-cell embryo replication 1

description:
4-cell embryo replication 1
Keywords = preimplantation
Keywords = development

source_name: 4-cell embryo


title: ref_v_20

source_name: Bacillus anthracis Sterne 34F2 from timepoint 20


title: 2-cell embryo replication 3

description:
2-cell embryo replication 3
Keywords = preimplantation
Keywords = development


title: ref_v_19

source_name: Bacillus anthracis Sterne 34F2 from timepoint 19


title: ref_v_16

source_name: Bacillus anthracis Sterne 34F2 from timepoint 16


title: ref_v_17

source_name: Bacillus anthracis Sterne 34F2 from timepoint 17


title: ref_v_15

source_name: Bacillus anthracis Sterne 34F2 from timepoint 15


title: ref_v_12

source_name: Bacillus anthracis Sterne 34F2 from timepoint 12


title: Fertilized egg replication 4

description:
Fertilized egg replication 4
Keywords = preimplantation
Keywords = development

source_name: Fertilized egg


title: ref_v_11

source_name: Bacillus anthracis Sterne 34F2 from timepoint 11


title: Fertilized egg replication 3

description:
Fertilized egg replication 3
Keywords = preimplantation
Keywords = development


title: ref_v_10

description:
Potetnial coding regions predicted by Glimmer 30 were arrayed onto glass microscope slides (Telechem, Inc).
RNA samples were reverse transcribed overnight using Random Hexamer Primers (Invitrogen, Rockville MD), Superscript II and dNTP mixture containing aminoallyl-dUTP (Sigma).
Arrays were scanned with a GenePix 4000B scanner (Axon Inc.).
Hybridization signals were quantitated using TIGR SPOTFINDER (software available at http://www.tigr.org/softlab).
Hybridization experiments were competitive usingprobes derived from B. anthracis Stern 34F2 pooled sample and B. anthracis Stern 34F2. Normalized signal intensities were used to generate relative hybridization ratio.
Samp_description: TIFF images were analyzed using the TIGR Spotfinder program (all TIGR software used in this study can be found at http://www.tigr.org/software/tm4/), which uses a dynamic thresholding algorithm to identify spots and calculate local background and integrated fluorescence intensity for each of the Cy3 and Cy5 channels.  This software was also useful in eliminating questionable spots (those for which shape deviates significantly from that of a true circle, or those with a low signal-to-noise ratio).  Each array was normalized globally using a mean-log2-centering approach to adjust the data to an average Cy5/Cy3 log2(ratio) of zero, then locally using a lowess (locally weighted linear regression) algorithm.  Finally, spots with very low intensity in one channel (and thus aberrantly high or low expression ratios) were removed and eliminated from future analyses.  All normalization was carried out using the TIGR MIDAS program.
Samp_description: Following normalization, the log2 ratios for each gene's in-slide replicates were averaged (median variance <0.01), and corresponding flip-dye replicates were averaged to compensate for dye-specific effects.  The data were then filtered in Microsoft Excel to remove those genes that were not present in at least 80% (16/20) of the data sets in order to ensure that subsequent clustering analyses were not confounded by genes with a high percentage of missing data.  All clustering analyses were performed using the TIGR MEV (MultiExperiment Viewer) program, and further statistical analysis was done using MEV or Excel plus the SAM (Significance Analysis for Microarrays) module available at http://www-stat.stanford.edu/~tibs/SAM/index.html .

source_name: Bacillus anthracis Sterne 34F2 from timepoint 10


title: ref_v_8

source_name: Bacillus anthracis Sterne 34F2 from timepoint 8


title: Unfertilized egg replication 4

description:
Unfertilized egg replication 4
Keywords = preimplantation
Keywords = development

source_name: Unfertilized egg


title: ref_v_4

source_name: Bacillus anthracis Sterne 34F2 from timepoint 4


title: Unfertilized egg replication 3

description:
Unfertilized egg replication 3
Keywords = preimplantation
Keywords = development

source_name: Universal Control


title: Unfertilized egg replication 2

description:
Unfertilized egg replication 2
Keywords = preimplantation
Keywords = development


title: ref_v_7

source_name: Bacillus anthracis Sterne 34F2 from timepoint 7


title: ref_v_1

description:
Potetnial coding regions predicted by Glimmer 30 were arrayed onto glass microscope slides (Telechem, Inc).
RNA samples were reverse transcribed overnight using  Random Hexamer Primers (Invitrogen, Rockville MD), Superscript II and dNTP mixture containing aminoallyl-dUTP (Sigma).
Arrays were scanned with a GenePix 4000B scanner (Axon Inc.).
Hybridization signals were quantitated using TIGR SPOTFINDER (software available at http://www.tigr.org/softlab).
Hybridization experiments were competitive usingprobes derived from B. anthracis Stern 34F2 pooled sample and B. anthracis Stern 34F2. Normalized signal intensities were used to generate relative hybridization ratio.
Samp_description: TIFF images were analyzed using the TIGR Spotfinder program (all TIGR software used in this study can be found at http://www.tigr.org/software/tm4/), which uses a dynamic thresholding algorithm to identify spots and calculate local background and integrated fluorescence intensity for each of the Cy3 and Cy5 channels.  This software was also useful in eliminating questionable spots (those for which shape deviates significantly from that of a true circle, or those with a low signal-to-noise ratio).  Each array was normalized globally using a mean-log2-centering approach to adjust the data to an average Cy5/Cy3 log2(ratio) of zero, then locally using a lowess (locally weighted linear regression) algorithm.  Finally, spots with very low intensity in one channel (and thus aberrantly high or low expression ratios) were removed and eliminated from future analyses.  All normalization was carried out using the TIGR MIDAS program.
Samp_description: Following normalization, the log2 ratios for each gene's in-slide replicates were averaged (median variance <0.01), and corresponding flip-dye replicates were averaged to compensate for dye-specific effects.  The data were then filtered in Microsoft Excel to remove those genes that were not present in at least 80% (16/20) of the data sets in order to ensure that subsequent clustering analyses were not confounded by genes with a high percentage of missing data.  All clustering analyses were performed using the TIGR MEV (MultiExperiment Viewer) program, and further statistical analysis was done using MEV or Excel plus the SAM (Significance Analysis for Microarrays) module available at http://www-stat.stanford.edu/~tibs/SAM/index.html .

source_name: Bacillus anthracis Sterne 34F2 pooled RNA

source_name: Bacillus anthracis Sterne 34F2 from timepoint 1


title: ref_v_3

source_name: Bacillus anthracis Sterne 34F2 from timepoint 3


title: ref_v_9

source_name: Bacillus anthracis Sterne 34F2 from timepoint 9


title: ref_v_2

source_name: Bacillus anthracis Sterne 34F2 from timepoint 2


title: 2-cell embryo replication 2

description:
2-cell embryo replication 2
Keywords = preimplantation
Keywords = development

source_name: 2-cell embryo


title: Unfertilized egg replication 1

description:
Unfertilized egg replication 1
Keywords = preimplantation
Keywords = development


title: Fertilized egg replication 1

description:
Fertilized egg replication 1
Keywords = preimplantation
Keywords = development


title: Blastocyst replication 3

description:
Blastocyst replication 3
Keywords = preimplantation
Keywords = development

source_name: Blastocyst


title: ref_v_6

source_name: Bacillus anthracis Sterne 34F2 from timepoint 6


title: 21h-Control replication 3

description:
21h-Control replication 3
Keywords = preimplantation
Keywords = development

source_name: 21h-Control, early 1-cell embryo

source_name: Universal Reference


title: 20_v_ref

description:
Potetnial coding regions predicted by Glimmer 30 were arrayed onto glass microscope slides (Telechem, Inc).
RNA samples were reverse transcribed overnight using Random Hexamer Primers (Invitrogen, Rockville MD), Superscript II and dNTP mixture containing aminoallyl-dUTP (Sigma).
Arrays were scanned with a GenePix 4000B scanner (Axon Inc.).
Hybridization signals were quantitated using TIGR SPOTFINDER (software available at http://www.tigr.org/softlab).
Hybridization experiments were competitive using probes derived from B. anthracis Stern 34F2 pooled sample and a B. anthracis Stern 34F2. Normalized signal intensities were used to generate relative hybridization ratios.
TIFF images were analyzed using the TIGR Spotfinder program (all TIGR software used in this study can be found at http://www.tigr.org/software/tm4/), which uses a dynamic thresholding algorithm to identify spots and calculate local background and integrated fluorescence intensity for each of the Cy3 and Cy5 channels.  This software was also useful in eliminating questionable spots (those for which shape deviates significantly from that of a true circle, or those with a low signal-to-noise ratio).  Each array was normalized globally using a mean-log2-centering approach to adjust the data to an average Cy5/Cy3 log2(ratio) of zero, then locally using a lowess (locally weighted linear regression) algorithm.  Finally, spots with very low intensity in one channel (and thus aberrantly high or low expression ratios) were removed and eliminated from future analyses.  All normalization was carried out using the TIGR MIDAS program.
Following normalization, the log2 ratios for each gene's in-slide replicates were averaged (median variance <0.01), and corresponding flip-dye replicates were averaged to compensate for dye-specific effects.  The data were then filtered in Microsoft Excel to remove those genes that were not present in at least 80% (16/20) of the data sets in order to ensure that subsequent clustering analyses were not confounded by genes with a high percentage of missing data.  All clustering analyses were performed using the TIGR MEV (MultiExperiment Viewer) program, and further statistical analysis was done using MEV or Excel plus the SAM (Significance Analysis for Microarrays) module available at http://www-stat.stanford.edu/~tibs/SAM/index.html .

source_name: Bacillus anthracis Sterne 34F2 timepoint 20


title: 18_v_ref

source_name: Bacillus anthracis Sterne 34F2 timepoint 18


title: 16_v_ref

source_name: Bacillus anthracis Sterne 34F2 timepoint 16


title: 15_v_ref

source_name: Bacillus anthracis Sterne 34F2 timepoint 15


title: 17_v_ref

source_name: Bacillus anthracis Sterne 34F2 timepoint 17


title: 19_v_ref

source_name: Bacillus anthracis Sterne 34F2 timepoint 19


title: 12_v_ref

source_name: Bacillus anthracis Sterne 34F2 timepoint 12


title: ref_v_5

source_name: Bacillus anthracis Sterne 34F2 pooled RNA

source_name: Bacillus anthracis Sterne 34F2 from timepoint 5


title: 8_v_ref

source_name: Bacillus anthracis Sterne 34F2 timepoint 8


title: Series 1; young; no fracture

description:
Study of rat femur fracture healing in young rats (6 weeks old at fracture).  RNA from two rats were pooled for each microarray.
Keywords = rat
Keywords = fracture
Keywords = age
Keywords = time
Keywords = femur
Lot batch = Sample 01

source_name: SD rat femur


title: Fertilized egg replication 2

description:
Fertilized egg replication 2
Keywords = preimplantation
Keywords = development

source_name: Fertilized egg

source_name: Universal Control


title: 10_v_ref

source_name: Bacillus anthracis Sterne 34F2 timepoint 10


title: 2-cell embryo replication 1

description:
2-cell embryo replication 1
Keywords = preimplantation
Keywords = development

