title: WGACON-6


title: WGACON-12

status: Public on Nov 04 2007

type: RNA

city: Miami

first: Amanda

last: Myers

state: FL

address: 1600 NW 10th Ave

department: Psychiatry and Behavioral Sciences

country: USA

institute: Miller School of Medicine, University of Miami

description: Human Cortex from neurologically normal control, Caucasian, male.

hyb_protocol: RNA: Illumina Whole Genome Gene Expression Rev. F (Illumina Doc #11763837)

scan_protocol: RNA: Illumina Beadstation

data_processing: RNA: Beadstudio software v 1.5.0.34, rank invariant normalization to extract, log10 transformation before analysis

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: neuropathologically normal frozen temporal cortex

label_protocol: RNA: per ambion manual for cat #IL1791, biotinylated cRNA created from in vitro translation targeting poly A tail, cy3 used to image RNA signal

extract_protocol: total RNA (Qiagen Rneasy Lipid Tissue cat #cat 74804, Qiagen Rnase free dnase set- cat # 79254)


title: NA12751 growth 3, replicate 5

status: Public on Aug 08 2007

city: Montreal

first: Tony

last: Kwan

state: Quebec

address: 740 Dr. Penfield

department: Human Genetics

country: Canada

institute: McGill University

description: Probeset expression data from NA12751 growth 3, replicate 5

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16-20 hr at 45C on GeneChip Human Exon 1.0 ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The data were analyzed with Affymetrix Power Tools package using Affymetrix default analysis settings and sketch quantile as normalization method.

source_name: CEU NA12751 Biological growth 3, Technical replicate 5

label_protocol: Biotinlabelled target for the microarray experiment were prepared using 1 ug of total RNA. The RNA was subjected to a rRNA removal procedure with the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen) and cDNA was synthesized using the GeneChip® WT (Whole Transcript) Sense Target Labeling and Control Reagents kit as described by the manufacturer (Affymetrix).

growth_protocol: Cells were grown at 37°C and 5% CO2 in RPMI 1640 medium supplemented with 15% heat-inactivated fetal bovine serum, 2 mM L-glutamine and penicillin/streptomycin

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

treatment_protocol: Cells were harvested at a density of 0.8-1.1 x 10e6 cells/mL. Cells were then resuspended and lysed in TRIzol reagent

tag: Gender

value: female, Cell-type:lymphoblasts

tag: Coriell cell line repository identifier


title: NA12751 growth 2, replicate 4

description: Probeset expression data from NA12751 growth 2, replicate 4

source_name: CEU NA12751 Biological growth 2, Technical replicate 4


title: NA12751 growth 3, replicate 4

description: Probeset expression data from NA12751 growth 3, replicate 4

source_name: CEU NA12751 Biological growth 3, Technical replicate 4


title: WGACON-7

hyb_protocol: RNA: per ambion manual for cat #IL1791, biotinylated cRNA created from in vitro translation targeting poly A tail, cy3 used to image RNA signal


