title: Col_control_2

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5�M IAA (IAA treated) or EtOH (control) for 2 h at 24 �C.

Line: Columbia wild-type
Treatment: Control
Replicate 2

Note: Correct data table for GSM9572 has been updated on Oct 26, 2005. If you have downloaded data at some previous time (the old version was duplicate of GSE9575), please download again.

source_name: liquid culture seedlings


title: 0hCy3_X_10hCy5_Exp1_Repl1

status: Public on Oct 19 2005

type: RNA

city: Santo André

first: Luiz

middle: R.

last: Nunes

state: SP

address: Rua Santa Adélia 166

department: Centro de Ciências Naturais e Humanas

country: Brazil

institute: UFABC - Universidade Federal do ABC

description: This hybridization is part of a time-course experiment aimed at evaluating gene expression modulation during the mycelium-to-yeast dimorphic shift in P. brasiliensis

hyb_protocol: Labelled cDNAs were mixed, dried in a Savant speed vacuum and resuspended in 100 ul of 1X Hybridization buffer, containing 6X SSC, 5X Denhardt�s solution, 0,25 mg/ml salmon sperm DNA, 0,01% SDS, 50% formamide and 92,5 ng/ul poly (dT) 25u (Amersham). Arrays were hybridized overnight (42oC) in a Gene-Tac Hybridization Station (Genomic Solutions, Inc., Ann Arbor, MI) and washed twice (42oC) in 0.5 X SSC, 0.01 % SDS, followed by two washes in 0.06 X SSC, 0.01 % SDS and two final washes in 0.06 X SSC. All washing steps consisted of 1 min of flow, followed by 5 min of incubation. Slides were then dried and subjected to fluorescent detection

scan_protocol: Slides were subjected to fluorescent detection with a GMS (Affymetrix) 418 Array Scanner (Affymetrix Inc., Santa Clara, CA) Cy3 channel was scanned at 100% laser power and 70% PMT gain Cy5 channel was scanned at 100% laser power and 70% PMT gain

data_processing: Images were analyzed with the TIGR Spotfinder program (v.2.2.4). All spots with less than 50% of the pixels with values lower than the median local background plus two SD have been flagged and excluded from further analyses. Raw data were submitted to a series of mathematical transformations with the aid of the software TIGR MIDAS v.2.19. These included filtering out all spots whose integrated intensities were below 10,000 a/d units, normalization between the two channels with the aid of the Lowess algorithm and SD regularization of the Cy5/Cy3 ratios across all sectors (blocks) of the array

molecule: total RNA

organism: Paracoccidioides brasiliensis

label_protocol: The RNA sample extracted with Trizol was further purified with aid of the RNA easy kit (Qiagen) and labeled by incorporation of Cy3- or Cy5-dCTP. Briefly, 30 ug of total P. brasiliensis RNA were mixed with 2 ug of oligo(dT)12-18 in 20 ul of water and heated to 65oC for 10 min. The tube was briefly chilled on ice and mixed with 4 ul of 5mM dNTPs, 4 ul of 0.1 M DTT, 8 ul of 5X first-strand buffer (Invitrogen) and 1.5 ul of Superscript II (200 units/ml) (Invitrogen). The reaction was then incubated at 42oC for 1.5 h and terminated by a 15-min incubation at 65oC. The RNA was degraded by adding 1 ul of 10 mg/ml RNAse A and incubation at 37oC for 1 hour. The resulting first strand cDNA was purified and concentrated with the aid of a Microcon YM-30 cartridge and final volume was adjusted to 29 ul. One microliter (1 ul) of 4 ug/ul random primer solution (9-mers) and 4 ul of 10X Klenow buffer were then added to the system. The tube was then heated at 65oC for 5 min and allowed to cool to room temperature for ten min for primer annealing. Finally, fluorescence incorporation was performed by the addition of 4 ul of 10X low dNTP solution (5mM dATP, 5mM dTTP, 5mM dGTP and 2mM dCTP), 1 ul of Cy3-labeled dCTP (1mM) (Amersham Biosciences) and 1 ul of the Klenow fragment (50 units/ul) (Invitrogen). The reaction was then incubated at 37oC for 2 h and the final labeled cDNA was purified in a Microcon YM-30 cartridge (3 washes)

extract_protocol: Yeast cells and mycelium were disrupted with glass beads and grinding in liquid nitrogen, respectively, and immediately mixed with Trizol (Gibco-BRL) for RNA extraction following the supplier�s recommendations. To verify the RNA integrity, twenty micrograms of RNA from each treatment were fractionated in 2.2-M formaldehyde, 1.2 % agarose gel, stained with ethidium bromide, and visualized with UV-light. The presence of intact 28S and 18S ribosomal RNA bands was used as a criterion to verify if the RNA was intact. RNAse-free DNA-se treatment was done in a final volume of 100 ul, containing 40 mM Tris-HCl pH 7.5 and 6 mM MgCl2, 1 ul of RNAsin (40 U/ul, Promega, USA), 10 ul of RNAse-free DNAse (1 U/ul, Promega or Life Technologies, USA), 2.5 ul of 200 mM DTT, and 10 mg of total RNA. The reaction was incubated at 37oC for 60 min and stopped by incubating at 70oC for 30 min. The absence of DNA contamination after the RNAse-free DNAse treatment was verified by PCR-amplification of the GP43 gene

tag: We used P. brasiliensis isolate 18, named Pb18 (provided by Dr. Z. P. Camargo, UNIFESP, S�o Paulo, Brazil). Fungal mycelium was cultivated in modified YPD medium (mYPD, 0.5% yeast extract, 0.5% casein peptone, 1.5% glucose, pH6.5) at 26oC (mycelium phase). To obtain mycelium cultures, yeast cells were recovered from the lungs of intratracheally infected mice and sub-cultured 3 successive times in mYPD slants, at 10-day intervals. In order to obtain the fungal mycelium phase, slant yeast cells were inoculated in 200 ml of the same medium and incubated at 26oC for approximately 9 days under shaking, when 100% of conversion was achieved.

label_protocol: The RNA sample extracted with Trizol was further purified with aid of the RNA easy kit (Qiagen) and labeled by incorporation of Cy3- or Cy5-dCTP. Briefly, 30 ug of total P. brasiliensis RNA were mixed with 2 ug of oligo(dT)12-18 in 20 ul of water and heated to 65oC for 10 min. The tube was briefly chilled on ice and mixed with 4 ul of 5mM dNTPs, 4 ul of 0.1 M DTT, 8 ul of 5X first-strand buffer (Invitrogen) and 1.5 ul of Superscript II (200 units/ml) (Invitrogen). The reaction was then incubated at 42oC for 1.5 h and terminated by a 15-min incubation at 65oC. The RNA was degraded by adding 1 ul of 10 mg/ml RNAse A and incubation at 37oC for 1 hour. The resulting first strand cDNA was purified and concentrated with the aid of a Microcon YM-30 cartridge and final volume was adjusted to 29 ul. One microliter (1 ul) of 4 ug/ul random primer solution (9-mers) and 4 ul of 10X Klenow buffer were then added to the system. The tube was then heated at 65oC for 5 min and allowed to cool to room temperature for ten min for primer annealing. Finally, fluorescence incorporation was performed by the addition of 4 ul of 10X low dNTP solution (5mM dATP, 5mM dTTP, 5mM dGTP and 2mM dCTP), 1 ul of Cy5-labeled dCTP (1mM) (Amersham Biosciences) and 1 ul of the Klenow fragment (50 units/ul) (Invitrogen). The reaction was then incubated at 37oC for 2 h and the final labeled cDNA was purified in a Microcon YM-30 cartridge (3 washes)

growth_protocol: Fungal mycelium, cultivated in mYPDfor 9 days, at 26oC was transfered to 37oC for a period of 10 hours, at 120 rpm in a rotatory shaker, when cells were harvested for RNA purification.

treatment_protocol: 10-hour incubation at 37oC in mYPD, at 120 rpm in a rotatory shaker

tag: We used P. brasiliensis isolate 18, named Pb18 (provided by Dr. Z. P. Camargo, UNIFESP, S�o Paulo, Brazil). Fungal mycelium, cultivated in modified YPD medium (mYPD, 0.5% yeast extract, 0.5% casein peptone, 1.5% glucose, pH6.5) for 9 days, at 26oC was transfered to 37oC for a period of 10 hours, when cells were harvested for RNA purification.


title: 0hCy3_X_10hCy5_Exp2_Repl2

hyb_protocol: Labelled cDNAs were mixed, dried in a Savant speed vacuum and resuspended in 100 ul of 1X Hybridization buffer, containing 6X SSC, 5X Denhardt´s solution, 0,25 mg/ml salmon sperm DNA, 0,01% SDS, 50% formamide and 92,5 ng/ul poly (dT) 25u (Amersham). Arrays were hybridized overnight (42oC) in a Gene-Tac Hybridization Station (Genomic Solutions, Inc., Ann Arbor, MI) and washed twice (42oC) in 0.5 X SSC, 0.01 % SDS, followed by two washes in 0.06 X SSC, 0.01 % SDS and two final washes in 0.06 X SSC. All washing steps consisted of 1 min of flow, followed by 5 min of incubation. Slides were then dried and subjected to fluorescent detection

scan_protocol: Slides were subjected to fluorescent detection with a GMS (Affymetrix) 418 Array Scanner (Affymetrix Inc., Santa Clara, CA) Cy3 channel was scanned at 100% laser power and 80% PMT gain Cy5 channel was scanned at 100% laser power and 70% PMT gain

extract_protocol: Yeast cells and mycelium were disrupted with glass beads and grinding in liquid nitrogen, respectively, and immediately mixed with Trizol (Gibco-BRL) for RNA extraction following the supplier’s recommendations. To verify the RNA integrity, twenty micrograms of RNA from each treatment were fractionated in 2.2-M formaldehyde, 1.2 % agarose gel, stained with ethidium bromide, and visualized with UV-light. The presence of intact 28S and 18S ribosomal RNA bands was used as a criterion to verify if the RNA was intact. RNAse-free DNA-se treatment was done in a final volume of 100 ul, containing 40 mM Tris-HCl pH 7.5 and 6 mM MgCl2, 1 ul of RNAsin (40 U/ul, Promega, USA), 10 ul of RNAse-free DNAse (1 U/ul, Promega or Life Technologies, USA), 2.5 ul of 200 mM DTT, and 10 mg of total RNA. The reaction was incubated at 37oC for 60 min and stopped by incubating at 70oC for 30 min. The absence of DNA contamination after the RNAse-free DNAse treatment was verified by PCR-amplification of the GP43 gene

tag: We used P. brasiliensis isolate 18, named Pb18 (provided by Dr. Z. P. Camargo, UNIFESP, São Paulo, Brazil). Fungal mycelium was cultivated in modified YPD medium (mYPD, 0.5% yeast extract, 0.5% casein peptone, 1.5% glucose, pH6.5) at 26oC (mycelium phase). To obtain mycelium cultures, yeast cells were recovered from the lungs of intratracheally infected mice and sub-cultured 3 successive times in mYPD slants, at 10-day intervals. In order to obtain the fungal mycelium phase, slant yeast cells were inoculated in 200 ml of the same medium and incubated at 26oC for approximately 9 days under shaking, when 100% of conversion was achieved.

tag: We used P. brasiliensis isolate 18, named Pb18 (provided by Dr. Z. P. Camargo, UNIFESP, São Paulo, Brazil). Fungal mycelium, cultivated in modified YPD medium (mYPD, 0.5% yeast extract, 0.5% casein peptone, 1.5% glucose, pH6.5) for 9 days, at 26oC was transfered to 37oC for a period of 10 hours, when cells were harvested for RNA purification.


title: Col_+IAA_2

city: Albany

first: Yoko

last: Okushima

state: CA

address: 800 Buchanan St.

department: Plant and Microbial Biology

country: USA

institute: Plant Gene Expression Center, U. C. Berkeley

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5µM IAA (IAA treated) or EtOH (control) for 2 h at 24 °C.