source_name: 2-cell embryo


title: 11_v_ref

source_name: Bacillus anthracis Sterne 34F2 timepoint 11


title: 9_v_ref

source_name: Bacillus anthracis Sterne 34F2 timepoint 9


title: HP-81c

status: Public on Jan 07 2004

city: Stockholm

first: Qiang

last: Pan-Hammarström

address: F79, Huddinge Hospital

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institute

description: Total RNA from corpus gastric biopsies

organism: Homo sapiens

source_name: gastric biopsies


title: 7_v_ref

source_name: Bacillus anthracis Sterne 34F2 timepoint 7


title: HP-45c

description: Total RNA from corpus gastric biopsies


title: 5_v_ref

source_name: Bacillus anthracis Sterne 34F2 timepoint 5


title: 4_v_ref

source_name: Bacillus anthracis Sterne 34F2 timepoint 4


title: HP-23c

description: Total RNA from corpus gastric biopsies


title: HP-13C

description: gastric biopsies


title: HP-54

description: Total RNA from antrum gastric biopsies


title: HP-9C

description: Total RNA from corpus gastric biopsies


title: HP-64

description: Total RNA from antrum gastric biopsies


title: HP-50

description: Total RNA from antrum gastric biopsies


title: HP-3

description: Total RNA from antrum gastric biopsies

source_name: gastric bipsies


title: HP-28

description: Total RNA from antrum gastric biopsies


title: 3_v_ref

description:
Potetnial coding regions predicted by Glimmer 30 were arrayed onto glass microscope slides (Telechem, Inc).
RNA samples were reverse transcribed overnight using Random Hexamer Primers (Invitrogen, Rockville MD), Superscript II and dNTP mixture containing aminoallyl-dUTP (Sigma).
Arrays were scanned with a GenePix 4000B scanner (Axon Inc.).
Hybridization signals were quantitated using TIGR SPOTFINDER (software available at http://www.tigr.org/softlab).
Hybridization experiments were competitive usingprobes derived from B. anthracis Stern 34F2 pooled sample and a B. anthracis Stern 34F2. Normalized signal intensities were used to generate relative hybridization ratios (query/reference).
TIFF images were analyzed using the TIGR Spotfinder program (all TIGR software used in this study can be found at http://www.tigr.org/software/tm4/), which uses a dynamic thresholding algorithm to identify spots and calculate local background and integrated fluorescence intensity for each of the Cy3 and Cy5 channels.  This software was also useful in eliminating questionable spots (those for which shape deviates significantly from that of a true circle, or those with a low signal-to-noise ratio).  Each array was normalized globally using a mean-log2-centering approach to adjust the data to an average Cy5/Cy3 log2(ratio) of zero, then locally using a lowess (locally weighted linear regression) algorithm.  Finally, spots with very low intensity in one channel (and thus aberrantly high or low expression ratios) were removed and eliminated from future analyses.  All normalization was carried out using the TIGR MIDAS program.
Following normalization, the log2 ratios for each gene's in-slide replicates were averaged (median variance <0.01), and corresponding flip-dye replicates were averaged to compensate for dye-specific effects.  The data were then filtered in Microsoft Excel to remove those genes that were not present in at least 80% (16/20) of the data sets in order to ensure that subsequent clustering analyses were not confounded by genes with a high percentage of missing data.  All clustering analyses were performed using the TIGR MEV (MultiExperiment Viewer) program, and further statistical analysis was done using MEV or Excel plus the SAM (Significance Analysis for Microarrays) module available at http://www-stat.stanford.edu/~tibs/SAM/index.html .

source_name: Bacillus anthracis Sterne 34F2 timepoint 3


title: 2_v_ref

description:
Potetnial coding regions predicted by Glimmer 30 were arrayed onto glass microscope slides (Telechem, Inc).
RNA samples were reverse transcribed overnight using Random Hexamer Primers (Invitrogen, Rockville MD), Superscript II and dNTP mixture containing aminoallyl-dUTP (Sigma).
Arrays were scanned with a GenePix 4000B scanner (Axon Inc.).
Hybridization signals were quantitated using TIGR SPOTFINDER (software available at http://www.tigr.org/softlab).
Hybridization experiments were competitive usingprobes derived from B. anthracis Stern 34F2 pooled sample (reference) and a B. anthracis Stern 34F2 (query). Normalized signal intensities were used to generate relative hybridization ratios (query/reference).
TIFF images were analyzed using the TIGR Spotfinder program (all TIGR software used in this study can be found at http://www.tigr.org/software/tm4/), which uses a dynamic thresholding algorithm to identify spots and calculate local background and integrated fluorescence intensity for each of the Cy3 and Cy5 channels.  This software was also useful in eliminating questionable spots (those for which shape deviates significantly from that of a true circle, or those with a low signal-to-noise ratio).  Each array was normalized globally using a mean-log2-centering approach to adjust the data to an average Cy5/Cy3 log2(ratio) of zero, then locally using a lowess (locally weighted linear regression) algorithm.  Finally, spots with very low intensity in one channel (and thus aberrantly high or low expression ratios) were removed and eliminated from future analyses.  All normalization was carried out using the TIGR MIDAS program.
Following normalization, the log2 ratios for each gene's in-slide replicates were averaged (median variance <0.01), and corresponding flip-dye replicates were averaged to compensate for dye-specific effects.  The data were then filtered in Microsoft Excel to remove those genes that were not present in at least 80% (16/20) of the data sets in order to ensure that subsequent clustering analyses were not confounded by genes with a high percentage of missing data.  All clustering analyses were performed using the TIGR MEV (MultiExperiment Viewer) program, and further statistical analysis was done using MEV or Excel plus the SAM (Significance Analysis for Microarrays) module available at http://www-stat.stanford.edu/~tibs/SAM/index.html .

source_name: Bacillus anthracis Sterne 34F2 timepoint 2


title: HP-12C

description: Total RNA from corpus gastric biopsies


title: 6_v_ref

source_name: Bacillus anthracis Sterne 34F2 timepoint 6

source_name: Bacillus anthracis Sterne 34F2 pooled RNA


title: 1_v_ref

source_name: Bacillus anthracis Sterne 34F2 timepoint 1


title: HP-27

description: Total RNA from antrum gastric biopsies

source_name: Gastric biopsies


title: HP-24

description: Total RNA from antrum gastric biopsies


title: HP-23

description: Total RNA from antrum gastric biopsies


title: RatU34_S1

city: New Haven

first: Mark

last: Kidd

state: CT

address: 333 Cedar Street

department: Surgery

institute: Yale University School of Medicine

description:
Analysis of gene expression in a population of enriched ECL cells obtained from the gastric mucosa of Mastomys that spontaneously developed a gastric ECL cell carcinoid
Keywords = ECL gastric Loxtidine Mastomys Affymetrix
Lot batch = S1

organism: Mastomys natalensis

source_name: Gastric mucosa


title: Mouseu74_T2

description:
Analysis of gene expression in the gastric mucosa of Mastomys treated with loxitidine for 16 weeks (neoplasia of ECL cells)
Keywords = ECL gastric Mastomys Mouse Affymetrix
Lot batch = T2


title: RatU34_T1

description:
Analysis of gene expression in a population of enriched ECL cells obtained from the gastric mucosa of Mastomys treated with Loxtidine for 16 weeks
Keywords = ECL gastric Loxtidine Mastomys Affymetrix
Lot batch = T3


title: HP-13

description: Total RNA from antrum gastric biopsies


title: HP-12

description: Total RNA from antrum gastric biopsies


title: HP-11

description: Total RNA from antrum gastric biopsies


title: HP-22

description: Total RNA from antrum gastric biopsies


title: MouseU74_T1

description:
Analysis of gene expression in the gastric mucosa of Mastomys treated with loxitidine for 16 weeks (neoplasia of ECL cells)
Keywords = ECL gastric Mastomys Mouse Affymetrix
Lot batch = T1


title: HP-2

description: Total RNA from antrum biopsies


title: HP-45

description: Total RNA from antumn gastric biopsies


title: HP-49

description: Total RNA from antrum gastric biopsies


title: MouseU74_H2

description:
Analysis of gene expression in the gastric mucosa of Mastomys treated with loxitidine for 8 weeks (hyerplasia of ECL cells)
Keywords = ECL gastric Mastomys Mouse Affymetrix
Lot batch = H2

source_name: Gastric Mucosa


title: MouseU74_H1

description:
Analysis of gene expression in the gastric mucosa of Mastomys treated with loxitidine for 8 weeks (hyerplasia of ECL cells)
Keywords = ECL gastric Mastomys Mouse Affymetrix
Lot batch = H1

source_name: Stomach-gastric mucosa


title: HP-9

status: Public on Jan 05 2004

description: Total RNA from antrum gastric biopsies


title: RatU34_H1

description:
Analysis of gene expression in a population of enriched ECL cells obtained from the gastric mucosa of Mastomys treated with Loxtidine for 8 weeks
Keywords = ECL gastric Loxtidine Mastomys Affymetrix
Lot batch = H3

source_name: Gastric ECL cells


title: wtPrE serumfree 2

city: Ann Arbor

first: Michael

middle: Thomas

last: McCabe

state: MI

address: 1500 E. Medical Center Drive

department: Urology

institute: University of Michigan

description:
control wild-type prostate epithelial cell line maintained in RPMI-1640 medium without fetal bovine serum for 48 hours
Keywords = prostate
Keywords = epithelial

source_name: wild-type prostate epithelial cell line


title: HP-1

description: Total RNA  from antrum biopsies


title: wtPrE serumfree 1


title: 21NT/OPbi

city: Tampa

first: Gregory

last: Bloom

state: FL

institute: Moffitt Cancer Center

description: breast carcinoma cells transfected to constitutively overexpress OPN

source_name: 21NT/OPbi cell line


title: HP-87

description: Total RNA from antrum gastric biopsies

source_name: gastric biopsies


title: Rb-/-PrE serum 1

description:
Rb-/- prostate epithelial cell line maintained in RPMI-1640 medium supplemented with 5% fetal bovine serum
Keywords = prostate
Keywords = epithelial

source_name: Rb-/- prostate epithelial cell line


title: Rb-/-PrE serum 2


title: Rb-/-PrE serumfree 2

description:
Rb-/- prostate epithelial cell line maintained in RPMI-1640 medium without fetal bovine serum for 48 hours
Keywords = prostate
Keywords = epithelial


title: 21NTCi

description: breast carcinoma cells transfected with empty vector

source_name: 21NTCi cell line


title: wtPrE serum 3

description:
control wild-type prostate epithelial cell line maintained in RPMI-1640 medium supplemented with 5% fetal bovine serum
Keywords = prostate
Keywords = epithelial


title: Rb-/-PrE serumfree 1


title: HP-8

description: Total RNA from antrum gastric biopsies


title: HP-65

description: Total RNA from antrum gastric biopsies


title: wtPrE serum 1


title: HP-81

description: Total RNA from antrum gastric biopsies


title: Blastocyst replication 1

description:
Blastocyst replication 1
Keywords = preimplantation
Keywords = development

source_name: Blastocyst

source_name: Universal Control


title: ref_v_13

description:
Potetnial coding regions predicted by Glimmer 30 were arrayed onto glass microscope slides (Telechem, Inc).
RNA samples were reverse transcribedovernight using Random Hexamer Primers (Invitrogen, Rockville MD), Superscript II and dNTP mixture containing aminoallyl-dUTP (Sigma).
Arrays were scanned with a GenePix 4000B scanner (Axon Inc.).
Hybridization signals were quantitated using TIGR SPOTFINDER (software available at http://www.tigr.org/softlab).
Hybridization experiments were competitive usingprobes derived from B. anthracis Stern 34F2 pooled sample and B. anthracis Stern 34F2. Normalized signal intensities were used to generate relative hybridization ratio.
Samp_description: TIFF images were analyzed using the TIGR Spotfinder program (all TIGR software used in this study can be found at http://www.tigr.org/software/tm4/), which uses a dynamic thresholding algorithm to identify spots and calculate local background and integrated fluorescence intensity for each of the Cy3 and Cy5 channels.  This software was also useful in eliminating questionable spots (those for which shape deviates significantly from that of a true circle, or those with a low signal-to-noise ratio).  Each array was normalized globally using a mean-log2-centering approach to adjust the data to an average Cy5/Cy3 log2(ratio) of zero, then locally using a lowess (locally weighted linear regression) algorithm.  Finally, spots with very low intensity in one channel (and thus aberrantly high or low expression ratios) were removed and eliminated from future analyses.  All normalization was carried out using the TIGR MIDAS program.
Samp_description: Following normalization, the log2 ratios for each gene's in-slide replicates were averaged (median variance <0.01), and corresponding flip-dye replicates were averaged to compensate for dye-specific effects.  The data were then filtered in Microsoft Excel to remove those genes that were not present in at least 80% (16/20) of the data sets in order to ensure that subsequent clustering analyses were not confounded by genes with a high percentage of missing data.  All clustering analyses were performed using the TIGR MEV (MultiExperiment Viewer) program, and further statistical analysis was done using MEV or Excel plus the SAM (Significance Analysis for Microarrays) module available at http://www-stat.stanford.edu/~tibs/SAM/index.html .

