title: GC2_SARB67_LT2_2D729_1


title: RE3_LT2_H2O2_20 min_3D179_3

status: Public on May 10 2004

type: RNA

city: Irvine

first: Michael

last: McClelland

state: CA

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

country: USA

institute: University of California, Irvine

description:
Salmonella typhimurium LT2 Expression after exposure to 2mM H2O2 for 20min
User - PCheng
Date_of_Scan = Thu Jul 31 10:47:38 2003
Sample_target_source3: LT2 genomic DNA cy5 lableled

molecule: total RNA

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: LT2 20 min post treatment

source_name: LT2 pretreatment


title: GC2_SARB67_LT2_2D729_2

type: genomic

description:
genomic comparison SARB67/LT2
User - PCheng
Date_of_Scan = Wed Apr 30 14:12:37 2003

molecule: genomic DNA

source_name: SARB67 gDNA overnight in LB

source_name: LT2 gDNA overnight in LB


title: RE3_LT2_H2O2_20 min_3D179_1


title: GC2_SARB48_LT2_2D727_3

description:
genomic comparison SARB48/LT2
User - PCheng
Date_of_Scan = Fri Apr 25 13:00:05 2003

organism:
Salmonella enterica subsp. enterica serovar Paratyphi C
Salmonella enterica subsp. enterica serovar Typhimurium

source_name: SARB48 gDNA overnight in LB


title: RE3_LT2_H2O2_20 min_3D286_1

description:
Salmonella typhimurium LT2 Expression after exposure to 2mM H2O2 for 20min
User - PCheng
Date_of_Scan = Mon Aug 18 09:25:03 2003
Sample_target_source3: LT2 Cy5 labeled genomic DNA


title: RE3_LT2_H2O2_20 min_3D179_2


title: GC2_SARB48_LT2_2D727_1


title: RE3_LT2_H2O2_20 min_3D148_2

description:
Salmonella typhimurium LT2 Expression after exposure to 2mM H2O2 for 20min
User - PCheng
Date_of_Scan = Tue Jul 29 13:17:28 2003
Sample_target_source3: LT2 genomic DNA


title: RE3_LT2_H2O2_120min_3D145_1

description:
Salmonella typhimurium LT2 Expression after exposure to 2mM H2O2 for 120min
User - PCheng
Date_of_Scan = Wed Jul 23 12:28:32 2003
Sample_target_source3: LT2 genomic DNA

source_name: LT2 120 min post treatment


title: GC2_SARB32_LT2_2D722_3

description:
genomic comparison SARB32/LT2
User - PCheng
Date_of_Scan = Wed Apr 23 15:05:03 2003

organism:
Salmonella enterica subsp. enterica serovar Muenchen
Salmonella enterica subsp. enterica serovar Typhimurium

source_name: SARB32 gDNA overnight in LB


title: RE3_LT2_H2O2_180 min_3D183_3

description:
Salmonella typhimurium LT2 Expression after exposure to 2mM H2O2
User - PCheng
Date_of_Scan = Thu Jul 24 10:39:43 2003
Sample_target_source3: LT2 pretreatment genomic DNA

source_name: LT2 180 min post treatment


title: GC2_SARB68_LT2_2D728_1

description:
genomic comparison SARB68/LT2
User - PCheng
Date_of_Scan = Wed Apr 30 13:52:35 2003

source_name: SARB68 gDNA overnight in LB


title: RE3_LT2_H2O2_180 min_3D183_2


title: RE3_LT2_H2O2_240 min_3D136_2

description:
Salmonella typhimurium LT2 Expression after exposure to 2mM H2O2 for 240min
User - PCheng
Date_of_Scan = Wed Jul 23 14:13:05 2003
Sample_target_source3: LT2 genomic DNA

source_name: LT2 240 min post treatment


title: RE3_LT2_H2O2_5 min_3D144_2

description:
Salmonella typhimurium LT2 Expression after exposure to 2mM H2O2 for 5min
User - PCheng
Date_of_Scan = Wed Jul 23 11:33:39 2003
Sample_target_source3: LT2 genomic DNA

source_name: LT2 5 min post treatment


title: GC2_SARB32_LT2_2D722_1


title: GC2_SARB48_LT2_2D727_2


title: RE3_LT2_H2O2_5 min_3D144_1


title: GC2_SARB66_LT2_2D718_3

description:
genomic comparison SARB66/LT2
User - PCheng
Date_of_Scan = Tue Apr 15 17:34:00 2003

source_name: SARB66 gDNA overnight in LB


title: RE3_LT2_H2O2_120min_3D145_3


title: GC2_011795_LT2_2D724_1

description:
genomic comparison 011795/LT2
User - PCheng
Date_of_Scan = Thu Apr 24 14:52:36 2003

source_name: 011795 gDNA overnight in LB


title: GC2_011795_LT2_2D724_3


title: RE3_LT2_H2O2_120min_3D145_2


title: RE3_LT2_H2O2_20 min_3D148_1


title: GC2_SARB32_LT2_2D722_2


title: GC2_SARB4_LT2_2D715_3

description:
genomic comparison SARB4/LT2
User - PCheng
Date_of_Scan = Tue Apr 15 16:48:10 2003

organism:
Salmonella enterica subsp. enterica serovar Typhimurium
Salmonella enterica subsp. enterica serovar Choleraesuis

source_name: SARB4 gDNA overnight in LB


title: RE3_LT2_H2O2_240 min_3D136_3


title: GC2_011795_LT2_2D724_2


title: GC2_LT2_T180_H2O2_3D130_2

description:
LT2 exposed to 2mM H2O2 for 180min compared to untreated log phase gDNA.
User - PCheng
Date_of_Scan = Tue Jul 08 10:15:46 2003

source_name: LT2 T0 untreated


title: RE3_LT2_H2O2_240 min_3D136_1


title: GC2_LT2_T180_H2O2_3D130_1


title: GC2_SARB66_LT2_2D718_2


title: GC2_LT2_T180_H2O2_3D130_3


title: RE3_LT2_H2O2_5 min_3D144_3


title: GC2_LT2_T180 H2O2 gDNA_3D154_2

description:
LT2 was exposed to 2mM H2O2 for 180 minutes and compared to untreated 0 minute LT2 gDNA. Same as slide 3d130.
User - Fblackmer
Date_of_Scan = Mon Jun 16 09:54:56 2003
Keywords = Salmonella

source_name: LT2 T180 H2O2 gDNA

source_name: LT2 T0 gDNA


title: GC2_SARB66_LT2_2D718_1


title: GC2_021785_LT2_2D714_3

description:
genomic comparison 021785/LT2
User - PCheng
Date_of_Scan = Wed Apr 09 16:19:35 2003

organism:
Salmonella enterica subsp. enterica serovar Muenster
Salmonella enterica subsp. enterica serovar Typhimurium

source_name: 021785 gDNA overnight in LB


title: RE3_LT2_H2O2_180 min_3D183_1

source_name: LT2 pretreatment


title: GC2_021785_LT2_2D714_2


title: GC2_LT2_T180 H2O2 gDNA_3D154_3


title: RRE2_LT2_H2O2_20min_3D125_3

description:
LT2 peroxide treatment time course
Keywords = Salmonella

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

source_name: LT2_ 20mins Post H2O2

source_name: LT2 Pretreatment


title: GC2_021173_LT2_2D713_2

description:
genomic comparison 021173/LT2
User - PCheng
Date_of_Scan = Wed Apr 09 15:51:24 2003

organism:
Salmonella enterica subsp. enterica serovar Senftenberg
Salmonella enterica subsp. enterica serovar Typhimurium

source_name: 021173 gDNA overnight in LB

source_name: LT2 gDNA overnight in LB


title: RRE2_LT2_H2O2_20min_3D125_2

source_name: LT2 20mins post H2O2


title: RRE2_LT2_MitomycinC_240min_3D120_2

description:
Salmonella typhimurium LT2 Expression after tratment with 2 ug/ml Mitomycin C  for 240 compared against untreated log phase RNA
User - PCheng
Date_of_Scan = Wed Jun 11 09:05:36 2003
Keywords = Salmonella


title: GC2_LT2_T180 H2O2 gDNA_3D154_1


title: RRE2_LT2_H2O2_20min_3D125_1

source_name: LT2 20min post H2O2


title: GC2_S1380_LT2_2D712_3

description:
genomic comparison S1380/LT2
User - PCheng
Date_of_Scan = Thu Apr 03 16:46:31 2003

source_name: S1380 gDNA overnight in LB


title: GC2_021173_LT2_2D713_3


title: RRE2_LT2_MitomycinC_240min_3D120_1

source_name: LT2 240 min post treatment


title: GC2_021173_LT2_2D713_1


title: GC2_022477_LT2_2D711_3

description:
genomic comparison 022477/LT2
User - PCheng
Date_of_Scan = Thu Apr 03 15:17:57 2003

organism:
Salmonella enterica subsp. enterica serovar Heidelberg
Salmonella enterica subsp. enterica serovar Typhimurium

source_name: 022477 gDNA overnight in LB


title: GC2_S1380_LT2_2D712_1


title: GC2_S1380_LT2_2D712_2


title: GC2_021998_LT2_2D710_3

description:
genomic comparison 021988/LT2
User - PCheng
Date_of_Scan = Thu Apr 03 14:48:09 2003

organism:
Salmonella enterica subsp. enterica serovar Saintpaul
Salmonella enterica subsp. enterica serovar Typhimurium

source_name: 021988 gDNA overnight in LB


title: RRE2_LT2_MitomycinC_180min_3D121_2

description:
Salmonella typhimurium LT2 Expression after tratment with 2 ug/ml Mitomycin C for 180 min compared to untreated log phase RNA
User - PCheng
Date_of_Scan = Wed Jun 11 09:26:19 2003
Keywords = Salmonella

source_name: LT2 180 min post treatment


title: RRE2_LT2_MitomycinC_180min_3D121_3


title: GC2_022477_LT2_2D711_2


title: RRE2_LT2_MitomycinC_20min_3D153_3

description:
Salmonella typhimurium LT2 Expression after tratment with 2 ug/ml Mitomycin C for 20min compared to untreated log phase RNA
User - PCheng
Date_of_Scan = Wed Jun 11 09:58:20 2003
Keywords = Salmonella

source_name: LT2 20 min post treatment


title: GC2_022007_LT2_2D658_1

description:
genomic comparison 022007/LT2
User - PCheng
Date_of_Scan = Mon Mar 17 10:16:16 2003

organism:
Salmonella enterica subsp. enterica serovar Typhimurium
Salmonella enterica subsp. enterica serovar Paratyphi B var. L(+) tartrate +

source_name: 022007 gDNA overnight in LB


title: GC2_SARB4_LT2_2D715_2

source_name: SARB4 gDNA overnight in LB


title: GC2_022477_LT2_2D711_1


title: RRE2_LT2_MitomycinC_180min_3D121_1


title: GC2_021785_LT2_2D714_1


title: RRE2_LT2_MitomycinC_120min_3D122_2

description:
Salmonella typhimurium LT2 Expression after tratment with 2 ug/ml Mitomycin C for 120min compared to untreated log phase RNA
User - PCheng
Date_of_Scan = Wed Jun 11 09:47:46 2003
Keywords = Salmonella

source_name: LT2 120 min post treatment


title: GC2_021998_LT2_2D710_2


title: RRE2_LT2_MitomycinC_120min_3D122_1


title: RRE2_LT2_MitomycinC_30min_3D123_3

description:
Salmonella typhimurium LT2 Expression after tratment with 2 ug/ml Mitomycin C for 30min compared to untreated log phase RNA
User - PCheng
Date_of_Scan = Wed Jun 11 10:11:55 2003
Keywords = Salmonella

source_name: LT2 30 min post treatment


title: GC2_022007_LT2_2D658_2


title: GC2_SARB43_LT2_2D654_1

description:
genomic comparison SARB43/LT2
User - PCheng
Date_of_Scan = Mon Mar 17 12:00:10 2003

organism:
Salmonella enterica subsp. enterica serovar Paratyphi B
Salmonella enterica subsp. enterica serovar Typhimurium

source_name: SARB43 gDNA overnight in LB


title: RRE2_LT2_MitomycinC_30min_3D123_2

source_name: LT2 pretreatment


title: RRE2_LT2_MitomycinC_30min_3D123_1


title: GC2_022007_LT2_2D658_3


title: GC2_15.5_LT2_4D281_2

description:
genomic comparison 15.5/LT2
User - Cchoy
Date_of_Scan = Wed Dec 17 13:23:26 2003

organism:
Salmonella enterica subsp. enterica serovar Abortusovis
Salmonella enterica subsp. enterica serovar Typhimurium

source_name: 15.5 gDNA overnight in LB


title: GC2_022226_LT2_2D653_3

description:
genomic comparison 022226/LT2
User - PCheng
Date_of_Scan = Sat Mar 15 13:01:36 2003

organism:
Salmonella enterica subsp. enterica serovar Infantis
Salmonella enterica subsp. enterica serovar Typhimurium