Line: Columbia wild-type
Treatment: IAA treated
Replicate 2

organism: Arabidopsis thaliana

source_name: Light grown liquid cultured seedlings (7-day old)


title: Col_+IAA_1

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5µM IAA (IAA treated) or EtOH (control) for 2 h at 24 °C.

Line: Columbia wild-type
Treatment: IAA treated
Replicate 1


title: 48 hour DMSO

status: Public on Oct 18 2005

city: Urbana

first: Michael

last: Spinella

state: IL

address: 2001 South Lincoln Ave

department: Comparative Biosciences

institute: University of Illinois

description: NT2 cells were treated for 48 hours with DMSO (control) or 10uM Retinoic Acid (RA). Total RNA was isolated using TriReagent, and subsequent cleanup with RNeasy columns (Qiagen) according to the manufacturer�s directions.  Hybridizations were performed according to Affymetrix guidelines using the Human HG-U133A chip containing 22,500 unique genetic elements.  Double-stranded cDNA was synthesized using Superscript II RT (Invitrogen).  In vitro transcription labeling was performed with biotin labeled nucleotides using the Bioarray High Yield RNA Labeling Kit (ENZO).  20 ul of labeled RNA per sample was added to the hybridization cocktail, with a total of 15 ug hybridized to the chip (16 hours, 45C).  RMA analysis was performed using Gene Traffic software (Iobion), where raw data for each hybridization was normalized, background corrected and filtered for signal intensity of 50 or greater in at least one comparison.

organism: Homo sapiens

source_name: NT2 cells


title: Col_control_3

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5�M IAA (IAA treated) or EtOH (control) for 2 h at 24 �C.

Line: Columbia wild-type
Treatment: Control
Replicate 3

Note: Correct data table for GSM9573 has been updated on Oct 26, 2005. If you have downloaded data at some previous time (the old version was duplicate of GSE9576), please download again.


title: Col_control_1

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5µM IAA (IAA treated) or EtOH (control) for 2 h at 24 °C.

Line: Columbia wild-type
Treatment: Control
Replicate 1


title: Wildtype 635

city: Salt Lake City

first: Robert

middle: J

last: Crisp

state: UT

address: 30 North Medical Drive

department: Dep't of Pathology

institute: University of Utah

description:
normal heme
iron deficient
6 hr

data_processing: Raw Data

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: mRNA

tag: normal heme

tag: iron deficient


title: heme deficient 532

description:
heme deficient
iron deficient
6 hr

tag: heme deficient


title: 48 hours RA


title: heme deficient 635

description:
heme deficient
iron deficient
6 hr


title: 0hCy5_X_24hCy3_Exp1_Repl1

scan_protocol: Slides were subjected to fluorescent detection with a GMS (Affymetrix) 418 Array Scanner (Affymetrix Inc., Santa Clara, CA) Cy3 channel was scanned at 100% laser power and 70% PMT gain Cy5 channel was scanned at 100% laser power and 100% PMT gain

growth_protocol: Fungal mycelium, cultivated in mYPDfor 9 days, at 26oC was transfered to 37oC for a period of 24 hours, at 120 rpm in a rotatory shaker, when cells were harvested for RNA purification.

treatment_protocol: 24-hour incubation at 37oC in mYPD, at 120 rpm in a rotatory shaker

tag: We used P. brasiliensis isolate 18, named Pb18 (provided by Dr. Z. P. Camargo, UNIFESP, S�o Paulo, Brazil). Fungal mycelium, cultivated in modified YPD medium (mYPD, 0.5% yeast extract, 0.5% casein peptone, 1.5% glucose, pH6.5) for 9 days, at 26oC was transfered to 37oC for a period of 24 hours, when cells were harvested for RNA purification.

growth_protocol: Fungal mycelium was cultivated in modified YPD medium (mYPD, 0.5% yeast extract, 0.5% casein peptone, 1.5% glucose, pH6.5) at 26oC (mycelium phase). To obtain mycelium cultures, yeast cells were recovered from the lungs of intratracheally infected mice and sub-cultured 3 successive times in mYPD slants, at 10-day intervals. In order to obtain the fungal mycelium phase, slant yeast cells were inoculated in 200 ml of the same medium and incubated at 26oC for approximately 9 days under shaking, when 100% of conversion was achieved.


title: Wildtype 532

description:
normal heme
iron deficient
6 hr


title: 0hCy5_X_10hCy3_Exp2_Repl1

scan_protocol: Slides were subjected to fluorescent detection with a GMS (Affymetrix) 418 Array Scanner (Affymetrix Inc., Santa Clara, CA) Cy3 channel was scanned at 100% laser power and 80% PMT gain Cy5 channel was scanned at 100% laser power and 90% PMT gain


title: 0hCy3_X_5hCy5_Exp1_Repl1

scan_protocol: Slides were subjected to fluorescent detection with a GMS (Affymetrix) 418 Array Scanner (Affymetrix Inc., Santa Clara, CA) Cy3 channel was scanned at 100% laser power and 70% PMT gain Cy5 channel was scanned at 100% laser power and 80% PMT gain

growth_protocol: Fungal mycelium, cultivated in mYPDfor 9 days, at 26oC was transfered to 37oC for a period of 5 hours, at 120 rpm in a rotatory shaker, when cells were harvested for RNA purification.

treatment_protocol: 5-hour incubation at 37oC in mYPD, at 120 rpm in a rotatory shaker

tag: We used P. brasiliensis isolate 18, named Pb18 (provided by Dr. Z. P. Camargo, UNIFESP, São Paulo, Brazil). Fungal mycelium, cultivated in modified YPD medium (mYPD, 0.5% yeast extract, 0.5% casein peptone, 1.5% glucose, pH6.5) for 9 days, at 26oC was transfered to 37oC for a period of 5 hours, when cells were harvested for RNA purification.


title: 0hCy5_X_10hCy3_Exp1_Repl2

scan_protocol: Slides were subjected to fluorescent detection with a GMS (Affymetrix) 418 Array Scanner (Affymetrix Inc., Santa Clara, CA) Cy3 channel was scanned at 100% laser power and 80% PMT gain Cy5 channel was scanned at 100% laser power and 80% PMT gain


title: 0hCy5_X_10hCy3_Exp2_Repl2


title: 0hCy5_X_10hCy3_Exp1_Repl1


title: 3328

status: Public on Oct 15 2005

city: San Diego

first: Tim

last: Jatkoe

institute: Veridex

description: Breast cancer

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

label: biotin

source_name: breast

label_protocol: Approximately 5 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Total RNA was isolated from breast cancer samples according to Standard Trizol protocol or Qiagen RNeasy Mini Kit protocol.

tag: Cancer


title: 3325

description: Breast cancer


title: 0hCy5_X_5hCy3_Exp2_Repl1

tag: We used P. brasiliensis isolate 18, named Pb18 (provided by Dr. Z. P. Camargo, UNIFESP, S�o Paulo, Brazil). Fungal mycelium, cultivated in modified YPD medium (mYPD, 0.5% yeast extract, 0.5% casein peptone, 1.5% glucose, pH6.5) for 9 days, at 26oC was transfered to 37oC for a period of 5 hours, when cells were harvested for RNA purification.


title: 3324

description: Breast cancer


title: 3326

description: Breast cancer


title: 3327

description: Breast cancer


title: Human FOS ChIP-chip S3 on Hela Biological Sample 2 (Nimblegen ENCODE Array)

type: genomic

city: Woodbridge

first: Can

last: Bruce

state: CT

address: 5 Chestnut Lane

institute: Sciomix

description:
HeLa S3 cells were grown in suspension in Joklik’s modified minimal essential medium (MEM), supplemented with 5% FBS at 37C in 5% CO2, to a density of 6 x10^5 cells/ml. Cells were fixed with 1% formaldehyde at room temperature for 10 min. Fixation was terminated with 125 mM glycine (2 M stock made in 1x PBS), and then cells were washed twice in cold 1x DulbeccoÃ•s PBS (Invitrogen). Cells were suspended in lysis buffer 1 (50 mM HEPES-KOH, pH 7.5; 140 mM NaCl; 1 mM EDTA; 10% glycerol; 0.5% NP-40; 0.25% Triton X-100; and 1X complete protease inhibitors (Roche)).  Cells were rocked for 15 min at 4C and collected by centrifugation at 3000 rpm for 5 min., and resuspended in lysis buffer 2 (10 mM Tris, pH 8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 1X protease inhibitors).  Cells were rocked as above and nuclei were collected by centrifugation at 3000 rpm.  Nuclei were lysed in lysis buffer 3 (10 mM Tris, pH 8.0; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% sodium deoxycholate; 0.5% N-lauroyl sarcosine; 1X protease inhibitors).  Chromatin was sheared with a Branson 250 Sonifier (power setting 2, 100% duty cycle, eight 30-second pulses) to an average of 500 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with 50 ul of anti-c-Fos (4-10G) from  Santa Cruz (sc-413) per 1x10^8 cells. Following this incubation Protein A/G agarose (Santa Cruz) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol.
For NimbleGen arrays, 16 ug (as measured by Nanodrop spectrophotomer) were directly labeled by Klenow (New England Biolabs) random priming with Cy5 nonamers (DNA from FOS ChIP) or Cy3 nonamers (total genomic DNA). The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and then hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, and 0.1 ug/ul herring sperm DNA. Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Arrays were scanned on an Axon 4000B scanner.
Keywords = Transcription Factor Binding, FOS, ChIP-chip, Human, Genome Tiling Arrays

data_processing: no processing; value = log_2( Signal for Cy5 / Signal for Cy3)

molecule: genomic DNA

source_name: FOS ChIP HeLa S3 Cells

tag: Hela S3 cells

source_name: Input DNA, total genomic DNA from HeLa S3 Cells


title: 0hCy5_X_5hCy3_Exp2_Repl2


title: 3323

description: Breast cancer


title: Human TAF II p250 ChIP-chip S3 on Hela Biological Sample 2 (Nimblegen ENCODE Array)