title: NA12751 growth 3, replicate 2

description: Probeset expression data from NA12751 growth 3, replicate 2

source_name: CEU NA12751 Biological growth 3, Technical replicate 2


title: NA12751 growth 3, replicate 3

description: Probeset expression data from NA12751 growth 3, replicate 3

source_name: CEU NA12751 Biological growth 3, Technical replicate 3


title: NA12751 growth 2, replicate 5

description: Probeset expression data from NA12751 growth 2, replicate 5

source_name: CEU NA12751 Biological growth 2, Technical replicate 5


title: WGACON-17


title: WGACON-1


title: NA12751 growth 3, replicate 1

description: Probeset expression data from NA12751 growth 3, replicate 1

source_name: CEU NA12751 Biological growth 3, Technical replicate 1


title: NA12751 growth 2, replicate 3

description: Probeset expression data from NA12751 growth 2, replicate 3

source_name: CEU NA12751 Biological growth 2, Technical replicate 3


title: NA12751 growth 1, replicate 5

description: Probeset expression data from NA12751 growth 1, replicate 5

source_name: CEU NA12751 Biological growth 1, Technical replicate 5


title: NA12751 growth 2, replicate 1

description: Probeset expression data from NA12751 growth 2, replicate 1

source_name: CEU NA12751 Biological growth 2, Technical replicate 1


title: NA12751 growth 1, replicate 4

description: Probeset expression data from NA12751 growth 1, replicate 4

source_name: CEU NA12751 Biological growth 1, Technical replicate 4


title: NA12751 growth 1, replicate 3

description: Probeset expression data from NA12751 growth 1, replicate 3

source_name: CEU NA12751 Biological growth 1, Technical replicate 3


title: NA12750 growth 3, replicate 5

description: Probeset expression data from NA12750 growth 3, replicate 5

source_name: CEU NA12750 Biological growth 3, Technical replicate 5

value: male, Cell-type:lymphoblasts


title: NA12751 growth 1, replicate 1

description: Probeset expression data from NA12751 growth 1, replicate 1

source_name: CEU NA12751 Biological growth 1, Technical replicate 1


title: NA12750 growth 3, replicate 4

description: Probeset expression data from NA12750 growth 3, replicate 4

source_name: CEU NA12750 Biological growth 3, Technical replicate 4


title: NA12751 growth 2, replicate 2

description: Probeset expression data from NA12751 growth 2, replicate 2

source_name: CEU NA12751 Biological growth 2, Technical replicate 2


title: NA12750 growth 1, replicate 3

description: Probeset expression data from NA12750 growth 1, replicate 3

source_name: CEU NA12750 Biological growth 1, Technical replicate 3


title: NA12751 growth 1, replicate 2

description: Probeset expression data from NA12751 growth 1, replicate 2

source_name: CEU NA12751 Biological growth 1, Technical replicate 2


title: GM18515

status: Public on Jun 06 2007

city: Chicago

first: Eileen

last: Dolan

state: IL

address: 5841 S. Maryland

department: Medicine

institute: University of Chicago

description: Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array.

hyb_protocol: Approximately 5.5ug of labeled DNA target was hybridized to the Affymetrix GeneChip Human Exon 1.0 ST Array at 45oC for 16 hours per manufacturers recommendation (see http://www.affymetrix.com/products/arrays/exon_application.affx for additional information).  Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450.

scan_protocol: All samples were scanned on a GCS3000 Scanner (Affymetrix, Inc.).

data_processing: dbSNP in Probe Filtering and Background Correction Protocol: The start and end coordinates of all probes of the Exon array were queried against the human genome (hg17). The coordinates for all SNPs were then queried in the dbSNP database (http://www.ncbi.nlm.nih.gov/projects/SNP/) (release 126) and then based on location, we identified probes harboring SNPs. In total, ~400,000 probes contained SNPs within their structure. Of the ~1.4 million probesets of the exon array, 255,676 contained at least one probe with SNP. Among these affected probesets, 105,000 harbored 2 or more probes with SNPs. Resulting probe signal intensity files were filtered by removing this group of 105,000probesets. After filtering, individual probe intensities were background corrected by subtracting the median intensity of a population of non-genomic probes with the same GC content to account for any non-specific hybridization. The resulting probe signal intensities were sketch quantile normalized over all 176 samples and gene-level expressions were summarized using the robust multi-array average (RMA) method with signals generated on a core set of exons.  A constant of 16 was added to all probeset intensities for variance stabilization and summarized signals were then log2 transformed with a median polish.

source_name: lymphoblastoid cell line

label_protocol: Ribosomal RNA was depleted from 1µg of total RNA using the RiboMinus Human/Mouse Transcriptome Isolation kit (Invitrogen Corp., Carlsbad, CA).  cDNA was generated using the GeneChip WT cDNA Synthesis and Amplification Kit (Affymetrix, Inc., Santa Clara, CA) per manufacturer's instructions.  cDNA was fragmented and end labeled using the GeneChip® WT Terminal Labeling Kit (Affymetrix, Inc.).

growth_protocol:
Each sample was collected while in exponential growth.
Lymphoblastoid cell lines were centrifuged at 400 × g to remove media and 5 mL fresh lymphoblastoid cell media (LCL media) containing RPMI 1640 (Mediatech)/1% l-glutamine (Mediatech) plus 20% FBS (HyClone Laboratories) for the initial passage and then passaged every 48 h with LCL medium and 15% FBS. Cell suspensions were transferred to 25 cm2 flasks and incubated at 37oC in a 90% humidified 5% CO2 atmosphere. Cell lines were maintained at a concentration of 3.5-4.0×105 cells/mL and harvested following the 4th passage, only if viability >= 85%.

extract_protocol: Lymphoblastoid cell line suspensions were spun at 400 × g for 5 min to remove media. Cell pellets were washed twice with ice-cold PBS and stored at -80°C. Total RNA was extracted using RNeasy Plus Kits according to the manufacturers protocol.

treatment_protocol: Untreated, baseline expression data.