source_name: 022226 gDNA overnight in LB


title: RRE2_LT2_MitomycinC_120min_3D122_3


title: GC2_SARB43_LT2_2D654_3

source_name: LT2 gDNA overnight in LB


title: GC2_SARB43_LT2_2D654_2


title: GC2_021998_LT2_2D710_1


title: GC2_15.5_LT2_4D281_1


title: GC2_021964_LT2_2D652_1

description:
genomic comparison 021964/LT2
User - PCheng
Date_of_Scan = Sat Mar 15 12:25:49 2003

source_name: 021964 gDNA overnight in LB


title: GC2_SS44_LT2_4D280_3

description:
genomic comparison SS44/LT2
User - Cchoy
Date_of_Scan = Wed Dec 17 12:27:22 2003

source_name: SS44 gDNA overnight in LB


title: RRE2_LT2_MitomycinC_20min_3D153_1


title: RRE2_LT2_MitomycinC_20min_3D153_2


title: GC2_SARB4_LT2_2D715_1

description:
genomic comparison SARB4/LT2
User - PCheng
Date_of_Scan = Tue Apr 15 16:48:10 2003


title: GC2_022226_LT2_2D653_2


title: GC2_022226_LT2_2D653_1


title: GC2_SS44_LT2_4D280_2


title: GC2_SS44_LT2_4D280_1


title: GC2_021964_LT2_2D652_3


title: GC2_15.5_LT2_4D281_3


title: GC2_995115_LT2_2D650_3

description:
genomic comparison 995115/LT2
User - PCheng
Date_of_Scan = Sat Mar 15 11:05:35 2003

organism:
Salmonella enterica subsp. enterica serovar Typhimurium
Salmonella enterica subsp. enterica serovar Newport

source_name: 995115 gDNA overnight in LB


title: GC2_024509_LT2_2D651_3

description:
genomic comparison 024509/LT2
User - PCheng
Date_of_Scan = Sat Mar 15 11:50:06 2003

source_name: 024509 gDNA overnight in LB


title: GC2_021964_LT2_2D652_2


title: GC2_995115_LT2_2D650_1


title: GC2_021834_LT2_2D649_3

description:
genomic comparison 021834/LT2
User - PCheng
Date_of_Scan = Wed Mar 26 09:58:41 2003

organism:
Salmonella enterica subsp. enterica serovar Typhimurium
Salmonella enterica subsp. enterica serovar Enteritidis

source_name: 021834 gDNA overnight in LB


title: GC2_SARB20_LT2_4D425_2

description:
genomic comparison SARB20/LT2
User - PCheng
Date_of_Scan = Fri Jan 30 10:39:28 2004

source_name: SARB20 (EN7) gDNA overnight in LB


title: RRE2_LT2_MitomycinC_240min_3D120_3

description:
Salmonella typhimurium LT2 Expression after tratment with 2 ug/ml Mitomycin C  for 240 compared against untreated log phase RNA
User - PCheng
Date_of_Scan = Wed Jun 11 09:05:36 2003
Keywords = Salmonella

source_name: LT2 240 min post treatment


title: GC2_SARB20_LT2_4D425_3


title: GC2_995115_LT2_2D650_2


title: GC2_SARA32_LT2_4D421_1

description:
genomic comparison SARA32/LT2
User - PCheng
Date_of_Scan = Tue Jan 27 13:12:33 2004

source_name: SARA32 gDNA overnight in LB


title: GC2_SARB44_LT2_4D426_3

description:
genomic comparison SARB44/LT2
User - PCheng
Date_of_Scan = Fri Jan 30 11:47:11 2004

source_name: SARB44 (Pb3) gDNA overnight in LB


title: GC2_SARB20_LT2_4D425_1


title: GC2_024509_LT2_2D651_1


title: GC2_021834_LT2_2D649_2


title: GC2_SARA27_LT2_4D406_3

description:
genomic comparison SARA27/LT2
User - PCheng
Date_of_Scan = Wed Jan 21 13:29:56 2004

source_name: SARA27 gDNA overnight in LB


title: GC2_024509_LT2_2D651_2


title: GC2_SARA27_LT2_4D406_1


title: GC2_SARA32_LT2_4D421_3


title: GC2_SARA32_LT2_4D421_2


title: GC2_SARB44_LT2_4D426_2


title: GC2_SARB44_LT2_4D426_1


title: GC2_024724_LT2_2D648_2

description:
genomic comparison 024724/LT2
User - PCheng
Date_of_Scan = Thu Mar 06 18:00:30 2003

organism:
Salmonella enterica subsp. enterica serovar Thompson
Salmonella enterica subsp. enterica serovar Typhimurium

source_name: 024724 gDNA overnight in LB


title: GC2_SARA25_LT2_4D405_2

description:
genomic comparison SARA25/LT2
User - PCheng
Date_of_Scan = Wed Jan 21 12:23:41 2004

source_name: SARA25 gDNA overnight in LB


title: GC2_021834_LT2_2D649_1


title: GC2_020420_LT2_2D647_1

description:
genomic comparison 020420/LT2
User - PCheng
Date_of_Scan = Thu Mar 06 18:36:52 2003

organism:
Salmonella enterica subsp. enterica serovar Oranienburg
Salmonella enterica subsp. enterica serovar Typhimurium

source_name: 020420 gDNA overnight in LB


title: GC2_024724_LT2_2D648_3


title: GC2_SARA27_LT2_4D406_2


title: GC2_SARA23_LT2_4D403_2

description:
genomic comparison SARA23/LT2
User - PCheng
Date_of_Scan = Thu Jan 15 11:59:02 2004

source_name: SARA23 gDNA overnight in LB


title: GC2_SARA22_LT2_4D402_3

description:
genomic comparison SARA22/LT2
User - PCheng
Date_of_Scan = Thu Jan 15 10:47:36 2004

source_name: SARA22 gDNA overnight in LB


title: GC2_SARA25_LT2_4D405_3


title: GC2_024724_LT2_2D648_1


title: GC2_SARB62_LT2_2D646_3

description:
genomic comparison SARB^@/LT2
User - PCheng
Date_of_Scan = Thu Feb 20 16:45:53 2003

source_name: SARB62 gDNA overnight in LB


title: GC2_SARB62_LT2_2D646_1

source_name: LT2 gDNA overnight in LB


title: GC2_SARA23_LT2_4D403_1


title: GC2_SARA23_LT2_4D403_3


title: GC2_SARB27_LT2_2D645_2

description:
genomic comparison SARB27/LT2
User - PCheng
Date_of_Scan =Thu Feb 20 16:26:29 2003

source_name: SARB27 gDNA overnight in LB


title: GC2_SARB62_LT2_2D646_2


title: GC2_SARB27_LT2_2D645_1


title: RE3_IB314-RpoH:PCN_HS_37C_100 min_4d202_3

description:
Salmonella typhimurium IB314-RpoH:PCN Expression after heatshock with 37C compared to 30C RNA and 30C DNA
User - PCheng
Date_of_Scan = Wed Oct 22 11:32:29 2003
Sample_target_source3: IB314 genomic DNA

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: IB314 100 min post treatment

source_name: IB314 pretreatment


title: GC2_SARB27_LT2_2D645_3


title: GC2_SARA25_LT2_4D405_1


title: GC2_SARA22_LT2_4D402_2


title: GC2_020420_LT2_2D647_3


title: GC2_020420_LT2_2D647_2


title: GC2_SARA22_LT2_4D402_1


title: RE3_IB314-RpoH:PCN_HS_37C_100 min_4d202_2


title: RE3_IB314-RpoH:PCN_HS_37C_100 min_4d202_1


title: GC2_SARB47_LT2_2D638_3

description:
genomic comparison SARB47/LT2
User - PCheng
Date_of_Scan = Mon Mar 17 12:25:15 2003

source_name: SARB47 gDNA overnight in LB


title: GC2_SARB17_LT2_2D644_1

description:
genomic comparison SARB17/LT2
User - PCheng
Date_of_Scan = Thu Feb 20 16:02:09 2003

source_name: SARB17 gDNA overnight in LB


title: GC2_SARB35_LT2_2D643_2

description:
genomic comparison SARB35/LT2
User - PCheng
Date_of_Scan = Thu Feb 20 15:41:07 2003

source_name: SARB35 gDNA overnight in LB


title: GC2_SARB35_LT2_2D643_3


title: GC2_SARB47_LT2_2D638_2


title: GC2_SARB17_LT2_2D644_2


title: GC2_SARB55_LT2_2D633_2

description:
genomic comparison SARB55/LT2
User - PCheng
Date_of_Scan = Thu Feb 13 18:21:55 2003

source_name: SARB55 gDNA overnight in LB


title: GC2_SARB35_LT2_2D643_1


title: GC2_SARB34_LT2_2D632_3

description:
genomic comparison SARB34/LT2
User - PCheng
Date_of_Scan = Thu Feb 13 17:43:13 2003

source_name: SARB34 gDNA overnight in LB


title: GC2_SARB47_LT2_2D638_1


title: GC2_SARB14_LT2_2D641_2

description:
genomic comparison SARB14/LT2
User - PCheng
Date_of_Scan = Thu Feb 20 14:36:55 2003

organism:
Salmonella enterica subsp. enterica serovar Typhimurium
Salmonella enterica subsp. enterica serovar Dublin

source_name: SARB14 gDNA overnight in LB


title: GC2_SARB34_LT2_2D632_2

organism:
Salmonella enterica subsp. enterica serovar Muenchen
Salmonella enterica subsp. enterica serovar Typhimurium


title: GC2_SARB14_LT2_2D641_1


title: GC2_SARB17_LT2_2D644_3


title: RE3_IB314-RpoH:PCN_HS_37C_80 min_4d201_2

description:
Salmonella typhimurium IB314-RpoH:PCN Expression after heatshock with 37C compared to 30C RNA vs 30C DNA
User - PCheng
Date_of_Scan = Wed Oct 22 10:39:13 2003
Sample_target_source3: IB314 genomic DNA

source_name: IB314 80 min post treatment


title: GC2_SARB14_LT2_2D641_3


title: GC2_SARB34_LT2_2D632_1


title: GC2_SARB55_LT2_2D633_1


title: RE3_IB314-RpoH:PCN_HS_37C_80 min_4d201_1


title: RE3_IB314-RpoH:PCN_HS_37C_140 min_4d200_3

description:
Salmonella typhimurium IB314-RpoH:PCN Expression after heatshock with 37C compared to 30C RNA and 30C DNA
User - PCheng
Date_of_Scan = Wed Oct 15 10:58:37 2003
Sample_target_source3: IB314 genomic DNA

source_name: IB314 140 min post treatment


title: GC2_SARB26_LT2_2D631_3

description:
genomic comparison SARB26/LT2
User - PCheng
Date_of_Scan = Thu Feb 13 16:36:14 2003

source_name: SARB26 gDNA overnight in LB


title: RE3_IB314-RpoH:PCN_HS_37C_140 min_4d200_1


title: RE3_IB314-RpoH:PCN_HS_37C_60 min_4d196_3

description:
Salmonella typhimurium IB314-RpoH:PCN Expression after heatshock with 37C compared to 30C RNA and 30C DNA.
User - PCheng
Date_of_Scan = Tue Oct 14 11:23:59 2003
Sample_target_source3: IB314 genomic DNA

source_name: IB314 60 min post treatment


title: RE3_IB314-RpoH:PCN_HS_37C_140 min_4d200_2


title: RE3_IB314-RpoH:PCN_HS_37C_80 min_4d201_3


title: RE3_IB314-RpoH:PCN_HS_37C_120 min_4d198_1

description:
Salmonella typhimurium IB314-RpoH:PCN Expression after heatshock with 37C compared to 30C RNA and 30C DNA
User - PCheng
Date_of_Scan = Tue Oct 14 12:22:06 2003
Sample_target_source3: IB314 genomic DNA

source_name: IB314 120 min post treatment


title: RE3_IB314-RpoH:PCN_HS_37C_120 min_4d198_2


title: GC2_SARB55_LT2_2D633_3


title: RE3_IB314-RpoH:PCN_HS_37C_120 min_4d198_3


title: Caco-2 cells, 3 week, filters B II

status: Public on May 08 2004

city: Epalinges

first: Pascale

last: Anderle

country: Switzerland

institute: ISREC

description: Caco-2 cells were cultured on filters for 5 days or 3 weeks. Log2 data [VALUE] were lowess corrected.

organism: Homo sapiens

source_name: Caco-2 cells, 5 days, filters B

source_name: Caco-2 cells, 3 week, filters B


title: Caco-2 cells, 2 week, filters B II

description: Caco-2 cells were cultured on filters for 5 days or 2 weeks. Log2 data [VALUE] were lowess corrected.

source_name: Caco-2 cells, 2 week, filters B


title: Caco-2 cells, 3 week, filters B I


title: RE3_IB314-RpoH:PCN_HS_37C_60 min_4d196_2


title: Caco-2 cells, 2 week, filters B I


title: GC2_SARB26_LT2_2D631_2

source_name: LT2 gDNA overnight in LB


title: Caco-2 cells, 1 week, filters B II

description: Caco-2 cells were cultured on filters for 5 days or 1 week. Log2 data [VALUE] were lowess corrected.

source_name: Caco-2 cells, 1 week, filters B


title: Caco-2 cells, 5 days, filters B II

description: Caco-2 cells were cultured on filters for 5 days. Log2 data [VALUE] were lowess corrected.