description:
HeLa S3 cells were grown in suspension in Joklik’s modified minimal essential medium (MEM), supplemented with 5% FBS at 37C in 5% CO2, to a density of 6 x10^5 cells/ml. Cells were fixed with 1% formaldehyde at room temperature for 10 min. Fixation was terminated with 125 mM glycine (2 M stock made in 1x PBS), and then cells were washed twice in cold 1x DulbeccoÃ•s PBS (Invitrogen). Cells were suspended in lysis buffer 1 (50 mM HEPES-KOH, pH 7.5; 140 mM NaCl; 1 mM EDTA; 10% glycerol; 0.5% NP-40; 0.25% Triton X-100; and 1X complete protease inhibitors (Roche)).  Cells were rocked for 15 min at 4C and collected by centrifugation at 3000 rpm for 5 min., and resuspended in lysis buffer 2 (10 mM Tris, pH 8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 1X protease inhibitors).  Cells were rocked as above and nuclei were collected by centrifugation at 3000 rpm.  Nuclei were lysed in lysis buffer 3 (10 mM Tris, pH 8.0; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% sodium deoxycholate; 0.5% N-lauroyl sarcosine; 1X protease inhibitors).  Chromatin was sheared with a Branson 250 Sonifier (power setting 2, 100% duty cycle, eight 30-second pulses) to an average of 500 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with 50 ul of  TAFII p250 (6B3) from  Santa Cruz (sc-735) per 1x10^8 cells. Following this incubation Protein A/G agarose (Santa Cruz) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol.
For NimbleGen arrays, 16 ug (as measured by Nanodrop spectrophotomer) were directly labeled by Klenow (New England Biolabs) random priming with Cy5 nonamers (DNA from TAF II p250 ChIP) or Cy3 nonamers (total genomic DNA). The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and then hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, and 0.1 ug/ul herring sperm DNA. Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Arrays were scanned on an Axon 4000B scanner.
Keywords = Transcription Factor Binding, TAF II p250, ChIP-chip, Human, Genome Tiling Arrays

source_name: TAF II p250 ChIP HeLa S3 Cells

tag: HeLa S3 Cells


title: 3320

description: Breast cancer


title: 3321

description: Breast cancer


title: 3319

description: Breast cancer


title: Human JUN ChIP-chip S3 on Hela Biological Sample 2 (Nimblegen ENCODE Array)

description:
HeLa S3 cells were grown in suspension in Joklik’s modified minimal essential medium (MEM), supplemented with 5% FBS at 37C in 5% CO2, to a density of 6 x10^5 cells/ml. Cells were fixed with 1% formaldehyde at room temperature for 10 min. Fixation was terminated with 125 mM glycine (2 M stock made in 1x PBS), and then cells were washed twice in cold 1x DulbeccoÃ•s PBS (Invitrogen). Cells were suspended in lysis buffer 1 (50 mM HEPES-KOH, pH 7.5; 140 mM NaCl; 1 mM EDTA; 10% glycerol; 0.5% NP-40; 0.25% Triton X-100; and 1X complete protease inhibitors (Roche)).  Cells were rocked for 15 min at 4C and collected by centrifugation at 3000 rpm for 5 min., and resuspended in lysis buffer 2 (10 mM Tris, pH 8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 1X protease inhibitors).  Cells were rocked as above and nuclei were collected by centrifugation at 3000 rpm.  Nuclei were lysed in lysis buffer 3 (10 mM Tris, pH 8.0; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% sodium deoxycholate; 0.5% N-lauroyl sarcosine; 1X protease inhibitors).  Chromatin was sheared with a Branson 250 Sonifier (power setting 2, 100% duty cycle, eight 30-second pulses) to an average of 500 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with 50 ul of anti-c-Jun rabbbit polyclonal antiserum (Upstate # 06-225) per 1x10^8 cells. Following this incubation Protein A/G agarose (Santa Cruz) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol.
For NimbleGen arrays, 16 ug (as measured by Nanodrop spectrophotomer) were directly labeled by Klenow (New England Biolabs) random priming with Cy5 nonamers (DNA from JUN ChIP) or Cy3 nonamers (total genomic DNA). The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and then hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, and 0.1 ug/ul herring sperm DNA. Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Arrays were scanned on an Axon 4000B scanner.

source_name: JUN ChIP HeLa S3 Cells


title: Human FOS ChIP-chip S3 on Hela Biological Sample 3 (Nimblegen ENCODE Array)


title: 3318

description: Breast cancer


title: Human JUN ChIP-chip S3 on Hela Biological Sample 1 (Nimblegen ENCODE Array)

description:
HeLa S3 cells were grown in suspension in Joklik’s modified minimal essential medium (MEM), supplemented with 5% FBS at 37C in 5% CO2, to a density of 6 x10^5 cells/ml. Cells were fixed with 1% formaldehyde at room temperature for 10 min. Fixation was terminated with 125 mM glycine (2 M stock made in 1x PBS), and then cells were washed twice in cold 1x DulbeccoÃ•s PBS (Invitrogen). Cells were suspended in lysis buffer 1 (50 mM HEPES-KOH, pH 7.5; 140 mM NaCl; 1 mM EDTA; 10% glycerol; 0.5% NP-40; 0.25% Triton X-100; and 1X complete protease inhibitors (Roche)).  Cells were rocked for 15 min at 4C and collected by centrifugation at 3000 rpm for 5 min., and resuspended in lysis buffer 2 (10 mM Tris, pH 8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 1X protease inhibitors).  Cells were rocked as above and nuclei were collected by centrifugation at 3000 rpm.  Nuclei were lysed in lysis buffer 3 (10 mM Tris, pH 8.0; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% sodium deoxycholate; 0.5% N-lauroyl sarcosine; 1X protease inhibitors).  Chromatin was sheared with a Branson 250 Sonifier (power setting 2, 100% duty cycle, eight 30-second pulses) to an average of 500 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with 50 ul of anti-c-Jun rabbbit polyclonal antiserum (Upstate # 06-225) per 1x10^8 cells. Following this incubation Protein A/G agarose (Santa Cruz) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol.
For NimbleGen arrays, 16 ug (as measured by Nanodrop spectrophotomer) were directly labeled by Klenow (New England Biolabs) random priming with Cy5 nonamers  (DNA from JUN ChIP) or Cy3 nonamers (total genomic DNA). The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and then hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, and 0.1 ug/ul herring sperm DNA. Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Arrays were scanned on an Axon 4000B scanner.


title: 3316

description: Breast cancer


title: 3315

description: Breast cancer


title: 3314

description: Breast cancer


title: 3313

description: Breast cancer


title: 3311

description: Breast cancer


title: 3312

description: Breast cancer


title: 3317

description: Breast cancer


title: Human TAF II p250 ChIP-chip S3 on Hela Biological Sample 1 (Nimblegen ENCODE Array)

description:
HeLa S3 cells were grown in suspension in Joklik’s modified minimal essential medium (MEM), supplemented with 5% FBS at 37C in 5% CO2, to a density of 6 x10^5 cells/ml. Cells were fixed with 1% formaldehyde at room temperature for 10 min. Fixation was terminated with 125 mM glycine (2 M stock made in 1x PBS), and then cells were washed twice in cold 1x DulbeccoÃ•s PBS (Invitrogen). Cells were suspended in lysis buffer 1 (50 mM HEPES-KOH, pH 7.5; 140 mM NaCl; 1 mM EDTA; 10% glycerol; 0.5% NP-40; 0.25% Triton X-100; and 1X complete protease inhibitors (Roche)).  Cells were rocked for 15 min at 4C and collected by centrifugation at 3000 rpm for 5 min., and resuspended in lysis buffer 2 (10 mM Tris, pH 8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 1X protease inhibitors).  Cells were rocked as above and nuclei were collected by centrifugation at 3000 rpm.  Nuclei were lysed in lysis buffer 3 (10 mM Tris, pH 8.0; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% sodium deoxycholate; 0.5% N-lauroyl sarcosine; 1X protease inhibitors).  Chromatin was sheared with a Branson 250 Sonifier (power setting 2, 100% duty cycle, eight 30-second pulses) to an average of 500 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with 50 ul of TAFII p250 (6B3) from  Santa Cruz (sc-735) per 1x10^8 cells. Following this incubation Protein A/G agarose (Santa Cruz) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol.
For NimbleGen arrays, 16 ug (as measured by Nanodrop spectrophotomer) were directly labeled by Klenow (New England Biolabs) random priming with Cy5 nonamers((DNA from TAF II p250 ChIP)  or Cy3 nonamers (total genomic DNA). The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and then hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, and 0.1 ug/ul herring sperm DNA. Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Arrays were scanned on an Axon 4000B scanner.
Keywords = Transcription Factor Binding, TAF II p250, ChIP-chip, Human, Genome Tiling Arrays


title: Human FOS ChIP-chip S3 on Hela Biological Sample 1 (Nimblegen ENCODE Array)

description:
HeLa S3 cells were grown in suspension in Joklik’s modified minimal essential medium (MEM), supplemented with 5% FBS at 37C in 5% CO2, to a density of 6 x10^5 cells/ml. Cells were fixed with 1% formaldehyde at room temperature for 10 min. Fixation was terminated with 125 mM glycine (2 M stock made in 1x PBS), and then cells were washed twice in cold 1x DulbeccoÃ•s PBS (Invitrogen). Cells were suspended in lysis buffer 1 (50 mM HEPES-KOH, pH 7.5; 140 mM NaCl; 1 mM EDTA; 10% glycerol; 0.5% NP-40; 0.25% Triton X-100; and 1X complete protease inhibitors (Roche)).  Cells were rocked for 15 min at 4C and collected by centrifugation at 3000 rpm for 5 min., and resuspended in lysis buffer 2 (10 mM Tris, pH 8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 1X protease inhibitors).  Cells were rocked as above and nuclei were collected by centrifugation at 3000 rpm.  Nuclei were lysed in lysis buffer 3 (10 mM Tris, pH 8.0; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% sodium deoxycholate; 0.5% N-lauroyl sarcosine; 1X protease inhibitors).  Chromatin was sheared with a Branson 250 Sonifier (power setting 2, 100% duty cycle, eight 30-second pulses) to an average of 500 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with 50 ul of anti-c-Fos (4-10G) from  Santa Cruz (sc-413) per 1x10^8 cells. Following this incubation Protein A/G agarose (Santa Cruz) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol.
For NimbleGen arrays, 16 ug (as measured by Nanodrop spectrophotomer) were directly labeled by Klenow (New England Biolabs) random priming with Cy5 nonamers((DNA from FOS ChIP)  or Cy3 nonamers (total genomic DNA). The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and then hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, and 0.1 ug/ul herring sperm DNA. Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Arrays were scanned on an Axon 4000B scanner.
Keywords = Transcription Factor Binding, FOS, ChIP-chip, Human, Genome Tiling Arrays


title: Human JUN ChIP-chip S3 on Hela Biological Sample 3 (Nimblegen ENCODE Array)


