title: F2-ob/ob(B) 327

description: (C57BL/6J X BTBR) F2-327. We selected 60 (C57BL/6J X BTBR) F2-ob/ob mice based on the selective phenotyping algorithm (Jin et al. 2004). The 60 mice used in this study were a subset of F2 mice segregating for phenotypes associated with obesity and diabetes (Stoehr et al. 2000). The framework map consists of 145 microsatellite markers spanning the 19 mouse autosomes, with average spacing of 20 cM, augmented by markers in identified regions.

tag: (C57BL/6J X BTBR) F2-ob/ob (leptin deficient) mice, Liver, 14 weeks, Gender = F, 4-hr fasting, MOE430A ArrayID = 327A100603, MOE430B ArrayID = 327B100703.


title: F2-ob/ob(B) 324

status: Public on Sep 21 2005

type: RNA

city: Madison

first: Alan

middle: D

last: Attie

state: WI

address: 433 Babcock Drive

department: Biochemistry

country: USA

institute: University of Wisconsin-Madison

description: (C57BL/6J X BTBR) F2-324. We selected 60 (C57BL/6J X BTBR) F2-ob/ob mice based on the selective phenotyping algorithm (Jin et al. 2004). The 60 mice used in this study were a subset of F2 mice segregating for phenotypes associated with obesity and diabetes (Stoehr et al. 2000). The framework map consists of 145 microsatellite markers spanning the 19 mouse autosomes, with average spacing of 20 cM, augmented by markers in identified regions.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: The data were processed with MAS5.0 to generate cell intensity files. Quantitative expression levels of all the transcripts were estimated using the RMA algorithm for normalization (Irizarry et al. 2003).

label: biotin.

molecule: total RNA

organism: Mus musculus

source_name: Liver

label_protocol: Approximately 10 µg of total RNA was processed to produce biotinylated cRNA targets according to Affymetrix Expression Analysis Technical Manual.

extract_protocol: Liver total RNA was extracted from frozen tissue samples with RNAzol reagent (Tel-Test, Inc.). Crude RNA samples were purified with RNeasy mini columns (Qiagen, Inc.) before being subjected to microarray studies. The RNA samples were processed according to the Affymetrix Expression Analysis Technical Manual. A total of 60 MOE430A and MOE430B arrays were used. Quantitative expression levels of all the transcripts were estimated using the RMA algorithm for normalization.

tag: (C57BL/6J X BTBR) F2-ob/ob (leptin deficient) mice, Liver, 14 weeks, Gender = F, 4-hr fasting, MOE430A ArrayID = 324A100603, MOE430B ArrayID = 324B100703.


title: F2-ob/ob(B) 343

description: (C57BL/6J X BTBR) F2-343. We selected 60 (C57BL/6J X BTBR) F2-ob/ob mice based on the selective phenotyping algorithm (Jin et al. 2004). The 60 mice used in this study were a subset of F2 mice segregating for phenotypes associated with obesity and diabetes (Stoehr et al. 2000). The framework map consists of 145 microsatellite markers spanning the 19 mouse autosomes, with average spacing of 20 cM, augmented by markers in identified regions.

tag: (C57BL/6J X BTBR) F2-ob/ob (leptin deficient) mice, Liver, 14 weeks, Gender = M, 4-hr fasting, MOE430A ArrayID = 343A100603, MOE430B ArrayID = 343B100703.


title: F2-ob/ob(B) 318

description: (C57BL/6J X BTBR) F2-318. We selected 60 (C57BL/6J X BTBR) F2-ob/ob mice based on the selective phenotyping algorithm (Jin et al. 2004). The 60 mice used in this study were a subset of F2 mice segregating for phenotypes associated with obesity and diabetes (Stoehr et al. 2000). The framework map consists of 145 microsatellite markers spanning the 19 mouse autosomes, with average spacing of 20 cM, augmented by markers in identified regions.

tag: (C57BL/6J X BTBR) F2-ob/ob (leptin deficient) mice, Liver, 14 weeks, Gender = F, 4-hr fasting, MOE430A ArrayID = 318A100603, MOE430B ArrayID = 318B100703.


title: F2-ob/ob(B) 310

description: (C57BL/6J X BTBR) F2-310. We selected 60 (C57BL/6J X BTBR) F2-ob/ob mice based on the selective phenotyping algorithm (Jin et al. 2004). The 60 mice used in this study were a subset of F2 mice segregating for phenotypes associated with obesity and diabetes (Stoehr et al. 2000). The framework map consists of 145 microsatellite markers spanning the 19 mouse autosomes, with average spacing of 20 cM, augmented by markers in identified regions.

tag: (C57BL/6J X BTBR) F2-ob/ob (leptin deficient) mice, Liver, 14 weeks, Gender = F, 4-hr fasting, MOE430A ArrayID = 310A100603, MOE430B ArrayID = 310B100703.


title: F2-ob/ob(B) 212

description: (C57BL/6J X BTBR) F2-212. We selected 60 (C57BL/6J X BTBR) F2-ob/ob mice based on the selective phenotyping algorithm (Jin et al. 2004). The 60 mice used in this study were a subset of F2 mice segregating for phenotypes associated with obesity and diabetes (Stoehr et al. 2000). The framework map consists of 145 microsatellite markers spanning the 19 mouse autosomes, with average spacing of 20 cM, augmented by markers in identified regions.

tag: (C57BL/6J X BTBR) F2-ob/ob (leptin deficient) mice, Liver, 14 weeks, Gender = F, 4-hr fasting, MOE430A ArrayID = 212A100303, MOE430B ArrayID = 212B100503.


title: F2-ob/ob(B) 253

description: (C57BL/6J X BTBR) F2-253. We selected 60 (C57BL/6J X BTBR) F2-ob/ob mice based on the selective phenotyping algorithm (Jin et al. 2004). The 60 mice used in this study were a subset of F2 mice segregating for phenotypes associated with obesity and diabetes (Stoehr et al. 2000). The framework map consists of 145 microsatellite markers spanning the 19 mouse autosomes, with average spacing of 20 cM, augmented by markers in identified regions.

tag: (C57BL/6J X BTBR) F2-ob/ob (leptin deficient) mice, Liver, 14 weeks, Gender = F, 4-hr fasting, MOE430A ArrayID = 253A100303, MOE430B ArrayID = 253B100503.


title: F2-ob/ob(B) 209

description: (C57BL/6J X BTBR) F2-209. We selected 60 (C57BL/6J X BTBR) F2-ob/ob mice based on the selective phenotyping algorithm (Jin et al. 2004). The 60 mice used in this study were a subset of F2 mice segregating for phenotypes associated with obesity and diabetes (Stoehr et al. 2000). The framework map consists of 145 microsatellite markers spanning the 19 mouse autosomes, with average spacing of 20 cM, augmented by markers in identified regions.

tag: (C57BL/6J X BTBR) F2-ob/ob (leptin deficient) mice, Liver, 14 weeks, Gender = F, 4-hr fasting, MOE430A ArrayID = 209A100303, MOE430B ArrayID = 209B100503.


title: F2-ob/ob(B) 224

description: (C57BL/6J X BTBR) F2-224. We selected 60 (C57BL/6J X BTBR) F2-ob/ob mice based on the selective phenotyping algorithm (Jin et al. 2004). The 60 mice used in this study were a subset of F2 mice segregating for phenotypes associated with obesity and diabetes (Stoehr et al. 2000). The framework map consists of 145 microsatellite markers spanning the 19 mouse autosomes, with average spacing of 20 cM, augmented by markers in identified regions.

tag: (C57BL/6J X BTBR) F2-ob/ob (leptin deficient) mice, Liver, 14 weeks, Gender = M, 4-hr fasting, MOE430A ArrayID = 224A100303, MOE430B ArrayID = 224B100503.


title: F2-ob/ob(B) 260

description: (C57BL/6J X BTBR) F2-260. We selected 60 (C57BL/6J X BTBR) F2-ob/ob mice based on the selective phenotyping algorithm (Jin et al. 2004). The 60 mice used in this study were a subset of F2 mice segregating for phenotypes associated with obesity and diabetes (Stoehr et al. 2000). The framework map consists of 145 microsatellite markers spanning the 19 mouse autosomes, with average spacing of 20 cM, augmented by markers in identified regions.

tag: (C57BL/6J X BTBR) F2-ob/ob (leptin deficient) mice, Liver, 14 weeks, Gender = F, 4-hr fasting, MOE430A ArrayID = 260A100603, MOE430B ArrayID = 260B100703.


title: F2-ob/ob(B) 254

description: (C57BL/6J X BTBR) F2-254. We selected 60 (C57BL/6J X BTBR) F2-ob/ob mice based on the selective phenotyping algorithm (Jin et al. 2004). The 60 mice used in this study were a subset of F2 mice segregating for phenotypes associated with obesity and diabetes (Stoehr et al. 2000). The framework map consists of 145 microsatellite markers spanning the 19 mouse autosomes, with average spacing of 20 cM, augmented by markers in identified regions.

tag: (C57BL/6J X BTBR) F2-ob/ob (leptin deficient) mice, Liver, 14 weeks, Gender = F, 4-hr fasting, MOE430A ArrayID = 254A100603, MOE430B ArrayID = 254B100703.


title: F2-ob/ob(B) 223

description: (C57BL/6J X BTBR) F2-223. We selected 60 (C57BL/6J X BTBR) F2-ob/ob mice based on the selective phenotyping algorithm (Jin et al. 2004). The 60 mice used in this study were a subset of F2 mice segregating for phenotypes associated with obesity and diabetes (Stoehr et al. 2000). The framework map consists of 145 microsatellite markers spanning the 19 mouse autosomes, with average spacing of 20 cM, augmented by markers in identified regions.

tag: (C57BL/6J X BTBR) F2-ob/ob (leptin deficient) mice, Liver, 14 weeks, Gender = M, 4-hr fasting, MOE430A ArrayID = 223A100303, MOE430B ArrayID = 223B100503.


title: F2-ob/ob(B) 200

description: (C57BL/6J X BTBR) F2-200. We selected 60 (C57BL/6J X BTBR) F2-ob/ob mice based on the selective phenotyping algorithm (Jin et al. 2004). The 60 mice used in this study were a subset of F2 mice segregating for phenotypes associated with obesity and diabetes (Stoehr et al. 2000). The framework map consists of 145 microsatellite markers spanning the 19 mouse autosomes, with average spacing of 20 cM, augmented by markers in identified regions.

tag: (C57BL/6J X BTBR) F2-ob/ob (leptin deficient) mice, Liver, 14 weeks, Gender = F, 4-hr fasting, MOE430A ArrayID = 200A100303, MOE430B ArrayID = 200B100503.


title: F2-ob/ob(B) 194

description: (C57BL/6J X BTBR) F2-194. We selected 60 (C57BL/6J X BTBR) F2-ob/ob mice based on the selective phenotyping algorithm (Jin et al. 2004). The 60 mice used in this study were a subset of F2 mice segregating for phenotypes associated with obesity and diabetes (Stoehr et al. 2000). The framework map consists of 145 microsatellite markers spanning the 19 mouse autosomes, with average spacing of 20 cM, augmented by markers in identified regions.

tag: (C57BL/6J X BTBR) F2-ob/ob (leptin deficient) mice, Liver, 14 weeks, Gender = M, 4-hr fasting, MOE430A ArrayID = 194A100303, MOE430B ArrayID = 194B100503.


title: F2-ob/ob(B) 173

description: (C57BL/6J X BTBR) F2-173. We selected 60 (C57BL/6J X BTBR) F2-ob/ob mice based on the selective phenotyping algorithm (Jin et al. 2004). The 60 mice used in this study were a subset of F2 mice segregating for phenotypes associated with obesity and diabetes (Stoehr et al. 2000). The framework map consists of 145 microsatellite markers spanning the 19 mouse autosomes, with average spacing of 20 cM, augmented by markers in identified regions.

tag: (C57BL/6J X BTBR) F2-ob/ob (leptin deficient) mice, Liver, 14 weeks, Gender = M, 4-hr fasting, MOE430A ArrayID = 173A100303, MOE430B ArrayID = 173B100503.