title: Caco-2 cells, 2 week, filters A III

source_name: Caco-2 cells, 5 days, filters A

source_name: Caco-2 cells, 2 week, filters A


title: Caco-2 cells, 3 week, filters A I

source_name: Caco-2 cells, 3 week, filters A


title: Caco-2 cells, 5 days, filters B I


title: Caco-2 cells, 1 week, filters B I


title: Caco-2 cells, 3 week, filters A III


title: RE3_IB314-RpoH:PCN_HS_37C_40 min_4d195_2

description:
Salmonella typhimurium IB314 Expression after heatshock with 37C compared to 30C RNA and 30C DNA
User - PCheng
Date_of_Scan = Wed Oct 15 13:05:04 2003
Sample_target_source3: IB314 genomic DNA

source_name: IB314 40 min post treatment

source_name: IB314 pretreatment


title: RE3_IB314-RpoH:PCN_HS_37C_20 min_4d193_1

description:
Salmonella typhimurium IB314-RpoH:PCN Expression after heatshock with 37C compared to 30C RNA and 30C DNA
User - PCheng
Date_of_Scan = Wed Oct 15 12:38:16 2003
Sample_target_source3: IB314 genomic DNA

source_name: IB314 20 min post treatment


title: RE3_IB314-RpoH:PCN_HS_37C_20 min_4d193_2


title: Caco-2 cells, 3 week, filters A II


title: RE3_IB314-RpoH:PCN_HS_37C_40 min_4d195_1


title: Caco-2 cells, 1 week, filters A I

source_name: Caco-2 cells, 1 week, filters A


title: Caco-2 cells, 1 week, filters A III


title: Caco-2 cells, 2 week, filters A II


title: RE3_IB314-RpoH:PCN_HS_37C_60 min_4d196_1


title: RE3_IB314-RpoH:PCN_HS_37C_40 min_4d195_3


title: Caco-2 cells, 5 days, filters A III


title: Caco-2 cells, 2 week, filters A I


title: Caco-2 cells, 1 week, filters A II


title: Caco-2 cells, 5 days, filters A II


title: Caco-2 cells, 5 days, filters A I


title: Caco-2 cells, 3 week, flasks III

description: Caco-2 cells were cultured in flasks for 5 days or 3 weeks. Log2 data [VALUE] were lowess corrected.

source_name: Caco-2 cells, 5 days, flasks

source_name: Caco-2 cells, 3 week, flasks


title: Caco-2 cells, 2 week, flasks I

description: Caco-2 cells were cultured in flasks for 5 days or 2 weeks. Log2 data [VALUE] were lowess corrected.

source_name: Caco-2 cells, 2 week, flasks


title: Caco-2 cells, 2 week, flasks III


title: Caco-2 cells, 2 week, flasks II


title: Caco-2 cells, 3 week, flasks II


title: Caco-2 cells, 3 week, flasks I


title: Caco-2 cells, 5 days, flasks II

description: Caco-2 cells were cultured in flasks for 5 days. Log2 data [VALUE] were lowess corrected.


title: Caco-2 cells, 1 week, flasks III

source_name: Caco-2 cells, 1 week, flasks


title: RE3_IB314-RpoH:PCN_HS_37C_20 min_4d193_3


title: 4 h (2)

status: Public on May 07 2004

city: Boston

first: Muralikrishna

last: Vemula

state: MA

department: Center for Engineering in Medicine/Department of Surgery

institute: Massachusetts General Hospital, Harvard Medical School and Shriners Hospital for Children

description: The mRNA was extracted from rat livers collected 4 hour after inflicting with a burn injury

organism: Rattus norvegicus

source_name: Rat liver


title: KSHV infected HDMEC 2nd array

city: Zurich

first: Jay

middle: Woo

last: Shin

state: Zurich

address: Wolfgang-Paulistrasse 10; HCI H394

department: Institute of Pharmaceutical Sciences

institute: ETH Zurich

description:
Primary human dermal endothelial cells were infected with isolated Kaposi's sarcoma associated herpes virus for 7 days. Total RNA was isolated using Trireagent and subjected to microarray.
Keywords = KSHV

source_name: HDMEC


title: 1 h (2)

description: The mRNA was extracted from rat livers collected 1 hour after inflicting with a burn injury


title: Caco-2 cells, 1 week, flasks I

description: Caco-2 cells were cultured in flasks for 5 days or 1 week. Log2 data [VALUE] were lowess corrected.


title: Caco-2 cells, 1 week, flasks II


title: KSHV infected HDMEC 1st array

description: Primary human dermal endothelial cells were infected with isolated Kaposi's sarcoma associated herpes virus for 7 days. Total RNA was isolated using Trireagent and subjected to microarray.


title: 8 h

description: The mRNA was extracted from rat livers collected 8 hour after inflicting with a burn injury


title: 13-Microgravity 1

city: Atlanta

first: Hanjoong

last: Jo

state: GA

department: Biomedical Engineering

institute: Emory University

description: Microgravity 1, where cells were cultured in Opticells and subjected to simulated microgravity using the Random Positioning Machine

organism: Mus musculus

source_name: Mouse


title: Uninfected control 2nd Array

description:
Primary human dermal endothelial cells were NOT infected with isolated Kaposi's sarcoma associated herpes virus for 7 days. Total RNA was isolated using Trireagent and subjected to microarray.
Keywords = KSHV


title: 15-Microgravity 3

description: Microgravity 3, where cells were cultured in Opticells and subjected to simulated microgravity using the Random Positioning Machine


title: 1 h


title: Caco-2 cells, 5 days, flasks III


title: 24 h (2)

description: The mRNA was extracted from rat livers collected 24 hour after inflicting with a burn injury


title: 8 h (2)


title: uninfected control 1st array

description: Primary human dermal endothelial cells were NOT infected with isolated Kaposi's sarcoma associated herpes virus for 7 days. Total RNA was isolated using Trireagent and subjected to microarray.


title: 14-Microgravity 2

description: Microgravity 2, where cells were cultured in Opticells and subjected to simulated microgravity using the Random Positioning Machine


title: 24 h


title: 12-Static 3

description: Static 3, where cells were cultured in Opticells and remained as a static control


title: 4 h


title: 11-Static 2

description: Static 2, where cells were cultured in Opticells and remained as a static control


title: TOL_48H_2nd

status: Public on May 05 2004

city: Meguro-ku

first: Makoto

last: Kano

state: Tokyo

address: 4-6-1 Komaba

country: Japan

institute: Research Center for Advanced Science and Technology, University of Tokyo

description:
tissue of hippocampus with hypoxia tolerant, at 48 hours after ischemia operation, 2nd experiment
Keywords = Rattus norvegicus, hippocampus, ischemic tolerance

source_name: hippocampus


title: 0 h (2) (Control sample)

description: The mRNA was collected from control rat liver (Sham, 0 h)


title: TOL_12H_2nd

description:
tissue of hippocampus with hypoxia tolerant, at 12 hours after ischemia operation, 2nd experiment
Keywords = Rattus norvegicus, hippocampus, ischemic tolerance


title: Caco-2 cells, 5 days, flasks I

description: Caco-2 cells were cultured in flasks for 5 days. Log2 data [VALUE] were lowess corrected.


title: TOL_48H_1st

description:
tissue of hippocampus with hypoxia tolerant, at 48 hours after ischemia operation, 1st experiment
Keywords = Rattus norvegicus, hippocampus, ischemic tolerance


title: 10-Static 1

description: Static 1, where cells were cultured in Opticells and remained as a static control


title: TOL_0H_2nd

description:
tissue of hippocampus with hypoxia tolerant, at 0 hours after ischemia operation, 2nd experiment
Keywords = Rattus norvegicus, hippocampus, ischemic tolerance


title: TOL_12H_1st

description:
tissue of hippocampus with hypoxia tolerant, at 12 hours after ischemia operation, 1st experiment
Keywords = Rattus norvegicus, hippocampus, ischemic tolerance


title: SHAM_48H_2nd

description:
tissue of hippocampus with hypoxia sensitive, at 48 hours after ischemia operation, 2nd experiment
Keywords = Rattus norvegicus, hippocampus, ischemic tolerance


title: TOL_0H_1st

description:
tissue of hippocampus with hypoxia tolerant, at 0 hours after ischemia operation, 1st experiment
Keywords = Rattus norvegicus, hippocampus, ischemic tolerance


title: SHAM_24H_2nd

description:
tissue of hippocampus with hypoxia sensitive, at 24 hours after ischemia operation, 2nd experiment
Keywords = Rattus norvegicus, hippocampus, ischemic tolerance


title: TOL_24H_1st

description:
tissue of hippocampus with hypoxia tolerant, at 24 hours after ischemia operation, 1st experiment
Keywords = Rattus norvegicus, hippocampus, ischemic tolerance


title: TOL_24H_2nd

description:
tissue of hippocampus with hypoxia tolerant, at 24 hours after ischemia operation, 2nd experiment
Keywords = Rattus norvegicus, hippocampus, ischemic tolerance


title: TOL_1H_2nd

description:
tissue of hippocampus with hypoxia tolerant, at 1 hours after ischemia operation, 2nd experiment
Keywords = Rattus norvegicus, hippocampus, ischemic tolerance


title: TOL_3H_2nd

description:
tissue of hippocampus with hypoxia tolerant, at 3 hours after ischemia operation, 2nd experiment
Keywords = Rattus norvegicus, hippocampus, ischemic tolerance


title: SHAM_24H_1st

description:
tissue of hippocampus with hypoxia sensitive, at 24 hours after ischemia operation, 1st experiment
Keywords = Rattus norvegicus, hippocampus, ischemic tolerance


title: SHAM_12H_2nd

description:
tissue of hippocampus with hypoxia sensitive, at 12 hours after ischemia operation, 2nd experiment
Keywords = Rattus norvegicus, hippocampus, ischemic tolerance


title: TOL_1H_1st

description:
tissue of hippocampus with hypoxia tolerant, at 1 hours after ischemia operation, 1st experiment
Keywords = Rattus norvegicus, hippocampus, ischemic tolerance


title: 0 h (control sample)

description: The mRNA was collected from control rat liver (Sham)


title: SHAM_12H_1st

description:
tissue of hippocampus with hypoxia sensitive, at 12 hours after ischemia operation, 1st experiment
Keywords = Rattus norvegicus, hippocampus, ischemic tolerance


title: SHAM_48H_1st

description:
tissue of hippocampus with hypoxia sensitive, at 48 hours after ischemia operation, 1st experiment
Keywords = Rattus norvegicus, hippocampus, ischemic tolerance


title: TOL_3H_1st

description:
tissue of hippocampus with hypoxia tolerant, at 3 hours after ischemia operation, 1st experiment
Keywords = Rattus norvegicus, hippocampus, ischemic tolerance


title: SHAM_3H_2nd

description:
tissue of hippocampus with hypoxia sensitive, at 3 hours after ischemia operation, 2nd experiment
Keywords = Rattus norvegicus, hippocampus, ischemic tolerance


title: SHAM_3H_1st

description:
tissue of hippocampus with hypoxia sensitive, at 3 hours after ischemia operation, 1st experiment
Keywords = Rattus norvegicus, hippocampus, ischemic tolerance


title: Knockout Mouse 3 vs Wild type Mouse 1

city: Tucson

first: Heddwen

last: Brooks

state: AZ

address: 1501 N Campbell Ave

department: Physiology

institute: University of Arizona

description: Knockout Mouse 3 Kidney Inner Medula (Channel 1) aRNA vs Wild Type Mouse 1 Kidney Inner Medula (Channel 2) aRNA

source_name: Knockout Mouse 3 Kidney Inner Medula aRNA

source_name: Wild type Mouse 1 Kidney Inner Medula aRNA


title: Knockout Mouse 2 vs Knockout Mouse 3

description: Knockout Mouse 2 Kidney Inner Medula (Channel 1) aRNA vs Knockout Mouse 3 Kidney Inner Medula (Channel 2) aRNA

source_name: Knockout Mouse 2 Kidney Inner Medula aRNA


title: Knockout Mouse 1 vs Knockout Mouse 2

description: Knockout Mouse 1 Kidney Inner Medula (Channel 1) aRNA vs Knockout Mouse 2 Kidney Inner Medula (Channel 2) aRNA

source_name: Knockout Mouse 1 Kidney Inner Medula aRNA


title: SHAM_1H_2nd

description:
tissue of hippocampus with hypoxia sensitive, at 1 hours after ischemia operation, 2nd experiment
Keywords = Rattus norvegicus, hippocampus, ischemic tolerance


title: Knockout Mouse 2 vs Wild type Mouse 1

description: Knockout Mouse 2 Kidney Inner Medula (Channel 1) aRNA vs Wild Type Mouse 1 Kidney Inner Medula (Channel 2) aRNA


title: Knockout Mouse 3 vs Wild type Mouse 2

description: Knockout Mouse 3 Kidney Inner Medula (Channel 1) aRNA vs Wild Type Mouse 2 Kidney Inner Medula (Channel 2) aRNA

source_name: Wild type Mouse 2 Kidney Inner Medula aRNA


title: SHAM_0H_2nd

description:
tissue of hippocampus with hypoxia sensitive, at 0 hours after ischemia operation, 2nd experiment
Keywords = Rattus norvegicus, hippocampus, ischemic tolerance