tag: Yoruban sample

value: Male

tag: Associated family

tag: Family relationship

value: child


title: NA12750 growth 1, replicate 1

description: Probeset expression data from NA12750 growth 1, replicate 1

source_name: CEU NA12750 Biological growth 1, Technical replicate 1


title: NA12750 growth 3, replicate 1

description: Probeset expression data from NA12750 growth 3, replicate 1

source_name: CEU NA12750 Biological growth 3, Technical replicate 1


title: GM18501

value: father


title: GM18517

value: Female

value: mother


title: GM18507


title: NA12750 growth 2, replicate 4

description: Probeset expression data from NA12750 growth 2, replicate 4

source_name: CEU NA12750 Biological growth 2, Technical replicate 4


title: NA12750 growth 2, replicate 2

description: Probeset expression data from NA12750 growth 2, replicate 2

source_name: CEU NA12750 Biological growth 2, Technical replicate 2


title: GM18516


title: GM18505


title: NA12750 growth 2, replicate 5

description: Probeset expression data from NA12750 growth 2, replicate 5

source_name: CEU NA12750 Biological growth 2, Technical replicate 5


title: NA12750 growth 1, replicate 2

description: Probeset expression data from NA12750 growth 1, replicate 2

source_name: CEU NA12750 Biological growth 1, Technical replicate 2


title: GM18504


title: GM18508


title: NA12750 growth 2, replicate 3

description: Probeset expression data from NA12750 growth 2, replicate 3

source_name: CEU NA12750 Biological growth 2, Technical replicate 3


title: GM18500


title: GM18503


title: NA12750 growth 1, replicate 4

description: Probeset expression data from NA12750 growth 1, replicate 4

source_name: CEU NA12750 Biological growth 1, Technical replicate 4


title: GM12892

tag: CEPH sample

value: maternal grandmother


title: GM18502


title: GM07034

value: paternal grandfather


title: GM18506


title: GM12878


title: NA12750 growth 1, replicate 5

description: Probeset expression data from NA12750 growth 1, replicate 5

source_name: CEU NA12750 Biological growth 1, Technical replicate 5


title: GM12872


title: GM12891

value: maternal grandfather


title: GM12875


title: GM12873

value: paternal grandmother


title: GM12865


title: GM12874


title: GM12813


title: GM07029


title: GM12762


title: GM12801


title: GM12812


title: GM12814


title: GM12864


title: GM07022


title: GM12763


title: GM12761


title: GM12753


title: GM12751


title: GM12815


title: GM12752


title: GM12802


title: GM12740


title: GM12717


title: GM12707


title: GM12264


title: GM12750


title: GM12249


title: GM12760


title: GM07019


title: GM12239


title: GM12234


title: GM12248


title: GM12156


title: GM12155


title: GM12057


title: GM12044


title: GM12144


title: GM12154


title: GM12003


title: GM12043


title: GM12145


title: GM12004


title: GM11993


title: GM12006


title: GM12056


title: GM12146


title: GM11995


title: GM11840


title: GM12005


title: GM11882


title: GM11994


title: GM06994


title: GM11992


title: GM11831


title: GM11881


title: GM07000


title: GM11839


title: GM11830


title: GM11829


title: GM11832


title: GM10863


title: GM10860


title: GM06993


title: GM10861


title: GM10846


title: GM10856


title: GM10835


title: GM10854


title: GM10857


title: GM10851


title: GM10859


title: GM06991


title: GM10839


title: GM19223


title: GM19240


title: GM10847


title: GM19222


title: GM19210


title: GM10831


title: GM10838


title: GM19239


title: GM19238


title: GM19221


title: GM19209


title: GM19208


title: GM19211


title: GM19206


title: GM19202


title: GM19207


title: GM19203


title: GM19204


title: GM19200


title: GM19173


title: GM10830


title: GM19201


title: GM19193


title: GM19205


title: GM19153


title: GM19172


title: GM19154


title: GM19142


title: GM19160


title: GM19144


title: GM19143


title: GM19171


title: GM19145


title: GM19141


title: GM07357


title: GM19161


title: GM19159


title: GM19140


title: GM07348


title: GM19152


title: GM19138


title: GM19116


title: GM19130


title: GM19131


title: GM19139


title: GM19128


title: GM19094


title: GM19192


title: GM19101


title: GM07345


title: GM19137


title: GM19194


title: GM19132


title: GM19102


title: GM19098


title: GM07056


title: GM19119


title: GM19129


title: GM19103


title: GM19120


title: GM19092


title: GM19099


title: GM19127


title: GM19100


title: GM19093


title: GM18912


title: GM18913


title: GM18914


title: GM18863


title: GM18870


title: GM18872


title: GM18862


title: GM18861


title: GM07055


title: GM18853


title: GM18858


title: GM18855


title: GM18859


title: GM18860


title: GM18856


title: GM18523


title: GM18522


title: GM18854


title: GM18516 (2)

status: Public on May 31 2007

data_processing: Gene expression profiles were assessed by using Affymetrix GeneChip Human Exon 1.0 ST array. Probe-signal intensities were sketch normalized using a subset of the 1.4 million probe sets. Transcript expression was summarized by using a robust multiarray average method (RMA) with the core set of well annotated exons (~200,000). The ExACT program developed by Affymetrix was used to determine gene signal estimates


title: GM18852


title: GM06985

description: Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array.Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array.


title: GM07048


title: GM18506 (2)


title: GM18505 (2)


title: GM18517 (2)


title: GM18515 (2)


title: GM18507 (2)


title: GM18508 (2)


title: GM18857


title: GM18503 (2)


title: GM18521


title: GM18502 (2)


title: GM07034 (2)


title: GM18500 (2)


title: GM18504 (2)


title: GM12892 (2)


title: GM12875 (2)


title: GM18501 (2)


title: GM12878 (2)


title: GM12891 (2)


title: GM12873 (2)


title: GM12872 (2)


title: GM12874 (2)


title: GM07029 (2)


title: GM12865 (2)


title: GM12864 (2)


title: GM12815 (2)


title: GM12801 (2)


title: GM12802 (2)


title: GM12812 (2)


title: GM12762 (2)


title: GM12813 (2)


title: GM12763 (2)


title: GM12814 (2)


title: GM12761 (2)


title: GM12760 (2)


title: GM07022 (2)


title: GM12707 (2)


title: GM12717 (2)


title: GM12249 (2)


title: GM12740 (2)


title: GM12750 (2)


title: GM12751 (2)


title: GM12248 (2)


title: GM07019 (2)


title: GM12234 (2)


title: GM12264 (2)


title: GM12156 (2)