title: 3309

description: Breast cancer


title: 3310

description: Breast cancer


title: 3308

description: Breast cancer


title: 3305

description: Breast cancer


title: 3303

description: Breast cancer


title: 3302

description: Breast cancer


title: 3301

description: Breast cancer


title: 3304

description: Breast cancer


title: 3306

description: Breast cancer


title: 3300

description: Breast cancer


title: 3307

description: Breast cancer


title: 3299

description: Breast cancer


title: 3296

description: Breast cancer


title: 3298

description: Breast cancer


title: 3297

description: Breast cancer


title: 3294

description: Breast cancer


title: 3293

description: Breast cancer


title: 3291

description: Breast cancer


title: 3290

description: Breast cancer


title: 3219

description: Breast cancer


title: 3218

description: Breast cancer


title: 3198

description: Breast cancer


title: 3197

description: Breast cancer


title: 3183

description: Breast cancer


title: 3185

description: Breast cancer


title: 3181

description: Breast cancer


title: 3186

description: Breast cancer


title: 3172

description: Breast cancer


title: 3179

description: Breast cancer


title: 3169

description: Breast cancer


title: 3196

description: Breast cancer


title: 3178

description: Breast cancer


title: Rice subspecies indica, OS_18654

city: New Haven

first: Xing-Wang

last: Deng

address: 165 Prospect

department: MCD Biology

institute: Yale University

description:
The four RNA population from seedling roots, seedling shoots, panicles, and suspension-cultured cells were pooled in equal amount and cDNAs were derived from the RNA mixture.
Total RNA and mRNA were isolated using the RNeasy Plant Mini kit (Qiagen, Valencia, CA) and the Oligotex mRNA kit (Qiagen), respectively.
First-strand cDNA was generated from 4 ¦Ìg poly(A)+ RNA with SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA).
The cDNAs were precipitated in ethanol:isopropanol (1:1 v/v) and resuspended in 0.1 M NaHCO3 to facilitate coupling of Alexa Fluor 555 NHS esters (Molecular Probes, Eugene, OR) to the reactive groups of the amino-allyl dUTPs and were purified with CyScribe GFX glass fiber spin columns (Amersham Bioscience, Piscataway, NJ).
Microarrays were hybridized with 4 ¦Ìg labeled cDNA in 300 ¦ÌL hybridization buffer (50 mM MES, 0.5 M NaCl, 10 mM EDTA, and 0.005% (v/v) Tween-20) for 16 hours at 50¡ãC in disposable adhesive chambers (Grace BioLabs, Bend, OR) in a hybridization oven with constant agitation.
Hybridized arrays were washed on an orbital Sample in non-stringent buffer (6¡Á SSPE, 0.01% [v/v] Tween-20) for 10 minutes at room temperature, then in stringent buffer (100 mM MES, 0.1 M NaCl, 0.01% Tween-20) for 30 minutes at 45¡ãC.
This was followed by a 5-minute wash in non-stringent buffer and a 2-minute wash in 0.1X SSC.
The arrays were dried with compressed nitrogen and scanned with an Axon 4000B laser scanner at 5 ¦Ìm resolution.
The fluorescence intensity data were extracted with the NimbleScan software (NimbleGen Systems, Madison, WI).

data_processing: Median fluorescence signal intensity of the array feature

organism: Oryza sativa

source_name: Poly(A)+ RNA derived from rice seedling roots, seedling shoots, panicles, and suspension cultured cells.

tag: Rice subspecies indica, OS_18654


title: Rice subspecies indica, OS_18766

tag: Rice subspecies indica, OS_18766


title: 3180

description: Breast cancer


title: Rice subspecies indica, OS_18922

tag: Rice subspecies indica, OS_18922


title: Rice subspecies indica, OS_18768

tag: Rice subspecies indica, OS_18768


title: 3162

description: Breast cancer


title: 3160

description: Breast cancer


title: 3159

description: Breast cancer


title: Rice subspecies indica, OS_18757

tag: Rice subspecies indica, OS_18757


title: Rice subspecies indica, OS_18767

tag: Rice subspecies indica, OS_18767


title: Rice subspecies indica, OS_18925

tag: Rice subspecies indica, OS_18925


title: 3158

description: Breast cancer


title: 3155

description: Breast cancer


title: 3157

description: Breast cancer


title: Rice subspecies indica, OS_18758

tag: Rice subspecies indica, OS_18758


title: 3152

description: Breast cancer


title: 3148

description: Breast cancer


title: 3151

description: Breast cancer


title: 3156

description: Breast cancer


title: 3150

description: Breast cancer


title: 3145

description: Breast cancer


title: Rice subspecies indica, OS_18924

tag: Rice subspecies indica, OS_18924


title: 3147

description: Breast cancer


title: 3146

description: Breast cancer


title: 3144

description: Breast cancer


title: Rice subspecies indica, OS_18923

tag: Rice subspecies indica, OS_18923


title: 3138

description: Breast cancer


title: 3140

description: Breast cancer


title: 3154

description: Breast cancer


title: 3141

description: Breast cancer


title: 3142

description: Breast cancer


title: 3136

description: Breast cancer


title: 3137

description: Breast cancer


title: 3133

description: Breast cancer


title: 3135

description: Breast cancer


title: 3132

description: Breast cancer


title: 3131

description: Breast cancer


title: 3129

description: Breast cancer


title: 3128

description: Breast cancer


title: 3127

description: Breast cancer


title: 3126

description: Breast cancer


title: 3125

description: Breast cancer


title: 3122

description: Breast cancer


title: 3110

description: Breast cancer


title: 3124

description: Breast cancer


title: 3123

description: Breast cancer


title: 3121

description: Breast cancer


title: 3120

description: Breast cancer


title: 3108

description: Breast cancer


title: 3106

description: Breast cancer


title: 3107

description: Breast cancer


title: 3102

description: Breast cancer


title: 3100

description: Breast cancer


title: 3103

description: Breast cancer


title: 3099

description: Breast cancer


title: 3098

description: Breast cancer


title: 3104

description: Breast cancer


title: MS02

city: Nashville

first: Zheng

last: Liu

state: TN

institute: Vanderbilt University

description: RAW DATA

data_processing: RAW

source_name: PBMC

tag: MS (MULTIPLE SCLEROSIS)


title: MS04

description: RAW DATA

tag: MS


title: MS01

description: RAW DATA


title: IDDM07

description: RAW DATA

tag: IDDM


title: IDDM06

description: RAW DATA


title: MS06

description: RAW DATA


title: IDDM05

description: RAW DATA


title: 3097

description: Breast cancer

tag: Cancer


title: 3096

description: Breast cancer


title: 3182

description: Breast cancer


title: 3093

description: Breast cancer


title: 3101

description: Breast cancer


title: 3105

description: Breast cancer


title: 3094

description: Breast cancer


title: 3095

description: Breast cancer


title: 3092

description: Breast cancer


title: IDDM04

description: RAW DATA


title: 3091

description: Breast cancer


title: SLE13

description: RAW DATA

tag: SLE


title: 3090

description: Breast cancer


title: 3089

description: Breast cancer


title: IDDM03

description: RAW DATA


title: FA4_1

description: raw data

tag: UNAFFECTED FAMILY MEMBERS OF AUTOIMMUNE DISEASES


title: SLE12

description: RAW DATA


title: SLE05

description: RAW DATA


title: SLE18

description: RAW DATA


title: FA3_4

description: raw data


title: 3088

description: Breast cancer


title: FA3_3

description: raw data

tag: UNAFFECTED FAMILY MEMBERS


title: 3087

description: Breast cancer


title: 3086

description: Breast cancer


title: 3085

description: Breast cancer


title: 3082

description: Breast cancer


title: 3079

description: Breast cancer


title: 3074

description: Breast cancer


title: 3081

description: Breast cancer


title: FA3_2

description: raw data


title: 3078

description: Breast cancer


title: 3080

description: Breast cancer


title: 3075

description: Breast cancer


title: FA2_2

description: raw data


title: FA3_1

description: raw data


title: FA2_1

description: raw data

tag: unaffected family members of autoimmune diseases


title: 3077

description: Breast cancer


title: 3076

description: Breast cancer


title: 3084

description: Breast cancer


title: 3073

description: Breast cancer


title: 3072

description: Breast cancer


title: 3070

description: Breast cancer


title: 3068

description: Breast cancer


title: 3069

description: Breast cancer


title: 3066

description: Breast cancer


title: 3071

description: Breast cancer


title: 3067

description: Breast cancer


title: 3065

description: Breast cancer


title: 3064

description: Breast cancer


title: 3062

description: Breast cancer


title: 3061

description: Breast cancer


title: 3055

description: Breast cancer


title: 3060

description: Breast cancer


title: 3057

description: Breast cancer


title: 3054

description: Breast cancer


title: 3050

description: Breast cancer


title: 3047

description: Breast cancer


title: 3049

description: Breast cancer


title: 3056

description: Breast cancer


title: 3053

description: Breast cancer


title: 3045

description: Breast cancer


title: 3051

description: Breast cancer


title: 3052

description: Breast cancer


title: 3059

description: Breast cancer


title: 3063

description: Breast cancer


title: 3042

description: Breast cancer


title: 3046

description: Breast cancer


title: 3043

description: Breast cancer


title: 3041

description: Breast cancer


title: 3044

description: Breast cancer


title: 3040

description: Breast cancer


title: 3038

description: Breast cancer


title: 3048

description: Breast cancer


title: 3039

description: Breast cancer


title: 3037

description: Breast cancer


title: 3036

description: Breast cancer


title: 3032

description: Breast cancer


title: 3033

description: Breast cancer


title: 3034

description: Breast cancer


title: 3029

description: Breast cancer


title: 3035

description: Breast cancer


title: 3030

description: Breast cancer


title: 3031

description: Breast cancer


title: 3025

description: Breast cancer


title: 3024

description: Breast cancer


title: 3022

description: Breast cancer


title: 3028

description: Breast cancer


title: 3058

description: Breast cancer


title: 3027

description: Breast cancer


title: 3023

description: Breast cancer


title: 3021

description: Breast cancer


title: 3026

description: Breast cancer


title: 3019

description: Breast cancer


title: 3017

description: Breast cancer


title: 3020

description: Breast cancer


title: 3016

description: Breast cancer


title: Rice subspecies indica, OS_18926

tag: Rice subspecies indica, OS_18926


title: 3018

description: Breast cancer


title: FA4_3

description: raw data


title: SpoY279

status: Public on Oct 13 2005

city: Bethesda

first: Rafael

middle: Dan

last: Camerini-Otero

state: MD

address: 5 Memorial Dr. Rm.205

department: GBB

institute: NIDDK

description: comparison of Spo11 knockout testes and wild type  testes from 15 day mice

data_processing: Primary data were flagged using four default parameters set in the Genepix 3.0 program. For further analysis, the data were imported into Excel (Microsoft) and normalized by the Median Centering Method

organism: Mus musculus

source_name: 15d wild type whole testis

tag: Strain:wild type

tag: Age:15 days

source_name: 15d Spo11-/- whole testis


title: SpoY281


title: SpoY278


title: SpoY280


title: Rice subspecies indica, OS_18779

tag: Rice subspecies indica, OS_18779


title: Rice subspecies indica, OS_18769

tag: Rice subspecies indica, OS_18769


title: Rice subspecies indica, OS_18928

tag: Rice subspecies indica, OS_18928


title: Rice subspecies indica, OS_18739

tag: Rice subspecies indica, OS_18739


title: Rice subspecies indica, OS_18791

tag: Rice subspecies indica, OS_18791


title: Rice subspecies indica, OS_18788

tag: Rice subspecies indica, OS_18788


title: Rice subspecies indica, OS_18780

tag: Rice subspecies indica, OS_18780


title: WT-MAC-SEV-1

status: Public on Oct 11 2005

city: St. Louis

first: Anand

middle: Champak

last: Patel

state: MO

address: Campus Box 8116, 660 S. Euclid Ave.

department: Pulmonary/Critical Care Medicine

institute: Washington University School of Medicine

description: Microarray normalization and statistical analysis were carried out using packages from the Bioconductor project (Gentleman RC et al, 2004), executed in the R programming environment. Data was normalized using the empirical Bayes version of the GCRMA algorithm as implemented in the GCRMA package (Wu Z et al, 2004). Differential expression was assessed by using linear models and empirical Bayes moderated F statistics as implemented in the LIMMA package (Smyth GK, 2004). Differences in gene expression were considered significant if the P values were <0.05 after adjustment for multiple testing (Benjamini & Hochberg, 1995), and thus, false discovery rate was controlled to be <5%. Visualization and plotting were performed using Spotfire DecisionSite for Functional Genomics (Spotfire, Somerville, MA).