title: SHAM_1H_1st

description:
tissue of hippocampus with hypoxia sensitive, at 1 hours after ischemia operation, 1st experiment
Keywords = Rattus norvegicus, hippocampus, ischemic tolerance


title: SHAM_0H_1st

description:
tissue of hippocampus with hypoxia sensitive, at 0 hours after ischemia operation, 1st experiment
Keywords = Rattus norvegicus, hippocampus, ischemic tolerance


title: Wild type Mouse 2 vs Wild type Mouse 3

description: Wild Type Mouse 2 Kidney Inner Medula (Channel 1) aRNA vs Wild Type Mouse 3 Kidney Inner Medula (Channel 2) aRNA

source_name: Wild type Mouse 3 Kidney Inner Medula aRNA


title: Wild type Mouse 3 vs Knockout Mouse 2

description: Wild Type Mouse 3 Kidney Inner Medula (Channel 1) aRNA vs Knockout Mouse 2 Kidney Inner Medula (Channel 2) aRNA


title: Pur_33CvRAS33C_3

status: Public on May 04 2004

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

country: Australia

institute: University of Canberra

description:
Hver 1.1.2
Cy3 Puro-3A 33C (3) (HMF3A with Puro control vector) cells were cultured at 33C. Media was changed a day before lysis. Cells were at 80% confluence when lysed.
Cy5 RAS-3A 33C (3) (HMF3A with activated RAS vector) cells were cultured at 33C. Media was changed a day before lysis. Cells were at 80% confluence when lysed.
Lot batch = 119-8


title: Wild type Mouse 1 vs Wild type Mouse 2

description: Wild Type Mouse 1 Kidney Inner Medula (Channel 1) aRNA vs Wild Type Mouse 2 Kidney Inner Medula (Channel 2) aRNA


title: Wild type Mouse 3 vs Knockout Mouse 1

description: Wild Type Mouse 3 Kidney Inner Medula (Channel 1) aRNA vs Knockout Mouse 1 Kidney Inner Medula (Channel 2) aRNA


title: Pur_33CvRAS33C_2

description:
Hver 1.1.2
Cy3 RAS-3A 33C (2) (HMF3A with activated RAS vector) cells were cultured at 33C. Media was changed a day before lysis. Cells were at 80% confluence when lysed.
Cy5 Puro-3A 33C (2) (HMF3A with Puro control vector) cells were cultured at 33C. Media was changed a day before lysis. Cells were at 80% confluence when lysed.
Lot batch = 121-36


title: Wild type Mouse 2 vs Knockout Mouse 1

description: Wild Type Mouse 2 Kidney Inner Medula (Channel 1) aRNA vs Knockout Mouse 1 Kidney Inner Medula (Channel 2) aRNA


title: Wild type Mouse 1 vs Wild type Mouse 3

description: Wild Type Mouse 1 Kidney Inner Medula (Channel 1) aRNA vs Wild Type Mouse 3 Kidney Inner Medula (Channel 2) aRNA

source_name: Wild Type Mouse 1 Kidney Inner Medula aRNA

source_name: Wild Type Mouse 3 Kidney Inner Medula aRNA


title: Knockout Mouse 1 vs Knockout Mouse 3

description: Knockout Mouse 1 Kidney Inner Medula (Channel 1) aRNA vs Knockout Mouse 3 Kidney Inner Medula (Channel 2) aRNA


title: RAS_33v39C_R2

description:
Hver 1.1.2
Cy3 RAS-3A 39C (1) cells were cultured at 33C. Cells were shifted to 39C for 7 days then lysed.
Cy5 RAS-3A 33C (1) (HMF3A with activated Ras vector) cells were cultured at 33C. Media was changed a day before lysis. Cells were at 80% confluence when lysed.
Lot batch = 121-34


title: RAS_33v39C_R1

description:
Hver 1.1.2
Cy3 RAS-3A (1) (HMF3A with activated RAS vector) cells were cultured at 33C. Media was changed a day before lysis. Cells were at 80% confluence when lysed.
Cy5 RAS-3A (1) cells were cultured at 33C. Cells were shifted to 39C for 7 days then lysed.
Lot batch = 87-35


title: RAS_33v39C_R3

description:
Hver 1.1.2
Cy3 RAS-3A 33C (2) (HMF3A with activated RAS vector) cells were cultured at 33C. Media was changed a day before lysis. Cells were at 80% confluence when lysed.
Cy5 RAS-3A 39C (2) cells were cultured at 33C. Cells were shifted to 39C for 7 days then lysed.
Lot batch = 119-5


title: Pur_33CvRAS33C_4

description:
Hver 1.1.2
Cy3 RAS-3A 33C (3) (HMF3A with activated RAS vector) cells were cultured at 33C. Media was changed a day before lysis. Cells were at 80% confluence when lysed.
Cy5 Puro-3A 33C (3) (HMF3A with Puro control vector) cells were cultured at 33C. Media was changed a day before lysis. Cells were at 80% confluence when lysed.
Lot batch = 119-7


title: Pur_33v39C_R1

description:
Hver 1.1.2
Cy3 Puro-3A (1) (HMF3A with Puro control vector) cells were cultured at 33C. Media was changed a day before lysis. Cells were at 80% confluence when lysed.
Cy5 Puro-3A (1) cells were cultured at 33C. Cells were shifted to 39C for 7 days then lysed.
Lot batch = 87-34


title: IgG1-3

city: Baltimore

first: Myriam

last: Gorospe

state: MD

address: 5600 Nathan Shock Drive

institute: NIA

description: RNA from IP reactions using an anti-IgG1 antibody. Biological repeat 3.

source_name: Hela cells


title: IgG1-2

description: RNA from IP reactions using an anti-IgG1 antibody. Biological repeat 2.


title: Pur_33v39C_R3

description:
Hver 1.1.2
Cy3 Puro-3A (2) (HMF3A with Puro control vector) cells were cultured at 33C. Media was changed a day before lysis. Cells were at 80% confluence when lysed.
Cy5 Puro-3A (2) cells were cultured at 33C. Cells were shifted to 39C for 7 days then lysed.
Lot batch = 119-3


title: RAS_33v39C_R4

description:
Hver 1.1.2
Cy3 RAS-3A 39C (2) cells were cultured at 33C. Cells were shifted to 39C for 7 days then lysed.
Cy5 RAS-3A 33C (2) (HMF3A with activated ras vector) cells were cultured at 33C. Media was changed a day before lysis. Cells were at 80% confluence when lysed.
Lot batch = 119-6


title: IgG1-1

description: RNA from IP reactions using an anti-IgG1 antibody. Biological repeat 1.


title: HuR-3

description: RNA from IP reactions using an anti-HuR antibody. Biological repeat 3.


title: AUF1-3

description: RNA from IP reactions using an anti-AUF1 antibody. Biological repeat 3.


title: EPC-120hrs-1

status: Public on May 02 2004

city: Scarborough

first: Diya

last: Zhang

email: WOJCHD@mmc.org , diya@northwestern.edu

state: ME

address: 81 Research Drive

department: Molecular Medicine

institute: Maine Medical Center Research Institute

description:
Developmentally synchronized erythroid progenitor cells (EPCs) were prepared from splenocytes at 80,100 and 120 hours after Thiamphenical(TAP) withdrawal (as stages I-III), and purified via MACS. Total RNA preparation, cRNA labeling and hybridization were performed according to recommendations by Affymetrix.
This is 1st replicate hybridization of stage III EPCs (Kit(-)neg/EpoR+ /Ter119+++/low FALS).
Array: Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74A
Keywords = erythroid progenitor erythropoiesis profiling

source_name: purified erythroid progenitor cells  from splenocytes, 120 hours after TAP withdrawel


title: AUF1-2

description: RNA from IP reactions using an anti-AUF1 antibody. Biological repeat 2.


title: EPC-120hrs-2

description:
Developmentally synchronized erythroid progenitor cells (EPCs) were prepared from splenocytes at 80,100 and 120 hours after Thiamphenical withdrawal (as stages I-III), and purified via MACS. Total RNA preparation, cRNA labeling and hybridization were performed according to recommendations by Affymetrix.
Here is 2nd replicate hybridization of stage III EPCs (Kit(-)neg/EpoR+ /Ter119+++/low FALS).
Array: Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74A
Keywords = erythroid progenitor erythropoiesis profiling


title: Antisense IL-10 treatment in Malignant Murine B-1 Cells (Untreated controls)

city: Newark

first: Brian

middle: A

last: McCarthy

state: NJ

address: 185 South Orange Ave

department: Pathology

institute: NJ Medical School/UMDNJ

description:
LNC, a cell line derived from an NZB mouse, was treated with 20uM IL-10 antisense and RNA was collected at 24h. These samples are from untreated control LNC.
Keywords = Interleukin 10
Keywords = Antisense
Keywords = Malignant
Keywords = B-1 Cell

source_name: Cell line from the Lymph Node of 1 yr old New Zealand Black mouse


title: Antisense IL-10 treatment in Malignant Murine B-1 Cells (Scrambled oligo control)

description:
LNC, a cell line derived from an NZB mouse, was treated with 20uM IL-10 antisense and RNA was collected at 24h. These samples are from 20um scrambled IL-10 antisense oligo treatment, used to control for the non-specific effects of oligonucleotide treatment.
Keywords = Interleukin 10
Keywords = Antisense
Keywords = Malignant
Keywords = B-1 Cell


title: AUF1-1

description: RNA from IP reactions using an anti-AUF1 antibody. Biological repeat 1.


title: EPC-100hrs-2

description:
Developmentally synchronized erythroid progenitor cells (EPCs) were prepared from splenocytes at 80,100 and 120 hours after Thiamphenical withdrawal (as stages I-III), and purified via MACS. Total RNA preparation, cRNA labeling and hybridization were performed according to recommendations by Affymetrix.
Here is 2nd replicate hybridization of stage II EPCs (Kit+/EpoR+++/Ter119+++/high FALS).
Array: Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74A
Keywords = erythroid progenitor erythropoiesis profiling

source_name: purified erythroid progenitor cells  from splenocytes, 100 hours after TAP withdrawel


title: HuR-2

description: RNA from IP reactions using an anti-HuR antibody. Biological repeat 2.

source_name: hela cells


title: Pur_33v39C_R4

description:
Hver 1.1.2
Cy3 Puro-3A (2) cells were cultured at 33C. Cells were shifted to 39C for 7 days then lysed.
Cy5 Puro-3A (2) (HMF3A with Puro control vector) cells were cultured at 33C. Media was changed a day before lysis. Cells were at 80% confluence when lysed.
Lot batch = 119-4


title: Operon agamous set3

city: Pasadena

first: Frank

last: Wellmer

address: 1200 E. California Blvd.

department: Biology 156-29

institute: California Institute of Technology

description:
Comparison of gene expression profiles of wild-type and agamous inflorescences.
The data were processed and normalized as described in Wellmer et al. (2004) Plant Cell 16(5).

organism: Arabidopsis thaliana

source_name: agamous inflorescences

source_name: wild-type inflorescences


title: Antisense IL-10 treatment in Malignant Murine B-1 Cells

description:
LNC, a cell line derived from an NZB mouse, was treated with 20uM IL-10 antisense and RNA was collected at 24h. These samples are from antisense treated LNC.
Keywords = Interleukin 10
Keywords = IL-10
Keywords = Antisense
Keywords = Malignant
Keywords = B-1 Cell


title: EPC-100hrs-1

description:
Developmentally synchronized erythroid progenitor cells (EPCs) were prepared from splenocytes at 80,100 and 120 hours after Thiamphenical withdrawal (as stages I-III), and purified via MACS. Total RNA preparation, cRNA labeling and hybridization were performed according to recommendations by Affymetrix.
Here is the 1st replicate hybridization of stage II EPCs (Kit+/EpoR+++/Ter119+++/high FALS).
Array: Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74A
Keywords = erythroid progenitor erythropoiesis profiling


title: Pur_33v39C_R2

description:
Hver 1.1.2
Cy3 Puro-3A (1) cells were cultured at 33C. Cells were shifted to 39C for 7 days then lysed.
Cy5 Puro-3A (1) (HMF3A with Puro control vector) cells were cultured at 33C. Media was changed a day before lysis. Cells were at 80% confluence when lysed.
Lot batch = 121-33


title: Pur_33CvRAS33C_1

description:
Hver 1.1.2
Cy3 Puro-3A 33C (2) (HMF3A with Puro control vector) cells were cultured at 33C. Media was changed a day before lysis. Cells were at 80% confluence when lysed.
Cy5 RAS-3A 33C (2) (HMF3A with activated RAS vector) cells were cultured at 33C. Media was changed a day before lysis. Cells were at 80% confluence when lysed.
Lot batch = 121-35


title: Operon agamous set2


title: EPC-80hrs-1

description:
Developmentally synchronized erythroid progenitor cells (EPCs) were prepared from splenocytes at 80,100 and 120 hours after Thiamphenical withdrawal (as stages I-III), and purified via MACS. Total RNA preparation, cRNA labeling and hybridization were performed according to recommendations by Affymetrix.
This is the first replicate hybridization with  stage I EPCs: Kit +++/ EpoR+++ /Ter119(-)neg, late CFU-e.
Array: Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74A