title: GM12239 (2)


title: GM12752 (2)


title: GM12145 (2)


title: GM12753 (2)


title: GM12146 (2)


title: GM12154 (2)


title: GM12155 (2)


title: GM07000 (2)


title: GM12057 (2)


title: GM12006 (2)


title: GM12144 (2)


title: GM12056 (2)


title: GM12043 (2)


title: GM12044 (2)


title: GM12005 (2)


title: GM11995 (2)


title: GM11882 (2)


title: GM11832 (2)


title: GM11881 (2)


title: GM12004 (2)


title: GM11992 (2)


title: GM12003 (2)


title: GM11840 (2)


title: GM06994 (2)


title: GM11831 (2)


title: GM11993 (2)


title: GM11839 (2)


title: GM10861 (2)


title: GM11829 (2)


title: GM11994 (2)


title: GM11830 (2)


title: GM06993 (2)


title: GM10863 (2)


title: GM10859 (2)


title: GM10857 (2)


title: GM10847 (2)


title: GM10856 (2)


title: GM10846 (2)


title: GM10860 (2)


title: GM10839 (2)


title: GM10854 (2)


title: GM10851 (2)


title: GM06991 (2)


title: GM19240 (2)


title: GM19238 (2)


title: GM19211 (2)


title: GM19221 (2)


title: GM19222 (2)


title: GM19239 (2)


title: GM10831 (2)


title: GM19203 (2)


title: GM19208 (2)


title: GM10835 (2)


title: GM10838 (2)


title: GM19207 (2)


title: GM19223 (2)


title: GM19204 (2)


title: GM19209 (2)


title: GM19210 (2)


title: GM19205 (2)


title: GM19206 (2)


title: GM19202 (2)


title: GM19193 (2)


title: GM10830 (2)


title: GM19192 (2)


title: GM19201 (2)


title: GM19194 (2)


title: GM19173 (2)


title: GM19200 (2)


title: GM19171 (2)


title: GM07357 (2)


title: GM19154 (2)


title: GM19152 (2)


title: GM19141 (2)


title: GM19161 (2)


title: GM19160 (2)


title: GM19153 (2)


title: GM19143 (2)


title: GM19140 (2)


title: GM19145 (2)


title: GM07348 (2)


title: GM19139 (2)


title: GM19172 (2)


title: GM19132 (2)


title: GM19138 (2)


title: GM19137 (2)


title: GM19131 (2)


title: GM19142 (2)


title: GM19128 (2)


title: GM19127 (2)


title: GM19144 (2)


title: GM19129 (2)


title: GM19120 (2)


title: GM19130 (2)


title: GM19159 (2)


title: GM19119 (2)


title: GM19101 (2)


title: GM19103 (2)


title: GM19099 (2)


title: GM07345 (2)


title: GM19100 (2)


title: GM19102 (2)


title: GM19098 (2)


title: GM19116 (2)


title: GM19093 (2)


title: GM18863 (2)


title: GM07056 (2)


title: GM19092 (2)


title: GM18912 (2)


title: GM18870 (2)


title: GM18913 (2)


title: GM18872 (2)


title: GM18857 (2)


title: GM18914 (2)


title: GM18861 (2)


title: GM18858 (2)


title: GM18855 (2)


title: GM19094 (2)


title: GM07055 (2)


title: GM18862 (2)


title: GM18860 (2)


title: GM18859 (2)


title: GM18856 (2)


title: GM18853 (2)


title: GM18852 (2)


title: GM18522 (2)


title: GM06985 (2)

description: Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array.Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array.!Sample_data_processing=Gene expression profiles were assessed by using Affymetrix GeneChip Human Exon 1.0 ST array. Probe-signal intensities were sketch normalized using a subset of the 1.4 million probe sets. Transcript expression was summarized by using a robust multiarray average method (RMA) with the core set of well annotated exons (~200,000). The ExACT program developed by Affymetrix was used to determine gene signal estimates


title: GM07048 (2)


title: GM18521 (2)


title: GM18854 (2)


title: Mtb.inf3

status: Public on Dec 31 2006

city: San Francisco

first: Andrea

middle: J

last: Barczak

state: CA

address: 1550 4th St Rock Hall 545

institute: UCSF Sandler Center Functional Genomics Core Facility

description:
11Mm_168.gpr
57BL/6 mice were exposed to aerosols (5 ml suspension) containing M. tuberculosis (H37RV; 470 cfu) for 40 min and analyzed 21 d later, rep 3.

hyb_protocol: Samples were hybridized for 20h at 63 degrees in a solution containing 2.8  SSC,0.025 M HEPES pH7.0,0.2% SDS,1 μg/μL yeast tRNA,and 0.6 μg/μL human Cot-1 DNA

scan_protocol: Scanned on an Axon 4000AB scanner. Images were quantified using GenePix 6.0 software.

data_processing: LOWESS normalized, no background subtraction was used

organism: Mus musculus

source_name: Mouse pooled whole lung lung reference

label_protocol: cDNA  reverse transcribed and indirectly labelled with amino-allyl Cy3 or Cy5