title: F2-ob/ob(B) 190

description: (C57BL/6J X BTBR) F2-190. We selected 60 (C57BL/6J X BTBR) F2-ob/ob mice based on the selective phenotyping algorithm (Jin et al. 2004). The 60 mice used in this study were a subset of F2 mice segregating for phenotypes associated with obesity and diabetes (Stoehr et al. 2000). The framework map consists of 145 microsatellite markers spanning the 19 mouse autosomes, with average spacing of 20 cM, augmented by markers in identified regions.

tag: (C57BL/6J X BTBR) F2-ob/ob (leptin deficient) mice, Liver, 14 weeks, Gender = F, 4-hr fasting, MOE430A ArrayID = 190A100303, MOE430B ArrayID = 190B100503.


title: F2-ob/ob(B) 207

description: (C57BL/6J X BTBR) F2-207. We selected 60 (C57BL/6J X BTBR) F2-ob/ob mice based on the selective phenotyping algorithm (Jin et al. 2004). The 60 mice used in this study were a subset of F2 mice segregating for phenotypes associated with obesity and diabetes (Stoehr et al. 2000). The framework map consists of 145 microsatellite markers spanning the 19 mouse autosomes, with average spacing of 20 cM, augmented by markers in identified regions.

tag: (C57BL/6J X BTBR) F2-ob/ob (leptin deficient) mice, Liver, 14 weeks, Gender = F, 4-hr fasting, MOE430A ArrayID = 207A100303, MOE430B ArrayID = 207B100503.


title: F2-ob/ob(B) 566

description: (C57BL/6J X BTBR) F2-566. We selected 60 (C57BL/6J X BTBR) F2-ob/ob mice based on the selective phenotyping algorithm (Jin et al. 2004). The 60 mice used in this study were a subset of F2 mice segregating for phenotypes associated with obesity and diabetes (Stoehr et al. 2000). The framework map consists of 145 microsatellite markers spanning the 19 mouse autosomes, with average spacing of 20 cM, augmented by markers in identified regions.

tag: (C57BL/6J X BTBR) F2-ob/ob (leptin deficient) mice, Liver, 14 weeks, Gender = M, 4-hr fasting, MOE430A ArrayID = 566A100703, MOE430B ArrayID = 566B100803.


title: F2-ob/ob(B) 156

description: (C57BL/6J X BTBR) F2-156. We selected 60 (C57BL/6J X BTBR) F2-ob/ob mice based on the selective phenotyping algorithm (Jin et al. 2004). The 60 mice used in this study were a subset of F2 mice segregating for phenotypes associated with obesity and diabetes (Stoehr et al. 2000). The framework map consists of 145 microsatellite markers spanning the 19 mouse autosomes, with average spacing of 20 cM, augmented by markers in identified regions.

tag: (C57BL/6J X BTBR) F2-ob/ob (leptin deficient) mice, Liver, 14 weeks, Gender = F, 4-hr fasting, MOE430A ArrayID = 156A100303, MOE430B ArrayID = 156B100503.


title: F2-ob/ob(B) 165

description: (C57BL/6J X BTBR) F2-165. We selected 60 (C57BL/6J X BTBR) F2-ob/ob mice based on the selective phenotyping algorithm (Jin et al. 2004). The 60 mice used in this study were a subset of F2 mice segregating for phenotypes associated with obesity and diabetes (Stoehr et al. 2000). The framework map consists of 145 microsatellite markers spanning the 19 mouse autosomes, with average spacing of 20 cM, augmented by markers in identified regions.

tag: (C57BL/6J X BTBR) F2-ob/ob (leptin deficient) mice, Liver, 14 weeks, Gender = M, 4-hr fasting, MOE430A ArrayID = 165A100303, MOE430B ArrayID = 165B100503.


title: F2-ob/ob(B) 046

description: (C57BL/6J X BTBR) F2-046. We selected 60 (C57BL/6J X BTBR) F2-ob/ob mice based on the selective phenotyping algorithm (Jin et al. 2004). The 60 mice used in this study were a subset of F2 mice segregating for phenotypes associated with obesity and diabetes (Stoehr et al. 2000). The framework map consists of 145 microsatellite markers spanning the 19 mouse autosomes, with average spacing of 20 cM, augmented by markers in identified regions.

tag: (C57BL/6J X BTBR) F2-ob/ob (leptin deficient) mice, Liver, 14 weeks, Gender = M, 4-hr fasting, MOE430A ArrayID = 046A100203, MOE430B ArrayID = 046B100503.


title: F2-ob/ob(B) 167

description: (C57BL/6J X BTBR) F2-167. We selected 60 (C57BL/6J X BTBR) F2-ob/ob mice based on the selective phenotyping algorithm (Jin et al. 2004). The 60 mice used in this study were a subset of F2 mice segregating for phenotypes associated with obesity and diabetes (Stoehr et al. 2000). The framework map consists of 145 microsatellite markers spanning the 19 mouse autosomes, with average spacing of 20 cM, augmented by markers in identified regions.

tag: (C57BL/6J X BTBR) F2-ob/ob (leptin deficient) mice, Liver, 14 weeks, Gender = M, 4-hr fasting, MOE430A ArrayID = 167A100303, MOE430B ArrayID = 167B100503.


title: F2-ob/ob(B) 105

description: (C57BL/6J X BTBR) F2-105. We selected 60 (C57BL/6J X BTBR) F2-ob/ob mice based on the selective phenotyping algorithm (Jin et al. 2004). The 60 mice used in this study were a subset of F2 mice segregating for phenotypes associated with obesity and diabetes (Stoehr et al. 2000). The framework map consists of 145 microsatellite markers spanning the 19 mouse autosomes, with average spacing of 20 cM, augmented by markers in identified regions.

tag: (C57BL/6J X BTBR) F2-ob/ob (leptin deficient) mice, Liver, 14 weeks, Gender = F, 4-hr fasting, MOE430A ArrayID = 105A100303, MOE430B ArrayID = 105B100503.


title: ssa1/2 deletion mutant 3

city: Tsukuba

first: Rena

last: Matsumoto

state: Ibaraki

address: 1-1-1 Higashi

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

description: The ratio of intensity Cy5/Cy3 was calculated and normalized with negative control spots. The functional categorization of genes was performed using GeneSpring (Silicon Genetics, Redwood City, CA, USA), and Comprehensive Yeast Genome Database (CYGD) at the Munich International Center of Protein Sequence (MIPS; http://mips.gsf.de/) database.

hyb_protocol: Synthesized cDNA were hybridized to Kuhara DNA chip (DNA Chip Research, Yokohama, Kanagawa, Japan) at 65 degrees C for 48 h.

data_processing: GeneSpring (Silicon Genetics)

organism: Saccharomyces cerevisiae

source_name: ssa1/2, Cy5

label_protocol: Cyscribe first-strand cDNA labeling kit (Amersham Biosciences)

growth_protocol: JN14 cells were incubated in 100 ml of YPD (1% yeast extract, 2% polypeptone and 2% glucose) medium at 30 degrees C to a logarithmic phase (OD660=1) using 500 ml Erlenmeyer flask.

extract_protocol: Hot-phenol and oligotex dt mRNA purification kit (TaKaRa)

tag: strain JN14

source_name: wild-type, Cy3

growth_protocol: JN54 cells were incubated in 100 ml of YPD (1% yeast extract, 2% polypeptone and 2% glucose) medium at 30 degrees C to a logarithmic phase (OD660=1) using 500 ml Erlenmeyer flask.

tag: strain JN54 (the parent strain of JN14)


title: F2-ob/ob(B) 186

description: (C57BL/6J X BTBR) F2-186. We selected 60 (C57BL/6J X BTBR) F2-ob/ob mice based on the selective phenotyping algorithm (Jin et al. 2004). The 60 mice used in this study were a subset of F2 mice segregating for phenotypes associated with obesity and diabetes (Stoehr et al. 2000). The framework map consists of 145 microsatellite markers spanning the 19 mouse autosomes, with average spacing of 20 cM, augmented by markers in identified regions.

tag: (C57BL/6J X BTBR) F2-ob/ob (leptin deficient) mice, Liver, 14 weeks, Gender = F, 4-hr fasting, MOE430A ArrayID = 186A100303, MOE430B ArrayID = 186B100503.


title: F2-ob/ob(B) 111

description: (C57BL/6J X BTBR) F2-111. We selected 60 (C57BL/6J X BTBR) F2-ob/ob mice based on the selective phenotyping algorithm (Jin et al. 2004). The 60 mice used in this study were a subset of F2 mice segregating for phenotypes associated with obesity and diabetes (Stoehr et al. 2000). The framework map consists of 145 microsatellite markers spanning the 19 mouse autosomes, with average spacing of 20 cM, augmented by markers in identified regions.

tag: (C57BL/6J X BTBR) F2-ob/ob (leptin deficient) mice, Liver, 14 weeks, Gender = F, 4-hr fasting, MOE430A ArrayID = 111A100303, MOE430B ArrayID = 111B100503.


title: F2-ob/ob(B) 123

description: (C57BL/6J X BTBR) F2-123. We selected 60 (C57BL/6J X BTBR) F2-ob/ob mice based on the selective phenotyping algorithm (Jin et al. 2004). The 60 mice used in this study were a subset of F2 mice segregating for phenotypes associated with obesity and diabetes (Stoehr et al. 2000). The framework map consists of 145 microsatellite markers spanning the 19 mouse autosomes, with average spacing of 20 cM, augmented by markers in identified regions.

tag: (C57BL/6J X BTBR) F2-ob/ob (leptin deficient) mice, Liver, 14 weeks, Gender = M, 4-hr fasting, MOE430A ArrayID = 123A100303, MOE430B ArrayID = 123B100503.


title: F2-ob/ob(B) 061

description: (C57BL/6J X BTBR) F2-061. We selected 60 (C57BL/6J X BTBR) F2-ob/ob mice based on the selective phenotyping algorithm (Jin et al. 2004). The 60 mice used in this study were a subset of F2 mice segregating for phenotypes associated with obesity and diabetes (Stoehr et al. 2000). The framework map consists of 145 microsatellite markers spanning the 19 mouse autosomes, with average spacing of 20 cM, augmented by markers in identified regions.

tag: (C57BL/6J X BTBR) F2-ob/ob (leptin deficient) mice, Liver, 14 weeks, Gender = M, 4-hr fasting, MOE430A ArrayID = 061A100203, MOE430B ArrayID = 061B100503.


title: ssa1/2 deletion mutant 2

molecule: polyA RNA

source_name: ssa1/2 Cy5


title: F2-ob/ob(B) 044

description: (C57BL/6J X BTBR) F2-044. We selected 60 (C57BL/6J X BTBR) F2-ob/ob mice based on the selective phenotyping algorithm (Jin et al. 2004). The 60 mice used in this study were a subset of F2 mice segregating for phenotypes associated with obesity and diabetes (Stoehr et al. 2000). The framework map consists of 145 microsatellite markers spanning the 19 mouse autosomes, with average spacing of 20 cM, augmented by markers in identified regions.

tag: (C57BL/6J X BTBR) F2-ob/ob (leptin deficient) mice, Liver, 14 weeks, Gender = M, 4-hr fasting, MOE430A ArrayID = 044A100203, MOE430B ArrayID = 044B100503.


title: F2-ob/ob(B) 100

description: (C57BL/6J X BTBR) F2-100. We selected 60 (C57BL/6J X BTBR) F2-ob/ob mice based on the selective phenotyping algorithm (Jin et al. 2004). The 60 mice used in this study were a subset of F2 mice segregating for phenotypes associated with obesity and diabetes (Stoehr et al. 2000). The framework map consists of 145 microsatellite markers spanning the 19 mouse autosomes, with average spacing of 20 cM, augmented by markers in identified regions.

tag: (C57BL/6J X BTBR) F2-ob/ob (leptin deficient) mice, Liver, 14 weeks, Gender = M, 4-hr fasting, MOE430A ArrayID = 100A100303, MOE430B ArrayID = 100B100503.


title: F2-ob/ob(B) 022

description: (C57BL/6J X BTBR) F2-022. We selected 60 (C57BL/6J X BTBR) F2-ob/ob mice based on the selective phenotyping algorithm (Jin et al. 2004). The 60 mice used in this study were a subset of F2 mice segregating for phenotypes associated with obesity and diabetes (Stoehr et al. 2000). The framework map consists of 145 microsatellite markers spanning the 19 mouse autosomes, with average spacing of 20 cM, augmented by markers in identified regions.

tag: (C57BL/6J X BTBR) F2-ob/ob (leptin deficient) mice, Liver, 14 weeks, Gender = M, 4-hr fasting, MOE430A ArrayID = 022A100203, MOE430B ArrayID = 022B100503.