source_name: Bacillus anthracis Sterne 34F2 from timepoint 13


title: Expression profile: wild type grown at pH3 vs fcc1 mutant grown at pH8; dye switch

status: Public on Jan 02 2004

city: West Lafayette

first: Charles

middle: P.

last: Woloshuk

state: IN

institute: Purdue University

description: RNA from the wild type grown at pH3 was labeled with Cy3 and RNA from the fcc1 mutant grown at pH8 was labeled with Cy5

organism: Fusarium verticillioides

source_name: wild type pH3

source_name: Fcc1 mutant pH 8


title: Expression profile: wild type grown at pH3 vs fcc1 mutant grown at pH8

description: RNA from the wild type grown at pH3 was labeled with Cy5 and RNA from the fcc1 mutant grown at pH8 was labeled with Cy3

source_name: Fcc1 mutant

source_name: Wild type


title: wtPrE serum 2


title: Expression profile: Wild type grown at pH3 vs pH8; dye switch

description: RNA from the wild type grown at pH3 was labeled with Cy5 and RNA from the wild type grown at pH8 was labeled with Cy3

source_name: wild type pH8


title: Expression profile: wild type grown vs fcc1 mutant grown at pH8

description: RNA from the wild type grown at pH8 was labeled with Cy5 and RNA from the fcc1 mutant grown at pH8 was labeled with Cy3

source_name: wild type


title: Expression profile:Wild type grown at pH3 vs pH8

description: RNA from the wild type grown at pH3 was labeled with Cy3 and RNA from the wild type grown at pH8 was labeled with Cy5


title: Expression profile: wild type grown vs fcc1 mutant grown on maize exp.3; dye switch

description: RNA from wild type was labeled with Cy3 and RNA from the fcc1 mutant was labeled with Cy5

source_name: fcc1 mutant


title: Expression profile: wild type grown vs fcc1 mutant grown on maize exp.3

description: RNA from wild type was labeled with Cy5 and RNA from the fcc1 mutant was labeled with Cy3


title: Expression profile: wild type grown vs fcc1 mutant grown on maize exp.2


title: Expression profile: wild type grown vs fcc1 mutant grown on maize exp.2; dye switch


title: Expression profile of fcc1 mutant and wild type grown under low (3) conditions

description: The fungal strains were grown in a defined medium adjusted to either pH 3.  The  RNA from the mutant was isolated and labeled with Cy3 and the wild type RNA was labeled with Cy5.

source_name: fcc1 mutant grown at pH 3

source_name: Wild-type strain grown at pH 3


title: Expression profile: fcc1 mutant grown at pH3 vs pH8; dye switch

description: RNA from the fcc1 mutant grown at pH8 was labeled with Cy3 and RNA from the fcc1 mutant grown at pH3 was labeled with Cy5

source_name: fcc1 mutant pH8

source_name: fcc1 mutant pH3


title: Expression profile: wild type grown vs fcc1 mutant grown at pH8; dye switch

description: RNA from the wild type grown at pH8 was labeled with Cy3 and RNA from the fcc1 mutant grown at pH8 was labeled with Cy5


title: Expression profile: fcc1 mutant grown at pH3 vs pH8

description: RNA from the fcc1 mutant grown at pH3 was labeled with Cy3 and RNA from the fcc1 mutant grown at pH8 was labeled with Cy5

source_name: Fcc1 mutant pH3

source_name: Fcc1 mutant pH8


title: Expression profile of wild type and fcc1 mutant grown in a medium adjusted to pH3.


title: Expression profile of wild type and fcc1 mutant grown on maize kernels


title: Expression profile: wild type grown at pH8 vs fcc1 mutant grown at pH3; dye switch


title: Vector-veh-1

status: Public on Jan 01 2004

city: Los Angeles

first: Charlie

last: Chen

state: CA

institute: University of California at Los Angeles

description: Human prostate cancer cells in different conditions

source_name: LNCaP


title: Vector-R-270pM


title: Vector-veh-2


title: Vector-R-30pM


title: Expression profile of wild type and fcc1 mutant grown on maize kernels-dye reverse


title: Vector-R-90pM


title: Expression profile of wild type grown in a medium adjusted to pH8 vs fcc1 mutant grown in a medium adjusted to pH3.

source_name: Wlid type


title: Vector-bic-1


title: AR-Veh-2


title: Vector-R-10pM


title: AR-R-30pM


title: AR-R-810pM


title: AR-R-270pM


title: Vector-bic-2


title: Vector-R-810pM


title: AR-Veh-1


title: AR-bic-10miM


title: exULMS781

city: Boston

first: Bradley

middle: J

last: Quade

state: MA

address: 75 Francis Street

department: Pathology

institute: Brigham and Women's Hospital

description: Comparison of Gene Expression in Uterine Smooth Muscle Tumors (including normal myometrium, benign uterine leiomyoma, malignant uterine and extra-uterine leiomyosarcoma. Total RNA was isolated with Trizol and converted to labeled cRNA by standard Affymetrix protocols. Before analysis, Avg Diff values were normalized to a sum of 3 million for each probe set on the chip and values less than 20 were adjusted to 20 to allow log scaling in subsequent analysis.

source_name: extra-uterine leiomyosarcoma


title: AR-R-10pM


title: exULMS2906


title: LMS19597

source_name: uterine leiomyosarcoma


title: exULMS92


title: LMS2103


title: exULMS91


title: LMS1775


title: LMS4578


title: LMS906


title: LMS11987


title: LMS818


title: LMS278


title: LNCaP-HS

description: Prostate cancer xenograft

source_name: human xenograft


title: Leio219

source_name: uterine leiomyoma


title: LUCaP35HR

description: Prostate cancer xenograft


title: Leio241


title: Leio242


title: LUCaP41HR

description: Prostate cancer xenograft


title: LNCaP-HR

description: Prostate cancer xenograft


title: Leio218


title: Leio240


title: Leio217


title: LUCaP23HS

description: Prostate cancer xenograft


title: 14_v_ref

description:
Potetnial coding regions predicted by Glimmer 30 were arrayed onto glass microscope slides (Telechem, Inc).
RNA samples were reverse transcribed overnight using Random Hexamer Primers (Invitrogen, Rockville MD), Superscript II and dNTP mixture containing aminoallyl-dUTP (Sigma).
Arrays were scanned with a GenePix 4000B scanner (Axon Inc.).
Hybridization signals were quantitated using TIGR SPOTFINDER (software available at http://www.tigr.org/softlab).
Hybridization experiments were competitive using probes derived from B. anthracis Stern 34F2 pooled sample and a B. anthracis Stern 34F2. Normalized signal intensities were used to generate relative hybridization ratios.
TIFF images were analyzed using the TIGR Spotfinder program (all TIGR software used in this study can be found at http://www.tigr.org/software/tm4/), which uses a dynamic thresholding algorithm to identify spots and calculate local background and integrated fluorescence intensity for each of the Cy3 and Cy5 channels.  This software was also useful in eliminating questionable spots (those for which shape deviates significantly from that of a true circle, or those with a low signal-to-noise ratio).  Each array was normalized globally using a mean-log2-centering approach to adjust the data to an average Cy5/Cy3 log2(ratio) of zero, then locally using a lowess (locally weighted linear regression) algorithm.  Finally, spots with very low intensity in one channel (and thus aberrantly high or low expression ratios) were removed and eliminated from future analyses.  All normalization was carried out using the TIGR MIDAS program.
Following normalization, the log2 ratios for each gene's in-slide replicates were averaged (median variance <0.01), and corresponding flip-dye replicates were averaged to compensate for dye-specific effects.  The data were then filtered in Microsoft Excel to remove those genes that were not present in at least 80% (16/20) of the data sets in order to ensure that subsequent clustering analyses were not confounded by genes with a high percentage of missing data.  All clustering analyses were performed using the TIGR MEV (MultiExperiment Viewer) program, and further statistical analysis was done using MEV or Excel plus the SAM (Significance Analysis for Microarrays) module available at http://www-stat.stanford.edu/~tibs/SAM/index.html .