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions

tag: tissue

value: whole lung

tag: type

value: pooled reference RNA

source_name: whole lung

tag: strain


title: Mtb.inf2

description:
11Mm_167.gpr
57BL/6 mice were exposed to aerosols (5 ml suspension) containing M. tuberculosis (H37RV; 470 cfu) for 40 min and analyzed 21 d later, rep 2.


title: Paerug.exoU1

description:
11Mm_181.gpr
P. aeruginosa exoU mutant strain (PA103: 5 x 107 cfu in 50 µl) was instilled intratracheally into BALB/c mice via the oropharynx. Mice were killed 2 h after treatment. Rep 1

value: BALB/c


title: Paerug.wild2

description:
11Mm_179.gpr
P. aeruginosa (PA103: 5 x 107 cfu in 50 µl) was instilled intratracheally into BALB/c mice via the oropharynx. Mice were killed 2 h after treatment. Rep 2


title: Bleo7d.S5

description:
11Mm_191.gpr
7 d Saline control(1.1 U/kg body weight in 60 µl saline was administered intratracheally to C57BL/6 mice. Mice were killed at 21 d, rep 5.


title: Nippo.S1

description:
11Mm_238.gpr
Saline control,BALB/c mice were injected with saline at the base of the tail and maintained on water supplemented with antibiotics for 5 d before being killed, rep 1


title: Nippo.N2

description:
11Mm_158.gpr
BALB/c mice were injected with 500 third-stage N. brasiliensis larvae at the base of the tail and maintained on water supplemented with antibiotics for 5 d before being killed, rep 2


title: Bleo21d.S6

description:
11Mm_198.gpr
21 d Saline control(1.1 U/kg body weight in 60 µl saline was administered intratracheally to C57BL/6 mice. Mice were killed at 21 d, rep 1.


title: Bleo21d.S9

description:
11Mm_200.gpr
21 d Saline control(1.1 U/kg body weight in 60 µl saline was administered intratracheally to C57BL/6 mice. Mice were killed at 21 d, rep 2.


title: Bleo21d.B9

description:
11Mm_197.gpr
A single dose of bleomycin (1.1 U/kg body weight in 60 µl saline was administered intratracheally to C57BL/6 mice. Mice were killed at 21 d, rep 5.


title: Paerug.cont2

description:
11Mm_247.gpr
Control: lactated Ringer's solution was instilled intratracheally into BALB/c mice via the oropharynx. Mice were killed 2 h after treatment. Rep 2


title: GM18523 (2)

description: Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array.


title: Mtb.inf1

description:
11Mm_166.gpr
57BL/6 mice were exposed to aerosols (5 ml suspension) containing M. tuberculosis (H37RV; 470 cfu) for 40 min and analyzed 21 d later, rep 1.


title: Nippo.S3

description:
11Mm_187.gpr
Saline control,BALB/c mice were injected with saline at the base of the tail and maintained on water supplemented with antibiotics for 5 d before being killed, rep 3


title: Bleo21d.B6

description:
11Mm_194.gpr
A single dose of bleomycin (1.1 U/kg body weight in 60 µl saline was administered intratracheally to C57BL/6 mice. Mice were killed at 21 d, rep 2.


title: Paerug.cont1

description:
11Mm_175.gpr
Control: lactated Ringer's solution was instilled intratracheally into BALB/c mice via the oropharynx. Mice were killed 2 h after treatment. Rep 1


title: Paerug.exoU3

description:
11Mm_183.gpr
P. aeruginosa exoU mutant strain (PA103: 5 x 107 cfu in 50 µl) was instilled intratracheally into BALB/c mice via the oropharynx. Mice were killed 2 h after treatment. Rep 3


title: Paerug.exoU2

description:
11Mm_182.gpr
P. aeruginosa exoU mutant strain (PA103: 5 x 107 cfu in 50 µl) was instilled intratracheally into BALB/c mice via the oropharynx. Mice were killed 2 h after treatment. Rep 2


title: Nippo.N3

description:
11Mm_159.gpr
BALB/c mice were injected with 500 third-stage N. brasiliensis larvae at the base of the tail and maintained on water supplemented with antibiotics for 5 d before being killed, rep 3


title: Mtb.cont3

description:
11Mm_171.gpr
Sterile water control, C57BL/6 mice were exposed to aerosols for 40 min and analyzed 21 d later, rep 3.


title: Bleo21d.B10

description:
11Mm_185.gpr
A single dose of bleomycin (1.1 U/kg body weight in 60 µl saline was administered intratracheally to C57BL/6 mice. Mice were killed at 21 d, rep 1.


title: Paerug.wild1

description:
11Mm_178.gpr
P. aeruginosa (PA103: 5 x 107 cfu in 50 µl) was instilled intratracheally into BALB/c mice via the oropharynx. Mice were killed 2 h after treatment. Rep 1


title: Mtb.cont2

description:
11Mm_170.gpr
Sterile water control, C57BL/6 mice were exposed to aerosols for 40 min and analyzed 21 d later, rep 2.


title: Nippo.S2

description:
11Mm_155.gpr
Saline control,BALB/c mice were injected with saline at the base of the tail and maintained on water supplemented with antibiotics for 5 d before being killed, rep 2


title: Mtb.cont1

description:
11Mm_169.gpr
Sterile water control, C57BL/6 mice were exposed to aerosols for 40 min and analyzed 21 d later, rep 1.