Keywords = erythroid progenitor erythropoiesis profiling

source_name: purified erythroid progenitor cells  from splenocytes, 80 hours after TAP withdrawel


title: EPC-80hrs-2

description:
Developmentally synchronized erythroid progenitor cells (EPCs) were prepared from splenocytes at 80,100 and 120 hours after Thiamphenical withdrawal (as stages I-III), and purified via MACS. Total RNA preparation, cRNA labeling and hybridization were performed according to recommendations by Affymetrix.
This is the 2nd  replicate hybridization with stage I EPCs (Kit +++/ EpoR+++ /Ter119(-)neg, late CFU-e).
Array: Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74A
Keywords = erythroid progenitor erythropoiesis profiling


title: Operon pistillata set3

description:
Comparison of gene expression profiles of wild-type and pistillata inflorescences.
The data were processed and normalized as described in Wellmer et al. (2004) Plant Cell 16(5).

source_name: pistillata inflorescences


title: cDNA agamous set2

description:
Comparison of gene expression profiles of wild-type and agamous inflorescences.
The data were preprocessed and normalized as described in Wellmer et al. (2004) Plant Cell 16(5).


title: cDNA agamous set1


title: Operon agamous set1


title: cDNA apetala3 set3

description:
Comparison of gene expression profiles of wild-type and apetala3 inflorescences.
The data were preprocessed and normalized as described in Wellmer et al. (2004) Plant Cell 16(5).

source_name: apetala3 inflorescences


title: Operon pistillata set4


title: cDNA pistillata set3

description:
Comparison of gene expression profiles of wild-type and pistillata inflorescences.
The data were preprocessed and normalized as described in Wellmer et al. (2004) Plant Cell 16(5).


title: Operon apetala3 set4

description:
Comparison of gene expression profiles of wild-type and apetala3 inflorescences.
The data were processed and normalized as described in Wellmer et al. (2004) Plant Cell 16(5).


title: Operon agamous set4


title: cDNA agamous set3


title: cDNA pistillata set2


title: Operon apetala3 set3


title: Operon pistillata set1


title: cDNA apetala3 set1


title: Operon apetala2 set4

description:
Comparison of gene expression profiles of wild-type and apetala2 inflorescences.
The data were processed and normalized as described in Wellmer et al. (2004) Plant Cell 16(5).

source_name: apetala2 inflorescences


title: Operon pistillata set2


title: Operon apetala2 set2


title: Operon apetala3 set1


title: cDNA apetala2 set2

description:
Comparison of gene expression profiles of wild-type and apetala2 inflorescences.
The data were preprocessed and normalized as described in Wellmer et al. (2004) Plant Cell 16(5).


title: Operon apetala1 set4

description:
Comparison of gene expression profiles of wild-type and apetala1 inflorescences.
The data were processed and normalized as described in Wellmer et al. (2004) Plant Cell 16(5).

source_name: apetala1 inflorescences


title: cDNA apetala3 set2


title: Operon apetala3 set2


title: cDNA pistillata set1


title: Operon apetala2 set3


title: cDNA apetala1 set2

description:
Comparison of gene expression profiles of wild-type and apetala1 inflorescences.
The data were preprocessed and normalized as described in Wellmer et al. (2004) Plant Cell 16(5).

source_name: wild type inflorescences


title: Operon apetala1 set1


title: cDNA apetala2 set1


title: Operon apetala1 set3


title: Operon apetala1 set2

source_name: apetela1 inflorescences


title: U2AF_nucleo_2

status: Public on May 01 2004

city: Kansas City

first: Marco

last: Blanchette

state: MO

institute: Stowers Institute for Medical Research

description: Nuclear RNA isolated using an hypotonic lysis from U2AF50 RNAi treated D. mel2 cells

organism: Drosophila melanogaster

source_name: D. mel2 cells


title: cDNA apetala2 set3


title: U2AF_cyto_1

description: Cytoplasmic RNA isolated using an hypotonic lysis from U2AF50 RNAi treated D. mel2 cells


title: E2+TOT 48h A

city: Urbana

first: Jonna

last: Frasor

state: IL

department: Molecular and Integrative Physiology

institute: University of Illinois

description: 10 nM estradiol + 1 uM trans-hydroxytamoxifen, 48h, Set A


title: NS_nucleo_3

description: Nuclear RNA isolated using an hypotonic lysis from Non-specific RNAi treated D. mel2 cells


title: U2AF_IP_5

description: RNA are immuno-affinity purified using anti-U2AF50 antibody from a Drosophila 0-12hrs embryonic RNP enriched fraction and compared to the RNA in the starting fraction. The ratio was computed from normalized data from the features with at least one channel above 2500 quanta and with a ratio of signal/background greater than 3.

source_name: Drosophila embryonic RNP

source_name: U2AF50 IPed RNA from RNP fraction


title: U2AF_nucleo_1


title: NS_cyto_2

description: Cytoplasmic RNA from non-specific RNAi treated D. mel2 cells

source_name: D. mel2


title: E2+TOT 48h B

description: 10 nM estradiol + 1 uM trans-hydroxytamoxifen, 48h, Set B


title: U2AF_nucleo_3


title: NS_nucleo_2


title: U2AF_cyto_3


title: NS_nucleo_1

description: Nuclear RNA from non-specific RNAi treated D. mel2 cells


title: U2AF_cyto_2


title: NS_cyto_1

source_name: D. mel-2 cells


title: NS_cyto_3

description: Cytoplasmic RNA isolated using an hypotonic lysis from Non-specific RNAi treated D. mel2 cells


title: E2+TOT 8h B

description: 10 nM estradiol + 1 uM trans-hydroxytamoxifen, 8h, Set B


title: U2AF_IP_4


title: E2+TOT 8h A

description: 10 nM estradiol + 1 uM trans-hydroxytamoxifen, 8h, Set A


title: E2+Ral 48h B

description: 10 nM estradiol + 1 uM Raloxifene, 48h, Set B


title: cDNA apetala1 set1


title: U2AF_IP_3


title: WT293 sample b

city: Galveston

first: Aaron

middle: M.

last: Domina

state: TX

address: 301 University Blvd

department: HBCG

institute: University of Texas Medical Branch

description:
WT293 cells are sensitive to Sindbis virus-induced cell death.
Keywords = Sindbis alphavirus functional phenotype

source_name: WT293 cells


title: Operon apetala2 set1

description:
Comparison of gene expression profiles of wild-type and apetala2 inflorescences.
The data were processed and normalized as described in Wellmer et al. (2004) Plant Cell 16(5).


title: WT293 sample c

source_name: WT 293 cells


title: WT293 sample a


title: E2+Ral 48h A

description: 10 nM estradiol + 1 uM Raloxifene, 48h, Set A


title: U2AF_IP_2


title: E2 48h B

description: 10 nM E2 treatment, 48h, set B


title: E2+ICI 48h A

description: 10 nM estradiol + 1 uM ICI 182780 48h, Set A


title: E2+ICI 48h B

description: 10 nM estradiol + 1 uM ICI 182780 48h, Set B


title: E2 48h A

description: 10 nM E2 treatment, 48h, set A


title: tg-2

city: Jerusalem

first: Eran

last: Meshorer

state: Israel

address: Givat Ram

department: Biological Chemistry

country: Israel

institute: Life Sciences

description: Pooled Total Prefrontal cortex RNA from 4 female mice overexpressing the human synaptic AChE.

source_name: Total Prefrontal cortex RNA


title: Clone 43 sample b

description:
Clone43 cells are resistant to Sindbis virus
Keywords = Sindbis alphavirus functional phenotype

source_name: Clone 43 cells


title: E2 8h B

description: 10 nM E2 treatment, 8h, set B


title: Control B

description: Control sample, set B


title: ct-2

description: Pooled Total Prefrontal cortex RNA from 4 female FVB/N mice.


title: E2+ICI 8h B

description: 10 nM estradiol + 1 uM ICI 182780 8h, Set B


title: Control A

description: Control sample, set A


title: U2-OS-ERb E2 48 hours 2

status: Public on Apr 30 2004

first: Fabio

last: Stossi

address: 285 Burrill Hall, 407 S Goodwin

institute: University of Illinois at Urbana-Champaign

description: U2-OS cells were stably transfected with low levels of ERb 1-530, this sample represents E2 10nM treated cells at 48 hours and was used in a time-course experiment


title: tg-1


title: ct-1


title: U2-OS-ERb E2 24 hours 2

description: U2-OS cells were stably transfected with low levels of ERb 1-530, this sample represents E2 10nM treated cells at 24 hours and was used in a time-course experiment


title: Clone9 sample a

description:
Clone9 cells are resistant to Sindbis virus
Keywords = Sindbis alphavirus functional phenotype

source_name: Clone9 cells


title: Clone9 sample b


title: Clone43 sample c

source_name: Clone43 cells


title: U2-OS-ERb E2 48 hours


title: Clone9 sample c

source_name: Clone 9 cells


title: E2+Ral 8h B

description: 10 nM estradiol + 1 uM Raloxifene, 8h, Set B


title: E2+Ral 8h A

description: 10 nM estradiol + 1 uM Raloxifene, 8h, Set A


title: U2-OS-ERb E2 24 hours


title: U2AF_IP_1

description: RNA are immuno-affinity purified using anti-U2AF50 antibody from a Drosophila 0-12hrs embryonic RNP enriched fraction and compared to the RNA in the starting fraction. The ratio was computed from normalized data from the features with at least one channel above 2500 quanta and with a ratio of signal/background greater than 3.


title: HuR-1

description: RNA from IP reactions using an anti-HuR antibody. Biological repeat 1.

source_name: Hela cells


title: E2 8h A

description: 10 nM E2 treatment, 8h, Set A


title: U2-OS-ERb E2 8 hrs

description: U2-OS cells were stably transfected with low levels of ERbeta1-530. This sample represents E2 10 nM treated cells for 8 hours.


title: U2-OS-ERb E2 8 hours 2

description: U2-OS cells were stably transfected with low levels of ERb 1-530, this sample represents E2 10nM treated cells at 8 hours and was used in a time-course experiment


title: U2-OS-ERb E2 4 hours

description: U2-OS cells were stably transfected with low levels of ERbeta1-530. This sample represents E2 10 nM treated cells for 4 hours.


title: Clone43 sample a


title: U2-OS-ERb vehicle 2

description: U2-OS cells were stably transfected with low levels of ERbeta1-530. This sample represents EtOH treated cells and was used as a control for a time-course experiment


title: U2-OS-ERb vehicle control 1


title: E2+ICI 8h A

description: 10 nM estradiol + 1 uM ICI 182780 8h, Set A


title: U2-OS-ERb E2 4 hours 2


title: Matrigel induced differentiation of HBC-3 cells , time 6-A days

status: Public on Apr 29 2004

city: New York

first: Leslie

last: Rogler

state: NY

address: 1300 Morris Park Ave

department: Liver Research Center/ Department of Medicine

institute: Albert Einstein College of Medicine

description:
HBC-3 cells were maintained as previously described (Rogler,L.E.,Am.J. Path. 150:591-602). Cells grown for microarray analysis were stripped of their STON+ feeder layer by trypsinization and replating on plastic in HBM
Undifferentiated cells were harvested the next A.M. for preparation of total RNA. Twenty 10cm plates were used to obtain sufficient quantities of undifferentiated reference total RNA. Total RNAs were prepared using Qiagen RNeasy maxi kit. The quality of each RNA preparation was determined using an Agilent 2100 Bioanalyzer. Five microgram aliquots of total RNA from undifferentiated HBC-3 cells were used to generate amplified RNA (aRNA) using the Ambion Message Amp Kit (cat.# 1750).  The quality of the aRNA was determined using an Agilent Bioanalyzer.  Amplified RNAs were stored as 5ug aliquots under 100% Ethanol at -80oC.
Cy 3 and Cy5 labeled targets were synthesized using a modified version of the AECOM functional Genomics facility protocol (http://microarray1k.aecom.yu.edu/) as previously described (Plescia et al, 2001,Differentiation 68:254-269).   Cy3 and Cy5 labeled targets were prepared using 5 ug of aRNA using random primers and Superscript reverse transcriptase (Invitrogen)
Cy3 labeled target prepared from undifferentiated HBC-3 cells provided the reference sample for all comparisons. The precipitated targets were then resuspended in hybridization buffer as previously described and applied to a microarray. Arrays were hybridized at 50oC for 20 hours. Washing was carried out as described at (http://microarray1k.aecom.yu.edu/
Cy3 and Cy5 labeled targets were synthesized using a modified version of the AECOM functional Genomics facility protocol (http://microarray1k.aecom.yu.edu/) as previously described (Plescia et al, 2001,Differentiation 68:254-269).   Cy3 and Cy5 labeled targets were prepared using 5 ug of aRNA using random primers and Superscript reverse transcriptase (Invitrogen).).  The purified Cy5 labeled targets were repared from aRNA made from HBC-3 cells treated with Matrigel for 6 day (to induce bile duct differentiation).Cy3 reference target and a Cy5 target prepared from an RNA isolated from cells at one of the time points of Matrigel treatment were combined and precipitated. The precipitated targets were then resuspended in hybridization buffer as previously described and applied to a microarray.  Arrays were hybridized at 50oC for 20 hours. Washing was carried out as described at (http://microarray1k.aecom.yu.edu/). "
In vitro bile ductular differentiation of HBC-3 cells was performed as previously described (Rogler,L.E.,Am.J. Path. 150:591-602) Cells grown for microarray analysis were stripped of their STON+ feeder layer by trypsinization and on a 1mm Matrigel cushion (differentiated). Cells undergoing Matrigel induced differentiation were harvested at 1 day of Matrigel treatment for preparation of total RNA.  Ten 10 cm plates were harvested for each time point to obtain total RNA sufficient for several target preparations at each time point.  Five microgram aliquots of total RNA from undifferentiated HBC-3 or  Matrigel treated HBC-3 cells were used to generate amplified RNA (aRNA) using the Ambion Message Amp Kit (cat.# 1750).  The quality of the aRNA was determined using an Agilent Bioanalyzer.  Amplified RNAs were stored as 5ug aliquots under 100% Ethanol at -80oC.
Following hybridization and washing, the arrays were scanned for Cy3 and y5 florescence using a scanner Genepix 3.0 scanner (Axon Instruments Inc., Union City, CA).  The signal intensity of a spot was considered to be significant if the signal intensity was greater by 200 units of the background for that spot and if it was not flagged as ""not found"" by GenePix software. These data were normalized using the Lowess implementation included in BASE. Following filtration and normalization, the ratio of red and green fluorescence, (RAT) was quantified for each qualified gene. The RAT values were then Log transformed and the LOG2 of the RAT is presented in the data table."
Keywords = HBC-3 cells, murine hepatoblast cells, matrigel