title: ssa1/2 deletion mutant 1

source_name: wild-type


title: F2-ob/ob(B) 012

description: (C57BL/6J X BTBR) F2-012. We selected 60 (C57BL/6J X BTBR) F2-ob/ob mice based on the selective phenotyping algorithm (Jin et al. 2004). The 60 mice used in this study were a subset of F2 mice segregating for phenotypes associated with obesity and diabetes (Stoehr et al. 2000). The framework map consists of 145 microsatellite markers spanning the 19 mouse autosomes, with average spacing of 20 cM, augmented by markers in identified regions.

tag: (C57BL/6J X BTBR) F2-ob/ob (leptin deficient) mice, Liver, 14 weeks, Gender = M, 4-hr fasting, MOE430A ArrayID = 012A100203, MOE430B ArrayID = 012B100503.


title: F2-ob/ob(B) 002

description: (C57BL/6J X BTBR) F2-002. We selected 60 (C57BL/6J X BTBR) F2-ob/ob mice based on the selective phenotyping algorithm (Jin et al. 2004). The 60 mice used in this study were a subset of F2 mice segregating for phenotypes associated with obesity and diabetes (Stoehr et al. 2000). The framework map consists of 145 microsatellite markers spanning the 19 mouse autosomes, with average spacing of 20 cM, augmented by markers in identified regions.

tag: (C57BL/6J X BTBR) F2-ob/ob (leptin deficient) mice, Liver, 14 weeks, Gender = M, 4-hr fasting, MOE430A ArrayID = 002A100203, MOE430B ArrayID = 002B100503.


title: Saccharomyces cerevisiae Sko1-HA, replicate 3

type: genomic

city: Boston

first: Francis

last: Gibbons

state: MA

address: 250 Longwood Ave

department: BCMP (Biological Chemistry and Molecular Pharamcology)

institute: Harvard Medical School

description: Chromosomal DNA from Saccharomyces cerevisiae Sko1-HA strain MAP37, W303-1A background

hyb_protocol: Cy5-labeled immunoprecipitated and Cy3-labeled total DNA samples were hybridized together over night at 46C with arrays containing all intergenic regions of Saccharomyces cerevisiae. Arrays were washed twice with 0.6x SSC before scanning.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon fluorescent scanner and image intensity data were extracted and analyzed with GenePix 4.0 analysis software.

data_processing: After background correction and elimination of all flagged values, p-values for each Sko1-intergenic region interaction were computed using the CHIPPER algorithm (http://llama.med.harvard.edu/Software.html)

molecule: genomic DNA

label_protocol: 40microL of chromosomal DNA samples were T4 DNA polymerase and Mung Bean Nuclease treated. After linker addition samples were amplified by standard PCR (Ligation mediated PCR). Cy5 (Clontech) labeling was performed for 1h and samples were purified with NucleoSpin extraction columns.

growth_protocol: Yeast cells were grown in liquid YPD medium to mid log phase

extract_protocol: Cells were incubated with 1% formaldehyde for 20min at room temperature followed by treatment with 0.36M glycine for 5min. Cells were washed twice with TBS and once with FA lysis buffer (50mM Hepes/KOH pH7.5, 150mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1mM PMSF) + 0.1% SDS. Cells were lysed in FA lysis buffer + 0.5% SDS with glass beads. Lysates were centrifuged for 1min at 13000rpm in minicentrifuge. Chromatin in the supernatant was solubilized by sonication and stored at -80C.  Immunoprecipitation was performed with approximately 1microgram of anti HA (12CA5) antibody and 25microL of protein A sepharose beads (Pharmacia) in FA lysis buffer + 0.1% SDS for 90min. Beads were washed 2 x with FA lysis buffer/0.1% SDS, 2 x with FA lysis buffer/0.1% SDS with 0.5M NaCl, 1 x with buffer B (10mM Tris/HCl pH 8.0, 0.25M LiCl, 1mM EDTA, 0.5% NP-40, 0.5% Na-deoxycholate), and 1 x with TE. Chromatin was eluted in 250microL of buffer C (50mM Tris/HCl pH 7.5, 10mM EDTA, 1% SDS) for 10min at 65C. 250microL of TE + 20_l Pronase (Roche, 20mg/ml) was added and protease treatment was performed for 1h at 37C and for 5h at 65C. Samples were phenol/chloroform extracted after addition of 50microL of 4M LiCl and DNA was precipitated with 1ml ethanol + 20_g glycogen (Roche). Chromosomal DNA fragments were resuspended in 100microL TE.

label_protocol: 5microL of total chromosomal DNA samples were T4 DNA polymerase and Mung Bean Nuclease treated. After linker addition, samples were amplified by standard PCR (Ligation mediated PCR). Cy3 (Clontech) labeling was performed for 1h and samples were purified with NucleoSpin extraction columns.

extract_protocol: Cells were incubated with 1% formaldehyde for 20min at room temperature followed by treatment with 0.36M glycine for 5min. Cells were washed twice with TBS and once with FA lysis buffer (50mM Hepes/KOH pH7.5, 150mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1mM PMSF) + 0.1% SDS. Cells were lysed in FA lysis buffer + 0.5% SDS with glass beads. Lysates were centrifuged for 1min at 13000rpm in minicentrifuge. Chromatin in the supernatant was solubilized by sonication and stored at -80C. 250microL of TE + 20_l Pronase (Roche, 20mg/ml) was added to 50microL of total chromatin and protease treatment was performed for 1h at 37C and for 5h at 65C. Samples were phenol/chloroform extracted after addition of 50microL of 4M LiCl and DNA was precipitated with 1ml ethanol + 20_g glycogen (Roche). Chromosomal DNA fragments were resuspended in 100microL TE.


title: Treated 5, 72 h

city: San Francisco

first: Philip

middle: L

last: Ballard

state: CA

address: 513 Parnassus St

department: Neonatology

institute: UCSF

description: RNA extracted with RNA STAT-60 and checked with Agilent gel

data_processing: Affymetrix algorithms (MAS 5.0)

label: Biotin-labeled cRNA

organism: Homo sapiens

source_name: Isolated epithelial cells from human fetal lung at 13-20 wk gestation

treatment_protocol: DCI (dexamethasone 10nM, 8-Bromo cyclic AMP 10µM, isobutylxanthine 10µM) added days 3-6 (72 h exposure) prior to extract preparation

tag: Human fetal lungs 13-20 wks gestation, both genders


title: Treated 4, 72 h


title: Saccharomyces cerevisiae Sko1-HA, replicate 2

source_name: Saccharomyces cerevisiae Sko1-HA strain MAP37, W303-1A background

treatment_protocol: Yeast cells were grown in liquid YPD medium to mid log phase


title: Control 2, 72 h

tag: Isolated epithelial cells 6 days in culture in Waymouth's medium (control)


title: Control 4, 72 h

treatment_protocol: Isolated epithelial cells 6 days in culture in Waymouth's medium


title: Control 5, 72 h


title: Control 3, 72 h


title: Treated 2, 72 h

tag: DCI (dexamethasone 10nM, 8-Bromo cyclic AMP 10µM, isobutylxanthine 10µM) added days 3-6 (72 h exposure)


title: Saccharomyces cerevisiae Sko1-HA, replicate 1

tag: Saccharomyces cerevisiae Sko1-HA strain MAP37


title: Control 1, 72 h


title: Nla18/DK1622, veg, E192, Exp#4

status: Public on Sep 20 2005

city: Davis

first: Mitchell

last: Singer

address: 1 Shields Ave

department: Microbiology

institute: The University of California, Davis

description: standard protocol

data_processing: GenePix, Excel

organism: Myxococcus xanthus

source_name: Nla18, veg

tag: Nla18, veg

source_name: DK1622, veg

tag: DK162, veg


title: Treated 3, 72 h


title: Nla18/DK1622, veg, E193, Exp#5

description: standard protocol

tag: DK1622, veg


title: Nla18/DK1622, veg, E189, Exp#1

description: standard protocol


title: Nla18/DK1622, veg, E190, Exp#2

description: standard protocol


title: HSC_collagen_2

city: Dresden

first: Martin

last: Bornhaeuser

address: Fetscherstrasse 74

department: Med. Klinik und Poliklinik

country: Germany

institute: Universitätsklinikum Carl Gustav Carus

description: further details in Oswald et al. "Gene expression profiling of CD34+ hematopoietic cells expanded in a collagen I matrix"

hyb_protocol: Standard Affymetrix hybridization protocol for eukaryotic samples

scan_protocol: Affymetrix standard procedure

data_processing: Affymetrix MAS 5.0, global scaling strategy, TGT 500

label: Biotin/Streptavidin Phycoerythrin

source_name: cord blood

label_protocol: Affymetrix GeneChip Eukaryotic Small Sample Target Labeling Assay Version II, starting the first amplification cycle with 100ng total RNA

extract_protocol: RNeasy Mini Kit

tag: CD34+ cells isolated from umbilical cord blood, cultured in collagen I gels


title: Nla18/DK1622, veg, E191, Exp#3

description: standard protocol


title: Treated 1, 72 h


title: mesenteric LN_CD4+CD25+_BDC2.5tg replicate4

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

data_processing: RMA

label: biotin

source_name: mesenteric lymph node CD4+CD25+ cells

tag: Strain

value: NOD

tag: Mutant

value: BDC2.5 TCR transgenic

tag: Age

value: 4 weeks

tag: Tissue

value: mesenteric lymph node


title: HSC_collagen_3


title: HSC_control_2

tag: CD34+ cells isolated from umbilical cord blood


title: mesenteric LN_CD4+CD25+_BDC2.5tg replicate5


title: Melanocytes replicate 2

city: New York

first: Michael

last: Rendl

state: NY

address: 1428 Madison Avenue

institute: Mount Sinai School of Medicine

description: Hair follicle melanocytes

data_processing: Affymetrix Microarray Suite version 5.0, scaled with the Affymetrix mask file to TGT=500

source_name: Skin

label_protocol: Approximately 1 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: 4 day old backskins were taken and Mx, ORS, DF, DP and Mc were FACSorted from Lef1-RFP/K14-H2BGFP mice. Total RNAs were prepared using the MicroPrep Kit (Stratagene)

tag: FACSorted skin cells, melanocytes


title: HSC_control_1


title: HSC_control_3

description: further details in Oswald et al. " Gene expression profiling of CD34+ hematopoietic cells expanded in a collagen I matrix"

hyb_protocol: Standard Affymetrix hybridization protocol for eucaryotic samples


title: Dermal papilla replicate 2

description: Hair follicle dermal papilla cells

tag: FACSorted skin cells, dermal papilla


title: Melanocytes replicate 1

description: Hair follicle melanocytes


title: HSC_collagen_1


title: Outer root sheath 2

description: Hair follicle outer root sheath cells

tag: FACSorted skin cells, outer root sheath


title: Dermal fraction replicate 1

description: Dermal fraction

tag: FACSorted skin cells, dermal fraction


title: Matrix replicate 1

description: Hair follicle matrix cells

tag: FACSorted skin cells, matrix


title: Outer root sheath 1

description: Hair follicle outer root sheath cells


title: Dermal papilla replicate 1

description: Hair follicle dermal papilla cells


title: Dermal fraction replicate 2

description: Dermal fraction


title: oocyte from primary follicle stage rep4 (430A)

status: Public on Sep 19 2005

city: Philadelphia

first: Hua

last: Pan

state: PA

address: 415 S University Avenue

department: Department of Biology

institute: University of Pennsylvania

description: none provided

data_processing: Affymetrix Microarray Suite version 5.0

source_name: oocyte

label_protocol: total RNA from 90 oocytes was processed to produce biotinylated cRNA targets using Affy Small Sample Target Labeling Assay Version II.

extract_protocol: 90 oocytes were collected from ovary of 6 day old SJLB6 female mouse.Total RNA was extracted and purified using an Picopure kit (Arcturus).