title: Bleo21d.B7

description:
11Mm_195.gpr
A single dose of bleomycin (1.1 U/kg body weight in 60 µl saline was administered intratracheally to C57BL/6 mice. Mice were killed at 21 d, rep 3.


title: Nippo.N1

description:
11Mm_152.gpr
BALB/c mice were injected with 500 third-stage N. brasiliensis larvae at the base of the tail and maintained on water supplemented with antibiotics for 5 d before being killed, rep 1


title: OVABalbc.Alum5

description:
GS.Mm_238.gpr
Control: BALB/c mice were sensitized with alum (10 mg alum, i.p.) on days 0, 7, and 14 and challenged with saline (50 µl saline). Mice were analyzed on Day 24. Rep 5


title: OVABalbc.OVA2

description:
GS.Mm_243.gpr
BALB/c mice were sensitized with OVA (50 µg in 10 mg alum, i.p.) on days 0, 7, and 14 and challenged with OVA (1 mg in 50 µl saline). Mice were analyzed on Day 24. Rep 2


title: Bleo21d.B8

description:
11Mm_196.gpr
A single dose of bleomycin (1.1 U/kg body weight in 60 µl saline was administered intratracheally to C57BL/6 mice. Mice were killed at 21 d, rep 4.


title: OVABalbc.OVA5

description:
GS.Mm_236.gpr
BALB/c mice were sensitized with OVA (50 µg in 10 mg alum, i.p.) on days 0, 7, and 14 and challenged with OVA (1 mg in 50 µl saline). Mice were analyzed on Day 24. Rep 5


title: OVABalbc.OVA4

description:
GS.Mm_245.gpr
BALB/c mice were sensitized with OVA (50 µg in 10 mg alum, i.p.) on days 0, 7, and 14 and challenged with OVA (1 mg in 50 µl saline). Mice were analyzed on Day 24. Rep 4


title: OVABalbc.OVA6

description:
GS.Mm_176.gpr
BALB/c mice were sensitized with OVA (50 µg in 10 mg alum, i.p.) on days 0, 7, and 14 and challenged with OVA (1 mg in 50 µl saline). Mice were analyzed on Day 24. Rep 6


title: OVABalbc.Alum4

description:
GS.Mm_237.gpr
Control: BALB/c mice were sensitized with alum (10 mg alum, i.p.) on days 0, 7, and 14 and challenged with saline (50 µl saline). Mice were analyzed on Day 24. Rep 4


title: OVABalbc.Alum1

description:
GS.Mm_239.gpr
Control: BALB/c mice were sensitized with alum (10 mg alum, i.p.) on days 0, 7, and 14 and challenged with saline (50 µl saline). Mice were analyzed on Day 24. Rep 1


title: OVABalbc.Alum2

description:
GS.Mm_174.gpr
Control: BALB/c mice were sensitized with alum (10 mg alum, i.p.) on days 0, 7, and 14 and challenged with saline (50 µl saline). Mice were analyzed on Day 24. Rep 2


title: Bleo7d.S1

description:
10Mm_243.gpr
7 d Saline control(1.1 U/kg body weight in 60 µl saline was administered intratracheally to C57BL/6 mice. Mice were killed at 21 d, rep 1.


title: OVABalbc.Alum3

description:
GS.Mm_175.gpr
Control: BALB/c mice were sensitized with alum (10 mg alum, i.p.) on days 0, 7, and 14 and challenged with saline (50 µl saline). Mice were analyzed on Day 24. Rep 3


title: IL13.S6ko.6

description:
10Mm_248.gpr
Control STAT6 -/-transgenic mice expressing IL-13 under the control of a Clara cell–specific promoter, mice were 6–8 wks of age, rep 6


title: IL13.S6wt.1

description:
10Mm_40.gpr
Transgenic mice expressing IL-13 under the control of a Clara cell–specific promoter, mice were 6–8 wks of age, rep 1


title: Bleo7d.S4

description:
10Mm_246.gpr
7 d Saline control(1.1 U/kg body weight in 60 µl saline was administered intratracheally to C57BL/6 mice. Mice were killed at 21 d, rep 4.


title: OVABalbc.OVA1

description:
GS.Mm_173.gpr
BALB/c mice were sensitized with OVA (50 µg in 10 mg alum, i.p.) on days 0, 7, and 14 and challenged with OVA (1 mg in 50 µl saline). Mice were analyzed on Day 24. Rep 1


title: IL13.S6ko.5

description:
10Mm_247.gpr
Control STAT6 -/-transgenic mice expressing IL-13 under the control of a Clara cell–specific promoter, mice were 6–8 wks of age, rep 5


title: Bleo7d.S3

description:
10Mm_245.gpr
7 d Saline control(1.1 U/kg body weight in 60 µl saline was administered intratracheally to C57BL/6 mice. Mice were killed at 21 d, rep 3.


title: IL13.S6wt.3

description:
10Mm_237.gpr
Transgenic mice expressing IL-13 under the control of a Clara cell–specific promoter, mice were 6–8 wks of age, rep 2


title: Bleo7d.S2

description:
10Mm_244.gpr
7 d Saline control(1.1 U/kg body weight in 60 µl saline was administered intratracheally to C57BL/6 mice. Mice were killed at 21 d, rep 2.