hyb_protocol: Samples were hybridized in duplicate to gene chip U74Av2 (Affymetrix, Santa Clara, CA) according to the manufacturer’s protocol.

scan_protocol: Chips were scanned, and hybridization data were acquired using Affymetrix MicroArray Suite (MAS) 5.0 software.

data_processing: gcRMA normalization, Bioconductor 1.5

source_name: macrophages, 4 days post SeV inoculation

label_protocol: RNA was labelled with biotin by using the BioArray High Yield RNA Transcript Labeling Kit (Enzo, Farmindale, NY).

growth_protocol: Cells were grown in 8-well Labtek chambers (2 x 105 cells per well) in RPMI medium with 10% FBS, 2 mM L-glutamine, and 1 mM non-essential amino acids. This method provided cultures in which 98.9 ± 0.7% of cells were CD68-positive and 100% of adherent cells were viable.

extract_protocol: Macrophage RNA was isolated using RNAqueous (Ambion, Austin, TX) and converted to Poly(A)+ RNA. RNA was assessed by formaldehyde agarose gel electrophoresis. Poly(A)+ RNA was amplified using RiboAmp (Arcturus, Mountain View, CA).

treatment_protocol: Five days after initial plating, cultures were inoculated with SeV (Sendai virus, MOI 20) for 4 d.

tag: Macrophage cultures were prepared from C57BL/6J, male, mouse peripheral blood by Optiprep (Accurate Chemical and Scientific, Westbury, NY) gradient centrifugation.


title: Rice subspecies indica, OS_18778

tag: Rice subspecies indica, OS_18778


title: Rice subspecies indica, OS_18756

tag: Rice subspecies indica, OS_18756


title: Rice subspecies indica, OS_18809

tag: Rice subspecies indica, OS_18809


title: WT-MAC-SEV-2


title: WT-MAC-UV-2

source_name: macrophages, 4 days post UV-SeV inoculation

treatment_protocol: Five days after initial plating, cultures were inoculated with SeV (MOI 20) or an equivalent amount of UV-inactivated SeV for 4 d.


title: Rice subspecies indica, OS_18740

tag: Rice subspecies indica, OS_18740


title: Rice subspecies indica, OS_18711

tag: Rice subspecies indica, OS_18711


title: Rice subspecies indica, OS_18741

tag: Rice subspecies indica, OS_18741


title: Rice subspecies indica, OS_18792

tag: Rice subspecies indica, OS_18792


title: Rice subspecies indica, OS_18743

tag: Rice subspecies indica, OS_18743


title: WT-MAC-UV-1


title: Rice subspecies indica, OS_18789

tag: Rice subspecies indica, OS_18789


title: Rice subspecies indica, OS_18733

tag: Rice subspecies indica, OS_18733


title: Rice subspecies indica, OS_18682

tag: Rice subspecies indica, OS_18682


title: Rice subspecies indica, OS_18787

tag: Rice subspecies indica, OS_18787


title: Rice subspecies indica, OS_18786

tag: Rice subspecies indica, OS_18786


title: Rice subspecies indica, OS_18826

tag: Rice subspecies indica, OS_18826


title: Triple-Fusion Transfected Embryonic Stem Cells Replicate 1

status: Public on Oct 12 2005

city: Stanford

first: Joshua

middle: M.

last: Spin

address: 300 Pasteur Drive

institute: Stanford University

description: Biological replicate 1 of 3. Stable triple-fusion-reporter-gene transfected embryonic stem cells, harvested after several passages.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially with 6x SSC/0.005% Triton X-102 and 0.1x SSC/0.005% Triton X-102 before scanning. Slides were hybridized for 17 h at 60°C in a rotating oven, and washed.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed Red signal/processed Green signal.

source_name: Total RNA from murine ES-D3 triple-transfected embryonic stem cells labeled with Cyanine-5 (red).

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy5-labeled dCTP (NEN Life Science, Boston, MA), and RNase inhibitor (Invitrogen). RNA was then degraded with RNase A, and labeled cDNAs were purified using QIAquick PCR columns (Qiagen).

growth_protocol: ES cells were kept in an undifferentiated, pluripotent state by using 1000 IU/ml leukemia inhibitory factor (LIF; Chemicon, ESGRO, ESG1107), and grown on top of murine embryonic fibroblasts feeder layer inactivated by 10 ug/ml of mitomycin C (Sigma, St. Louis).  ES cells were cultured on 0.1% gelatin-coated plastic dishes in ES medium containing Dulbecco modified Eagle medium supplemented with 15% fetal calf serum, 0.1 mM beta-mercaptoethanol, 2 mM glutamine, and 0.1 mN non-essential amino acids.

treatment_protocol: PCR amplification and standard cloning techniques were used to insert fluc and mrfp genes from plasmids pCDNA 3.1-CMV-fluc (Promega, Madison, WI) and pCDNA3.1-CMV-mrfp in frame with the ttk gene into the pCDNA3.1-truncated sr39tk.  This triple fusion (TF) reporter gene fragment (3.3 kbp) was released from the plasmid with Not1 and BamH1 restriction enzymes before blunt-end ligation into the multiple cloning site of lentiviral transfer vector, FUG, driven by the human ubiquitin-C promoter. Self-inactivating (SIN) lentivirus was prepared by transient transfection of 293T cells.  Briefly, pFUG-TF containing the triple fusion reporter gene was co-transfected into 293T cells with HIV-1 packaging vector (δ8.9) and vesicular stomatitis virus G glycoprotein-pseudotyped envelop vector (pVSVG).  Lentivirus supernatant was concentrated by sediment centrifugation using a SW29 rotor at 50,000 x g for two hours.  Concentrated virus was titered on 293T cells.  Murine ES cells were transfected with LV-pUb-fluc-mrfp-ttk at a multiplicity of infection (MOI) of 10.

tag: ES-D3 cell line (CRL-1934)

tag: Transfected with pUb-fluc-mrfp-ttk triple fusion reporter gene.

tag: Age

value: day 4

tag: Tissue

value: blastocytes

tag: Strain

value: 129/Sv mice

source_name: Total RNA from pooled whole mouse embryos e17.5, labeled with Cyanine-3 (green).

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-labeled dCTP (NEN Life Science, Boston, MA), and RNase inhibitor (Invitrogen). RNA was then degraded with RNase A, and labeled cDNAs were purified using QIAquick PCR columns (Qiagen).

value: whole embryo


title: Control Embyronic Stem Cell Replicate 2

description: Biological replicate 2 of 4. Control embryonic stem cells, untreated, harvested after several passages.

source_name: Total RNA from murine ES-D3 embryonic stem cells labeled with Cyanine-5 (red).


title: Control Embyronic Stem Cell Replicate 1

description: Biological replicate 1 of 4. Control embryonic stem cells, untreated, harvested after several passages.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5).


title: Triple-Fusion Transfected Embryonic Stem Cells Replicate 2

description: Biological replicate 2 of 3. Stable triple-fusion-reporter-gene transfected embryonic stem cells, harvested after several passages.


title: Rice subspecies indica, OS_18735

tag: Rice subspecies indica, OS_18735


title: Rice subspecies indica, OS_18730

tag: Rice subspecies indica, OS_18730


title: APL,case 12,8NF,CL

status: Public on Oct 06 2005

city: Modena

first: Rossana

last: Maffei

state: Modena

address: Via del Pozzo 71

department: Dept of Hematology and Oncology

country: Italy

institute: University of Modena and Reggio Emilia

description:
APL patient with FLT3 WILD TYPE, 65 years at diagnosis (24/9/02), female, GB=0.8, Hb(g/dl)=13.1, PLT=128, circulant blasts=0%, DIC no, LDH (IU/L)=342, fibrinogen(mg/dl)=205,bcr1, classical M3 morphology, ATRA syndrome no.
Keywords = APL
Keywords = FLT3
Keywords = ITD
Keywords = mutation
Lot batch = US22502667_251209731755

source_name: FLT3, WILD TYPE, Cy5

source_name: Universal Human reference Stratagene,Cy3


title: Triple-Fusion Transfected Embryonic Stem Cells Replicate 3

description: Biological replicate 3 of 3. Stable triple-fusion-reporter-gene transfected embryonic stem cells, harvested after several passages.


title: Control Embyronic Stem Cell Replicate 4

description: Biological replicate 4 of 4. Control embryonic stem cells, untreated, harvested after several passages.


title: Control Embyronic Stem Cell Replicate 3

description: Biological replicate 3 of 4. Control embryonic stem cells, untreated, harvested after several passages.


title: APL,case 11,7NF,BB

description:
APL patient with FLT3 WILD TYPE, 68 years at diagnosis (15/5/03), male, GB=1.0, Hb(g/dl)=9, PLT=4, circulant blasts=10%, DIC yes, LDH (IU/L)=441, fibrinogen(mg/dl)=346,bcr1, classical M3 morphology, ATRA syndrome no.
Keywords = APL
Keywords = FLT3
Keywords = ITD
Keywords = mutation
Lot batch = US22502667_251209731636


title: APL,case 28,1IF,BA

description:
APL patient with FLT3 ITD mutation, 34 years at diagnosis (30/3/94), female, GB=65.6,Hb(g/dl)=11.3, PLT=17, circulant blasts=86%, DIC yes, LDH (IU/L)=392, fibrinogen(mg/dl)=94,bcr3, variant M3 morphology, ATRA syndrome NO.
Keywords = APL
Keywords = FLT3
Keywords = ITD
Keywords = mutation
Lot batch = US22502667_251209731842

source_name: FLT3, ITD, Cy5


title: APL,case 18,2IF,GD

description:
APL patient with FLT3 ITD mutation, 61 years at diagnosis (3/12/02), male, GB=0.9,Hb(g/dl)=4.6, PLT=4, circulant blasts=85%, DIC yes, LDH (IU/L)=490, fibrinogen(mg/dl)=114,bcr1, variant M3 morphology, ATRA syndrome NO.
Keywords = APL
Keywords = FLT3
Keywords = ITD
Keywords = mutation
Lot batch = US22502667_251209731843


title: APL,case 1,4NF,SE

description:
APL patient with FLT3 WILD TYPE, 22 years at diagnosis (16/10/02), male, GB=1.9, Hb(g/dl)=12, PLT=53, circulant blasts=21%, DIC NO, LDH (IU/L)=489, fibrinogen(mg/dl)=178,bcr1, classical M3 morphology, ATRA syndrome no.
Keywords = APL
Keywords = FLT3
Keywords = ITD
Keywords = mutation
Lot batch = US22502667_251209731634


title: APL,case 4,5NF,VR

description:
APL patient with FLT3 WILD TYPE, 34 years at diagnosis (26/3/02), male, GB=1.3, Hb(g/dl)=10.5, PLT=7, circulant blasts=39%, DIC yes, LDH (IU/L)=638, fibrinogen(mg/dl)=85,bcr3, classical M3 morphology, ATRA syndrome no.
Keywords = APL
Keywords = FLT3
Keywords = ITD
Keywords = mutation
Lot batch = US22502667_251209731635


title: APL,case 19,2NF,AD

description:
APL patient with FLT3 WILD TYPE, 56 years at diagnosis (02/05/02), female, GB=18.1, Hb(g/dl)=11.4, PLT=18, circulant blasts=94%, DIC NO, LDH (IU/L)=NA, fibrinogen(mg/dl)=152,bcr3, classical M3 morphology, ATRA syndrome no.
Keywords = APL
Keywords = FLT3
Keywords = ITD
Keywords = mutation
Lot batch = US22502667_251209729798


title: H2A.Z Biological Replicate 1 vs input | array 11_123

status: Public on Oct 07 2005

city: Worcester

first: Oliver

last: Rando

state: MA

address: 364 Plantation St.