tag: in vivo,primary follicle stage, oocyte


title: oocyte from primary follicle stage rep3 (430A)

description: none provided


title: oocyte from primary follicle stage rep3 (430B)

description: none provided


title: oocyte from primary follicle stage rep2 (430A)

description: none provided


title: Matrix replicate 2

description: Hair follicle matrix cells


title: oocyte from primary follicle stage rep4 (430B)

description: none provided


title: oocyte from primary follicle stage rep1 (430B)

description: none provided


title: oocyte from primary follicle stage rep1 (430A)

description: none provided


title: 18 month PCA rep 3

status: Public on Sep 17 2005

city: Lexington

first: Colleen

middle: A

last: McMullen

state: KY

address: 800 Rose St MS508

department: Physiology

institute: University of Kentucky

description: Age-related laryngeal dysfunction

label: Cy3, Cy5

organism: Rattus norvegicus

source_name: posterior cricoarytenoid

tag: Fischer 344-Brown Norway F1 hybrid rats

tag: 6,18, and 30 months of age

tag: Male


title: 30 month PCA rep 1

description: Age-related laryngeal dysfunction

tag: 6, 18, and 30 months of age


title: 30 month PCA rep 2

description: Age-related laryngeal dysfunction


title: 6 month PCA rep 1

description: Age-related laryngeal dysfunction

tag: Fischer 344-Brown Norway F1 hybrid rats 6,18,30 months of age


title: 6 month PCA rep 3

description: Age-related laryngeal dysfunction

tag: 6,18,and 30 months of age


title: 18 month EOM rep 3

description: profile of extraocular muscles  and extensor digitorum longus muscles with age

source_name: extraocular muscles

tag: Fischer 344/Brown Norway F1 hybrid rats at 6-, 18- and 30-months of age.


title: 30 month PCA rep 3

description: Age-related laryngeal dysfunction


title: oocyte from primary follicle stage rep2 (430B)

description: none provided


title: 30 month EOM rep 2

tag: Fischer 344/Brown Norway F1 hybrid rats at 6-, 18- and 30-months of age


title: 30 month EOM rep 1


title: 6 month PCA rep 2

description: Age-related laryngeal dysfunction


title: 30 month EOM rep 3


title: 18 month PCA rep 2

description: Age-related laryngeal dysfunction

tag: 6,18 and 30 months of age


title: 18 month EOM rep 4


title: 18 month EOM rep 2


title: 18 month PCA rep 1

description: Age-related laryngeal dysfunction


title: 30 month EOM rep 4


title: 6 month EOM rep 4


title: 18 month EOM rep 1


title: 30 month EDL rep 4

source_name: extensor digitorum longus muscles

tag: male


title: 6 month EOM rep 2


title: 30 month EDL rep 2


title: 6 month EOM rep 1


title: 30 month EDL rep 1


title: 18 month EDL rep 4


title: PG_cKGM/KGM_001

type: protein

city: Seattle

first: Murray

last: Hackett

state: WA

address: HSB H330 1959 NE Pacific Street

department: Chemical Engineering

institute: University of Washington

description: P. gingivalis in cKGM or KGM media

data_processing: Number of unique peptides identified

molecule: protein

organism: Porphyromonas gingivalis

source_name: keratinocyte growth medium (KGM_001)

tag: P. gingivalis exposed to control keratinocyte growth medium

source_name: conditioned keratinocyte growth medium (PG_cKGM)

tag: P. gingivalis exposed to conditioned keratinocyte growth medium


title: 30 month EDL rep 3


title: F2-ob/ob(B) 484

description: (C57BL/6J X BTBR) F2-484. We selected 60 (C57BL/6J X BTBR) F2-ob/ob mice based on the selective phenotyping algorithm (Jin et al. 2004). The 60 mice used in this study were a subset of F2 mice segregating for phenotypes associated with obesity and diabetes (Stoehr et al. 2000). The framework map consists of 145 microsatellite markers spanning the 19 mouse autosomes, with average spacing of 20 cM, augmented by markers in identified regions.

source_name: Liver

tag: (C57BL/6J X BTBR) F2-ob/ob (leptin deficient) mice, Liver, 14 weeks, Gender = F, 4-hr fasting, MOE430A ArrayID = 484A100603, MOE430B ArrayID = 484B100803.


title: 18 month spinal cord rep 1

description: 6,18,30 month oculomotor nucleus and spinal cord

source_name: 18 month spinal cord

tag: 18 months


title: 18 month spinal cord rep 3


title: 30 month spinal cord rep 2

source_name: 30 month spinal cord

tag: 30 months


title: 30 month oculomotor nucleus rep 1

source_name: 30 month oculomotor nucleus


title: 6 month spinal cord rep 1

source_name: 6 month spinal cord

tag: 6 months


title: 18 month EDL rep 2


title: 18 month spinal cord rep 2


title: 18 month oculomotor nucleus rep 3

source_name: 18 month oculomotor


title: 6 month spinal cord rep 3


title: 6 month EDL rep 4


title: 6 month EDL rep 3


title: 18 month EDL rep 1


title: 30 month oculomotor nucleus rep 3


title: 18 month EDL rep 3


title: 6 month spinal cord rep 2

source_name: 6 months spinal cord


title: 30 month spinal cord rep 3


title: 30 month oculomotor nucleus rep 2


title: 30 month spinal cord rep 1


title: 6 month EDL rep 2


title: 6 month EDL rep 1

tag: Fischer 344/Brown Norway F1 hybrid rats

tag: 6-, 18- and 30-months of age


title: 6 month EOM rep 3


title: 6 month oculomotor nucleus rep 2

description: 6, 18, 30 month F344BN oculomotor nucleus and spinal cord

source_name: 6 month oculomotor nucleus rep2

tag: Strain F344BN

tag: 6 month


title: 6 month oculomotor nucleus rep 1

source_name: 6 month oculomotor nucleus rep 1

tag: Strain Fischer 344 brown Norway

tag: Male

tag: oculomotor nucleus


title: 18 month oculomotor nucleus rep 1

source_name: 18 month oculomotor nucleus


title: Control adult zebrafish retina, 5d post-lesion

status: Public on Sep 16 2005

city: Syracuse

first: David

last: Cameron

address: 750 E Adams St

department: Neuroscience & Physiology

institute: SUNY Upstate

description: Cameron, Gentile, Middleton, Yurco (2005). Gene expression profiles of intact and regenerating zebrafish retina. Molecular Vision 11 (in press).

data_processing: Normalized and scaled to a mean target intensity value of 500 using the Gene Chip Operating System (GCOS) software.

organism: Danio rerio

source_name: retina

tag: wildtype adult


title: 6 month oculomotor nucleus rep 3

source_name: 6 month oculomotor rep 3


title: Lesioned adult zebrafish retina, 5d post-lesion


title: Control adult zebrafish retina, 7d post-lesion


title: Control adult zebrafish retina, 3d post-lesion


title: Lesioned adult zebrafish retina, 2d post-lesion


title: peripheral LN_CD4+CD25+_BDC2.5tg replicate3

status: Public on Sep 15 2005

source_name: peripheral lymph node CD4+CD25+ cells

tag: Strain

tag: Mutant

tag: Age

tag: Tissue


title: Control Adult Zebrafish Brain

source_name: Brain


title: Lesioned adult zebrafish retina, 3d post-lesion


title: peripheral LN_CD4+CD25+_BDC2.5tg replicate2


title: peripheral LN_CD4+CD25-_BDC2.5tg replicate2

source_name: peripheral lymph node CD4+CD25- cells


title: peripheral LN_CD4+CD25+_BDC2.5tg replicate1


title: mesenteric LN_CD4+CD25-_BDC2.5tg_rep3

source_name: mesenteric lymph node CD4+CD25- cells


title: 18 month oculomotor nucleus rep 2


title: ppsA mutant 30 min (1) slide 2

status: Public on Sep 14 2005

city: Los Angeles

first: Katy

last: Kao

address: 420 Westwood Plaza/5805 Boelter Hall

institute: University of California, Los Angeles

description: Ratio reported in the database is reference/time course sample.  However, ratio reported in paper is time course sample/reference sample.

data_processing: normalized using lcDNA

organism: Escherichia coli

source_name: time course sample harvested after 30 min of glucose to acetate shift

tag: strain BW25113 ppsA deletion

source_name: reference sample harvested immediately prior to glucose to acetate shift


title: mesenteric LN_CD4+CD25+_BDC2.5tg replicate3

source_name: mesenteric lymph node CD4+CD25+ cells


title: Control adult zebrafish retina, 14d post-lesion


title: ppsA mutant 5 min (1) slide 1

source_name: time course sample harvested after 5 min of glucose to acetate shift


title: peripheral LN_CD4+CD25-_BDC2.5tg replicate1


title: ppsA mutant 15 min (1) slide 1

source_name: time course sample harvested after 15 min of glucose to acetate shift


title: Control adult zebrafish retina, 2d post-lesion


title: mesenteric LN_CD4+CD25-_BDC2.5tg_rep1

extract_protocol: Cells were separated using FACS.  RNA was extracted using the Trizol method.  2 rounds of amplification with the Ambion technique.


title: mesenteric LN_CD4+CD25+_BDC2.5tg replicate2


title: ppsA mutant 15 min (1) slide 2


title: "true" control adult zebrafish retina


title: mesenteric LN_CD4+CD25-_BDC2.5tg_rep2


title: ppsA mutant 5 min (1) slide 2


title: ppsA mutant 30 min (1) slide 1


title: peripheral LN_CD4+CD25-_BDC2.5tg replicate3


title: Lesioned adult zebrafish retina, 7d post-lesion


title: mesenteric LN_CD4+CD25+_BDC2.5tg replicate1


title: wild-type 30 min (2) slide 2

tag: strain BW25113


title: wild-type 30 min (2) slide 1


title: wild-type 30 min (1) slide 2


title: wild-type 15 min (1) slide 2


title: Lesioned adult zebrafish retina, 14d post-lesion


title: wild-type 15 min (2) slide 2


title: wild-type 5min (1) slide 1


title: wild-type 15 min (2) slide 1


title: wild-type 30 min (1) slide 1


title: Control 4

city: La Jolla

first: Sunil

last: Kurian

address: 10550 N Torrey Pines Road

department: Molecular and Experimental Medicine

institute: The Scripps Research Institute

description: Biopsy RNA

data_processing: Raw GCOS signal values

label: SAPE

source_name: Kidney

tag: 15 gauge biopsy


title: Control 6

description: Biopsy RNA


title: wild-type 5min (2) slide 1


title: wild-type 5min (1) slide 2


title: Laparoscopic Donor 5

description: Biopsy RNA

tag: 15 Gauge Biopsy


title: wild-type 15 min (1) slide 1


title: Control 1

description: Biopsy RNA


title: Laparoscopic Donor 2

description: Biopsy RNA

tag: 15 Gauge biopsy


title: CR1_Lysis_24_32290689_10036417_A_

first: Wenzhong Xiao

address: 55 Fruit Street, GRV 1302

department: Department of Surgery

institute: Massachusetts General Hospital

description: Data for Inflamation and Host Reponse to Injury, NIH Glue Grant, Study or Experiment