source_name: HBC-3 cells after 6 day of differentiation

source_name: HBC-3 cells control


title: Matrigel induced differentiation of HBC-3 cells , time 7-B days

description:
HBC-3 cells were maintained as previously described (Rogler,L.E.,Am.J. Path. 150:591-602). Cells grown for microarray analysis were stripped of their STON+ feeder layer by trypsinization and replating on plastic in HBM
Undifferentiated cells were harvested the next A.M. for preparation of total RNA. Twenty 10cm plates were used to obtain sufficient quantities of undifferentiated reference total RNA. Total RNAs were prepared using Qiagen RNeasy maxi kit. The quality of each RNA preparation was determined using an Agilent 2100 Bioanalyzer. Five microgram aliquots of total RNA from undifferentiated HBC-3 cells were used to generate amplified RNA (aRNA) using the Ambion Message Amp Kit (cat.# 1750).  The quality of the aRNA was determined using an Agilent Bioanalyzer.  Amplified RNAs were stored as 5ug aliquots under 100% Ethanol at -80oC.
Cy 3 and Cy5 labeled targets were synthesized using a modified version of the AECOM functional Genomics facility protocol (http://microarray1k.aecom.yu.edu/) as previously described (Plescia et al, 2001,Differentiation 68:254-269).   Cy3 and Cy5 labeled targets were prepared using 5 ug of aRNA using random primers and Superscript reverse transcriptase (Invitrogen)
Cy3 labeled target prepared from undifferentiated HBC-3 cells provided the reference sample for all comparisons. The precipitated targets were then resuspended in hybridization buffer as previously described and applied to a microarray. Arrays were hybridized at 50oC for 20 hours. Washing was carried out as described at (http://microarray1k.aecom.yu.edu/
Cy3 and Cy5 labeled targets were synthesized using a modified version of the AECOM functional Genomics facility protocol (http://microarray1k.aecom.yu.edu/) as previously described (Plescia et al, 2001,Differentiation 68:254-269).   Cy3 and Cy5 labeled targets were prepared using 5 ug of aRNA using random primers and Superscript reverse transcriptase (Invitrogen).).  The purified Cy5 labeled targets were repared from aRNA made from HBC-3 cells treated with Matrigel for 7 day (to induce bile duct differentiation).Cy3 reference target and a Cy5 target prepared from an RNA isolated from cells at one of the time points of Matrigel treatment were combined and precipitated. The precipitated targets were then resuspended in hybridization buffer as previously described and applied to a microarray.  Arrays were hybridized at 50oC for 20 hours. Washing was carried out as described at (http://microarray1k.aecom.yu.edu/). "
In vitro bile ductular differentiation of HBC-3 cells was performed as previously described (Rogler,L.E.,Am.J. Path. 150:591-602) Cells grown for microarray analysis were stripped of their STON+ feeder layer by trypsinization and on a 1mm Matrigel cushion (differentiated). Cells undergoing Matrigel induced differentiation were harvested at 1 day of Matrigel treatment for preparation of total RNA.  Ten 10 cm plates were harvested for each time point to obtain total RNA sufficient for several target preparations at each time point.  Five microgram aliquots of total RNA from undifferentiated HBC-3 or  Matrigel treated HBC-3 cells were used to generate amplified RNA (aRNA) using the Ambion Message Amp Kit (cat.# 1750).  The quality of the aRNA was determined using an Agilent Bioanalyzer.  Amplified RNAs were stored as 5ug aliquots under 100% Ethanol at -80oC.
Following hybridization and washing, the arrays were scanned for Cy3 and y5 florescence using a scanner Genepix 3.0 scanner (Axon Instruments Inc., Union City, CA).  The signal intensity of a spot was considered to be significant if the signal intensity was greater by 200 units of the background for that spot and if it was not flagged as ""not found"" by GenePix software. These data were normalized using the Lowess implementation included in BASE. Following filtration and normalization, the ratio of red and green fluorescence, (RAT) was quantified for each qualified gene. The RAT values were then Log transformed and the LOG2 of the RAT is presented in the data table."
Keywords = HBC-3 cells, murine hepatoblast cells, matrigel

source_name: HBC-3 cells after 7 day of differentiation


title: Matrigel induced differentiation of HBC-3 cells , time 6-C day


title: Matrigel induced differentiation of HBC-3 cells , time 7-C days


title: Matrigel induced differentiation of HBC-3 cells , time 3-B days

description:
HBC-3 cells were maintained as previously described (Rogler,L.E.,Am.J. Path. 150:591-602). Cells grown for microarray analysis were stripped of their STON+ feeder layer by trypsinization and replating on plastic in HBM
Undifferentiated cells were harvested the next A.M. for preparation of total RNA. Twenty 10cm plates were used to obtain sufficient quantities of undifferentiated reference total RNA. Total RNAs were prepared using Qiagen RNeasy maxi kit. The quality of each RNA preparation was determined using an Agilent 2100 Bioanalyzer. Five microgram aliquots of total RNA from undifferentiated HBC-3 cells were used to generate amplified RNA (aRNA) using the Ambion Message Amp Kit (cat.# 1750).  The quality of the aRNA was determined using an Agilent Bioanalyzer.  Amplified RNAs were stored as 5ug aliquots under 100% Ethanol at -80oC.
Cy 3 and Cy5 labeled targets were synthesized using a modified version of the AECOM functional Genomics facility protocol (http://microarray1k.aecom.yu.edu/) as previously described (Plescia et al, 2001,Differentiation 68:254-269).   Cy3 and Cy5 labeled targets were prepared using 5 ug of aRNA using random primers and Superscript reverse transcriptase (Invitrogen)
Cy3 labeled target prepared from undifferentiated HBC-3 cells provided the reference sample for all comparisons. The precipitated targets were then resuspended in hybridization buffer as previously described and applied to a microarray. Arrays were hybridized at 50oC for 20 hours. Washing was carried out as described at (http://microarray1k.aecom.yu.edu/
Cy3 and Cy5 labeled targets were synthesized using a modified version of the AECOM functional Genomics facility protocol (http://microarray1k.aecom.yu.edu/) as previously described (Plescia et al, 2001,Differentiation 68:254-269).   Cy3 and Cy5 labeled targets were prepared using 5 ug of aRNA using random primers and Superscript reverse transcriptase (Invitrogen).).  The purified Cy5 labeled targets were repared from aRNA made from HBC-3 cells treated with Matrigel for 3 day (to induce bile duct differentiation).Cy3 reference target and a Cy5 target prepared from an RNA isolated from cells at one of the time points of Matrigel treatment were combined and precipitated. The precipitated targets were then resuspended in hybridization buffer as previously described and applied to a microarray.  Arrays were hybridized at 50oC for 20 hours. Washing was carried out as described at (http://microarray1k.aecom.yu.edu/). "
In vitro bile ductular differentiation of HBC-3 cells was performed as previously described (Rogler,L.E.,Am.J. Path. 150:591-602) Cells grown for microarray analysis were stripped of their STON+ feeder layer by trypsinization and on a 1mm Matrigel cushion (differentiated). Cells undergoing Matrigel induced differentiation were harvested at 1 day of Matrigel treatment for preparation of total RNA.  Ten 10 cm plates were harvested for each time point to obtain total RNA sufficient for several target preparations at each time point.  Five microgram aliquots of total RNA from undifferentiated HBC-3 or  Matrigel treated HBC-3 cells were used to generate amplified RNA (aRNA) using the Ambion Message Amp Kit (cat.# 1750).  The quality of the aRNA was determined using an Agilent Bioanalyzer.  Amplified RNAs were stored as 5ug aliquots under 100% Ethanol at -80oC.
Following hybridization and washing, the arrays were scanned for Cy3 and y5 florescence using a scanner Genepix 3.0 scanner (Axon Instruments Inc., Union City, CA).  The signal intensity of a spot was considered to be significant if the signal intensity was greater by 200 units of the background for that spot and if it was not flagged as ""not found"" by GenePix software. These data were normalized using the Lowess implementation included in BASE. Following filtration and normalization, the ratio of red and green fluorescence, (RAT) was quantified for each qualified gene. The RAT values were then Log transformed and the LOG2 of the RAT is presented in the data table."
Keywords = HBC-3 cells, murine hepatoblast cells, matrigel

source_name: HBC-3 cells after 3 day of differentiation


title: Matrigel induced differentiation of HBC-3 cells , time 4-A days

description:
HBC-3 cells were maintained as previously described (Rogler,L.E.,Am.J. Path. 150:591-602). Cells grown for microarray analysis were stripped of their STON+ feeder layer by trypsinization and replating on plastic in HBM
Undifferentiated cells were harvested the next A.M. for preparation of total RNA. Twenty 10cm plates were used to obtain sufficient quantities of undifferentiated reference total RNA. Total RNAs were prepared using Qiagen RNeasy maxi kit. The quality of each RNA preparation was determined using an Agilent 2100 Bioanalyzer. Five microgram aliquots of total RNA from undifferentiated HBC-3 cells were used to generate amplified RNA (aRNA) using the Ambion Message Amp Kit (cat.# 1750).  The quality of the aRNA was determined using an Agilent Bioanalyzer.  Amplified RNAs were stored as 5ug aliquots under 100% Ethanol at -80oC.
Cy 3 and Cy5 labeled targets were synthesized using a modified version of the AECOM functional Genomics facility protocol (http://microarray1k.aecom.yu.edu/) as previously described (Plescia et al, 2001,Differentiation 68:254-269).   Cy3 and Cy5 labeled targets were prepared using 5 ug of aRNA using random primers and Superscript reverse transcriptase (Invitrogen)
Cy3 labeled target prepared from undifferentiated HBC-3 cells provided the reference sample for all comparisons. The precipitated targets were then resuspended in hybridization buffer as previously described and applied to a microarray. Arrays were hybridized at 50oC for 20 hours. Washing was carried out as described at (http://microarray1k.aecom.yu.edu/
Cy3 and Cy5 labeled targets were synthesized using a modified version of the AECOM functional Genomics facility protocol (http://microarray1k.aecom.yu.edu/) as previously described (Plescia et al, 2001,Differentiation 68:254-269).   Cy3 and Cy5 labeled targets were prepared using 5 ug of aRNA using random primers and Superscript reverse transcriptase (Invitrogen).).  The purified Cy5 labeled targets were repared from aRNA made from HBC-3 cells treated with Matrigel for 4 day (to induce bile duct differentiation).Cy3 reference target and a Cy5 target prepared from an RNA isolated from cells at one of the time points of Matrigel treatment were combined and precipitated. The precipitated targets were then resuspended in hybridization buffer as previously described and applied to a microarray.  Arrays were hybridized at 50oC for 20 hours. Washing was carried out as described at (http://microarray1k.aecom.yu.edu/). "
In vitro bile ductular differentiation of HBC-3 cells was performed as previously described (Rogler,L.E.,Am.J. Path. 150:591-602) Cells grown for microarray analysis were stripped of their STON+ feeder layer by trypsinization and on a 1mm Matrigel cushion (differentiated). Cells undergoing Matrigel induced differentiation were harvested at 1 day of Matrigel treatment for preparation of total RNA.  Ten 10 cm plates were harvested for each time point to obtain total RNA sufficient for several target preparations at each time point.  Five microgram aliquots of total RNA from undifferentiated HBC-3 or  Matrigel treated HBC-3 cells were used to generate amplified RNA (aRNA) using the Ambion Message Amp Kit (cat.# 1750).  The quality of the aRNA was determined using an Agilent Bioanalyzer.  Amplified RNAs were stored as 5ug aliquots under 100% Ethanol at -80oC.
Following hybridization and washing, the arrays were scanned for Cy3 and y5 florescence using a scanner Genepix 3.0 scanner (Axon Instruments Inc., Union City, CA).  The signal intensity of a spot was considered to be significant if the signal intensity was greater by 200 units of the background for that spot and if it was not flagged as ""not found"" by GenePix software. These data were normalized using the Lowess implementation included in BASE. Following filtration and normalization, the ratio of red and green fluorescence, (RAT) was quantified for each qualified gene. The RAT values were then Log transformed and the LOG2 of the RAT is presented in the data table."
Keywords = HBC-3 cells, murine hepatoblast cells, matrigel