source_name: Bacillus anthracis Sterne 34F2 timepoint 14

source_name: Bacillus anthracis Sterne 34F2 pooled RNA


title: LUCaP41HS

description: Prostate cancer xenograft


title: Leio216


title: LUCaP35HS

description: Prostate cancer xenograft


title: LAPC9HR

description: Prostate cancer xenograft


title: LUCaP23HR

description: Prostate cancer xenograft


title: LAPC4HS

description: Prostate cancer xenograft


title: LAPC4HR

description: Prostate cancer xenograft


title: LMS19825


title: LAPC9HS

description: Prostate cancer xenograft


title: CWR22HS

description: Prostate cancer xenograft


title: CWR22HR

description: Prostate cancer xenograft


title: Myo220

source_name: myomtrium


title: Myo44


title: VREI_B042_6-10-02

first: Valerie

last: Reinke

address: 333 Cedar St

department: Genetics

description: glp-4;him-5 adult males prep 4 vs reference

organism: Caenorhabditis elegans

source_name: wt mixed reference mRNA

source_name: glp-4;him-5 adult males prep 4 mRNA


title: Myo243


title: AR-R-90pM


title: Blood60

status: Public on Dec 31 2003

city: Kirkland

first: Mao

last: Mao

state: WA

department: Biology

institute: Rosetta Inpharmatics

description: Blood cell RNA

source_name: pool of individual blood

source_name: 7/24/01 740 Buffy Coat Male


title: Blood68

description: Blood cell RNA

source_name: 7/18/01 843 Buffy Coat Female


title: VREI_A046_4-22-02

description: glp-4;him-5 adult males prep 2 vs reference

source_name: glp-4;him-5 adult males prep 2 mRNA


title: VREI_A041_6-05-02

description: glp-4;him-5 adult males prep 3 vs reference

source_name: glp-4;him-5 adult males prep 3 mRNA


title: Blood69

description: Blood cell RNA

source_name: 7/24/01 843 Buffy Coat Female


title: Blood67

description: Blood cell RNA

source_name: 7/10/01 843 Buffy Coat Female


title: 13_v_ref

source_name: Bacillus anthracis Sterne 34F2 timepoint 13


title: Blood63

description: Blood cell RNA

source_name: 7/24/01 827 Buffy Coat Female


title: Blood61

description: Blood cell RNA

source_name: 7/10/01 827 Buffy Coat Female


title: Blood64

description: Blood cell RNA

source_name: 6/12/01 843 Buffy Coat Female


title: Blood62

description: Blood cell RNA

source_name: 7/18/01 827 Buffy Coat Female


title: Blood54

description: Blood cell RNA

source_name: 7/10/01 730 Buffy Coat Female


title: Blood66

description: Blood cell RNA

source_name: 6/26/01 843 Buffy Coat Female


title: Blood57

description: Blood cell RNA

source_name: 6/12/01 740 Buffy Coat Male


title: Blood65

description: Blood cell RNA

source_name: 6/20/01 843 Buffy Coat Female


title: Blood50

description: Blood cell RNA

source_name: 6/12/01 710 Buffy Coat Male


title: Blood59

description: Blood cell RNA

source_name: pool of individual blood

source_name: 7/10/01 740 Buffy Coat Male


title: Blood53

description: Blood cell RNA

source_name: 6/26/01 730 Buffy Coat Female


title: VREI_A048_4-19-02

description: glp-4;him-5 adult males prep 1 vs reference

source_name: wt mixed reference mRNA

source_name: glp-4;him-5 adult males prep 1 mRNA


title: Myo43

source_name: myomtrium


title: Blood51

description: Blood cell RNA

source_name: 6/20/01 710 Buffy Coat Male


title: Blood56

description: Blood cell RNA

source_name: 7/24/01 730 Buffy Coat Female


title: Blood58

description: Blood cell RNA

source_name: 6/20/01 740 Buffy Coat Male


title: Blood55

description: Blood cell RNA

source_name: 7/18/01 730 Buffy Coat Female


title: Blood52

description: Blood cell RNA

source_name: 6/20/01 730 Buffy Coat Female


title: Blood48

description: Blood cell RNA

source_name: 7/18/01 619 Buffy Coat Female


title: Blood49

description: Blood cell RNA

source_name: 7/24/01 619 Buffy Coat Female


title: Blood47

description: Blood cell RNA

source_name: 7/5/01 619 Buffy Coat Female


title: Blood46

description: Blood cell RNA

source_name: 6/20/01 619 Buffy Coat Female


title: Blood44

description: Blood cell RNA

source_name: 7/18/01 604 Buffy Coat Male


title: Blood45

description: Blood cell RNA

source_name: 6/12/01 619 Buffy Coat Female


title: Blood41

description: Blood cell RNA

source_name: pool of individual blood

source_name: 6/26/01 604 Buffy Coat Male


title: Blood42

description: Blood cell RNA

source_name: 7/5/01 604 Buffy Coat Male


title: Blood43

description: Blood cell RNA

source_name: 7/10/01 604 Buffy Coat Male


title: Blood40

description: Blood cell RNA

source_name: 6/20/01 604 Buffy Coat Male


title: Blood39

description: Blood cell RNA

source_name: 6/12/01 604 Buffy Coat Male


title: Blood38

description: Blood cell RNA

source_name: 7/18/01 483 Buffy Coat Female


title: Blood35

description: Blood cell RNA

source_name: 6/12/01 483 Buffy Coat Female


title: Blood34

description: Blood cell RNA

source_name: 7/24/01 404 Buffy Coat Male


title: Blood37

description: Blood cell RNA

source_name: 7/5/01 483 Buffy Coat Female


title: Blood29

description: Blood cell RNA

source_name: 7/18/01 368 Buffy Coat Male


title: Blood26

description: Blood cell RNA

source_name: 6/26/01 368 Buffy Coat Male


title: Blood36

description: Blood cell RNA

source_name: 6/20/01 483 Buffy Coat Female


title: Blood30

description: Blood cell RNA

source_name: 7/24/01 368 Buffy Coat Male


title: Blood33

description: Blood cell RNA

source_name: 7/18/01 404 Buffy Coat Male


title: Blood20

description: Blood cell RNA

source_name: 7/5/01 367 Buffy Coat Female


title: Blood25

description: Blood cell RNA

source_name: 6/20/01 368 Buffy Coat Male


title: Blood31

description: Blood cell RNA

source_name: pool of individual blood

source_name: 6/12/01 404 Buffy Coat Male


title: Blood17

description: Blood cell RNA

source_name: 7/24/01 315 Buffy Coat Male


title: Blood18

description: Blood cell RNA

source_name: 6/12/01 367 Buffy Coat Female


title: Blood27

description: Blood cell RNA

source_name: 7/5/01 368 Buffy Coat Male


title: Blood23

description: Blood cell RNA

source_name: 7/24/01 367 Buffy Coat Female


title: Blood28

description: Blood cell RNA

source_name: 7/10/01 368 Buffy Coat Male


title: Blood24

description: Blood cell RNA

source_name: 6/12/01 368 Buffy Coat Male


title: Blood21

description: Blood cell RNA

source_name: 7/10/01 367 Buffy Coat Female


title: Blood22

description: Blood cell RNA

source_name: 7/18/01 367 Buffy Coat Female


title: Blood16

description: Blood cell RNA

source_name: 7/18/01 315 Buffy Coat Male


title: Blood19

description: Blood cell RNA

source_name: 6/20/01 367 Buffy Coat Female


title: Blood14

description: Blood cell RNA

source_name: 7/18/01 297 Buffy Coat Male


title: Blood32

description: Blood cell RNA

source_name: 6/20/01 404 Buffy Coat Male


title: Blood11

description: Blood cell RNA

source_name: 6/12/01 297 Buffy Coat Male


title: Blood8

description: Blood cell RNA

source_name: 7/10/01 287 Buffy Coat Female


title: Blood15

description: Blood cell RNA

source_name: 7/24/01 297 Buffy Coat Male


title: Blood13

description: Blood cell RNA

source_name: pool of individual blood

source_name: 7/10/01 297 Buffy Coat Male


title: Blood10

description: Blood cell RNA

source_name: 7/24/01 287 Buffy Coat Female


title: Blood7

description: Blood cell RNA

source_name: 7/5/01 287 Buffy Coat Female


title: Blood12

description: Blood cell RNA

source_name: 6/20/01 297 Buffy Coat Male


title: VREI_SJ020_2-18-01

description: wt adult prep 3 vs mixed reference

source_name: wt mixed reference mRNA

source_name: wt adult prep 3 mRNA


title: Blood9

description: Blood cell RNA

source_name: 7/18/01 287 Buffy Coat Female


title: Blood5

description: Blood cell RNA

source_name: 6/12/01 287 Buffy Coat Female


title: Blood1

description: Blood cell RNA

source_name: 6/12/01 277 Buffy Coat Female


title: Blood6

description: Blood cell RNA

source_name: 6/26/01 287 Buffy Coat Female


title: VREI_SI099_3-17-01

description: wt L4 prep 2 vs mixed reference

source_name: wt L4 prep 2 mRNA


title: VREI_SJ102_3-19-01

description: wt L4 prep 1 vs mixed reference

source_name: wt L4 prep 1 mRNA


title: Blood4

description: Blood cell RNA

source_name: 7/24/01 277 Buffy Coat Female


title: VREI_SH132_3-07-01

description: wt L4 prep 3 vs mixed reference

source_name: wt L4 prep 3 mRNA


title: VREI_SJ098_3-19-01

description: wt L3 prep 1 vs mixed reference

source_name: wt mixed reference

source_name: wt L3 prep 1 mRNA


title: VREI_SI064_2-18-01

description: wt L3 prep 3 vs mixed reference

source_name: wt L3 prep 3 mRNA


title: Blood2

description: Blood cell RNA

source_name: pool of individual blood

source_name: 6/20/01 277 Buffy Coat Female


title: VREI_SL019_3-20-01

description: wt L2 prep 2 vs mixed reference

source_name: wt L2 prep 2 mRNA


title: VREI_SJ106_3-19-01

description: wt adult prep 1 vs mixed reference

source_name: wt adult prep 1 mRNA


title: VREI_SJ070_3-19-01

description: wt L2 prep 1 vs mixed reference

source_name: wt mixed reference mRNA

source_name: wt L2 prep 1 mRNA


title: VREI_SG069_2-22-01

description: wt L2 prep 4 vs mixed reference

source_name: wt L2 prep 4 mRNA


title: Blood3

description: Blood cell RNA

source_name: 7/18/01 277 Buffy Coat Female


title: VREI_SL066_2-22-01

description: wt L3 prep 4 vs mixed reference

source_name: wt L3 prep 4 mRNA


title: VREI_SJ033_3-18-01

description: wt L3 prep 2 vs mixed reference

source_name: wt L3 prep 2 mRNA


title: VREI_SJ042_2-18-01

description: wt L4 prep 4 vs mixed reference

source_name: wt L4 prep 4 mRNA


title: VREI_SJ048_2-18-01

description: wt adult prep 4 vs mixed reference

source_name: wt adult prep 4 mRNA


title: VREI_SL020_3-20-01

description: wt adult prep 2 vs mixed reference

source_name: wt adult prep 2 mRNA


title: VREI_SL021_2-19-01

description: glp-4 adult prep 4 vs reference

source_name: wt mixed reference RNA

source_name: glp-4 adult prep 4 mRNA


title: VREI_SL048_2-20-01

description: wt L2 prep 3 vs mixed reference

source_name: wt L2 prep 3 mRNA


title: VREI_SJ064_2-19-01

description: glp-4 adult prep 3 vs reference

source_name: glp-4 adult prep 3 mRNA


title: VREI_SI041_2-15-01

description: glp-4 adult prep 2 vs reference

source_name: glp-4 adult prep 2 mRNA


title: VREI_A039_7-31-01

description: TP12 adult w/ emb 3 prep 3 hermaphrodites vs mixed reference

source_name: TP12 adult w/ emb 3 prep 3 mRNA


title: VREI_A014_7-24-01

description: TP12 adult w/ emb 3 prep 1 hermaphrodites vs mixed reference

source_name: TP12 adult w/ emb 3 prep 1 mRNA


title: VREI_A025_7-26-01

description: TP11 adult w/ emb 2 prep 2 hermaphrodites vs mixed reference

source_name: TP11 adult w/ emb 2 prep 2 mRNA


title: VREI_A013_7-24-01

description: TP11 adult w/ emb 2 prep 1 hermaphrodites vs mixed reference

source_name: wt mixed reference mRNA

source_name: TP11 adult w/ emb 2 prep 1 mRNA


title: VREI_A024_7-26-01

description: TP10 adult w/ emb 1 prep 2 hermaphrodites vs mixed reference

source_name: TP10 adult w/ emb 1 prep 2 mRNA


title: VREI_SJ090_2-19-01

description: glp-4 L4 prep 4 vs mixed reference

source_name: wt mixed stage reference

source_name: glp-4 L4 prep 4


title: VREI_SJ088_2-19-01

description: glp-4 L3 prep 4 vs wt mixed reference

source_name: wt mixed reference

source_name: glp-4 L3 prep 4


title: VREI_A011_7-24-01

description: TP09 adult  prep 1 hermaphrodites vs mixed reference

source_name: TP09 adult prep 1 mRNA


title: VREI_SG041_2-10-01

description: glp-4 L4 prep 1 vs mixed reference

source_name: glp-4 L4


title: VREI_A026_7-26-01

description: TP12 adult w/ emb 3 prep 2 hermaphrodites vs mixed reference

source_name: TP12 adult w/ emb 3 prep 2 mRNA


title: VREI_SJ059_2-19-01

description: glp-4 L4 prep 3 vs mixed reference

source_name: glp-4 L4 prep 3


title: Human Limb Muscle 12 (M12)

city: Philadelphia

first: Dominik

last: Fischer

state: PA

institute: Pennsylvania Muscle Institute

description:
Specimen was collected at biopsy
Keywords = Muscle
Keywords = DMD
Keywords = Myasthenia Gravis
Keywords = Limb