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Affymetrix GCOS version 1.2.0

label: paper supplemental material "A Network-Based Analysis of Systemic Inflammation in Humans" at www.gluegrant.org

source_name: blood

tag: age 18-40; control or endotoxin at 0,2,4,6,9,24 hrs


title: Laparoscopic Donor 6

description: Biopsy RNA


title: Control 5

description: Biopsy RNA


title: CR1_Lysis_9_33644801_18184487_A_


title: CR1_Lysis_24_30617740_33314489_A_


title: Laparoscopic Donor 1

description: Biopsy RNA


title: CR1_Lysis_24_339423_1567260_A_


title: Laparoscopic Donor 4

description: Biopsy RNA


title: CR1_Lysis_24_1626809_14198042_A_


title: Control 3

description: Biopsy RNA


title: CR1_Lysis_24_27596703_27142447_A_


title: CR1_Lysis_24_24581684_26086916_A_


title: Laparoscopic Donor 3

description: Biopsy RNA


title: CR1_Lysis_9_32290689_31118687_A_


title: CR1_Lysis_24_21572677_4479275_A_


title: CR1_Lysis_9_339423_11275230_A_


title: CR1_Lysis_24_33644801_18770658_A_


title: Control 2

description: Biopsy RNA


title: wild-type 5min (2) slide 2


title: CR1_Lysis_9_30617740_32209377_A_


title: CR1_Lysis_24_33644801_18770658_B_


title: CR1_Lysis_6_30617740_20779368_A_


title: CR1_Lysis_4_30617740_21123328_A_


title: CR1_Lysis_4_32290689_8317408_A_


title: CR1_Lysis_24_21572677_4479275_B_


title: CR1_Lysis_9_24581684_6336377_A_


title: CR1_Lysis_24_30617740_33314489_B_


title: CR1_Lysis_24_24581684_26086916_B_


title: CR1_Lysis_9_27596703_5944600_A_


title: CR1_Lysis_6_33644801_3892180_A_


title: CR1_Lysis_24_1626809_14198042_B_


title: CR1_Lysis_9_21572677_21949161_A_


title: CR1_Lysis_4_33644801_3716598_A_


title: CR1_Lysis_6_27596703_19918478_A_


title: CR1_Lysis_4_27596703_34012992_A_


title: CR1_Lysis_24_339423_1567260_B_


title: CR1_Lysis_9_33644801_18184487_B_


title: CR1_Lysis_24_27596703_27142447_B_


title: CR1_Lysis_6_24581684_21757491_A_


title: CR1_Lysis_9_339423_11275230_B_


title: CR1_Lysis_6_32290689_18473389_A_


title: CR1_Lysis_4_21572677_22199230_A_


title: CR1_Lysis_6_339423_21406854_A_


title: CR1_Lysis_2_33644801_13519166_A_


title: CR1_Lysis_6_21572677_4488426_A_


title: CR1_Lysis_24_32290689_10036417_B_


title: CR1_Lysis_4_339423_31962126_A_


title: CR1_Lysis_2_339423_7889957_A_


title: CR1_Lysis_4_24581684_2248086_A_


title: CR1_Lysis_9_1626809_29945956_A_


title: CR1_Lysis_9_32290689_31118687_B_


title: CR1_Lysis_2_32290689_20990830_A_


title: CR1_Lysis_9_21572677_21949161_B_


title: ppsA mutant 6 hour (2) slide 2

source_name: time course sample harvested after 6 hour of glucose to acetate shift


title: CR1_Lysis_2_27596703_13177053_A_


title: ppsA mutant 3 hour (2) slide 2

source_name: time course sample harvested after 3 hour of glucose to acetate shift


title: ppsA mutant 4 hour (2) slide 2

source_name: time course sample harvested after 4 hour of glucose to acetate shift


title: ppsA mutant 5 hour (2) slide 2

source_name: time course sample harvested after 5 hour of glucose to acetate shift


title: ppsA mutant 4 hour (2) slide 1


title: CR1_Lysis_6_339423_21406854_B_


title: CR1_Lysis_9_24581684_6336377_B_


title: CR1_Lysis_9_30617740_32209377_B_


title: CR1_Lysis_2_30617740_399966_A_


title: CR1_Lysis_9_27596703_5944600_B_


title: ppsA mutant 5 hour (2) slide 1


title: ppsA mutant 6 hour (2) slide 1


title: CR1_Lysis_9_1626809_29945956_B_


title: CR1_Lysis_6_33644801_3892180_B_


title: CR1_Lysis_2_24581684_17910322_A_


title: ppsA mutant 2 hour (2) slide 1

source_name: time course sample harvested after 2 hour of glucose to acetate shift


title: CR1_Lysis_6_32290689_18473389_B_


title: CR1_Lysis_2_21572677_4979401_A_


title: CR1_Lysis_0_339423_19292507_A_


title: ppsA mutant 3 hour (2) slide 1


title: CR1_Lysis_2_1626809_26146952_A_


title: CR1_Lysis_0_33644801_23267004_A_


title: ppsA mutant 2 hour (2) slide 2


title: ppsA mutant 1 hour (2) slide 2

source_name: time course sample harvested after 1 hour of glucose to acetate shift


title: CR1_Lysis_0_32290689_27334033_A_


title: CR1_Lysis_6_30617740_20779368_B_


title: ppsA mutant 1 hour (2) slide 1


title: CR1_Lysis_0_30617740_25813640_A_


title: wild-type 6 hour (2) slide 1


title: wild-type 5 hour (2) slide 2


title: CR1_Lysis_6_24581684_21757491_B_


title: wild-type 3 hour (2) slide 1


title: CR1_Lysis_6_27596703_19918478_B_


title: wild-type 4 hour (2) slide 2


title: wild-type 6 hour (2) slide 2


title: CR1_Lysis_4_339423_31962126_B_


title: wild-type 4 hour (2) slide 1


title: wild-type 2 hour (2) slide 2


title: wild-type 3 hour (2) slide 2


title: ppsA mutant 3 hour (3) slide 1


title: CR1_Lysis_0_1626809_11996035_A_


title: ppsA mutant 6 hour (1) slide 1


title: CR1_Lysis_6_21572677_4488426_B_


title: ppsA mutant 6 hour (1) slide 2


title: CR1_Lysis_0_27596703_27512821_A_


title: CR1_Lysis_4_27596703_34012992_B_


title: CR1_Lysis_4_32290689_8317408_B_


title: CR1_Lysis_4_30617740_21123328_B_


title: ppsA mutant 4 hour (3) slide 1


title: wild-type 5 hour (2) slide 1


title: ppsA mutant 4 hour (3) slide 2


title: ppsA mutant 5 hour (1) slide 2


title: ppsA mutant 3 hour (3) slide 2


title: CR1_Lysis_4_33644801_3716598_B_


title: wild-type 2 hour (2) slide 1


title: CR1_Lysis_4_24581684_2248086_B_


title: CR1_Lysis_0_21572677_22931099_A_


title: CR1_Lysis_0_24581684_33693110_A_


title: ppsA mutant 5 hour (1) slide 1


title: CR1_Lysis_4_21572677_22199230_B_


title: CR1_Lysis_2_339423_7889957_B_


title: ppsA mutant 2 hour (3) slide 1


title: CR1_Lysis_2_33644801_13519166_B_


title: ppsA mutant 2 hour (3) slide 2


title: CR1_Lysis_2_30617740_399966_B_


title: ppsA mutant 1 hour (3) slide 1


title: ppsA mutant 1 hour (3) slide 2


title: wild-type 6 hour (1) slide 2


title: ppsA mutant 2 hour (1) slide 1


title: ppsA mutant 4 hour (1) slide 1


title: wild-type 6 hour (1) slide 1


title: ppsA mutant 2 hour (1) slide 2


title: CR1_Lysis_2_24581684_17910322_B_


title: ppsA mutant 3 hour (1) slide 2


title: ppsA mutant 3 hour (1) slide 1


title: CR1_Lysis_2_21572677_4979401_B_


title: CR1_Lysis_2_32290689_20990830_B_


title: ppsA mutant 1 hour (1) slide 1


title: CR1_Lysis_2_27596703_13177053_B_


title: wild-type 5 hour (1) slide 2


title: ppsA mutant 1 hour (1) slide 2


title: CR1_Lysis_2_1626809_26146952_B_


title: wild-type 4 hour (3) slide 2


title: CR1_Lysis_0_339423_19292507_B_


title: wild-type 4 hour (1) slide 2


title: wild-type 3 hour (3) slide 2


title: wild-type 4 hour (1) slide 1


title: CR1_Lysis_0_33644801_23267004_B_


title: wild-type 1 hour (2) slide 2


title: wild-type 3 hour (1) slide 2


title: CR1_Lysis_0_32290689_27334033_B_


title: ppsA mutant 4 hour (1) slide 2


title: CR1_Lysis_0_30617740_25813640_B_


title: wild-type 4 hour (3) slide 1


title: wild-type 3 hour (3) slide 1


title: wild-type 3 hour (1) slide 1


title: wild-type 2 hour (3) slide 2


title: wild-type 5 hour (1) slide 1


title: wild-type 2 hour (3) slide 1


title: CR1_Lysis_0_27596703_27512821_B_


title: wild-type 2 hour (1) slide 2


title: wild-type 1 hour (3) slide 2


title: wild-type 1 hour (1) slide 2


title: CR1_Lysis_0_24581684_33693110_B_


title: wild-type 1 hour (3) slide 1


title: wild-type 2 hour (1) slide 1


title: CR1_Lysis_0_21572677_22931099_B_


title: Ductus arteriosus 3hours chip B

status: Public on Sep 13 2005

city: Pisa

first: Flavio

last: Coceani

address: Piazza Martiri della Libertà, 33

department: Settore di Scienze Mediche

country: Italy

institute: Scuola Superiore S. Anna

description: Isolation of rat DA and Ao. Rats were mated for 24 hours and the end of this period was marked as day zero of pregnancy. Near-term fetuses (gestational age, 19 days) were delivered by Cesarean section from a normoxic or hyperoxic dam, while newborns were used 3 hours after vaginal delivery. Pregnant rats were made hyperoxic to reproduce the neonatal condition in utero. They breathed 100% oxygen inside a box for 3 hours. All animals were killed by cervical dislocation and, to isolate the DA and Ao (arch and thoracic sections), were secured inside a chamber filled with ice-cold Krebs medium through which was bubbled a gas mixture with 2.5 (fetus) or 12.5% (newborn) oxygen. Special care was taken to obtain the blood vessels free of any adhering tissue.

data_processing: Original Affymetrix output files

label: Standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001)

source_name: ductus Arteriosus

tag: Ductus Arteriosus


title: Aorta 3hours  chip B

source_name: Aorta

tag: Aorta


title: Ductus Arteriosus 19 days post coitum chipB

source_name: Ductus Arteriosus


title: CR1_Lysis_0_1626809_11996035_B_


title: Ductus Art. 19 days post coitum +O2 chipB


title: Ductus Arteriosus 3hours chip C

data_processing: Original Affymetrix .dat proprietory output files

tag: ductus arteriosus


title: wild-type 1 hour (1) slide 1

tag: Strain BW25113


title: Aorta 19 days post coitum chip B

description: Isolation of rat Ao. Rats were mated for 24 hours and the end of this period was marked as day zero of pregnancy. Near-term fetuses (gestational age, 19 days) were delivered by Cesarean section from a normoxic dam. All animals were killed by cervical dislocation and, to isolate the DA and Ao (arch and thoracic sections), were secured inside a chamber filled with ice-cold Krebs medium through which was bubbled a gas mixture with 2.5 (fetus) or 12.5% (newborn) oxygen. Special care was taken to obtain the blood vessels free of any adhering tissue.


title: Ductus arteriosus 19 days post coitum+O2chipC

tag: Ductus arteriosus


title: Ductus Arteriosus 19 days post c. chipC

source_name: Ductus arteriosus


title: Aorta 19 days post coitum chip C


title: Ductus Arteriosus 3 hours post natal

description: Isolation of rat DA . Newborn Rats were used 3 hours after vaginal delivery. All animals were killed by cervical dislocation and, to isolate the DA  were secured inside a chamber filled with ice-cold Krebs medium through which was bubbled a gas mixture with 2.5 (fetus) or 12.5% (newborn) oxygen. Special care was taken to obtain the blood vessels free of any adhering tissue.

data_processing: Affymetrix Microarray Suite 5.0 was used for image analysis and feature extraction

tag: Rat   Long Evans


title: Kidneys of CD1 mice subjected 4 weeks to normal atmospheric conditions, array N4B

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description: Chronic hypoxia alters the level, maturation and control of gene expression in mouse kidney

hyb_protocol: Hybridization protocol ("multiple yellow" strategy) described in Fan C, Iacobas DA, Zhou D, et al. Physiol Genomics. 22: 292-307

scan_protocol: Slides were scanned with GenePix 4100A scanner (Axon Instruments, CA) and images were primarily analyzed with GenePixPro 4.1 (Axon Instruments, CA).

data_processing: Data were normalized and analyzed with in house developed algorithms described in Iacobas DA, Iacobas S, Li WEI, et al. Physiol Genomics 20: 211-223, 2005.

source_name: Male mouse subjected 4 weeks to normal atmospheric conditions (N4MB)

label_protocol: 60 ug total RNA was used to synthesize fluorescent labeled cDNA probe by direct incorporation with Cy5 fluorescent dye (Amersham Biosciences, NJ)

extract_protocol: RNA samples were extracted in Trizol (Invitrogen, CA) from the kidneys

treatment_protocol: P2 CD1 mice were subjected to 4 weeks normal atmospheric conditions. The animals were decapitated under aseptic conditions and organs were removed and immediately stored into -80 ºC freezer for later total RNA extraction.