institute: UMass Medical School

description: Nucleosomal DNA was isolated and amplified using TLAD, and labeled with Cy3 fluorescent dye (green).  DNA from a ChIP with 10 ul rabbit anti-H2A.Z was amplified using TLAD, and labeled with Cy5 fluorescent dye (red).  These two probes were mixed together and hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner at 5 micron resolution and image intensity data were extracted and analyzed with GenePix Pro 5.1 analysis software.

data_processing: After background correction and removal of flagged values, data was block normalized by dilation and log base 2 expression ratios were calculated to produce the values given in the data table.

source_name: aRNA-amplifed MNase digested ChIP input DNA

label_protocol: The cDNA were covalently coupled separately with either Cy5 or Cy3 monoreactive fluors in 50 mM sodium bicarbonate, pH 9.0. The Cy5 and Cy3 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and suspended in 50 µl of 3.4X SSC, 2 mg/ml of yeast tRNA, and 0.3% SDS for hybridization to the microarray.

source_name: H2A.Z ChIP, 10 ul Ab, IVT #637


title: APL,case 27,4IF,GN

description:
APL patient with FLT3 ITD mutation, 83 years at diagnosis (22/8/96), male, GB=12.7,Hb(g/dl)=5.5, PLT=14, circulant blasts=78%, DIC yes, LDH (IU/L)=882, fibrinogen(mg/dl)=136,bcr3, variant M3 morphology, ATRA syndrome NO.
Keywords = APL
Keywords = FLT3
Keywords = ITD
Keywords = mutation
Lot batch = US22502667_251209729796


title: APL,case 9,3AF,MG

description:
APL patients with FLT3 TK mutation, 60 years at diagnosis (5/6/01), male, GB=2.8,Hb(g/dl)=6.5, PLT=21, circulant blasts=80%, DIC yes, LDH (IU/L)=621, fibrinogen(mg/dl)=139,bcr1, variant M3 morphology, ATRA syndrome NO.
Keywords = APL
Keywords = FLT3
Keywords = ITD
Keywords = mutation
Lot batch = US22502667_251209731595

source_name: FLT3, asp mutation, Cy5


title: APL,case 16,6IF,PL

description:
APL patient with FLT3 ITD mutation, 70 years at diagnosis (11/6/99), male, GB=21.2,Hb(g/dl)=7.9, PLT=17, circulant blasts=83%, DIC NO, LDH (IU/L)=415, fibrinogen(mg/dl)=344,bcr3, variant M3 morphology, ATRA syndrome NO.
Keywords = APL
Keywords = FLT3
Keywords = ITD
Keywords = mutation
Lot batch = US22502667_25120972980


title: APL,case 23,7IF,AM

description:
APL patient with FLT3 ITD mutation, 71 years at diagnosis (20/5/98), female, GB=10.1,Hb(g/dl)=7.4, PLT=8, circulant blasts=90%, DIC yes, LDH (IU/L)=1807, fibrinogen(mg/dl)=148,bcr3, variant M3 morphology, ATRA syndrome NO.
Keywords = APL
Keywords = FLT3
Keywords = ITD
Keywords = mutation
Lot batch = US22502667_251209731633


title: Male Striatum

city: Seattle

first: Di

middle: Kim

last: Nguyen

state: WA

address: 1959 NE Pacific St.

department: Pathology

institute: University of Washington

description: Studies of X-linked gene expression in male brain Tissues

data_processing: GCOS 1.3

label: Biotin

source_name: Male Striatum

tag: Male


title: Male Heart

description: Studies of X-linked gene expression in male somatic Tissues

source_name: Male Heart


title: APL,case 8,5IF,VA

description:
APL patient with FLT3 ITD mutation, 26 years at diagnosis (23/10/99), male, GB=18.4,Hb(g/dl)=12.7, PLT=17, circulant blasts=86%, DIC yes, LDH (IU/L)=1581, fibrinogen(mg/dl)=85,bcr3, variant M3 morphology, ATRA syndrome NO.
Keywords = APL
Keywords = FLT3
Keywords = ITD
Keywords = mutation
Lot batch = US22502667_251209729797


title: APL,case 13,3NF,FrC

description:
APL patient with FLT3 WILD TYPE, 72 years at diagnosis (23/04/01), male, GB=3.8, Hb(g/dl)=10.5, PLT=15, circulant blasts=61%, DIC NO, LDH (IU/L)=957, fibrinogen(mg/dl)=323,bcr2, classical M3 morphology, ATRA syndrome no.
Keywords = APL
Keywords = FLT3
Keywords = ITD
Keywords = mutation
Lot batch = US22502667_251209729799


title: Female Heart

description: Studies of X-linked gene expression in female somatic Tissues

source_name: Female Heart

tag: Female


title: H2A.Z Biological Replicate 2 vs input | array 11_127

source_name: H2A.Z ChIP, 10 ul Ab, IVT #655


title: H2A.Z Biological Replicate 2 vs input | array 11_155


title: H2A.Z Biological Replicate 2 vs input | array 11_156


title: H2A.Z Biological Replicate 1 vs input | array 11_130


title: Pax6 homozygous Hindbrain 2nd

city: Sendai

last: Arai

state: Miyagi

address: 2-1, Seiryo-machi, Aoba-ku,

department: Div. Devel. Neurosci

country: Japan

institute: Tohoku Univ. Sch. of Med

description:
E12.5 wild-type and Pax6 homozygous rat embryos were dissected from the uterus obtained from pregnant female rats under deep anesthesia.  To prepare RNA of distinct brain regions, the rostral part of wild-type and Pax6 homozygous rat embryos were first cut off at the upper forelimb level, and then subdivided into two parts including the forebrain (FB) and the hindbrain (HB), respectively, by cutting at the isthmus.  Thus, the FB tissue also included the eye and nose primordia and the midbrain, and the HB tissue included pharyngeal arches as well.  Total RNA was prepared using TRIzol Reagent (Invitrogen) according to the manufacture’s instructions.  mRNA was purified from 250µg of total RNA by OligotexTM-dT30 <Super> mRNA Purification Kit (Takara).  Approximately 2µg of mRNA was reverse-transcribed by Superscript II reverse transcriptase (Invitrogen) with T7- (dT)24 primer containing a T7 RNA polymerase promoter sequence.  Then, double strand DNA (dsDNA) was synthesized by SuperScriptTMChoice System (Invitrogen).  The following procedures including preparation of cRNA targets, hybridization, washing, staining, and scanning were performed as described in the Expression Analysis Technical Manual (Affymetrix, CA).  Briefly, biotin-labeled antisense cRNA were synthesized by in vitro transcription reaction with BioArrayTMHighYieldTMRNA Transcript Labeling Kit (ENZO Diagnostics).   The cRNA targets were size-fragmented to 35-200 bp in a buffer containing potassium and magnesium acetate at 94 °C for 35 minutes and were used for hybridization as cRNA targets.  The hybridization cocktail [containing 15 ug of target cRNA, control oligo BS (Affymetrix), and Eukaryotic Hybridization controls (Affymetrix)] was hybridized with a rat U34A array at 45 °C for 16 hours in GeneChip Hybridization Oven 640.  Washing and staining were performed after hybridization under the fluidics station protocol, EuGE-WS2, on GeneChip Fluidics Station 400.  Then, we scanned the array on HP GeneArrayTM scanner.  Experiments were repeated twice with independent mRNA preparation.  To quantify the expression level of a transcript, the average difference value (Adv) was calculated from the intensities against the probe set using the global methods of normalization by Microarray Suite ver. 4.0 (Affymetrix).
Keywords = Pax6 transcription factor
Keywords = wild-type rat embryos
Keywords = Pax6 homozygous mutant rat embryos
Keywords = forebrain
Keywords = hindbrain
Keywords = up-regulated genes
Keywords = down-regulated genes.

organism: Rattus norvegicus

source_name: E12.5 rat hindbrain region


title: Pax6 homozygous Hindbrain 1st


title: Wild-type Hindbrain 2nd


title: Wild-type Forebrain 2nd

source_name: E12.5 rat forebrain region


title: Female Whole Brain

description: Studies of X-linked gene expression in female brain Tissues

source_name: Female Whole Brain


title: Male Liver

source_name: Male Liver


title: Wild-type Hindbrain 1st


title: Male Whole Brain 2

description: Studies of X-linked gene expression in female brain

source_name: Whole Brain


title: APL,case 26,2AF,AL

description:
APL patients with FLT3 TK mutation, 64 years at diagnosis (26/2/98), female, GB=14,Hb(g/dl)=11.5, PLT=47, circulant blasts=74%, DIC yes, LDH (IU/L)=1777, fibrinogen(mg/dl)=95,bcr3, variant M3 morphology, ATRA syndrome YES.
Keywords = APL
Keywords = FLT3
Keywords = ITD
Keywords = mutation
Lot batch = US22502667_251209729788


title: APL,case 21,1IAF,MV

description:
APL patients with FLT3 TK mutation plus internal tandem duplication, 82 years at diagnosis (3/9/02), female, GB=12.3,Hb=10.4, PLT=15, circulant blasts=28%, DIC yes, LDH (IU/L)=711, fibrinogen(mg/dl)=387,bcr1, classical M3 morphology, ATRA syndrome yes
Keywords = APL
Keywords = FLT3
Keywords = ITD
Keywords = mutation
Lot batch = US22502667_251209729783

source_name: FLT3, asp mutation, ITD, Cy5


title: Female Spleen

source_name: Female Spleen


title: Pax6 homozygous Forebrain 1st


title: Female Occipital Cortex

source_name: Occipital Cortex


title: APL,case 10,6NF,RC

description:
APL patients with FLT3 WILD TYPE, 25 years at diagnosis (12/9/01), female, GB=2.8,Hb(g/dl)=10.6, PLT=23, circulant blasts=36%, DIC yes, LDH (IU/L)=594, fibrinogen(mg/dl)=83,bcr1, classical M3 morphology, ATRA syndrome no.
Keywords = APL
Keywords = FLT3
Keywords = ITD
Keywords = mutation
Lot batch = US22502667_251209729785

source_name: FLT3, WILD TYPE, Cy5

source_name: Universal Human reference Stratagene,Cy3


title: Normal control serum (Test-102)

status: Public on Oct 04 2005

type: protein

city: Ann Arbor

first: Xiaoju

last: Wang

state: MI

address: 1500 E. Medical Center Drive

institute: University of Michigan

description: Serum sample from normal control subject

molecule: protein

source_name: Human Serum IgG

source_name: T7 Phage Capsid Protein 10B


title: Normal control serum (Test-98)

source_name: Human serum IgG


title: Wild-type Forebrain 1st


title: Pax6 homozygous Forebrain 2nd


title: Gene expression profiling of MBC at 24 hours compared with MBN at 24 hour (B).