source_name: HBC-3 cells after 4 day of differentiation


title: Matrigel induced differentiation of HBC-3 cells , time 4-B days


title: Matrigel induced differentiation of HBC-3 cells , time 2-B days

description:
HBC-3 cells were maintained as previously described (Rogler,L.E.,Am.J. Path. 150:591-602). Cells grown for microarray analysis were stripped of their STON+ feeder layer by trypsinization and replating on plastic in HBM
Undifferentiated cells were harvested the next A.M. for preparation of total RNA. Twenty 10cm plates were used to obtain sufficient quantities of undifferentiated reference total RNA. Total RNAs were prepared using Qiagen RNeasy maxi kit. The quality of each RNA preparation was determined using an Agilent 2100 Bioanalyzer. Five microgram aliquots of total RNA from undifferentiated HBC-3 cells were used to generate amplified RNA (aRNA) using the Ambion Message Amp Kit (cat.# 1750).  The quality of the aRNA was determined using an Agilent Bioanalyzer.  Amplified RNAs were stored as 5ug aliquots under 100% Ethanol at -80oC.
Cy 3 and Cy5 labeled targets were synthesized using a modified version of the AECOM functional Genomics facility protocol (http://microarray1k.aecom.yu.edu/) as previously described (Plescia et al, 2001,Differentiation 68:254-269).   Cy3 and Cy5 labeled targets were prepared using 5 ug of aRNA using random primers and Superscript reverse transcriptase (Invitrogen)
Cy3 labeled target prepared from undifferentiated HBC-3 cells provided the reference sample for all comparisons. The precipitated targets were then resuspended in hybridization buffer as previously described and applied to a microarray. Arrays were hybridized at 50oC for 20 hours. Washing was carried out as described at (http://microarray1k.aecom.yu.edu/
Cy3 and Cy5 labeled targets were synthesized using a modified version of the AECOM functional Genomics facility protocol (http://microarray1k.aecom.yu.edu/) as previously described (Plescia et al, 2001,Differentiation 68:254-269).   Cy3 and Cy5 labeled targets were prepared using 5 ug of aRNA using random primers and Superscript reverse transcriptase (Invitrogen).).  The purified Cy5 labeled targets were repared from aRNA made from HBC-3 cells treated with Matrigel for 2 day (to induce bile duct differentiation).Cy3 reference target and a Cy5 target prepared from an RNA isolated from cells at one of the time points of Matrigel treatment were combined and precipitated. The precipitated targets were then resuspended in hybridization buffer as previously described and applied to a microarray.  Arrays were hybridized at 50oC for 20 hours. Washing was carried out as described at (http://microarray1k.aecom.yu.edu/). "
In vitro bile ductular differentiation of HBC-3 cells was performed as previously described (Rogler,L.E.,Am.J. Path. 150:591-602) Cells grown for microarray analysis were stripped of their STON+ feeder layer by trypsinization and on a 1mm Matrigel cushion (differentiated). Cells undergoing Matrigel induced differentiation were harvested at 1 day of Matrigel treatment for preparation of total RNA.  Ten 10 cm plates were harvested for each time point to obtain total RNA sufficient for several target preparations at each time point.  Five microgram aliquots of total RNA from undifferentiated HBC-3 or  Matrigel treated HBC-3 cells were used to generate amplified RNA (aRNA) using the Ambion Message Amp Kit (cat.# 1750).  The quality of the aRNA was determined using an Agilent Bioanalyzer.  Amplified RNAs were stored as 5ug aliquots under 100% Ethanol at -80oC.
Following hybridization and washing, the arrays were scanned for Cy3 and y5 florescence using a scanner Genepix 3.0 scanner (Axon Instruments Inc., Union City, CA).  The signal intensity of a spot was considered to be significant if the signal intensity was greater by 200 units of the background for that spot and if it was not flagged as ""not found"" by GenePix software. These data were normalized using the Lowess implementation included in BASE. Following filtration and normalization, the ratio of red and green fluorescence, (RAT) was quantified for each qualified gene. The RAT values were then Log transformed and the LOG2 of the RAT is presented in the data table."
Keywords = HBC-3 cells, murine hepatoblast cells, matrigel

source_name: HBC-3 cells after 2 day of differentiation


title: Matrigel induced differentiation of HBC-3 cells , time 5-A days

description:
HBC-3 cells were maintained as previously described (Rogler,L.E.,Am.J. Path. 150:591-602). Cells grown for microarray analysis were stripped of their STON+ feeder layer by trypsinization and replating on plastic in HBM
Undifferentiated cells were harvested the next A.M. for preparation of total RNA. Twenty 10cm plates were used to obtain sufficient quantities of undifferentiated reference total RNA. Total RNAs were prepared using Qiagen RNeasy maxi kit. The quality of each RNA preparation was determined using an Agilent 2100 Bioanalyzer. Five microgram aliquots of total RNA from undifferentiated HBC-3 cells were used to generate amplified RNA (aRNA) using the Ambion Message Amp Kit (cat.# 1750).  The quality of the aRNA was determined using an Agilent Bioanalyzer.  Amplified RNAs were stored as 5ug aliquots under 100% Ethanol at -80oC.
Cy 3 and Cy5 labeled targets were synthesized using a modified version of the AECOM functional Genomics facility protocol (http://microarray1k.aecom.yu.edu/) as previously described (Plescia et al, 2001,Differentiation 68:254-269).   Cy3 and Cy5 labeled targets were prepared using 5 ug of aRNA using random primers and Superscript reverse transcriptase (Invitrogen)
Cy3 labeled target prepared from undifferentiated HBC-3 cells provided the reference sample for all comparisons. The precipitated targets were then resuspended in hybridization buffer as previously described and applied to a microarray. Arrays were hybridized at 50oC for 20 hours. Washing was carried out as described at (http://microarray1k.aecom.yu.edu/
Cy3 and Cy5 labeled targets were synthesized using a modified version of the AECOM functional Genomics facility protocol (http://microarray1k.aecom.yu.edu/) as previously described (Plescia et al, 2001,Differentiation 68:254-269).   Cy3 and Cy5 labeled targets were prepared using 5 ug of aRNA using random primers and Superscript reverse transcriptase (Invitrogen).).  The purified Cy5 labeled targets were repared from aRNA made from HBC-3 cells treated with Matrigel for 5 day (to induce bile duct differentiation).Cy3 reference target and a Cy5 target prepared from an RNA isolated from cells at one of the time points of Matrigel treatment were combined and precipitated. The precipitated targets were then resuspended in hybridization buffer as previously described and applied to a microarray.  Arrays were hybridized at 50oC for 20 hours. Washing was carried out as described at (http://microarray1k.aecom.yu.edu/). "
In vitro bile ductular differentiation of HBC-3 cells was performed as previously described (Rogler,L.E.,Am.J. Path. 150:591-602) Cells grown for microarray analysis were stripped of their STON+ feeder layer by trypsinization and on a 1mm Matrigel cushion (differentiated). Cells undergoing Matrigel induced differentiation were harvested at 1 day of Matrigel treatment for preparation of total RNA.  Ten 10 cm plates were harvested for each time point to obtain total RNA sufficient for several target preparations at each time point.  Five microgram aliquots of total RNA from undifferentiated HBC-3 or  Matrigel treated HBC-3 cells were used to generate amplified RNA (aRNA) using the Ambion Message Amp Kit (cat.# 1750).  The quality of the aRNA was determined using an Agilent Bioanalyzer.  Amplified RNAs were stored as 5ug aliquots under 100% Ethanol at -80oC.
Following hybridization and washing, the arrays were scanned for Cy3 and y5 florescence using a scanner Genepix 3.0 scanner (Axon Instruments Inc., Union City, CA).  The signal intensity of a spot was considered to be significant if the signal intensity was greater by 200 units of the background for that spot and if it was not flagged as ""not found"" by GenePix software. These data were normalized using the Lowess implementation included in BASE. Following filtration and normalization, the ratio of red and green fluorescence, (RAT) was quantified for each qualified gene. The RAT values were then Log transformed and the LOG2 of the RAT is presented in the data table."
Keywords = HBC-3 cells, murine hepatoblast cells, matrigel

source_name: HBC-3 cells after 5 day of differentiation


title: Matrigel induced differentiation of HBC-3 cells , time 3-A days


title: Matrigel induced differentiation of HBC-3 cells , time 5-B days


title: Matrigel induced differentiation of HBC-3 cells , time 6-B day


title: Matrigel induced differentiation of HBC-3 cells , time 5-C day


title: Matrigel induced differentiation of HBC-3 cells , time 7-A day


title: Matrigel induced differentiation of HBC-3 cells , time 2-C days


title: Matrigel induced differentiation of HBC-3 cells , time 4-C days


title: Matrigel induced differentiation of HBC-3 cells , time 3-C days


title: Matrigel induced differentiation of HBC-3 cells , time 1-C day

description:
HBC-3 cells were maintained as previously described (Rogler,L.E.,Am.J. Path. 150:591-602). Cells grown for microarray analysis were stripped of their STON+ feeder layer by trypsinization and replating on plastic in HBM
Undifferentiated cells were harvested the next A.M. for preparation of total RNA. Twenty 10cm plates were used to obtain sufficient quantities of undifferentiated reference total RNA. Total RNAs were prepared using Qiagen RNeasy maxi kit. The quality of each RNA preparation was determined using an Agilent 2100 Bioanalyzer. Five microgram aliquots of total RNA from undifferentiated HBC-3 cells were used to generate amplified RNA (aRNA) using the Ambion Message Amp Kit (cat.# 1750).  The quality of the aRNA was determined using an Agilent Bioanalyzer.  Amplified RNAs were stored as 5ug aliquots under 100% Ethanol at -80oC.
Cy 3 and Cy5 labeled targets were synthesized using a modified version of the AECOM functional Genomics facility protocol (http://microarray1k.aecom.yu.edu/) as previously described (Plescia et al, 2001,Differentiation 68:254-269).   Cy3 and Cy5 labeled targets were prepared using 5 ug of aRNA using random primers and Superscript reverse transcriptase (Invitrogen)
Cy3 labeled target prepared from undifferentiated HBC-3 cells provided the reference sample for all comparisons. The precipitated targets were then resuspended in hybridization buffer as previously described and applied to a microarray. Arrays were hybridized at 50oC for 20 hours. Washing was carried out as described at (http://microarray1k.aecom.yu.edu/
Cy3 and Cy5 labeled targets were synthesized using a modified version of the AECOM functional Genomics facility protocol (http://microarray1k.aecom.yu.edu/) as previously described (Plescia et al, 2001,Differentiation 68:254-269).   Cy3 and Cy5 labeled targets were prepared using 5 ug of aRNA using random primers and Superscript reverse transcriptase (Invitrogen).).  The purified Cy5 labeled targets were repared from aRNA made from HBC-3 cells treated with Matrigel for 1 day (to induce bile duct differentiation).Cy3 reference target and a Cy5 target prepared from an RNA isolated from cells at one of the time points of Matrigel treatment were combined and precipitated. The precipitated targets were then resuspended in hybridization buffer as previously described and applied to a microarray.  Arrays were hybridized at 50oC for 20 hours. Washing was carried out as described at (http://microarray1k.aecom.yu.edu/). "
In vitro bile ductular differentiation of HBC-3 cells was performed as previously described (Rogler,L.E.,Am.J. Path. 150:591-602) Cells grown for microarray analysis were stripped of their STON+ feeder layer by trypsinization and on a 1mm Matrigel cushion (differentiated). Cells undergoing Matrigel induced differentiation were harvested at 1 day of Matrigel treatment for preparation of total RNA.  Ten 10 cm plates were harvested for each time point to obtain total RNA sufficient for several target preparations at each time point.  Five microgram aliquots of total RNA from undifferentiated HBC-3 or  Matrigel treated HBC-3 cells were used to generate amplified RNA (aRNA) using the Ambion Message Amp Kit (cat.# 1750).  The quality of the aRNA was determined using an Agilent Bioanalyzer.  Amplified RNAs were stored as 5ug aliquots under 100% Ethanol at -80oC.
Following hybridization and washing, the arrays were scanned for Cy3 and y5 florescence using a scanner Genepix 3.0 scanner (Axon Instruments Inc., Union City, CA).  The signal intensity of a spot was considered to be significant if the signal intensity was greater by 200 units of the background for that spot and if it was not flagged as ""not found"" by GenePix software. These data were normalized using the Lowess implementation included in BASE. Following filtration and normalization, the ratio of red and green fluorescence, (RAT) was quantified for each qualified gene. The RAT values were then Log transformed and the LOG2 of the RAT is presented in the data table."
Keywords = HBC-3 cells, murine hepatoblast cells, matrigel