tag: Kidneys of one CD1 (Charles River, MA, U.S.A.) male mouse subjected 4 weeks to normal atmospheric conditions

source_name: Female mouse subjected 4 weeks to normal atmospheric conditions (N4FB)

label_protocol: 60 ug total RNA was used to synthesize fluorescent labeled cDNA probe by direct incorporation with Cy3 fluorescent dye (Amersham Biosciences, NJ)

tag: Kidneys of one CD1 (Charles River, MA, U.S.A.) female mouse subjected 4 weeks to normal atmospheric conditions


title: Kidneys of CD1 mice subjected 4 weeks to normal atmospheric conditions, array N4A

source_name: Male mouse subjected 4 weeks to normal atmospheric conditions (N4MA)

source_name: Female mouse subjected 4 weeks to normal atmospheric conditions (N4FA)


title: Kidneys of CD1 mice subjected 2 weeks to normal atmospheric conditions, array N2A

source_name: Male mouse subjected 2 week to normal atmospheric conditions (N2MA)

treatment_protocol: P2 CD1 mice were subjected to 2 weeks normal atmospheric conditions. The animals were decapitated under aseptic conditions and organs were removed and immediately stored into -80 ºC freezer for later total RNA extraction.

tag: Kidneys of one CD1 (Charles River, MA, U.S.A.) male mouse subjected 2 weeks to normal atmospheric conditions

source_name: Female mouse subjected 2 weeks to normal atmospheric conditions (N2FA)

tag: Kidneys of one CD1 (Charles River, MA, U.S.A.) female mouse subjected 2 weeks to normal atmospheric conditions


title: Kidneys of CD1 mice subjected 1 week to normal atmospheric conditions, array N1A

source_name: Male mouse subjected 1 week to normal atmospheric conditions (N1MA)

treatment_protocol: P2 CD1 mice were subjected to 1 week normal atmospheric conditions. The animals were decapitated under aseptic conditions and organs were removed and immediately stored into -80 ºC freezer for later total RNA extraction.

tag: Kidneys of one CD1 (Charles River, MA, U.S.A.) male mouse subjected 1 week to normal atmospheric conditions

source_name: Female mouse subjected 1 week to normal atmospheric conditions (N1FA)

tag: Kidneys of one CD1 (Charles River, MA, U.S.A.) female mouse subjected 1 week to normal atmospheric conditions


title: Ductus Arteriosus 19 days post coitum

description: Isolation of rat DA . Rats were mated for 24 hours and the end of this period was marked as day zero of pregnancy. Near-term fetuses (gestational age, 19 days) were delivered by Cesarean section from a normoxic  dam.  All animals were killed by cervical dislocation and, to isolate the DA  the paps, were secured inside a chamber filled with ice-cold Krebs medium through which was bubbled a gas mixture with 2.5 (fetus) or 12.5% (newborn) oxygen. Special care was taken to obtain the blood vessels free of any adhering tissue.

source_name: Ductus arteriusus


title: Aorta 3 hours post coitum

description: Isolation of rat  Ao.  newborn rats were used 3 hours after vaginal delivery.  All animals were killed by cervical dislocation and, to isolate the DA and Ao (arch and thoracic sections), were secured inside a chamber filled with ice-cold Krebs medium through which was bubbled a gas mixture with 2.5 (fetus) or 12.5% (newborn) oxygen. Special care was taken to obtain the blood vessels free of any adhering tissue.

source_name: aorta

tag: Rat -Long Evans


title: Kidneys of CD1 mice subjected 4 weeks to chronic intermittent hypoxia, array I4B

source_name: Male mouse subjected 4 weeks to chronic intermittent hypoxia (I4MB)

treatment_protocol: P2 CD1 mice were subjected to 4 weeks chronic intermittent hypoxia  in which [O2] was switched between 21% and 11% every four minutes. The animals were decapitated under aseptic conditions and organs were removed and immediately stored into -80 ºC freezer for later total RNA extraction.

tag: Kidneys of one CD1 (Charles River, MA, U.S.A.) male mouse subjected 4 weeks to chronic intermittent hypoxia

source_name: Female mouse subjected 4 weeks to chronic intermittent hypoxia (I4FB)

tag: Kidneys of one CD1 (Charles River, MA, U.S.A.) female mouse subjected 4 weeks to chronic intermittent hypoxia


title: Ductus Arteriosus 19 days post coitum+3hours O2

description: Isolation of rat DA . Rats were mated for 24 hours and the end of this period was marked as day zero of pregnancy. Near-term fetuses (gestational age, 19 days) were delivered by Cesarean section from a hyperoxic dam. Pregnant rats were made hyperoxic to reproduce the neonatal condition in utero. They breathed 100% oxygen inside a box for 3 hours. All animals were killed by cervical dislocation and, to isolate the DA and Ao (arch and thoracic sections), were secured inside a chamber filled with ice-cold Krebs medium through which was bubbled a gas mixture with 2.5 (fetus). Special care was taken to obtain the blood vessels free of any adhering tissue.


title: Kidneys of CD1 mice subjected 4 weeks to chronic intermittent hypoxia, array I4A

source_name: Male mouse subjected 4 weeks to chronic intermittent hypoxia (I4MA)

source_name: Female mouse subjected 4 weeks to chronic intermittent hypoxia (I4FA)


title: Kidneys of CD1 mice subjected 1 week to normal atmospheric conditions, array N1B

source_name: Male mouse subjected 1 week to normal atmospheric conditions (N1MBA)

source_name: Female mouse subjected 1 week to normal atmospheric conditions (N1FB)


title: Kidneys of CD1 mice subjected 2 weeks to chronic intermittent hypoxia, array I2A

source_name: Male mouse subjected 2 weeks to chronic intermittent hypoxia (I2MA)

treatment_protocol: P2 CD1 mice were subjected to 2 weeks chronic intermittent hypoxia  in which [O2] was switched between 21% and 11% every four minutes. The animals were decapitated under aseptic conditions and organs were removed and immediately stored into -80 ºC freezer for later total RNA extraction.

tag: Kidneys of one CD1 (Charles River, MA, U.S.A.) male mouse subjected 2 weeks to chronic intermittent hypoxia

source_name: Female mouse subjected 1 week to chronic intermittent hypoxia (I1FA)

tag: Kidneys of one CD1 (Charles River, MA, U.S.A.) female mouse subjected 2 weeks to chronic intermittent hypoxia


title: Kidneys of CD1 mice subjected 2 weeks to normal atmospheric conditions, array N2B

source_name: Male mouse subjected 2 weeks to normal atmospheric conditions (N2MB)

source_name: Female mouse subjected 2 weeks to normal atmospheric conditions (N2FB)


title: Kidneys of CD1 mice subjected 2 weeks to chronic intermittent hypoxia, array I2B

source_name: Male mouse subjected 2 weeks to chronic intermittent hypoxia (I2MB)

source_name: Female mouse subjected 2 weeks to chronic intermittent hypoxia (I2FB)


title: Aorta 19 days post coitum

description: Isolation of rat Ao. Rats were mated for 24 hours and the end of this period was marked as day zero of pregnancy. Near-term fetuses (gestational age, 19 days) were delivered by Cesarean section from a normoxic dam. To isolate the  Ao (arch and thoracic sections), was secured inside a chamber filled with ice-cold Krebs medium through which was bubbled a gas mixture with 2.5 (fetus) oxygen. Special care was taken to obtain the blood vessels free of any adhering tissue.

data_processing: Data selection and transformation procedures.

source_name: Aorta

tag: Long Evans


title: Kidneys of CD1 mice subjected 1 week to chronic intermittent hypoxia, array I1B

source_name: Male mouse subjected 1 week to chronic intermittent hypoxia (I1MB)

treatment_protocol: P2 CD1 mice were subjected to 1 week chronic intermittent hypoxia  in which [O2] was switched between 21% and 11% every four minutes. The animals were decapitated under aseptic conditions and organs were removed and immediately stored into -80 ºC freezer for later total RNA extraction.

tag: Kidneys of one CD1 (Charles River, MA, U.S.A.) male mouse subjected 1 week to chronic intermittent hypoxia

source_name: Female mouse subjected 1 week to chronic intermittent hypoxia (I1FB)

tag: Kidneys of one CD1 (Charles River, MA, U.S.A.) female mouse subjected 1 week to chronic intermittent hypoxia


title: Kidneys of CD1 mice subjected 1 week to chronic intermittent hypoxia, array I1A

source_name: Male mouse subjected 1 week to chronic intermittent hypoxia (I1MA)


title: Brain_Aged_LPSip_4hr_mouse2 (OL2_#68)

status: Public on Sep 12 2005

city: Urbana

first: Rodney

middle: W.

last: Johnson

state: IL

address: 1207 W. Gregory Dr.

department: Animal Sciences

institute: Univ of Illinois in Urbana

description: The aged mouse was injected intraperitoneal (ip) with Escherichia coli lipopolysaccharide (LPS, 0.33mg/kg body weight (BW), ~10ug/mouse; serotype O127:B8, Sigma) and was killed 4 hours after injection by CO2 asphyxiation. Brain was removed, separated in half at the longitudinal fissure, frozen in liquid nitrogen and stored at -80C until use.

data_processing: Scaling was used: All probe sets, target signal 150. Data parameters: Alpha1 (0.05), Alpha2 (0.065), Tau (0.015), Gamma1L (0.002), Gamma1H (0.002), Gamma2L (0.002667), Gamma2H (0.002667), Perturbation (1.1). Algorithm: Statistical, GCOS 1.1.

label: Biotin-labeled

source_name: Mouse brain, Aged, 4hr post LPS ip injection

tag: Strain

value: In-house BALB/c mice; Gender:Male; Age:22 months old; Tissue:Brain; Treatment:4 hours post LPS 0.33mg/kg BW ip.


title: Brain_Aged_LPSip_4hr_mouse3 (OL3_#69)


title: Kidneys of CD1 mice subjected 4 weeks to chronic constant hypoxia, array C4B

source_name: Male mouse subjected 4 weeks to chronic constant hypoxia (C4MB)

treatment_protocol: P2 CD1 mice were subjected to 4 weeks chronic constant hypoxia  in which [O2] was kept constant at 11%. The animals were decapitated under aseptic conditions and organs were removed and immediately stored into -80 ºC freezer for later total RNA extraction.

tag: Kidneys of one CD1 (Charles River, MA, U.S.A.) male mouse subjected 4 weeks to chronic constant hypoxia

source_name: Female mouse subjected 4 weeks to chronic constant hypoxia (C4FB)

tag: Kidneys of one CD1 (Charles River, MA, U.S.A.) female mouse subjected 4 weeks to chronic constant hypoxia


title: Kidneys of CD1 mice subjected 1 week to chronic constant hypoxia, array C1B

source_name: Male mouse subjected 1 week to chronic constant hypoxia (C1MB)

treatment_protocol: P2 CD1 mice were subjected to 1 week chronic constant hypoxia  in which [O2] was kept constant at 11%. The animals were decapitated under aseptic conditions and organs were removed and immediately stored into -80 ºC freezer for later total RNA extraction.

tag: Kidneys of one CD1 (Charles River, MA, U.S.A.) male mouse subjected 1 week to chronic constant hypoxia

source_name: Female mouse subjected 1 week to chronic constant hypoxia (C1FB)

tag: Kidneys of one CD1 (Charles River, MA, U.S.A.) female mouse subjected 1 week to chronic constant hypoxia


title: Brain_Adult_LPSip_4hr_mouse2 (YL2_#65)

description: The adult mouse was injected intraperitoneal (ip) with Escherichia coli lipopolysaccharide (LPS, 0.33mg/kg body weight (BW), ~10ug/mouse; serotype O127:B8, Sigma) and was killed 4 hours after injection by CO2 asphyxiation. Brain was removed, separated in half at the longitudinal fissure, frozen in liquid nitrogen and stored at -80C until use.

source_name: Mouse brain, Adult, 4hr post LPS ip injection

value: In-house BALB/c mice; Gender:Male; Age:4 months old; Tissue:Brain; Treatment:4 hours post LPS 0.33mg/kg BW ip.


title: Kidneys of CD1 mice subjected 2 weeks to chronic constant hypoxia, array C2B

source_name: Male mouse subjected 2 weeks to chronic constant hypoxia (C2MB)

treatment_protocol: P2 CD1 mice were subjected to 2 weeks chronic constant hypoxia  in which [O2] was kept constant at 11%. The animals were decapitated under aseptic conditions and organs were removed and immediately stored into -80 ºC freezer for later total RNA extraction.