title: Bleo7d.B4

description:
10Mm_236.gpr
A single dose of bleomycin (1.1 U/kg body weight in 60 µl saline was administered intratracheally to C57BL/6 mice. Mice were killed at 7 d, rep 4.


title: Bleo7d.B1

description:
10Mm_233.gpr
A single dose of bleomycin (1.1 U/kg body weight in 60 µl saline was administered intratracheally to C57BL/6 mice. Mice were killed at 7 d, rep 1.


title: Bleo7d.B2

description:
10Mm_234.gpr
A single dose of bleomycin (1.1 U/kg body weight in 60 µl saline was administered intratracheally to C57BL/6 mice. Mice were killed at 7 d, rep 2.


title: IL13.S6ko.1

description:
10Mm_239.gpr
Control STAT6 -/-transgenic mice expressing IL-13 under the control of a Clara cell–specific promoter, mice were 6–8 wks of age, rep 1


title: IL13.S6wt.5

description:
10Mm_252.gpr
Transgenic mice expressing IL-13 under the control of a Clara cell–specific promoter, mice were 6–8 wks of age, rep 4


title: IL13.S6ko.4

description:
10Mm_225.gpr
Control STAT6 -/-transgenic mice expressing IL-13 under the control of a Clara cell–specific promoter, mice were 6–8 wks of age, rep 4


title: Bleo7d.B5

description:
11Mm_188.gpr
A single dose of bleomycin (1.1 U/kg body weight in 60 µl saline was administered intratracheally to C57BL/6 mice. Mice were killed at 7 d, rep 5.


title: Mpulm.inf2

description:
10Mm_199.gpr
C3H mice were inoculated intranasally with M. pulmonis (strain CT7; 105 cfu; n = 5). Mice were killed after 7 d, rep 2


title: Mpulm.inf5

description:
10Mm_230.gpr
C3H mice were inoculated intranasally with M. pulmonis (strain CT7; 105 cfu; n = 5). Mice were killed after 7 d, rep 5


title: Bleo7d.B3

description:
10Mm_235.gpr
A single dose of bleomycin (1.1 U/kg body weight in 60 µl saline was administered intratracheally to C57BL/6 mice. Mice were killed at 7 d, rep 3.


title: Mpulm.noinf4

description:
10Mm_201.gpr
PBS control, C3H mice were inoculated intranasally and were killed after 7d, rep 4


title: Mpulm.inf1

description:
10Mm_197.gpr
C3H mice were inoculated intranasally with M. pulmonis (strain CT7; 105 cfu; n = 5). Mice were killed after 7 d, rep 1


title: Mpulm.inf3

description:
10Mm_200.gpr
C3H mice were inoculated intranasally with M. pulmonis (strain CT7; 105 cfu; n = 5). Mice were killed after 7 d, rep 3


title: Mpulm.inf4

description:
10Mm_195.gpr
C3H mice were inoculated intranasally with M. pulmonis (strain CT7; 105 cfu; n = 5). Mice were killed after 7 d, rep 4


title: IL13.S6wt.4

description:
10Mm_218.gpr
Transgenic mice expressing IL-13 under the control of a Clara cell–specific promoter, mice were 6–8 wks of age, rep 3


title: Asp.noAsp3

description:
10Mm_149.gpr
C57BL/6 mice controls  sensitized via intranasal administration of saline, rep 3


title: OVAC57.OVA2

description:
10Mm_206.gpr
C57BL/6 mice were sensitized with OVA (50 µg in 10 mg alum, i.p.) on days 0, 7, and 14 and challenged with OVA (1 mg in 50 µl saline). Mice were analyzed on Day 24. Rep 2


title: Asp.Asp3

description:
10Mm_141.gpr
C57BL/6 mice were sensitized via intranasal administration of Aspergillus fumigatus antigen, rep 3


title: OVAC57.OVA1

description:
10Mm_143.gpr
C57BL/6 mice were sensitized with OVA (50 µg in 10 mg alum, i.p.) on days 0, 7, and 14 and challenged with OVA (1 mg in 50 µl saline). Mice were analyzed on Day 24. Rep 1


title: OVAC57.OVA4

description:
10Mm_207.gpr
C57BL/6 mice were sensitized with OVA (50 µg in 10 mg alum, i.p.) on days 0, 7, and 14 and challenged with OVA (1 mg in 50 µl saline). Mice were analyzed on Day 24. Rep 4


title: OVAC57.Alum4

description:
10Mm_204.gpr
ControL: C57BL/6 mice were sensitized with alum (10 mg alum, i.p.) on days 0, 7, and 14 and challenged with saline (50 µl saline). Mice were analyzed on Day 24. Rep 4


title: Asp.noAsp2

description:
10Mm_152.gpr
C57BL/6 mice controls  sensitized via intranasal administration of saline, rep 2


title: Mpulm.noinf2

description:
10Mm_198.gpr
PBS control, C3H mice were inoculated intranasally and were killed after 7d, rep 2


title: Asp.noAsp1

description:
10Mm_148.gpr
C57BL/6 mice controls  sensitized via intranasal administration of saline, rep 1