source_name: HBC-3 cells after 1 day of differentiation


title: Matrigel induced differentiation of HBC-3 cells , time 0-C day

description:
HBC-3 cells were maintained as previously described (Rogler,L.E.,Am.J. Path. 150:591-602). Cells grown for microarray analysis were stripped of their STON+ feeder layer by trypsinization and replating on plastic in HBM
Undifferentiated cells were harvested the next A.M. for preparation of total RNA. Twenty 10cm plates were used to obtain sufficient quantities of undifferentiated reference total RNA. Total RNAs were prepared using Qiagen RNeasy maxi kit. The quality of each RNA preparation was determined using an Agilent 2100 Bioanalyzer. Five microgram aliquots of total RNA from undifferentiated HBC-3 cells were used to generate amplified RNA (aRNA) using the Ambion Message Amp Kit (cat.# 1750).  The quality of the aRNA was determined using an Agilent Bioanalyzer.  Amplified RNAs were stored as 5ug aliquots under 100% Ethanol at -80oC.
Cy 3 and Cy5 labeled targets were synthesized using a modified version of the AECOM functional Genomics facility protocol (http://microarray1k.aecom.yu.edu/) as previously described (Plescia et al, 2001,Differentiation 68:254-269).   Cy3 and Cy5 labeled targets were prepared using 5 ug of aRNA using random primers and Superscript reverse transcriptase (Invitrogen)
Cy3 labeled target prepared from undifferentiated HBC-3 cells provided the reference sample for all comparisons. The precipitated targets were then resuspended in hybridization buffer as previously described and applied to a microarray. Arrays were hybridized at 50oC for 20 hours. Washing was carried out as described at (http://microarray1k.aecom.yu.edu/
Cy3 and Cy5 labeled targets were synthesized using a modified version of the AECOM functional Genomics facility protocol (http://microarray1k.aecom.yu.edu/) as previously described (Plescia et al, 2001,Differentiation 68:254-269).   Cy3 and Cy5 labeled targets were prepared using 5 ug of aRNA using random primers and Superscript reverse transcriptase (Invitrogen).).  The purified Cy5 labeled targets were repared from aRNA made from HBC-3 cells treated with Matrigel for 1 day (to induce bile duct differentiation).Cy3 reference target and a Cy5 target prepared from an RNA isolated from cells at one of the time points of Matrigel treatment were combined and precipitated. The precipitated targets were then resuspended in hybridization buffer as previously described and applied to a microarray.  Arrays were hybridized at 50oC for 20 hours. Washing was carried out as described at (http://microarray1k.aecom.yu.edu/). "
Following hybridization and washing, the arrays were scanned for Cy3 and y5 florescence using a scanner Genepix 3.0 scanner (Axon Instruments Inc., Union City, CA).  The signal intensity of a spot was considered to be significant if the signal intensity was greater by 200 units of the background for that spot and if it was not flagged as ""not found"" by GenePix software. These data were normalized using the Lowess implementation included in BASE. Following filtration and normalization, the ratio of red and green fluorescence, (RAT) was quantified for each qualified gene. The RAT values were then Log transformed and the LOG2 of the RAT is presented in the data table."
Keywords = HBC-3 cells, murine hepatoblast cells, matrigel


title: HD12E1

status: Public on Apr 26 2004

first: Robert

middle: C

last: De Lisle

state: KS

address: 3901 Rainbow Blvd

department: Anatomy & Cell Biology

institute: Univ Kansas Med Ctr

description: Total RNA was prepared from the entire small intestine of one 40 day old CFTR control female mouse, CFTR(+/+), congenic on the black6 background, using TRIzol reagent. Mice were fed Peptamen from age 10 days to prevent intestinal obstruction.

source_name: Small intestine


title: Matrigel induced differentiation of HBC-3 cells , time 2-A days


title: Matrigel induced differentiation of HBC-3 cells , time 0-B day


title: Trauma Burn PAX 70373

status: Public on Apr 24 2004

city: Gainesville

first: Lyle

last: Moldawer

state: FL

address: 1600 SW Archer Road

department: Surgery

institute: University of Florida College of Medicine

description: Blood sample obtained from a trauma/burn subject and processed using the PAXgene system

source_name: Human Blood PAXgene


title: Trauma Burn PAX 70318

description: gene expression analysis performed on a whole blood (PAXgene) preparation from a burn/trauma patient.


title: Trauma Burn PAX 70330


title: Trauma Burn PAX 70331


title: Trauma Burn BC 70369

description: gene expression analysis performed on a whole blood buffy coat (leukocyte) preparation from a burn/trauma patient.

source_name: Human Blood Buffy Coat


title: Trauma Burn BC 70329


title: Unfed males - 2A

status: Public on Apr 21 2004

city: Stillwater

first: Richard

middle: C.

last: Essenberg

state: OK

address: 246 NRC

department: Department of Biochemistry and Molecular Biology

institute: Oklahoma State University

description: Complementary DNAs were synthesized from total RNA obtained from the salivary glands of unfed males using MMLV reverse transcriptase, then amplified using primers A1 + A3 in the presence of digoxigenin 11-dUTP.  The membranes were then hybridized in 0.25 M sodium phosphate hybridization buffer (pH 7.2) containing 7% SDS and 1 mM ethylene diamine tetra-acetic acid (EDTA) at 65oC. The hybridized membranes were then washed and visualized using CPD-star following a protocol from Tropix (Applied Biosystems, Bedford, MA).  Antidigoxigenin Fab fragments conjugated to alkaline phosphatase (Boehringer-Mannheim, Indianapolis, IN), diluted 1: 10,000 in blocking buffer, were used to detect the digoxigenin-labelled probe. The membranes were exposed to X-ray film for 1 min or 5 min and then scanned into a GS-700 imaging densitometer (BioRad, Hercules, CA).

organism: Dermacentor andersoni

source_name: Unfed male salivary glands


title: Trauma Burn PAX 70319


title: Trauma Burn BC 70316


title: cDNA apetala1 set2

state: CA

description:
Comparison of gene expression profiles of wild-type and apetala1 inflorescences.
The data were preprocessed and normalized as described in Wellmer et al. (2004) Plant Cell 16(5).

source_name: wild type inflorescences

source_name: apetala1 inflorescences


title: Matrigel induced differentiation of HBC-3 cells , time 0-A day


title: Trauma Burn PAX 70324


title: Matrigel induced differentiation of HBC-3 cells , time 1-B day


title: Human Trauma BC 70315

source_name: blood buffy coat preparation


title: Trauma Burn BC 70314


title: Trauma Burn BC 70372


title: Normal basal cell - 40mJ

status: Public on Apr 17 2004

city: Boston

first: Jeff

last: Shearstone

state: MA

address: 70 Fargo Street

department: Biology

institute: Acetylon Pharmaceuticals

description:
This data set was generated as part of Biogen Community Lab's science fair mentorship program. In brief, human basal cells (ATCC: CRL-7761, designation TE 353.Sk) were cultured to 80% confluence. After removing media, cells were treated with a titration of ultraviolet light (Biorad GS GeneLinker, 254 nm energy maximum). Media was then added and cells were grown for 24 hours. Total RNA was harvested using RLT buffer and Qiagen RNeasy kit. 5 ug of total RNA was labeled using standard Affymetrix protocols for Eukaryotic target preparation (GeneChip Expression Analysis Technical Manual Revision 4).
Keywords = UV
Keywords = ultraviolet
Keywords = basal cell

source_name: Human skin; normal


title: Trauma Burn PAX 70370


title: Matrigel induced differentiation of HBC-3 cells , time 1-A day


title: Trauma Burn BC 70327


title: MCF7_U133_CHA2

status: Public on Apr 16 2004

city: Albuquerque

first: Scott

middle: A.

last: Ness

state: NM

department: Internal Medicine

institute: U. of New Mexico HSC

description:
MCF7 cells were infected with adenovirus expressing Green Fluorescent protein and CHA, a recombinant protein with the DNA binding domain of c-Myb and the transactivation domain of A-Myb. After 16 hours, RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA. Initial data analysis was performed using Affymetrix MAS software.
Keywords = human, MCF7 cells, breast cancer, Myb oncogene

source_name: MCF7 breast cancer cells


title: MCF7_U133_AHC2

description:
MCF7 cells were infected with adenovirus expressing Green Fluorescent protein and AHC, a recombinant protein with the DNA binding domain of A-Myb and the transactivation domain of c-Myb. After 16 hours, RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA. Initial data analysis was performed using Affymetrix MAS software.
Keywords = human, MCF7 cells, breast cancer, Myb oncogene


title: Normal basal cell - 20mJ


title: MCF7_U133_CHA1


title: MCF7_U133_cMyb1

description:
MCF7 cells were infected with adenovirus expressing Green Fluorescent protein and c-Myb. After 16 hours, RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA. Initial data analysis was performed using Affymetrix MAS software.
Keywords = human, MCF7 cells, breast cancer, Myb oncogene


title: Normal basal cell - 0mJ

description:
This data set was generated as part of Biogen Community Lab's science fair mentorship program.  In brief, human basal cells (ATCC: CRL-7761, designation TE 353.Sk) were cultured to 80% confluence.  After removing media, cells were treated with a titration of ultraviolet light (Biorad GS GeneLinker, 254 nm energy maximum).  Media was then added and cells were grown for 24 hours.  Total RNA was harvested using RLT buffer and Qiagen RNeasy kit.  5 ug of total RNA was labeled using standard Affymetrix protocols for Eukaryotic target preparation (GeneChip Expression Analysis Technical Manual Revision 4).
Keywords = UV
Keywords = ultraviolet
Keywords = basal cell


title: MCF7_U133_AHC1


title: MCF7_U133_cMyb2

description:
MCF7 cells were infected with adenovirus expressing Green Fluorescent protein anc c-Myb. After 16 hours, RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA. Initial data analysis was performed using Affymetrix MAS software.
Keywords = human, MCF7 cells, breast cancer, Myb oncogene


title: Trauma Burn PAX 70325


title: Trauma Burn BC 70320

source_name: Human blood buffy coat


title: NHEK control

status: Public on Apr 14 2004

city: Seattle

first: Cosette

last: LeCiel

state: WA

institute: ZymoGenetics

description: Gene Expression Array Analysis using NHEK control vs Il31 tx RNA

source_name: NHEK cells


title: MCF7_U133_AdCont1

description:
MCF7 cells were infected with adenovirus expressing Green Fluorescent protein. After 16 hours, RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA. Initial data analysis was performed using Affymetrix MAS software.
Keywords = human, MCF7 cells, breast cancer, Myb oncogene


title: MCF7_U133_AMyb2

description:
MCF7 cells were infected with adenovirus expressing Green Fluorescent protein and A-Myb. After 16 hours, RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA. Initial data analysis was performed using Affymetrix MAS software.
Keywords = human, MCF7 cells, breast cancer, Myb oncogene


title: amlrrays 2251

status: Public on Apr 15 2004

city: Houston

first: Roel

last: Verhaak

address: 1400 Pressler St

department: Bioinformatics and Comp Bio

institute: MD Anderson Cancer Center

description: Blasts and mononuclear cells were purified from bone marrow or peripheral blood aspirates of acute myeloid patients. Samples contained 80-100 percent blast cells. Total RNA was extracted by lyses with guanidium isothiocyanate followed by cesium chloride gradient purification. FAB=M2, Karyotype=Complex, FLT3 ITD=neg, FLT3 TKD=neg, N-RAS=neg, K-RAS=neg, EVI1=neg, cEBPa=neg

source_name: blasts and mononuclear cells


title: NHEK Il-31 tx


title: 95d GW7845_4

status: Public on Apr 13 2004

first: Brig

last: Mecham

address: 20 Shattuck St

institute: Harvard Medical School

description: Primary cultures of human trophoblasts were established from normal, term placenta.  Cells were treated five hours after plating.  This sample was treated with 1 uM GW7845.  RNA was extracted after 48 hours of treatment using Tri-reagent. Each sample was pooled from three individual placentas prior to target generation.  Targets were produced using standard Affymetrix procedures from 30ug of total RNA.  This sample is also known as Treatment 3, replicate 4

source_name: human primary trophoblast


title: amlrrays 2307

description: Blasts and mononuclear cells were purified from bone marrow or peripheral blood aspirates of acute myeloid patients. Samples contained 80-100 percent blast cells. Total RNA was extracted by lyses with guanidium isothiocyanate followed by cesium chloride gradient purification. FAB=M3, Karyotype="t(15;17)", FLT3 ITD=neg, FLT3 TKD=neg, N-RAS=neg, K-RAS=neg, EVI1=neg, cEBPa=neg


title: MCF7_U133_AdCont2


title: 95d GW7845_5

description: Primary cultures of human trophoblasts were established from normal, term placenta.  Cells were treated five hours after plating.  This sample was treated with 1 uM GW7845.  RNA was extracted after 48 hours of treatment using Tri-reagent. Each sample was pooled from three individual placentas prior to target generation.  Targets were produced using standard Affymetrix procedures from 30ug of total RNA.  This sample is also known as Treatment 3, replicate 5


title: 95d GW7845_1

description: Primary cultures of human trophoblasts were established from normal, term placenta.  Cells were treated five hours after plating.  This sample was treated with 1 uM GW7845.  RNA was extracted after 48 hours of treatment using Tri-reagent. Each sample was pooled from three individual placentas prior to target generation.  Targets were produced using standard Affymetrix procedures from 30ug of total RNA.  This sample is also known as Treatment 3, replicate 1