tag: Kidneys of one CD1 (Charles River, MA, U.S.A.) male mouse subjected 2 weeks to chronic constant hypoxia

source_name: Female mouse subjected 2 weeks to chronic constant hypoxia (C2FB)

tag: Kidneys of one CD1 (Charles River, MA, U.S.A.) female mouse subjected 2 weeks to chronic constant hypoxia


title: Brain_Adult_LPSip_4hr_mouse1 (YL1_#64)


title: Kidneys of CD1 mice subjected 4 weeks to chronic constant hypoxia, array C4A

source_name: Male mouse subjected 4 weeks to chronic constant hypoxia (C4MA)

source_name: Female mouse subjected 4 weeks to chronic constant hypoxia (C4FA)


title: Kidneys of CD1 mice subjected 2 weeks to chronic constant hypoxia, array C2A

source_name: Male mouse subjected 2 weeks to chronic constant hypoxia (C2MA)

source_name: Female mouse subjected 2 weeks to chronic constant hypoxia (C2FA)


title: Kidneys of CD1 mice subjected 1 week to chronic constant hypoxia, array C1A

source_name: Male mouse subjected 1 week to chronic constant hypoxia (C1MA)

source_name: Female mouse subjected 1 week to chronic constant hypoxia (C1FA)


title: Brain_Adult_Salineip_4hr_mouse3(YP3_#60)

description: The adult mouse was injected intraperitoneal (ip) with saline (~100ul/mouse) and was killed 4 hours after injection by CO2 asphyxiation. Brain was removed, separated in half at the longitudinal fissure, frozen in liquid nitrogen and stored at -80C until use.

source_name: Mouse brain, Adult, 4hr post Saline ip injection

value: In-house BALB/c mice; Gender:Male; Age:4 months old; Tissue:Brain; Treatment:4 hours post Saline ip.


title: Brain_Adult_LPSip_4hr_mouse3 (YL3_#66)


title: Brain_Adult_Salineip_4hr_mouse2 (YP2_#59)

source_name: Mouse brain, Adult, 4hr post saline ip injection

value: In-house BALB/c mice; Gender:Male; Age:4 months old; Tissue:Brain; Treatment:4 hours post saline ip.


title: Brain_Adult_Salineip_4hr_mouse1 (YP1_#58)


title: Brain_Aged_Salineip_4hr_mouse3(OP3_#63)

description: The aged mouse was injected intraperitoneal (ip) with saline (~100ul/mouse) and was killed 4 hours after injection by CO2 asphyxiation. Brain was removed, separated in half at the longitudinal fissure, frozen in liquid nitrogen and stored at -80C until use.

source_name: Mouse brain, Aged, 4hr post saline ip injection

value: In-house BALB/c mice; Gender:Male; Age:22 months old; Tissue:Brain; Treatment:4 hours post saline ip.


title: Squamous cell lung cancer X36sqm

status: Public on Sep 09 2005

first: Shinichiro

last: Wachi

address: 1 Shields Avenue

department: Internal Medicine

institute: University of California, Davis

description: Tumor cells

data_processing: Robust Microarray Analysis (RMA), Bioconductor Suite Version 2.0.0

source_name: Squamous cell lung cancer patient 36

label_protocol: 15~25 ug of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Tissue sample double extraction using TRIzol

tag: Human squamous cell lung cancer cells


title: Squamous cell lung cancer X42sqm

description: Tumor cells

source_name: Squamous cell lung cancer patient 42


title: Brain_Aged_LPSip_4hr_mouse1 (OL1_#67)

source_name: Mouse brain, Aged, 4hr post LPS ip injection


title: Brain_Aged_Salineip_4hr_mouse1 (OP1_#61)


title: Squamous cell lung cancer X33sqm

description: Tumor cells

source_name: Squamous cell lung cancer patient 33


title: Squamous cell lung cancer X35nml

description: Normal cells

source_name: Squamous cell lung cancer patient 35


title: Squamous cell lung cancer X33nml

description: Normal cells


title: Squamous cell lung cancer X35sqm

description: Tumor cells


title: Squamous cell lung cancer X31nml

description: Normal cells

source_name: Squamous cell lung cancer patient 31


title: Squamous cell lung cancer X42nml

description: Normal cells


title: 218m8d15

status: Public on Sep 08 2005

city: London

first: Claudine

last: James

email: claudinegj@hotmail.com, fbeier@uwo.ca

state: Ontario

address: 1151 Richmond Street, Suite 2

department: Physiology and Pharmacology

country: Canada

institute: University of Western Ontario

description: MOE430A CHIP HYBRIDIZATION, CHIP DESIGNATION:218m8, TIME COURSE DAY:15, REPLICATE:#3

source_name: TOTAL RNA


title: 217m8d12

description: MOE430A CHIP HYBRIDIZATION, CHIP DESIGNATION:217m8, TIME COURSE DAY:12, REPLICATE:#3


title: 162m6d9n

description: MOE430A CHIP HYBRIDIZATION, CHIP DESIGNATION:162m6, TIME COURSE DAY:9, REPLICATE:#2


title: 216m8d9

description: MOE430A CHIP HYBRIDIZATION, CHIP DESIGNATION:216m8, TIME COURSE DAY:9, REPLICATE:#3


title: 215m8d6

description: MOE430A CHIP HYBRIDIZATION, CHIP DESIGNATION:215m8, TIME COURSE DAY:6, REPLICATE:#3


title: 161m6d6

description: MOE430A CHIP HYBRIDIZATION, CHIP DESIGNATION:161m6, TIME COURSE DAY:6, REPLICATE:#2


title: 214m8d3

description: MOE430A CHIP HYBRIDIZATION, CHIP DESIGNATION:214m8, TIME COURSE DAY:3, REPLICATE:#3


title: Aorta 3 hours chip C

description: Isolation of rat DA and Ao. Rats were mated for 24 hours and the end of this period was marked as day zero of pregnancy. Near-term fetuses (gestational age, 19 days) were delivered by Cesarean section from a normoxic or hyperoxic dam, while newborns were used 3 hours after vaginal delivery. Pregnant rats were made hyperoxic to reproduce the neonatal condition in utero. They breathed 100% oxygen inside a box for 3 hours. All animals were killed by cervical dislocation and, to isolate the DA and Ao (arch and thoracic sections), were secured inside a chamber filled with ice-cold Krebs medium through which was bubbled a gas mixture with 2.5 (fetus) or 12.5% (newborn) oxygen. Special care was taken to obtain the blood vessels free of any adhering tissue.

source_name: Aorta

tag: aorta


title: 164m6d15

description: MOE430A CHIP HYBRIDIZATION, CHIP DESIGNATION:164m6, TIME COURSE DAY:15, REPLICATE:#2


title: 163m6d12

description: MOE430A CHIP HYBRIDIZATION, CHIP DESIGNATION:163m6, TIME COURSE DAY:12, REPLICATE:#2


title: 148m4d15

description: MOE430A CHIP HYBRIDIZATION, CHIP DESIGNATION:148m4, TIME COURSE DAY:15, REPLICATE:#1


title: 160m6d3

description: MOE430A CHIP HYBRIDIZATION, CHIP DESIGNATION:160m6, TIME COURSE DAY:3, REPLICATE:#2


title: Brain_Aged_Salineip_4hr_mouse2 (OP2_#62)


title: 147m4d12

description: MOE430A CHIP HYBRIDIZATION, CHIP DESIGNATION:147m4, TIME COURSE DAY:12, REPLICATE:#1


title: 145m4d6

description: MOE430A CHIP HYBRIDIZATION, CHIP DESIGNATION:145m4, TIME COURSE DAY:6, REPLICATE:#1


title: 146m4d9

description: MOE430A CHIP HYBRIDIZATION, CHIP DESIGNATION:146m4, TIME COURSE DAY:9, REPLICATE:#1


title: 27939vsS8228

city: Rockville

first: Norman

middle: H

last: Lee

state: MD

address: 9712 Medical Center Drive

department: Department of Mammalian Genomics

institute: The Institute for Genomic Research

data_processing: LOWESS Normalized


title: Squamous cell lung cancer X36nml

description: Normal cells


title: 27954vs8229


title: 27928vsS8218.txt


title: 27920vs8209


title: 144m4d3

description:
MOE430A CHIP HYBRIDIZATION,
CHIP DESIGNATION:144m4,
TIME COURSE DAY:3,
REPLICATE:#1


title: 27932vs8211.txt


title: Cerebellum_nontransgenic control A61_8 months_replicate 1

status: Public on Sep 07 2005

first: Andrew

last: Strand

address: 1100 Fairview Ave N.

institute: Fred Hutchinson Cancer Research Center

description: A61 WT1	F6/20	A61	wild type	Mouse	8 months	Cerebellum	Male

data_processing: MAS 5 global scaling at defalut values; normalization factor=1, target value=500

source_name: cerebellum


title: Cerebellum_transgenic nuclear exclusion signal Htt exon1 142Q A39_4 months_replicate 3

description: A39 NES 142Q TG3	F7/4	A39	NES Htt exon 1 142Q	Mouse	4 months	Cerebellum	Male


title: 27923vs8219.txt


title: 27926vsS8210.txt


title: Cerebellum_nontransgenic control S46_10 months_replicate 2

description: S46 WT6	F5/54	S46	wild type	Mouse	10 months	Cerebellum	Female


title: Cerebellum_nontransgenic control A39_4 months_replicate 2

description: A39 WT2	F5/53	A39	wild type	Mouse	4 months	Cerebellum	Female


title: Cerebellum_nontransgenic control S46_10 months_replicate 1

description: S46 WT5	F5/53	S46	wild type	Mouse	10 months	Cerebellum	Female


title: Cerebellum_transgenic nuclear exclusion signal Htt exon1 142Q A61_8 months_replicate 3

description: A61 NES 142Q TG3	F6/23	A61	NES Htt exon 1 142Q	Mouse	8 months	Cerebellum	Male


title: Cerebellum_transgenic nuclear exclusion signal Htt exon1 142Q A61_8 months_replicate 1

description: A61 NES 142Q TG1	F6/13	A61	NES Htt exon 1 142Q	Mouse	8 months	Cerebellum	Male


title: Cerebellum_transgenic nuclear exclusion signal Htt exon1 142Q A61_8 months_replicate 2

description: A61 NES 142Q TG2	F6/22	A61	NES Htt exon 1 142Q	Mouse	8 months	Cerebellum	Male


title: Cerebellum_transgenic nuclear exclusion signal Htt exon1 142Q A39_4 months_replicate 2

description: A39 NES 142Q TG2	F5/52	A39	NES Htt exon 1 142Q	Mouse	4 months	Cerebellum	Female


title: Squamous cell lung cancer X31sqm

description: Tumor cells


title: Cerebellum_nontransgenic control A39_4 months_replicate 3

description: A39 WT3	F7/3	A39	wild type	Mouse	4 months	Cerebellum	Male


title: Cerebellum_transgenic nuclear localization signal Htt exon1 142Q S46_3 months_replicate 2

description: S46 NLS 142Q TG2	F5/9	S46	NLS Htt exon 1 142Q	Mouse	3.5 months	Cerebellum	Female


title: Cerebellum_transgenic nuclear exclusion signal Htt exon1 142Q A39_4 months_replicate 1

description: A39 NES 142Q TG1	F5/51	A39	NES Htt exon 1 142Q	Mouse	4 months	Cerebellum	Female


title: Cerebellum_transgenic nuclear exclusion signal Htt exon1 142Q A39_4 months_replicate 4

description: A39 NES 142Q TG4	F7/5	A39	NES Htt exon 1 142Q	Mouse	4 months	Cerebellum	Male


title: Cerebellum_nontransgenic control S46_3.5 months_replicate 2

description: S46 WT2	F5/8	S46	wild type	Mouse	3.5 months	Cerebellum	Female


title: Cerebellum_nontransgenic control S46_10 months_replicate 3

description: S46 WT7	F5/55	S46	wild type	Mouse	10 months	Cerebellum	Female


title: Cerebellum_nontransgenic control A39_8 months_replicate 2

description: A61 WT2	F6/21	A61	wild type	Mouse	8 months	Cerebellum	Male


title: Cerebellum_transgenic nuclear localization signal Htt exon1 142Q S25_3 months_replicate 3

description: S25 NLS 142Q TG3	F4/34	S25	NLS Htt exon 1 142Q	Mouse	3 months	Cerebellum	Male