source_name: Human Quadriceps Femoris Muscle


title: VREI_A022_7-26-01

description: TP08 YA 2 prep 2 hermaphrodites vs mixed reference

source_name: TP08 YA2 prep 2 mRNA


title: VREI_A038_7-31-01

description: TP11 adult w/ emb 2 prep 3 hermaphrodites vs mixed reference

source_name: TP11 adult w/ emb 2 prep 3 mRNA


title: VREI_A012_7-24-01

description: TP10 adult w/ emb 1 prep 1 hermaphrodites vs mixed reference

source_name: TP10 adult w/ emb 1 prep 1 mRNA


title: VREI_A023_7-26-01

description: TP09 adult  prep 2 hermaphrodites vs mixed reference

source_name: TP09 adult prep 2 mRNA


title: VREI_SI032_2-15-01

description: glp-4 L4 prep 2 vs mixed reference

source_name: glp-4 L4 prep 2


title: VREI_SI053_2-15-01

description: glp-4 L2 prep 1 vs mixed reference

source_name: wt mixed reference mRNA

source_name: glp-4 L2 prep 1 mRNA


title: VREI_A035_7-31-01

description: TP08 YA 2 prep 3 hermaphrodites vs mixed reference

source_name: TP08 YA2 prep 3 mRNA


title: VREI_SJ053_2-19-01

description: glp-4 L3 prep 3 vs wt mixed reference

source_name: glp-4 L3 prep 3


title: VREI_A037_7-31-01

description: TP10 adult w/ emb 1 prep 3 hermaphrodites vs mixed reference

source_name: TP10 adult w/ emb 1 prep 3 mRNA


title: VREI_A036_7-31-01

description: TP09 adult  prep 3 hermaphrodites vs mixed reference

source_name: TP09 adult prep 3 mRNA


title: VREI_SL022_2-21-01

description: glp-4 L2 prep 2 vs mixed reference

source_name: glp-4 L2 prep 2 mRNA


title: VREI_A008_7_21_01

description: TP08 YA 2 prep 1 hermaphrodites vs mixed reference

source_name: TP08 YA2 prep 1 mRNA


title: VREI_A040_8-21-01

description: TP07 YA 1 prep 3 hermaphrodites vs mixed reference

source_name: TP07 YA 1 prep 3 mRNA


title: VREI_A007_7-21-01

description: TP07 YA 1 prep 1 hermaphrodites vs mixed reference

source_name: TP07 YA 1 prep 1 mRNA


title: VREI_A021_7-26-01

description: TP07 YA 1 prep 2 hermaphrodites vs mixed reference

source_name: TP07 YA 1 prep 2 mRNA


title: VREI_SL098_2-22-01

description: glp-4 L3 prep 1 vs wt mixed reference

source_name: wt mixed reference

source_name: glp-4 L3 prep 1


title: Human Limb Muscle 6 (M6)

source_name: Human Quadriceps Femoris Muscle


title: VREI_A033_7-29-01

description: TP06 L4/YA prep 3 hermaphrodites vs mixed reference

source_name: TP06 L4/YA prep 3 mRNA


title: VREI_SI009_2-12-01

description: glp-4 adult prep 1 vs reference

source_name: wt mixed reference RNA

source_name: glp-4 adult prep 1 mRNA


title: Human Limb Muscle 5 (M5)


title: Human Extraocular Muscle 3 (hEOM3)

description:
Specimen was collected at autopsy
Keywords = EOM
Keywords = DMD
Keywords = Myasthenia Gravis
Keywords = Eye

source_name: Human extraocular muscle


title: Syracuse Low Avoidance (SLA) learning rats 3

city: Dallas

first: Shumin

last: Zhang

state: TX

institute: UT Southwestern

description: Rats were sacrificed 2 weeks after the two-way active avoidance testing and the whole hippocampus were collected and pooled, 3 rats/pool.

source_name: hippocampi pool from 3 SLA rats


title: VREI_A032_7-29-01

description: TP05 late L4 prep 3 hermaphrodites vs mixed reference

source_name: wt mixed reference mRNA

source_name: TP05 late L4 prep 3 mRNA


title: VREI_A009_7-24-01

description: TP06 L4/YA prep 1 hermaphrodites vs mixed reference

source_name: TP06 L4/young adult prep 1 mRNA


title: Human Extraocular Muscle 2 (hEOM2)

source_name: Human superior rectus extraocular muscle


title: Syracuse High Avoidance (SHA) learning rats 3

source_name: hippocampi pool from 3 SHA rats


title: VREI_A019_7-25-01

description: TP05 late L4 prep 2 hermaphrodites vs mixed reference

source_name: TP05 late L4 prep 2 mRNA


title: VREI_A018_7-25-01

description: TP04 early L4 prep 2 hermaphrodites vs mixed reference

source_name: TP04 early L4 prep 2 mRNA


title: Syracuse Low Avoidance (SLA) learning rats 1


title: VREI_A020_7-25-01

description: TP06 L4/YA prep 2 hermaphrodites vs mixed reference

source_name: TP06 L4/young adult prep 2 mRNA


title: Syracuse High Avoidance (SHA) learing rats 2

description: Rats were sacrificed 2 weeks after the two-way active avoidance testing and the whole hippocampus were collected.


title: VREI_A002_7-22-01

description: TP02 late L3 prep 1 hermaphrodites vs mixed reference

source_name: TP02 late L3 prep 1 mRNA


title: VREI_A006_7-24-01

description: TP05 late L4 prep 1 hermaphrodites vs mixed reference

source_name: TP05 late L4 prep 1 mRNA


title: Syracuse High Avoidance (SHA) learning rats 1

source_name: Hippocampus pool from three SHA rats


title: VREI_A003_7-22-01

description: TP03 L3/L4 prep 1 hermaphrodites vs mixed reference

source_name: TP03 L3/L4 prep 1 mRNA


title: VREI_A028_7-29-01

description: TP02 late L3 prep 3 hermaphrodites vs mixed reference

source_name: TP02 late L3 prep 3 mRNA


title: VREI_A027_7-29-01

description: TP01 mid-L3 prep 3 hermaphrodites  vs mixed reference

source_name: TP01 mid-L3 prep 3 mRNA


title: VREI_A029_7-29-01

description: TP03 L3/L4 prep 3 hermaphrodites vs mixed reference

source_name: TP03 L3/L4 prep 3 mRNA


title: VREI_A016_7-25-01

description: TP02 late L3 prep 2 hermaphrodites vs mixed reference

source_name: TP02 late L3 prep 2 mRNA


title: Syracuse Low Avoidance (SLA) learning rats 2

source_name: hippocampi pool from 3 SLA rats


title: VREI_A042_6-05-02

description: him-5 adult males prep 3 vs mixed reference

source_name: wt mixed reference mRNA

source_name: him-5 adult males prep 3 mRNA


title: VREI_A030_7-29-01

description: TP04 early L4 prep 3 hermaphrodites vs mixed reference

source_name: TP04 early L4 prep 3 mRNA


title: VREI_A047_4-22-02

description: him-5 adult males prep 1 vs mixed reference

source_name: wt mixed stage reference mRNA

source_name: him-5 adult males prep 1 mRNA


title: WT sample 4:Comparison of WT and YODA

status: Public on Dec 30 2003

city: Stanford

first: Chris

last: Somerville

institute: Carnegie Institution

description:
Wild type and yda-2 plants were germinated and grown on commercial potting mix in walk-in chambers with constant illumination at 22oC. The aerial parts of the plants were harvested at the rosette stage, prior to bolting. Total RNA was prepared using Trizol reagent (Invitrogen) with the additional steps recommended for polysaccharide-rich tissues. Hybridization probes for the GeneChip AtGenome1 microarrays (Affymetrix) were prepared from 20 mg total RNA. All procedures followed Affymetrix protocols. Briefly, cDNA was synthesized using Superscript reverse transcriptase (Invitrogen) and a T7-(dT)24 primer, purified by phenol/chloroform extraction using Phase Lock Gel tubes (Eppendorf), and precipitated with ethanol. Labeled antisense RNA was generated with a BioArray kit (Enzo) and purified using an RNeasy kit (Qiagen). 25 mg of the fragmented cRNAs were used for hybridization to the arrays. Affymetrix instruments were used for hybridization, washing, staining and scanning of the arrays according to the provided instructions.
Data from four biological replications representing tissue grown and harvested at different times was collected. The average signals of all eight experiments were scaled to the target value of 500.
Keywords = yoda
Keywords = yda
Lot batch = Wild type 4

organism: Arabidopsis thaliana

source_name: Aerial parts harvested at rosette stage


title: VREI_A043_6-03-02

description: him-5 adult males prep 4 vs mixed reference

source_name: him-5 adult males prep 4 mRNA


title: YODA sample 4:Comparison of WT and YODA

description:
Wild type and yda-2 plants were germinated and grown on commercial potting mix in walk-in chambers with constant illumination at 22oC. The aerial parts of the plants were harvested at the rosette stage, prior to bolting. Total RNA was prepared using Trizol reagent (Invitrogen) with the additional steps recommended for polysaccharide-rich tissues. Hybridization probes for the GeneChip AtGenome1 microarrays (Affymetrix) were prepared from 20 mg total RNA. All procedures followed Affymetrix protocols. Briefly, cDNA was synthesized using Superscript reverse transcriptase (Invitrogen) and a T7-(dT)24 primer, purified by phenol/chloroform extraction using Phase Lock Gel tubes (Eppendorf), and precipitated with ethanol. Labeled antisense RNA was generated with a BioArray kit (Enzo) and purified using an RNeasy kit (Qiagen). 25 mg of the fragmented cRNAs were used for hybridization to the arrays. Affymetrix instruments were used for hybridization, washing, staining and scanning of the arrays according to the provided instructions.
Data from four biological replications representing tissue grown and harvested at different times was collected. The average signals of all eight experiments were scaled to the target value of 500.
Keywords = yoda
Keywords = yda
Lot batch = YODA 4


title: VREI_A015_7-25-01

description: TP01 mid-L3 prep 2 hermaphrodites  vs mixed reference

source_name: TP01 mid-L3 prep 2 mRNA


title: VREI_A005_7-22-01

description: TP04 early L4 prep 1 hermaphrodites vs mixed reference

source_name: TP04 early L4 prep 1 mRNA


title: YODA sample 3:Comparison of WT and YODA

description:
Wild type and yda-2 plants were germinated and grown on commercial potting mix in walk-in chambers with constant illumination at 22oC. The aerial parts of the plants were harvested at the rosette stage, prior to bolting. Total RNA was prepared using Trizol reagent (Invitrogen) with the additional steps recommended for polysaccharide-rich tissues. Hybridization probes for the GeneChip AtGenome1 microarrays (Affymetrix) were prepared from 20 mg total RNA. All procedures followed Affymetrix protocols. Briefly, cDNA was synthesized using Superscript reverse transcriptase (Invitrogen) and a T7-(dT)24 primer, purified by phenol/chloroform extraction using Phase Lock Gel tubes (Eppendorf), and precipitated with ethanol. Labeled antisense RNA was generated with a BioArray kit (Enzo) and purified using an RNeasy kit (Qiagen). 25 mg of the fragmented cRNAs were used for hybridization to the arrays. Affymetrix instruments were used for hybridization, washing, staining and scanning of the arrays according to the provided instructions.
Data from four biological replications representing tissue grown and harvested at different times was collected. The average signals of all eight experiments were scaled to the target value of 500.
Keywords = yoda
Keywords = yda
Lot batch = YODA 3


title: Chemokine and receptor expression by Ag104Ld tumor tissue

city: Chicago

first: Yang-Xin

last: Fu

state: IL

institute: U. of Chicago

description: Chemokine and receptor array on mRNA from murine tumor tissue

source_name: murine tumor tissue


title: Chemokine and receptor expression by Ag104Ld-LIGHT

description: Chemokine and receptor array on mRNA from LIGHT-expressing murine tumor tissue


title: WT sample 3:Comparison of WT and YODA

description:
Wild type and yda-2 plants were germinated and grown on commercial potting mix in walk-in chambers with constant illumination at 22oC. The aerial parts of the plants were harvested at the rosette stage, prior to bolting. Total RNA was prepared using Trizol reagent (Invitrogen) with the additional steps recommended for polysaccharide-rich tissues. Hybridization probes for the GeneChip AtGenome1 microarrays (Affymetrix) were prepared from 20 mg total RNA. All procedures followed Affymetrix protocols. Briefly, cDNA was synthesized using Superscript reverse transcriptase (Invitrogen) and a T7-(dT)24 primer, purified by phenol/chloroform extraction using Phase Lock Gel tubes (Eppendorf), and precipitated with ethanol. Labeled antisense RNA was generated with a BioArray kit (Enzo) and purified using an RNeasy kit (Qiagen). 25 mg of the fragmented cRNAs were used for hybridization to the arrays. Affymetrix instruments were used for hybridization, washing, staining and scanning of the arrays according to the provided instructions.
Data from four biological replications representing tissue grown and harvested at different times was collected. The average signals of all eight experiments were scaled to the target value of 500.
Keywords = yoda
Keywords = yda
Lot batch = Wild type 3


title: LBP6

city: Suita, Osaka

first: Yoshihiro

last: Asano

country: Japan

institute: Osaka Univ.