status: Public on Oct 05 2005

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

institute: University of Padova

description: Myoblasts were incubated with control (MBN) or CAPAN-1 pancreatic cancer conditioned media (MBC) for 0, 14 and 24 hours. RNAs purified from MBC at 14 and 24 hours were compared with RNA from MBN at 0 hour and at the corresponding stages. These samples were labeled and hybridized to muscle specific microarrays produced by our group (Human Array 2.0).

hyb_protocol: Microarray hybridisation was carried out in a dual slide chamber (HybChamber, Gene Machines, San Carlos, CA, USA) humidified with 100 µl of 3 x SSC. Labeled cDNA was dissolved in 40 µl of hybridisation buffer, denatured at 90°C for 2 min in a thermal cycler and applied directly to the slides. Microarrays were covered with 22 x 40 mm cover slip and hybridized overnight at 42°C by immersion in a high precision water bath (W28, Grant, Cambridge, UK). Post-hybridization washing was performed by serial incubations in buffers with decreasing SSC and SDS concentrations, at 42° C.

scan_protocol: Digital images were generated in a GSI Lumonics LITE dual confocal laser scanner (ScanArray Microarray Analysis Software) and processed with QuantArray Analysis Software (GSI Lumonics, Ottawa, Canada).

data_processing: The gene expression data analysis tool SNOMAD (http://pevsnerlab.kennedykrieger.org/snomadinput.html) was used for microarray data normalization and standardization. Log2 transformation was performed for each normalized expression value.

source_name: MBN24 (Reference)

label_protocol: Total RNA , 15 ug, was retro-transcribed and directly labeled in the presence of Cy5 modified dCTP.

extract_protocol: Total RNA from myoblasts was purified following the standard Trizol standard protocol. The RNA 6000 LabChip kit (Agilent Technologies) was used for RNA quantification and quality control in conjunction with an Agilent Bioanalyzer 2001.

tag: C2C12 cell line; Tissue

value: muscle; Morphology:Myoblast; Properties:differentiation, muscle proteins express, myogenesis; Growing medium:DMEM + 2mM Glutamine + 10% Fetal Bovine Serum (FBS).

source_name: MBC24 (Test)

label_protocol: Total RNA , 15 ug, was retro-transcribed and directly labeled in the presence of Cy3 modified dCTP.

tag: C2C12 cell incubated CAPAN-1 pancreatic cancer conditioned media for 24 hours.


title: Normal control serum (Test-95)


title: Normal control serum (Test-52)


title: Normal control serum (Test-101)


title: Normal control serum (Test-94)


title: Gene expression profiling of MBC at 24 hours compared with MBN at 24 hour (A).


title: Normal control serum (Test-100)


title: Normal control serum (Test-93)


title: Gene expression profiling of MBC at 14 hours compared with MBN at 0 hour (A).

source_name: MBN0 (Reference)

label_protocol: Total RNA, 15 ug, was retro-transcribed and directly labeled in the presence of Cy3 modified dCTP.

extract_protocol: Total RNA from C2C12 was purified following the standard Trizol standard protocol. The RNA 6000 LabChip kit (Agilent Technologies) was used for RNA quantification and quality control in conjunction with an Agilent Bioanalyzer 2001.

value: muscle; Morphology:Myoblast; Properties:differentiation, muscle proteins express, myogenesis; Growing medium:DMEM + 2mM Glutamine + 10% Fetal Bovine Serum (FBS)

source_name: MBC14 (Test)

label_protocol: Total RNA, 15 ug, was retro-transcribed and directly labeled in the presence of Cy5 modified dCTP.

extract_protocol: Total RNA from MBC14 myoblasts was purified following the standard Trizol standard protocol. The RNA 6000 LabChip kit (Agilent Technologies) was used for RNA quantification and quality control in conjunction with an Agilent Bioanalyzer 2001.

tag: C2C12 cell incubated CAPAN-1 pancreatic cancer conditioned media for 14 hours.


title: Gene expression profiling of MBC at 14 hours compared with MBN at 14 hour (B).

source_name: MBN14 (Reference)


title: Normal control serum (Test-103)


title: Gene expression profiling of MBC at 14 hours compared with MBN at 14 hour (A).


title: Gene expression profiling of MBC at 14 hours compared with MBN at 0 hour (B)


title: Normal control serum (Test-55)


title: Gene expression profiling of MBC at 24 hours compared with MBN at 0 hour (B).


title: Normal control serum (Test-51)


title: Normal control serum (Test-50)


title: Normal control serum (TestSet-88)


title: Normal control serum (Test-49)


title: Normal control serum (Test-89)


title: Normal control serum (Test-56)


title: Normal control serum (Test-87)


title: Normal control serum (Test-90)


title: Localized Prostate Cancer Serum (Test-10)

description: Serum sample from localized prostate cancer patient


title: Gene expression profiling of MBC at 24 hours compared with MBN at 0 hour (A).


title: Normal control serum (Test-92)


title: Normal control serum (Test-53)


title: Normal control serum (Test-54)


title: Localized Prostate Cancer Serum (Test-9)


title: Localized Prostate Cancer Serum (Test-8)


title: Localized Prostate Cancer Serum (Test-7)


title: Localized Prostate Cancer Serum (Test-3)


title: Localized Prostate Cancer Serum (Test-5)


title: Localized Prostate Cancer Serum (Test-2)


title: Localized Prostate Cancer Serum (Test-1)


title: Localized Prostate Cancer Serum (Test-4)


title: Localized Prostate Cancer Serum (Test-6)


title: Localized Prostate Cancer Serum (Test-128)


title: Localized Prostate Cancer Serum (Test-125)


title: Localized Prostate Cancer Serum (Test-127)


title: Localized Prostate Cancer Serum (Test-126)


title: Localized Prostate Cancer Serum (Test-120)


title: Localized Prostate Cancer Serum (Test-124)


title: Localized Prostate Cancer Serum (Test-122)


title: Localized Prostate Cancer Serum (TestSet-42)


title: Localized Prostate Cancer Serum (Test-121)


title: Lung Cancer Serum (AD149)

description: Serum sample from lung adenocarcinoma patient


title: Lung Cancer Serum (AD150)


title: Localized Prostate Cancer Serum (Test-119)


title: Localized Prostate Cancer Serum (Test-118)


title: Localized Prostate Cancer Serum (TestSet-48)


title: Localized Prostate Cancer Serum (Test-123)


title: Localized Prostate Cancer Serum (TestSet-47)


title: Lung Cancer Serum (AD147)


title: Lung Cancer Serum (AD152)


title: Lung Cancer Serum (AD148)


title: Lung Cancer Serum (AD155)


title: Localized Prostate Cancer Serum (TestSet-40)


title: Localized Prostate Cancer Serum (TestSet-41)


title: Lung Cancer Serum (AD145)


title: Localized Prostate Cancer Serum (Test-117)


title: Lung Cancer Serum (AD142)


title: Lung Cancer Serum (AD143)


title: Localized Prostate Cancer Serum (TestSet-45)


title: Localized Prostate Cancer Serum (TestSet-44)


title: Lung Cancer Serum (AD140)


title: Lung Cancer Serum (AD136)


title: Lung Cancer Serum (AD129)


title: Lung Cancer Serum (AD138)


title: Lung Cancer Serum (AD141)


title: Normal control serum (TestSet-112)


title: Normal control serum (TestSet-104)


title: Lung Cancer Serum (AD125)


title: Normal control serum (TestSet-108)


title: Lung Cancer Serum (AD130)


title: Normal control serum (TestSet-109)


title: Normal control serum (TestSet-110)


title: Lung Cancer Serum (AD124)


title: Normal control serum (TestSet-105)


title: Lung Cancer Serum (AD127)


title: Normal control serum (Test-111)


title: Normal control serum (TestSet-106)


title: Lung Cancer Serum (AD120)


title: Normal control serum (TestSet-107)


title: Lung Cancer Serum (AD122)


title: Normal control serum (TestSet-114)


title: Normal control serum (TestSet-115)


title: Normal control serum (TestSet-113)


title: Normal control serum (TestSet-116)


title: Localized Prostate Cancer Serum (Test-43)


title: Lung Cancer Serum (AD114)


title: Lung Cancer Serum (AD111)


title: Localized Prostate Cancer Serum (Test-46)


title: Lung Cancer Serum (AD104)


title: Lung Cancer Serum (AD109)


title: Lung Cancer Serum (AD89)


title: Lung Cancer Serum (AD31)


title: Post-prostatectomy cancer serum (pt13)

description: Serum sample from post-prostatectomy prostate cancer patient


title: Hormone-refractory prostate cancer serum (P11)

description: Serum sample from hormone-refractory (HR) prostate cancer patient


title: Lung Cancer Serum (AD32)


title: Post-prostatectomy cancer serum (pt11)


title: Hormone-refractory prostate cancer serum (P10)


title: Post-prostatectomy cancer serum (pt14)


title: Lung Cancer Serum (AD108)


title: Post-prostatectomy cancer serum (pt12)


title: Lung Cancer Serum (AD10)


title: Post-prostatectomy cancer serum (pt10)


title: Lung Cancer Serum (AD7)


title: Hormone-refractory prostate cancer serum (P9)


title: Hormone-refractory prostate cancer serum (P5)


title: Hormone-refractory prostate cancer serum (P6)


title: Post-prostatectomy cancer serum (pt9)


title: Post-prostatectomy cancer serum (pt8)


title: Hormone-refractory prostate cancer serum (P8)


title: Hormone-refractory prostate cancer serum (P7)


title: Hormone-refractory prostate cancer serum (P3)


title: Post-prostatectomy cancer serum (pt6)


title: Post-prostatectomy cancer serum (pt7)


title: Hormone-refractory prostate cancer serum (P4)


title: Post-prostatectomy cancer serum (pt5)


title: Hormone-refractory prostate cancer serum (P2)


title: Post-prostatectomy cancer serum (pt4)


title: Post-prostatectomy cancer serum (pt3)


title: Post-prostatectomy cancer serum (pt2)


title: Post-prostatectomy cancer serum (pt1)


title: Normal control serum (Test-75)


title: Normal control serum (Test-82)


title: Hormone-refractory prostate cancer serum (P1)


title: SpoID_8_d0_1

city: Tuebingen

first: Janko

last: Dietzsch

address: Sand 14

department: ZBIT (Center for Bioinformatics Tuebingen)

country: Germany

institute: University Tuebingen

description: time point 1 vs. time point 0 of SpoID_8 after normalization (Loess-correction, averaging over all sub-arrays, dye-swap correction)

source_name: peripheral blood time point 0

source_name: peripheral blood time point 1


title: Normal control serum (Test-69)


title: Normal control serum (Test-68)


title: SpoID_5_d0_1

description: time point 1 vs. time point 0 of SpoID_5 after normalization (Loess-correction, averaging over all sub-arrays, dye-swap correction)


title: SpoID_7_d0_1

description: time point 1 vs. time point 0 of SpoID_7 after normalization (Loess-correction, averaging over all sub-arrays, dye-swap correction)


title: SpoID_2_d0_1

description: time point 1 vs. time point 0 of SpoID_2 after normalization (Loess-correction, averaging over all sub-arrays, dye-swap correction)


title: Normal control serum (Test-62)


title: Normal control serum (Test-70)