title: Cerebellum_nontransgenic control S25_3 months_replicate 3

description: S25 WT2	F41/390	S25	wild type	Mouse	2.5 months	Cerebellum	Female


title: Cerebellum_nontransgenic control S25_3 months_replicate 2

description: S25 WT1	F4/27	S25	wild type	Mouse	3 months	Cerebellum	Male


title: Cerebellum_transgenic nuclear localization signal Htt exon1 142Q S46_3 months_replicate 4

description: S46 NLS 142Q TG4	F5/12	S46	NLS Htt exon 1 142Q	Mouse	3.5 months	Cerebellum	Female


title: Cerebellum_nontransgenic control S46_3.5 months_replicate 3

description: S46 WT3	F5/11	S46	wild type	Mouse	3.5 months	Cerebellum	Female


title: Cerebellum_transgenic nuclear localization signal Htt exon1 18Q x50_16 months_replicate 3

description: X50 NLS 18Q TG3	F2/49	X50	NLS Htt exon 1 18Q	Mouse	16 months	Cerebellum	Male


title: Cerebellum_transgenic nuclear localization signal Htt exon1 142Q S46_10 months_replicate 3

description: S46 NLS 142Q TG7	F4/3	S46	NLS Htt exon 1 142Q	Mouse	10 months	Cerebellum	Female


title: Cerebellum_transgenic nuclear localization signal Htt exon1 142Q S46_3 months_replicate 1

description: S46 NLS 142Q TG1	F5/2	S46	NLS Htt exon 1 142Q	Mouse	3.5 months	Cerebellum	Male


title: Cerebellum_transgenic nuclear localization signal Htt exon1 142Q S46_10 months_replicate 2

description: S46 NLS 142Q TG6	F4/2	S46	NLS Htt exon 1 142Q	Mouse	10 months	Cerebellum	Female


title: Cerebellum_transgenic nuclear localization signal Htt exon1 142Q S25_3 months_replicate 2

description: S25 NLS 142Q TG2	F4/26	S25	NLS Htt exon 1 142Q	Mouse	3 months	Cerebellum	Male


title: Cerebellum_nontransgenic control S46_3.5 months_replicate 1

description: S46 WT1	F5/3	S46	wild type	Mouse	3.5 months	Cerebellum	Male


title: Cerebellum_nontransgenic control A39_8 months_replicate 4

description: A61 WT4	F24/5	A61	wild type	Mouse	8 months	Cerebellum	Female


title: Cerebellum_transgenic nuclear exclusion signal Htt exon1 142Q A61_8 months_replicate 4

description: A61 NES 142Q TG4	F5/1	A61	NES Htt exon 1 142Q	Mouse	8 months	Cerebellum	Male


title: Cerebellum_nontransgenic control A39_4 months_replicate 4

description: A39 WT4	F25/17	A39	wild type	Mouse	4 months	Cerebellum	Female


title: Cerebellum_transgenic nuclear exclusion signal Htt exon1 142Q A39_10 months_replicate 3

description: A39 NES 142Q TG7	F2/13	A39	NES Htt exon 1 142Q	Mouse	10 months	Cerebellum	Male


title: Cerebellum_transgenic nuclear localization signal Htt exon1 142Q S25_3 months_replicate 1

description: S25 NLS 142Q TG1	F4/23	S25	NLS Htt exon 1 142Q	Mouse	3 months	Cerebellum	Male


title: Cerebellum_nontransgenic control X50_16 months_replicate 2

description: X50 WT2	F2/9	X50	wild type	Mouse	16 months	Cerebellum	Male


title: Cerebellum_transgenic nuclear localization signal Htt exon1 142Q S46_10 months_replicate 1

description: S46 NLS 142Q TG5	F4/1	S46	NLS Htt exon 1 142Q	Mouse	10 months	Cerebellum	Female


title: Cerebellum_nontransgenic control A39_10 months_replicate 2

description: A39 WT6	F2/11	A39	wild type	Mouse	10 months	Cerebellum	Male


title: Cerebellum_transgenic nuclear localization signal Htt exon1 18Q x50_16 months_replicate 2

description: X50 NLS 18Q TG2	F2/35	X50	NLS Htt exon 1 18Q	Mouse	16 months	Cerebellum	Male


title: Cerebellum_nontransgenic control A39_8 months_replicate 3

description: A61 WT3	F24/2	A61	wild type	Mouse	8 months	Cerebellum	Male


title: Cerebellum_nontransgenic control S25_3 months_replicate 1

description: S25 WT3	F41/391	S25	wild type	Mouse	2.5 months	Cerebellum	Female


title: Cerebellum_transgenic nuclear localization signal Htt exon1 18Q x50_16 months_replicate 1

description: X50 NLS 18Q TG1	F2/34	X50	NLS Htt exon 1 18Q	Mouse	16 months	Cerebellum	Male


title: Cerebellum_nontransgenic control X50_16 months_replicate 3

description: X50 WT3	F2/33	X50	wild type	Mouse	16 months	Cerebellum	Male


title: Cerebellum_transgenic nuclear exclusion signal Htt exon1 142Q A39_10 months_replicate 2

description: A39 NES 142Q TG6	F1/4	A39	NES Htt exon 1 142Q	Mouse	10.5 months	Cerebellum	Female


title: Cerebellum_nontransgenic control A39_10 months_replicate 1

description: A39 WT5		F1/1	A39	wild type	Mouse	10.5 months	Cerebellum	Male

data_processing: MAS 5 global scaling at default values; normalization factor=1, target value=500

tag: Line A39 control cerebellum, mouse, male, 10 months


title: Cerebellum_transgenic nuclear localization signal Htt exon1 142Q S46_3 months_replicate 3

description: S46 NLS 142Q TG3	F5/10	S46	NLS Htt exon 1 142Q	Mouse	3.5 months	Cerebellum	Female


title: Cerebellum_transgenic nuclear exclusion signal Htt exon1 142Q A39_10 months_replicate 1

description: A39 NES 142Q TG5	F1/2	A39	NES Htt exon 1 142Q	Mouse	10.5 months	Cerebellum	Male

tag: Line A39 transgenic cerebellum, mouse, male, 10 months


title: Cerebellum_nontransgenic control S46_3.5 months_replicate 4

description: S46 WT4	F5/13	S46	wild type	Mouse	3.5 months	Cerebellum	Female


title: Cerebellum_nontransgenic control A39_10 months_replicate 3

description: A39 WT7	F2/14	A39	wild type	Mouse	10 months	Cerebellum	Male


title: Cerebellum_nontransgenic control X50_16 months_replicate 1

description: X50 WT1	F2/8	X50	wild type	Mouse	16 months	Cerebellum	Male


title: CSS651

status: Public on Aug 29 2005

city: Cincinnati

first: Bruce

middle: J

last: Aronow

state: OH

institute: Cincinnati Children's Hospital Medical Center

description: epithelium cell type comparison

data_processing: We used a normalization and referencing strategy that consisted of BioConductor/RMA Express RMA processing of the entire series of cel files followed by a per gene normalization in which the median value of expression for each gene was derived from the cultured samples only, and this was used as a reference for all samples including the cultured skin substitute. This approach allowed for the identification of genes that were higher and lower-expressed in the cultured skin relative to the individual cell types that were also expressed strongly or weakly in normal skin relative to the median value established by the three cell types.

source_name: cultured skin substitute - individual 651

label_protocol: standard Affymetrix

tag: Tissue type

value: epithelium

tag: Sample type

value: cultured skin substitute

tag: idv ID

tag: Donor Age

tag: Site

value: breast

tag: indivRep


title: CF639

description: epithelium cell type comparison

source_name: cultured fibroblast - individual _639

value: cultured fibroblast

value: abdomen


title: CK651

description: epithelium cell type comparison

source_name: cultured keratinocyte - individual 651

value: cultured keratinocyte


title: C_1_REF

description: epithelium cell type comparison

source_name: human skin - ref

value: human skin

value: ref


title: CK633

description: epithelium cell type comparison

source_name: cultured keratinocyte - individual 633


title: NHS639

description: epithelium cell type comparison

source_name: human skin - individual 639


title: CF633

description: epithelium cell type comparison

source_name: cultured fibroblast - individual 633


title: CF634

description: epithelium cell type comparison

source_name: cultured fibroblast - individual 634


title: CK634

description: epithelium cell type comparison

source_name: cultured keratinocyte - individual 634


title: CK639

description: epithelium cell type comparison

source_name: cultured keratinocyte - individual 639


title: CSS633

description: epithelium cell type comparison

source_name: cultured skin substitute - individual 633


title: PPS2-4C

status: Public on Jul 27 2004

city: Laramie

first: Mark

last: Gomelsky

state: WY

department: Molecular Biology

institute: University of Wyoming

description: PPS2-4 strain was derived from R.sphaeroides 2.4.1. It has two point mutations in the chromosomal ppsR gene resulting in amino acid substitutions C251->S and C424->S. Growth at 20% O2, 1% CO2, 79% N2 in the dark. Cells are collected at OD 0.18. RNA was isolated with bead beater + RNeasy kits

organism: Cereibacter sphaeroides

source_name: Rhodobacter sphaeroides PPS2-4


title: PPS2-4A


title: pancreatic T effector cells 2300

status: Public on Jun 07 2004

city: Boston

first: CBDM

last: Lab

institute: Harvard Medical School

description:
T effector cells isolated from the pancreas of BDC2.5 tg NOD mice, mice were treated with Rat IgG.  RNA prep by Trizol, followed by two rounds of amplification.  Detailed method in Herman et al, J.Exp. Med., Vol 199, Number 11, June 7,2004.
Keywords = diabetes
Keywords = immune regulation

source_name: pancreatic CD4+CD25lo/-CD69+/- cells


title: CF651

description: epithelium cell type comparison

source_name: cultured fibroblast - individual 651


title: CSS639

description: epithelium cell type comparison

source_name: cultured skin substitute - individual 639_1_H


title: CSS634

description: epithelium cell type comparison

source_name: cultured skin substitute - individual 634


title: NHS636

description: epithelium cell type comparison

source_name: human skin - individual _636


title: pancreatic T effector cell 2284


title: pancreatic T effector cells 2297


title: PPS2-4D


title: pancreatic T regulatory cell 2016

description:
T regulatory cells isolated from BDC2.5 tg NOD mouse pancreata,
mice were treated with Rat IgG.  RNA prep by Trizol, followed by two rounds of amplification.  Detailed method in Herman et al, J Exp. Med., Vol 199, Number 11, June 7,2004.
Keywords = diabetes
Keywords = immune regulation

source_name: pancreatic CD4+CD25+CD69- cells


title: pancreatic T regulatory cell 2298

description:
T regulatory cells isolated from BDC2.5 tg NOD mouse pancreata,
mice were treated with Rat IgG.  RNA prep by Trizol, followed by two rounds of amplification.  Detailed method in Herman et al, J.Exp. Med., Vol 199, Number 11, June 7,2004.
Keywords = diabetes
Keywords = immune regulation


title: pancreatic T effector cell 2018


title: NHS633

description: epithelium cell type comparison

source_name: human skin - individual 633


title: pancreatic T effector cell 2020

source_name: pancreatic CD4+CD25lo/-CD69+/-


title: pancreatic T regulatory cell 2286


title: Eye Discs iso4 lm29

status: Public on Jan 21 2003

city: Basel

first: Lydia

last: Michaut

address: Klingelbergstrasse 70

department: Cell Biology

country: Switzerland

institute: Biozentrum

description: To analyze gene expression in Drosophila eye primordia (third instar wandering larvae), the eye part was separated from the antennal part of the eye-antennal disc. One hundred eye imaginal discs were dissected, immediately transferred into 800ul Trizol (GIBCO Life Technologies) and stored at -70C. RNA extraction was performed according to the manufacturer's instructions. Quantity and quality of total RNA were determined by capillary electrophoresis on a RNA6000 bioanalyzer (Agilent Technologies). Two successive rounds of cDNA synthesis were applied to prepare 20ug of biotinylated target from one to two micrograms of total RNA (see Michaut et al., 2003).

organism: Drosophila melanogaster

source_name: Drosophila wandering larvae eye imaginal discs


title: Cerebellum_nontransgenic control A39_4 months_replicate 1

description: A39 WT1	F5/50	A39	wild type	Mouse	4 months	Cerebellum	Female

source_name: cerebellum