description: neonatal mouse cardiomyocyte (6 hrs after the infection)

source_name: cacrdiomyocyte


title: Control6

source_name: cardiomyocyte


title: Mutant6


title: WT sample 2:Comparison of WT and YODA

description:
Wild type and yda-2 plants were germinated and grown on commercial potting mix in walk-in chambers with constant illumination at 22oC. The aerial parts of the plants were harvested at the rosette stage, prior to bolting. Total RNA was prepared using Trizol reagent (Invitrogen) with the additional steps recommended for polysaccharide-rich tissues. Hybridization probes for the GeneChip AtGenome1 microarrays (Affymetrix) were prepared from 20 mg total RNA. All procedures followed Affymetrix protocols. Briefly, cDNA was synthesized using Superscript reverse transcriptase (Invitrogen) and a T7-(dT)24 primer, purified by phenol/chloroform extraction using Phase Lock Gel tubes (Eppendorf), and precipitated with ethanol. Labeled antisense RNA was generated with a BioArray kit (Enzo) and purified using an RNeasy kit (Qiagen). 25 mg of the fragmented cRNAs were used for hybridization to the arrays. Affymetrix instruments were used for hybridization, washing, staining and scanning of the arrays according to the provided instructions.
Data from four biological replications representing tissue grown and harvested at different times was collected. The average signals of all eight experiments were scaled to the target value of 500.
Keywords = yoda
Keywords = yda
Lot batch = wild type 2


title: delta sus1-2

status: Public on Dec 29 2003

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description:
Total RNA isolated from a exponentially growing culture of sus1 mutant yeast cells. cDNA labelling using oligo(dT)15VN and 33P-dCTP.
Keywords = yeast
Keywords = SUS1

organism: Saccharomyces cerevisiae

source_name: Exponentially growing sus1 mutant yeast strain


title: WT sample 1: Comparison of WT and YODA

description:
Wild type and yda-2 plants were germinated and grown on commercial potting mix in walk-in chambers with constant illumination at 22oC. The aerial parts of the plants were harvested at the rosette stage, prior to bolting. Total RNA was prepared using Trizol reagent (Invitrogen) with the additional steps recommended for polysaccharide-rich tissues. Hybridization probes for the GeneChip AtGenome1 microarrays (Affymetrix) were prepared from 20 mg total RNA. All procedures followed Affymetrix protocols. Briefly, cDNA was synthesized using Superscript reverse transcriptase (Invitrogen) and a T7-(dT)24 primer, purified by phenol/chloroform extraction using Phase Lock Gel tubes (Eppendorf), and precipitated with ethanol. Labeled antisense RNA was generated with a BioArray kit (Enzo) and purified using an RNeasy kit (Qiagen). 25 mg of the fragmented cRNAs were used for hybridization to the arrays. Affymetrix instruments were used for hybridization, washing, staining and scanning of the arrays according to the provided instructions.
Data from four biological replications representing tissue grown and harvested at different times was collected. The average signals of all eight experiments were scaled to the target value of 500.
Keywords = yoda
Keywords = yda
Lot batch = wild type 1


title: delta sus1-3


title: YODA sample 1: Comparison of WT and YODA

description:
Wild type and yda-2 plants were germinated and grown on commercial potting mix in walk-in chambers with constant illumination at 22oC. The aerial parts of the plants were harvested at the rosette stage, prior to bolting. Total RNA was prepared using Trizol reagent (Invitrogen) with the additional steps recommended for polysaccharide-rich tissues. Hybridization probes for the GeneChip AtGenome1 microarrays (Affymetrix) were prepared from 20 mg total RNA. All procedures followed Affymetrix protocols. Briefly, cDNA was synthesized using Superscript reverse transcriptase (Invitrogen) and a T7-(dT)24 primer, purified by phenol/chloroform extraction using Phase Lock Gel tubes (Eppendorf), and precipitated with ethanol. Labeled antisense RNA was generated with a BioArray kit (Enzo) and purified using an RNeasy kit (Qiagen). 25 mg of the fragmented cRNAs were used for hybridization to the arrays. Affymetrix instruments were used for hybridization, washing, staining and scanning of the arrays according to the provided instructions.
Data from four biological replications representing tissue grown and harvested at different times was collected. The average signals of all eight experiments were scaled to the target value of 500.
Keywords = yoda
Keywords = yda
Lot batch = YODA 1


title: wt 1

description:
Total RNA isolated from a exponentially growing culture of wild type yeast cells. cDNA labelling using oligo(dT)15VN and 33P-dCTP.
Keywords = yeast

source_name: Exponentially growing wild type yeast strain


title: VREI_A001_7-21-01

description: TP01 mid-L3 prep 1 hermaphrodites vs mixed reference

source_name: TP01 mid-L3 prep 1 mRNA


title: delta grx5 3

description:
Total RNA isolated from a exponentially growing culture of grx5 mutant yeast cells. cDNA labelling using oligo(dT)15VN and 33P-dCTP.
Keywords = yeast
Keywords = grx5
Keywords = glutaredoxin

source_name: Exponentially growing grx5 mutant MML100 yeast strain


title: YODA sample 2:Comparison of WT and YODA

description:
Wild type and yda-2 plants were germinated and grown on commercial potting mix in walk-in chambers with constant illumination at 22oC. The aerial parts of the plants were harvested at the rosette stage, prior to bolting. Total RNA was prepared using Trizol reagent (Invitrogen) with the additional steps recommended for polysaccharide-rich tissues. Hybridization probes for the GeneChip AtGenome1 microarrays (Affymetrix) were prepared from 20 mg total RNA. All procedures followed Affymetrix protocols. Briefly, cDNA was synthesized using Superscript reverse transcriptase (Invitrogen) and a T7-(dT)24 primer, purified by phenol/chloroform extraction using Phase Lock Gel tubes (Eppendorf), and precipitated with ethanol. Labeled antisense RNA was generated with a BioArray kit (Enzo) and purified using an RNeasy kit (Qiagen). 25 mg of the fragmented cRNAs were used for hybridization to the arrays. Affymetrix instruments were used for hybridization, washing, staining and scanning of the arrays according to the provided instructions.
Data from four biological replications representing tissue grown and harvested at different times was collected. The average signals of all eight experiments were scaled to the target value of 500.
Keywords = yoda
Keywords = yda
Lot batch = YODA 2


title: wt 2


title: delta pet117 2

description:
Total RNA isolated from a exponentially growing culture of pet117 mutant yeast cells. cDNA labelling using oligo(dT)15VN and 33P-dCTP.
Keywords = yeast
Keywords = PET117