title: OVAC57.Alum3

description:
10Mm_139.gpr
ControL: C57BL/6 mice were sensitized with alum (10 mg alum, i.p.) on days 0, 7, and 14 and challenged with saline (50 µl saline). Mice were analyzed on Day 24. Rep 3


title: Asp.Asp4

description:
10Mm_147.gpr
C57BL/6 mice were sensitized via intranasal administration of Aspergillus fumigatus antigen, rep 4


title: OVAC57.Alum1

description:
10Mm_135.gpr
ControL: C57BL/6 mice were sensitized with alum (10 mg alum, i.p.) on days 0, 7, and 14 and challenged with saline (50 µl saline). Mice were analyzed on Day 24. Rep 1


title: ADA.ko.1

description:
7Mm_159.gpr
ADA-/- rep 1


title: LPSA.aero2

description:
7Mm_155.gpr
LPS (7 ml of 1.0 mg/ml solution) was delivered to C57BL/6 mice as a continuous aerosol generated by a small-volume nebulizer over 30 min. Mice were killed 4 h after exposure, rep 1


title: LPSIP.IP3

description:
7Mm_166.gpr
LPS (5 µg/g BW) as administered to C57BL/6 mice via a single i.p. injection. Mice were killed 4 h after injection, rep 3


title: Mpulm.noinf5

description:
10Mm_229.gpr
PBS control, C3H mice were inoculated intranasally and were killed after 7d, rep 5


title: LPSIP.IP1

description:
7Mm_164.gpr
LPS (5 µg/g BW) as administered to C57BL/6 mice via a single i.p. injection. Mice were killed 4 h after injection, rep 1


title: ADA.wt.2

description:
7Mm_112.gpr
ADA +/+ control rep 2


title: Asp.Asp1

description:
10Mm_136.gpr
C57BL/6 mice were sensitized via intranasal administration of Aspergillus fumigatus antigen, rep 1


title: ADA.wt.3

description:
7Mm_128.gpr
ADA +/+ control rep 3


title: Mpulm.noinf1

description:
10Mm_196.gpr
PBS control, C3H mice were inoculated intranasally and were killed after 7d, rep 1


title: LPS.noLPS1

description:
7Mm_153.gpr
Saline control was administered to C57BL/6 mice via a single i.p. injection. Mice were killed 4 h after injection, rep 1


title: OVAC57.Alum2

description:
10Mm_137.gpr
ControL: C57BL/6 mice were sensitized with alum (10 mg alum, i.p.) on days 0, 7, and 14 and challenged with saline (50 µl saline). Mice were analyzed on Day 24. Rep 2


title: LPS.noLPS2

description:
7Mm_154.gpr
Saline control was administered to C57BL/6 mice via a single i.p. injection. Mice were killed 4 h after injection, rep 2


title: ADA.ko.3

description:
7Mm_130.gpr
ADA-/- rep 3


title: Asp.Asp2

description:
10Mm_138.gpr
C57BL/6 mice were sensitized via intranasal administration of Aspergillus fumigatus antigen, rep 2


title: LPSA.aero3

description:
7Mm_156.gpr
LPS (7 ml of 1.0 mg/ml solution) was delivered to C57BL/6 mice as a continuous aerosol generated by a small-volume nebulizer over 30 min. Mice were killed 4 h after exposure, rep 2


title: LPS.noLPS3

description:
7Mm_111.gpr
Saline control was administered to C57BL/6 mice via a single i.p. injection. Mice were killed 4 h after injection, rep 3


title: ADA.ko.2

description:
7Mm_129.gpr
ADA-/- rep 2


title: ADA.wt.1

description:
7Mm_117.gpr
ADA +/+ control rep 1


title: LPSIP.IP2

description:
7Mm_152.gpr
LPS (5 µg/g BW) as administered to C57BL/6 mice via a single i.p. injection. Mice were killed 4 h after injection, rep 2


title: WGAAD-175

status: Public on Apr 10 2009

description: Human Cortex from Alzheimer's Disease

data_processing: RNA: Beadstudio software v 1.5.0.34, rank invariant normalization to extract

source_name: Alzheimer's Disease frozen cortical tissue

tag: gender

tag: age

tag: pmi


title: WGAAD-125

description: Human Cortex from Alzheimer's Disease

value: Alzheimer's Disease frozen cortical tissue


title: Normal RLL pairing AS3 at Day 10, biological rep3

status: Public on Apr 02 2009

city: Jacksonville

first: Catherine

last: Dumur

address: 5008 Mustang Rd

department: Anatomic Pathology

institute: Sonic Healthcare USA

description: Gene expression data from Normal RLL at Day 10 from rat# 3

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

scan_protocol: GeneChips were scanned using the GCS 3000 scanner.

data_processing: The data were analyzed using the Robust Multiarray Analysis (RMA) method.

organism: Rattus norvegicus

source_name: Normal RLL, Day 10

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Tissues were snap-frozen immediately after extirpation from the animal.

extract_protocol: Trizol extraction of total RNA was performed followed by a Qiagen cleanup step, according to manufacturers' instructions.

tag: rat number

value: normal liver

value: Fischer 344

value: male

value: Young adult