source_name: Exponentially growing pet117 mutant MML511 yeast strain


title: delta grx5 2


title: delta pet117 1


title: delta sus1-1


title: delta pet117 3


title: wt 3


title: delta grx5 1


title: wild type 3

source_name: Exponentially growing wild type W303-1A yeast strain


title: wild type 1


title: wild type 2


title: VREI_A044_4-24-02

description: him-5 adult males prep 2 vs mixed reference

source_name: wt mixed reference mRNA

source_name: him-5 adult males prep 2 mRNA


title: S3WT-4hr-R3 hyb

status: Public on Dec 28 2003

city: Bronx

first: Weijia

state: NY

address: 1300 Morris Park Ave

department: Medicine

institute: Albert Einstein College of Medicine

description: S3WT-4hr-R3 hyb


title: S3KO-1hr-R3 hyb

description: S3KO-1hr-R3 hyb


title: S3WT-4hr-R2 hyb

description: S3WT-4hr-R2 hyb


title: S3WT-1hr-R1 hyb

description: S3WT-1hr-R1 hyb


title: S3WT-4hr-R1 hyb

description: S3WT-4hr-R1 hyb


title: S3WT-0.3hr-R2 hyb

description: S3WT-0.3hr-R2 hyb


title: S3KO-4hr-R2 hyb

description: S3KO-4hr-R2 hyb


title: S3KO-4hr-R1 hyb

description: S3KO-4hr-R1 hyb


title: S3WT-2hr-R3 hyb

description: S3WT-2hr-R3 hyb


title: S3WT-0hr-R1 hyb

description: S3WT-0hr-R1 hyb


title: S3KO-2hr-R1 hyb

description: S3KO-2hr-R1 hyb


title: S3WT-0hr-R2 hyb

description: S3WT-0hr-R2 hyb


title: S3WT-0hr-R3 hyb

description: S3WT-0hr-R3 hyb


title: S3KO-2hr-R3 hyb

description: S3KO-2hr-R3 hyb


title: S3WT-0.3hr-R1 hyb

description: S3WT-0.3hr-R1 hyb


title: S3KO-4hr-R3 hyb

description: S3KO-4hr-R3 hyb


title: S3WT-2hr-R1 hyb

description: S3WT-2hr-R1 hyb


title: S3WT-1hr-R2 hyb

description: S3WT-1hr-R2 hyb


title: S3KO-1hr-R2 hyb

description: S3KO-1hr-R2 hyb


title: S3KO-0hr-R2 hyb

description: S3KO-0hr-R2 hyb


title: S3WT-1hr-R3 hyb

description: S3WT-1hr-R3 hyb


title: S3KO-0hr-R3 hyb

description: S3KO-0hr-R3 hyb


title: S3KO-0.3hr-R3 hyb

description: S3KO-0.3hr-R3 hyb


title: S2WT_vs_U0126-4hr-R3 hyb

description: S2WT_vs_U0126-4hr-R3 hyb


title: S3WT-2hr-R2 hyb

description: S3WT-2hr-R2 hyb


title: S3WT-0.3hr-R3 hyb

description: S3WT-0.3hr-R3 hyb


title: S3KO-0hr-R1 hyb

description: S3KO-0hr-R1 hyb


title: S3KO-0.3hr-R2 hyb

description: S3KO-0.3hr-R2 hyb


title: S3KO-2hr-R2 hyb

description: S3KO-2hr-R2 hyb


title: VREI_A017_7-25-01

description: TP03 L3/L4 prep 2 hermaphrodites vs mixed reference

source_name: TP03 L3/L4 prep 2 mRNA


title: S3KO-0.3hr-R1 hyb

description: S3KO-0.3hr-R1 hyb


title: S2WT_vs_U0126-4hr-R1 hyb

description: S2WT_vs_U0126-4hr-R1 hyb


title: S2WT_vs_U0126-2hr-R1 hyb

description: S2WT_vs_U0126-2hr-R1 hyb


title: S2WT_vs_U0126-4hr-R2 hyb

description: S2WT_vs_U0126-4hr-R2 hyb


title: S2WT-1hr-R1 hyb

description: S2WT-1hr-R1 hyb


title: S2WT_vs_U0126-2hr-R3 hyb

description: S2WT_vs_U0126-2hr-R3 hyb


title: S2WT_vs_U0126-2hr-R2 hyb

description: S2WT_vs_U0126-2hr-R2 hyb


title: S2WT-2hr-R1 hyb

description: S2WT-2hr-R1 hyb


title: S2WT-4hr-R1 hyb

description: S2WT-4hr-R1 hyb


title: S2WT-2hr-R3 hyb

description: S2WT-2hr-R3 hyb


title: S2WT-0.3hr-R3 hyb

description: S2WT-0.3hr-R3 hyb


title: S2WT_vs_U0126-0hr-R1 hyb

description: S2WT_vs_U0126-0hr-R1 hyb


title: S2WT-0hr-R2 hyb

description: S2WT-0hr-R2 hyb


title: S2WT_vs_U0126-0.3hr-R2 hyb

description: S2WT_vs_U0126-0.3hr-R2 hyb


title: S2WT-2hr-R2 hyb

description: S2WT-2hr-R2 hyb


title: S2WT_vs_U0126-1hr-R2 hyb

description: S2WT_vs_U0126-1hr-R2 hyb


title: S2WT_vs_U0126-0.3hr-R1 hyb

description: S2WT_vs_U0126-0.3hr-R1 hyb


title: S2WT-0.3hr-R2 hyb

description: S2WT-0.3hr-R2 hyb


title: S2WT_vs_U0126-0hr-R3 hyb

description: S2WT_vs_U0126-0hr-R3 hyb


title: S2WT-4hr-R3 hyb

description: S2WT-4hr-R3 hyb


title: S2WT-4hr-R2 hyb

description: S2WT-4hr-R2 hyb


title: S2WT-0hr-R3 hyb

description: S2WT-0hr-R3 hyb


title: S2WT_vs_U0126-0hr-R2 hyb

description: S2WT_vs_U0126-0hr-R2 hyb


title: S2WT-1hr-R3 hyb

description: S2WT-1hr-R3 hyb


title: S2WT_vs_U0126-1hr-R1 hyb

description: S2WT_vs_U0126-1hr-R1 hyb


title: S2WT-0hr-R1 hyb

description: S2WT-0hr-R1 hyb


title: S2WT-1hr-R2 hyb

description: S2WT-1hr-R2 hyb


title: S2WT_vs_U0126-0.3hr-R3 hyb

description: S2WT_vs_U0126-0.3hr-R3 hyb


title: S2WT_vs_U0126-1hr-R3 hyb

description: S2WT_vs_U0126-1hr-R3 hyb


title: S2KO-4hr-R3 hyb

description: S2KO-4hr-R3 hyb


title: S2WT-0.3hr-R1 hyb

description: S2WT-0.3hr-R1 hyb


title: S2KO-4hr-R2 hyb

description: S2KO-4hr-R2 hyb


title: S2KO-2hr-R3 hyb

description: S2KO-2hr-R3 hyb


title: S2KO-4hr-R1 hyb

description: S2KO-4hr-R1 hyb


title: Normal Megakaryocytes

status: Public on Dec 25 2003

city: Modena

first: Enrico

last: Tagliafico

state: MO

address: Via Campi 287

department: Center for Genome Research

country: Italy

institute: University of Modena and Reggio Emilia

description: Normal donors BM CD34+ cells were differentiated in thrombopoietin-treated liquid suspension cultures. Briefly, CD34+ cells (80,000 /mL) were resuspended in a serum-free medium in the presence of 100 ng/mL of human recombinant thrombopoietin (TPO; Genzyme, Boston, MA). Every 3 days, viable cells were scored by Trypan blue dye exclusion and cultures were amplified with fresh serum-free medium. Each well was then supplemented with 100 ng/mL TPO. After 14 to 16 days of liquid culture, CD34-derived megakaryocytes (MKs) were purified by means of an anti-CD41a monoclonal antibody (MoAb) (Dako, Milan, Italy) directed against the glycoproteic alpha2B-beta3 complex and immunobeads (MPC 450 Dynabeads; Dynal, Oslo, Norway). The purity of MKs was determined for each isolation by indirect immunofluorescence, using an anti-CD41b MoAb which reacts with a different epitope of alpha2B-beta3 subunit (Immunotech Inc., Westbrook, ME), followed by a goat anti-mouse IgG, covalently linked to fluorescein (Becton Dickinson, San Jose, CA).

source_name: Bone marrow, TPO treated, CD34 positive cells (6 donors pool)


title: S2KO-1hr-R3 hyb

description: S2KO-1hr-R3 hyb


title: S2KO-2hr-R1 hyb

description: S2KO-2hr-R1 hyb


title: S2KO-2hr-R2 hyb

description: S2KO-2hr-R2 hyb


title: Essential Thrombocythemia (ET) Megakaryocytes

description: Essential Thrombocythemia (ET) patients BM CD34+ cells were differentiated in thrombopoietin-treated liquid suspension cultures. Briefly, CD34+ cells (80,000 /mL) were resuspended in a serum-free medium in the presence of 100 ng/mL of human recombinant thrombopoietin (TPO; Genzyme, Boston, MA). Every 3 days, viable cells were scored by Trypan blue dye exclusion and cultures were amplified with fresh serum-free medium. Each well was then supplemented with 100 ng/mL TPO. After 14 to 16 days of liquid culture, CD34-derived megakaryocytes (MKs) were purified by means of an anti-CD41a monoclonal antibody (MoAb) (Dako, Milan, Italy) directed against the glycoproteic alpha2B-beta3 complex and immunobeads (MPC 450 Dynabeads; Dynal, Oslo, Norway). The purity of MKs was determined for each isolation by indirect immunofluorescence, using an anti-CD41b MoAb which reacts with a different epitope of alpha2B-beta3 subunit (Immunotech Inc., Westbrook, ME), followed by a goat anti-mouse IgG, covalently linked to fluorescein (Becton Dickinson, San Jose, CA).

source_name: Bone marrow, TPO treated, CD34 positive cells (6 ET patients pool)


title: S2KO-1hr-R1 hyb

description: S2KO-1hr-R1 hyb


title: HS27a+CD14-6

status: Public on Dec 22 2003

city: Seattle

first: Lynn

last: Graf

address: 1100 Fairview Ave. N. D1-100

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

description: Comparison of gene expression profile of human bone marrrow stromal cell line HS27a cultured 3 days with and without monocytes. Values are ratio of 3-day HS27a plus monocyte coculture to HS27a alone.

source_name: HS27a alone

source_name: HS27a + monocyte coculture, Donor 6


title: HS27a+CD14-4

source_name: HS27a + monocyte coculture, Donor 4


title: S2KO-0.3hr-R3 hyb

description: S2KO-0.3hr-R3 hyb


title: HS27a-CD14-3

source_name: HS27a + monocyte coculture, Donor 1


title: S2KO-0hr-R2 hyb

description: S2KO-0hr-R2 hyb


title: rat sham 3 (1.2)

status: Public on Dec 20 2003

city: Durham

first: Mihai

middle: Victor

last: Podgoreanu

address: Genome Science Research Bldg.1, 595 LaSalle St, Ste#1027

department: Anesthesiology

institute: Duke University Medical Center

description:
rat heart from sham operated controls
Keywords = rat
Keywords = cardiac
Keywords = cytokine
Keywords = inflammation
Keywords = CPB

source_name: total heart


title: S2KO-1hr-R2 hyb

description: S2KO-1hr-R2 hyb


title: HS27a+CD14-7

source_name: HS27a + monocyte coculture, Donor 7


title: S2KO-0hr-R1 hyb

description: S2KO-0hr-R1 hyb


title: rat sham 3


title: S2KO-0hr-R3 hyb

description: S2KO-0hr-R3 hyb


title: VREI_SI065_10-11-00

status: Public on Dec 24 2003

city: New Haven

institute: Yale University School of Medicine

description: fem-1(lf) vs fem-3(gf) prep 3

source_name: fem-3(gf) prep 3 mRNA

source_name: fem-1(lf) prep 3 mRNA


title: S2KO-0.3hr-R1 hyb

description: S2KO-0.3hr-R1 hyb


title: VREI_SI045_10-11-00

description: fem-1(lf) vs fem-3(gf) prep 1

source_name: fem-3(gf) prep 1 mRNA

source_name: fem-1(lf) prep 1 mRNA


title: HS27a+CD14-5


title: HS27a+CD14-2

source_name: HS27a + monocyte coculture, Donor 2


title: HS27a+CD14-1


title: rat sham 2 (1.2)


title: S2KO-0.3hr-R2 hyb

description: S2KO-0.3hr-R2 hyb


title: rat sham 1


title: rat sham 1 (1.2)


title: rat CPB 2 (1.2)

description:
rat heart exposed to cardiopulmonary bypass
Keywords = rat
Keywords = cardiac
Keywords = cytokine
Keywords = inflammation
Keywords = CPB


title: rat CPB 1 (1.2)


title: rat sham 2


title: rat CPB 3

description:
rat heart subjected to cardiopulmonary bypass
Keywords = rat
Keywords = cardiac
Keywords = cytokine
Keywords = inflammation
Keywords = CPB


title: VREI_SI055_10-11-00

description: fem-1(lf) vs fem-3(gf) prep 2

source_name: fem-3(gf) prep 2 mRNA

source_name: fem-1(lf) prep 2 mRNA


title: rat CPB 2


title: rat CPB 1


title: Leukemia Promyelocytic (HL-60) [JunctionChip 5 of 5]

status: Public on Dec 19 2003

first: John

last: Castle

department: Informatics

institute: Merck

description:
Samples were purchased from Clontech as mRNA.
Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end.  shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3'  shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3'  1.5  g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was  degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C.  The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick).
The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification.  Multiple polymerase chain reactions were run using 0.15  g of double stranded DNA and standard reaction conditions.  Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase)  DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3'  T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3'  followed by Qiaquick purification.
Further amplification was achieved using in vitro transcription reactions with X0.5  g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and  reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II).
The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray.
Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66",  Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003.
Keywords = junction alternate splicing oligonucleotide

source_name: Leukemia Promyelocytic (HL-60)


title: Leukemia Lymphoblastic (MOLT-4) [JunctionChip 5 of 5]

source_name: Leukemia Lymphoblastic (MOLT-4)


title: Hour 11 No Yeast (NY)

city: Providence

first: Boris

last: Gershman

state: RI

address: Attn: Marc Tatar, Box G-W

department: Ecology and Evolutionary Biology

institute: Brown University

description:
Hour 11 No Yeast Treatment (NY).

Larvae were reared on standard diet until early third instar, at which time they were washed and transferred to standard diet lacking yeast.  The animals remained on this diet until four days after emergence, when one group of adults was switched back to standard diet containing yeast (group Y) while another remained on the diet lacking yeast (group NY).  Flies from both groups were killed every hour for the next twelve hours, creating 24 samples across the two treatments.  In addition, four samples of flies were killed just before the start of the time course and used as baseline replicates for the no yeast (NY) and yeast (Y) treatments.  Baseline replicates were temporally ordered as noted for change-point analysis.  No yeast (NY) treatment samples at hours four and eight did not yield microarray data due to insufficient RNA.

Total RNA was extracted from whole animals using Trizol (Invitrogen).  Sample processing and microarray hybridization/scanning were performed at the Brown University Center for Genetics and Genomics according to Affymetrix protocol.  Microarray data was normalized by DNA-Chip Analyzer  (dChip, http://www.dchip.org), which utilizes an invariant difference selection (IDS) algorithm to construct a normalization relation.
Keywords = insulin, diet, nutrition

organism: Drosophila melanogaster

source_name: Whole animal (Drosophila)


title: Hour 12 Yeast (Y)

description:
Hour 12 Yeast Treatment (Y).

Larvae were reared on standard diet until early third instar, at which time they were washed and transferred to standard diet lacking yeast.  The animals remained on this diet until four days after emergence, when one group of adults was switched back to standard diet containing yeast (group Y) while another remained on the diet lacking yeast (group NY).  Flies from both groups were killed every hour for the next twelve hours, creating 24 samples across the two treatments.  In addition, four samples of flies were killed just before the start of the time course and used as baseline replicates for the no yeast (NY) and yeast (Y) treatments.  Baseline replicates were temporally ordered as noted for change-point analysis.  No yeast (NY) treatment samples at hours four and eight did not yield microarray data due to insufficient RNA.

Total RNA was extracted from whole animals using Trizol (Invitrogen).  Sample processing and microarray hybridization/scanning were performed at the Brown University Center for Genetics and Genomics according to Affymetrix protocol.  Microarray data was normalized by DNA-Chip Analyzer  (dChip, http://www.dchip.org), which utilizes an invariant difference selection (IDS) algorithm to construct a normalization relation.
Keywords = insulin, diet, nutrition


title: Brain (caudate nucleus) [JunctionChip 5 of 5]

source_name: Brain (caudate nucleus)


title: Hour 11 Yeast (Y)

description:
Hour 11 Yeast Treatment (Y).

Larvae were reared on standard diet until early third instar, at which time they were washed and transferred to standard diet lacking yeast.  The animals remained on this diet until four days after emergence, when one group of adults was switched back to standard diet containing yeast (group Y) while another remained on the diet lacking yeast (group NY).  Flies from both groups were killed every hour for the next twelve hours, creating 24 samples across the two treatments.  In addition, four samples of flies were killed just before the start of the time course and used as baseline replicates for the no yeast (NY) and yeast (Y) treatments.  Baseline replicates were temporally ordered as noted for change-point analysis.  No yeast (NY) treatment samples at hours four and eight did not yield microarray data due to insufficient RNA.

Total RNA was extracted from whole animals using Trizol (Invitrogen).  Sample processing and microarray hybridization/scanning were performed at the Brown University Center for Genetics and Genomics according to Affymetrix protocol.  Microarray data was normalized by DNA-Chip Analyzer  (dChip, http://www.dchip.org), which utilizes an invariant difference selection (IDS) algorithm to construct a normalization relation.
Keywords = insulin, diet, nutrition


title: Hour 10 Yeast (Y)

description:
Hour 10 Yeast Treatment (Y).

Larvae were reared on standard diet until early third instar, at which time they were washed and transferred to standard diet lacking yeast.  The animals remained on this diet until four days after emergence, when one group of adults was switched back to standard diet containing yeast (group Y) while another remained on the diet lacking yeast (group NY).  Flies from both groups were killed every hour for the next twelve hours, creating 24 samples across the two treatments.  In addition, four samples of flies were killed just before the start of the time course and used as baseline replicates for the no yeast (NY) and yeast (Y) treatments.  Baseline replicates were temporally ordered as noted for change-point analysis.  No yeast (NY) treatment samples at hours four and eight did not yield microarray data due to insufficient RNA.

Total RNA was extracted from whole animals using Trizol (Invitrogen).  Sample processing and microarray hybridization/scanning were performed at the Brown University Center for Genetics and Genomics according to Affymetrix protocol.  Microarray data was normalized by DNA-Chip Analyzer  (dChip, http://www.dchip.org), which utilizes an invariant difference selection (IDS) algorithm to construct a normalization relation.
Keywords = insulin, diet, nutrition


title: Jejunum 2 [JunctionChip 5 of 5]

source_name: Jejunum


title: Hour 10 No Yeast (NY)

description:
Hour 10 No Yeast Treatment (NY).

Larvae were reared on standard diet until early third instar, at which time they were washed and transferred to standard diet lacking yeast.  The animals remained on this diet until four days after emergence, when one group of adults was switched back to standard diet containing yeast (group Y) while another remained on the diet lacking yeast (group NY).  Flies from both groups were killed every hour for the next twelve hours, creating 24 samples across the two treatments.  In addition, four samples of flies were killed just before the start of the time course and used as baseline replicates for the no yeast (NY) and yeast (Y) treatments.  Baseline replicates were temporally ordered as noted for change-point analysis.  No yeast (NY) treatment samples at hours four and eight did not yield microarray data due to insufficient RNA.

Total RNA was extracted from whole animals using Trizol (Invitrogen).  Sample processing and microarray hybridization/scanning were performed at the Brown University Center for Genetics and Genomics according to Affymetrix protocol.  Microarray data was normalized by DNA-Chip Analyzer  (dChip, http://www.dchip.org), which utilizes an invariant difference selection (IDS) algorithm to construct a normalization relation.
Keywords = insulin, diet, nutrition


title: Brain (postcentral gyrus) [JunctionChip 5 of 5]

source_name: Brain (postcentral gyrus)


title: Hour 12 No Yeast (NY)

description:
Hour 12 No Yeast Treatment (NY).

Larvae were reared on standard diet until early third instar, at which time they were washed and transferred to standard diet lacking yeast.  The animals remained on this diet until four days after emergence, when one group of adults was switched back to standard diet containing yeast (group Y) while another remained on the diet lacking yeast (group NY).  Flies from both groups were killed every hour for the next twelve hours, creating 24 samples across the two treatments.  In addition, four samples of flies were killed just before the start of the time course and used as baseline replicates for the no yeast (NY) and yeast (Y) treatments.  Baseline replicates were temporally ordered as noted for change-point analysis.  No yeast (NY) treatment samples at hours four and eight did not yield microarray data due to insufficient RNA.

Total RNA was extracted from whole animals using Trizol (Invitrogen).  Sample processing and microarray hybridization/scanning were performed at the Brown University Center for Genetics and Genomics according to Affymetrix protocol.  Microarray data was normalized by DNA-Chip Analyzer  (dChip, http://www.dchip.org), which utilizes an invariant difference selection (IDS) algorithm to construct a normalization relation.
Keywords = insulin, diet, nutrition


title: Epididymis [JunctionChip 5 of 5]

source_name: Epididymis


title: Testis [JunctionChip 5 of 5]

source_name: Testis


title: Mislabeled (was labeled Heart (interventricular septum)) [JunctionChip 5 of 5]


title: Colon (descending) [JunctionChip 5 of 5]

source_name: Colon (descending)


title: Hour 9 No Yeast (NY)

description:
Hour 9 No Yeast Treatment (NY).

Larvae were reared on standard diet until early third instar, at which time they were washed and transferred to standard diet lacking yeast.  The animals remained on this diet until four days after emergence, when one group of adults was switched back to standard diet containing yeast (group Y) while another remained on the diet lacking yeast (group NY).  Flies from both groups were killed every hour for the next twelve hours, creating 24 samples across the two treatments.  In addition, four samples of flies were killed just before the start of the time course and used as baseline replicates for the no yeast (NY) and yeast (Y) treatments.  Baseline replicates were temporally ordered as noted for change-point analysis.  No yeast (NY) treatment samples at hours four and eight did not yield microarray data due to insufficient RNA.

Total RNA was extracted from whole animals using Trizol (Invitrogen).  Sample processing and microarray hybridization/scanning were performed at the Brown University Center for Genetics and Genomics according to Affymetrix protocol.  Microarray data was normalized by DNA-Chip Analyzer  (dChip, http://www.dchip.org), which utilizes an invariant difference selection (IDS) algorithm to construct a normalization relation.
Keywords = insulin, diet, nutrition


title: Hour 8 Yeast (Y)

description:
Hour 8 Yeast Treatment (Y).

Larvae were reared on standard diet until early third instar, at which time they were washed and transferred to standard diet lacking yeast.  The animals remained on this diet until four days after emergence, when one group of adults was switched back to standard diet containing yeast (group Y) while another remained on the diet lacking yeast (group NY).  Flies from both groups were killed every hour for the next twelve hours, creating 24 samples across the two treatments.  In addition, four samples of flies were killed just before the start of the time course and used as baseline replicates for the no yeast (NY) and yeast (Y) treatments.  Baseline replicates were temporally ordered as noted for change-point analysis.  No yeast (NY) treatment samples at hours four and eight did not yield microarray data due to insufficient RNA.

Total RNA was extracted from whole animals using Trizol (Invitrogen).  Sample processing and microarray hybridization/scanning were performed at the Brown University Center for Genetics and Genomics according to Affymetrix protocol.  Microarray data was normalized by DNA-Chip Analyzer  (dChip, http://www.dchip.org), which utilizes an invariant difference selection (IDS) algorithm to construct a normalization relation.
Keywords = insulin, diet, nutrition


title: Lymphoma (Burkitts Daudi) [JunctionChip 5 of 5]

source_name: Lymphoma (Burkitts Daudi)


title: Lung (fetal) [JunctionChip 5 of 5]

source_name: Lung (fetal)


title: Tonsil [JunctionChip 5 of 5]

source_name: Tonsil


title: Hour 9 Yeast (Y)

description:
Hour 9 Yeast Treatment (Y).

Larvae were reared on standard diet until early third instar, at which time they were washed and transferred to standard diet lacking yeast.  The animals remained on this diet until four days after emergence, when one group of adults was switched back to standard diet containing yeast (group Y) while another remained on the diet lacking yeast (group NY).  Flies from both groups were killed every hour for the next twelve hours, creating 24 samples across the two treatments.  In addition, four samples of flies were killed just before the start of the time course and used as baseline replicates for the no yeast (NY) and yeast (Y) treatments.  Baseline replicates were temporally ordered as noted for change-point analysis.  No yeast (NY) treatment samples at hours four and eight did not yield microarray data due to insufficient RNA.

Total RNA was extracted from whole animals using Trizol (Invitrogen).  Sample processing and microarray hybridization/scanning were performed at the Brown University Center for Genetics and Genomics according to Affymetrix protocol.  Microarray data was normalized by DNA-Chip Analyzer  (dChip, http://www.dchip.org), which utilizes an invariant difference selection (IDS) algorithm to construct a normalization relation.
Keywords = insulin, diet, nutrition


title: Kidney [JunctionChip 5 of 5]

source_name: Kidney


title: Hour 7 No Yeast (NY)

description:
Hour 7 No Yeast Treatment (NY).

Larvae were reared on standard diet until early third instar, at which time they were washed and transferred to standard diet lacking yeast.  The animals remained on this diet until four days after emergence, when one group of adults was switched back to standard diet containing yeast (group Y) while another remained on the diet lacking yeast (group NY).  Flies from both groups were killed every hour for the next twelve hours, creating 24 samples across the two treatments.  In addition, four samples of flies were killed just before the start of the time course and used as baseline replicates for the no yeast (NY) and yeast (Y) treatments.  Baseline replicates were temporally ordered as noted for change-point analysis.  No yeast (NY) treatment samples at hours four and eight did not yield microarray data due to insufficient RNA.

Total RNA was extracted from whole animals using Trizol (Invitrogen).  Sample processing and microarray hybridization/scanning were performed at the Brown University Center for Genetics and Genomics according to Affymetrix protocol.  Microarray data was normalized by DNA-Chip Analyzer  (dChip, http://www.dchip.org), which utilizes an invariant difference selection (IDS) algorithm to construct a normalization relation.
Keywords = insulin, diet, nutrition


title: Jejunum [JunctionChip 5 of 5]


title: rat CPB 3 (1.2)

source_name: total heart


title: Brain (hippocampus) [JunctionChip 5 of 5]

source_name: Brain (hippocampus)


title: Hour 5 Yeast (Y)

description:
Hour 5 Yeast Treatment (Y).

Larvae were reared on standard diet until early third instar, at which time they were washed and transferred to standard diet lacking yeast.  The animals remained on this diet until four days after emergence, when one group of adults was switched back to standard diet containing yeast (group Y) while another remained on the diet lacking yeast (group NY).  Flies from both groups were killed every hour for the next twelve hours, creating 24 samples across the two treatments.  In addition, four samples of flies were killed just before the start of the time course and used as baseline replicates for the no yeast (NY) and yeast (Y) treatments.  Baseline replicates were temporally ordered as noted for change-point analysis.  No yeast (NY) treatment samples at hours four and eight did not yield microarray data due to insufficient RNA.

Total RNA was extracted from whole animals using Trizol (Invitrogen).  Sample processing and microarray hybridization/scanning were performed at the Brown University Center for Genetics and Genomics according to Affymetrix protocol.  Microarray data was normalized by DNA-Chip Analyzer  (dChip, http://www.dchip.org), which utilizes an invariant difference selection (IDS) algorithm to construct a normalization relation.
Keywords = insulin, diet, nutrition