title: SpoID_4_d0_1

description: time point 1 vs. time point 0 of SpoID_4 after normalization (Loess-correction, averaging over all sub-arrays, dye-swap correction)


title: Normal control serum (Test-66)


title: Normal control serum (Test-64)


title: Normal control serum (Test-72)


title: Normal control serum (Test-61)

description: Serum sample from normal control set


title: SpoID_3_d0_1

description: time point 1 vs. time point 0 of SpoID_3 after normalization (Loess-correction, averaging over all sub-arrays, dye-swap correction)


title: Normal control serum (Test-97)


title: Normal control serum (Test-91)


title: Normal control serum (Test-78)


title: Normal control serum (Test-85)


title: SpoID_1_d0_1

description:
time point 1 vs. time point 0 of SpoID_1
after normalization (Loess-correction, averaging over all sub-arrays, dye-swap correction)


title: SpoID_6_d0_1

description: time point 1 vs. time point 0 of SpoID_6 after normalization (Loess-correction, averaging over all sub-arrays, dye-swap correction)


title: Normal control serum (Test-99)


title: Normal control serum (Test-58)


title: Normal control serum (Test-83)


title: Kidney_8weeks_on_High_Salt+Fat_Diet_replicate5

city: Collegeville

first: Shawn

last: O'Brien

state: PA

address: 1250 Collegeville Rd

institute: GSK

description: SHR-SP Rat Kidney

source_name: Kidney

extract_protocol: Whole kidneys were pulverized on dry ice, approx 100mg tissue was further homogenized in a mixer mill with steel bead in 1ml Trizol reagent. Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: SHR-SP strain


title: Normal control serum (Test-81)


title: Normal control serum (Test-79)


title: Normal control serum (Test-84)


title: Normal control serum (Test-74)


title: Kidney_8weeks_on_High_Salt+Fat_Diet_replicate6

description: SHR-SP Rat Kidney


title: Normal control serum (Test-76)


title: Normal control serum (Test-73)


title: Normal control serum (Test-77)


title: Kidney_8weeks_on_High_Salt+Fat_Diet_replicate4

description: SHR-SP Rat Kidney


title: Normal control serum (Test-65)


title: Normal control serum (Test-71)


title: Normal control serum (Test-67)


title: Normal control serum (Test-60)


title: Normal control serum (Test-63)


title: Kidney_8weeks_on_High_Salt+Fat_Diet_replicate3

description: SHR-SP Rat Kidney


title: Kidney_8weeks_on_Normal Diet_replicate5

description: SHR-SP Rat Kidney


title: Kidney_8weeks_on_High_Salt+Fat_Diet_replicate1

description: SHR-SP Rat Kidney


title: Kidney_8weeks_on_High_Salt+Fat_Diet_replicate2

description: SHR-SP Rat Kidney


title: Normal control serum (Test-59)


title: Kidney_8weeks_on_Normal Diet_replicate6

description: SHR-SP Rat Kidney


title: Normal control serum (Test-86)


title: Localized Prostate Cancer Serum (Test-38)


title: Kidney_8weeks_on_Normal Diet_replicate4

description: SHR-SP Rat Kidney


title: Localized Prostate Cancer Serum (Test-33)


title: Localized Prostate Cancer Serum (Test-37)


title: Localized Prostate Cancer Serum (Test-36)


title: Kidney_8weeks_on_Normal Diet_replicate3

description: SHR-SP Rat Kidney


title: Normal control serum (Test-96)


title: Kidney_2weeks_on_High_Salt+Fat_Diet_replicate3

description: SHR-SP Rat Kidney


title: Kidney_2weeks_on_High_Salt+Fat_Diet_replicate6

description: SHR-SP Rat Kidney


title: Kidney_8weeks_on_Normal Diet_replicate2

description: SHR-SP Rat Kidney


title: Kidney_8weeks_on_Normal Diet_replicate1

description: SHR-SP Rat Kidney


title: Localized Prostate Cancer Serum (Test-32)


title: Normal control serum (Test-57)


title: Localized Prostate Cancer Serum (Test-30)


title: Localized Prostate Cancer Serum (Test-31)


title: Localized Prostate Cancer Serum (Test-28)


title: Localized Prostate Cancer Serum (Test-25)


title: Localized Prostate Cancer Serum (Test-23)


title: Kidney_2weeks_on_High_Salt+Fat_Diet_replicate5

description: SHR-SP Rat Kidney


title: Localized Prostate Cancer Serum (Test-19)


title: Localized Prostate Cancer Serum (Test-24)


title: Localized Prostate Cancer Serum (Test-20)


title: Localized Prostate Cancer Serum (Test-29)


title: Kidney_2weeks_on_High_Salt+Fat_Diet_replicate4

description: SHR-SP Rat Kidney


title: Localized Prostate Cancer Serum (Test-27)


title: Kidney_2weeks_on_High_Salt+Fat_Diet_replicate2

description: SHR-SP Rat Kidney


title: Normal control serum (Test-80)


title: Localized Prostate Cancer Serum (Test-21)


title: Localized Prostate Cancer Serum (Test-17)


title: Localized Prostate Cancer Serum (Test-35)


title: Localized Prostate Cancer Serum (Test-16)


title: Kidney_2weeks_on_Normal Diet_replicate5

description: SHR-SP Rat Kidney


title: Kidney_2weeks_on_Normal Diet_replicate6

description: SHR-SP Rat Kidney


title: Localized Prostate Cancer Serum (Test-18)


title: Localized Prostate Cancer Serum (Test-34)


title: Localized Prostate Cancer Serum (Test-14)


title: Localized Prostate Cancer Serum (Test-13)


title: Localized Prostate Cancer Serum (Test-39)


title: Localized Prostate Cancer Serum (Test-22)


title: Localized Prostate Cancer Serum (Test-12)


title: Kidney_2weeks_on_High_Salt+Fat_Diet_replicate1

description: SHR-SP Rat Kidney


title: Localized Prostate Cancer Serum (Test-11)


title: Localized Prostate Cancer Serum (Test-15)


title: Localized Prostate Cancer Serum (Test-26)


title: Normal control serum (TraingSet_202)


title: Kidney_2weeks_on_Normal Diet_replicate2

description: SHR-SP Rat Kidney


title: Normal control serum (TraingSet_176)


title: Kidney_2weeks_on_Normal Diet_replicate3

description: SHR-SP Rat Kidney


title: Kidney_2weeks_on_Normal Diet_replicate1

description: SHR-SP Rat Kidney


title: Control Proximal, Small Intestine 3 21 days old

city: Vers-chez-les-Blancs

first: Alexandra

last: Schumann

address: PO box 44

department: Nutrition and Health

country: Switzerland

institute: Nestle Research Center

description:
Whole tissues corresponding to the proximal and distal small intestine and to the colon were dissected from each rat, washed with ice-cold saline solution and immediately frozen in liquid nitrogen. Rats were either control or treated with Amoxicillin (100mg/kg/day). Small intestine was divided in two identical length considered as the proximal and distal part. In each intestinal part 1 cm of tissue was taken in the middle of this part to perform the RNA extraction and then the GeneArray analysis.
Keywords = gastrointestinal tract, microarray, antibiotic, suckling rats, amoxicillin

source_name: Proximal, Small Intestine 21 days old


title: Normal control serum (TrainSet_209)


title: Normal control serum (TraingSet_201)


title: Normal control serum (TrainSet_227)


title: Control Proximal, Small Intestine 3 17 days old

source_name: Proximal, Small Intestine 17 days old


title: Control Proximal, Small Intestine 2 21 days old


title: Normal control serum (TrainSet_172)


title: Normal control serum (TrainSet_226)


title: Normal control serum (TrainSet_206)


title: Control Proximal, Small Intestine 2 17 days old


title: Normal control serum (TraingSet_183)


title: Normal control serum (TrainSet_228)


title: Normal control serum (TraingSet_188)


title: Normal control serum (TraingSet_180)


title: Control Proximal, Small Intestine 1 17 days old


title: Control Proximal, Small Intestine 1 21 days old


title: Kidney_2weeks_on_Normal Diet_replicate4

description: SHR-SP Rat Kidney


title: Control Distal, Small Intestine 3 21 days old

source_name: Distal, Small Intestine 21 days old


title: Normal control serum (TraingSet_185)


title: Normal control serum (TrainSet_186)


title: Normal control serum (TrainSet_205)


title: Normal control serum (TraingSet_211)


title: Normal control serum (TrainSet_216)


title: Normal control serum (TraingSet_222)


title: Control Distal, Small Intestine 3 17 days old

source_name: Distal, Small Intestine 17 days old


title: Normal control serum (TrainSet_220)


title: Normal control serum (TrainSet_204)


title: Control Distal, Small Intestine 2 17 days old


title: Control Distal, Small Intestine 1 21 days old


title: Normal control serum (TrainSet_224)


title: Control Distal, Small Intestine 2 21 days old


title: Normal control serum (TraingSet_171)


title: Normal control serum (TrainSet_218)


title: Localized Prostate Cancer Serum (TrainSet_136)


title: Localized Prostate Cancer Serum (TrainSet_135)


title: Localized Prostate Cancer Serum (TrainSet_198)


title: Localized Prostate Cancer Serum (TrainSet_106)


title: Control Distal, Small Intestine 1 17 days old


title: Normal control serum (TraingSet_110)


title: Normal control serum (TraingSet_229)


title: Localized Prostate Cancer Serum (TrainSet_157)


title: Control Colon 2 21 days old

source_name: Colon 21 days old


title: Localized Prostate Cancer Serum (TrainSet_133)


title: Normal control serum (TraingSet_213)


title: Normal control serum (TraingSet_101)


title: Normal control serum (TraingSet_221)


title: Normal control serum (TraingSet_217)


title: Normal control serum (TraingSet_212)


title: Control Colon 1 17 days old

source_name: Colon 17 days old


title: Control Colon 1 21 days old


title: Amoxicillin treated Proximal, Small Intestine 3 17 days old


title: Amoxicillin treated Proximal, Small Intestine 2 21 days old


title: Normal control serum (TraingSet_210)


title: Localized Prostate Cancer Serum (TrainSet_143)

source_name: Human Serum IgG


title: Localized Prostate Cancer Serum (TrainSet_140)

source_name: T7 Phage Capsid Protein 10B


title: Normal control serum (TraingSet_173)

source_name: Human serum IgG


title: Localized Prostate Cancer Serum (TrainSet_159)


title: Localized Prostate Cancer Serum (TrainSet_131)


title: Normal control serum (TraingSet_102)


title: Normal control serum (TraingSet_177)


title: Localized Prostate Cancer Serum (TrainSet_156)


title: Localized Prostate Cancer Serum (TrainSet_196)


title: Localized Prostate Cancer Serum (TrainSet_162)


title: Normal control serum (TraingSet_105)


title: Localized Prostate Cancer Serum (TrainSet_193)


title: Localized Prostate Cancer Serum (TrainSet_160)


title: Normal control serum (TraingSet_169)


title: Amoxicillin treated Proximal, Small Intestine 1 21 days old


title: Control Colon 2 17 days old


title: Localized Prostate Cancer Serum (TrainSet_161)


title: Amoxicillin treated Distal, Small Intestine 3 21 days old


title: Amoxicillin treated Proximal, Small Intestine 2 17 days old


title: Amoxicillin treated Distal, Small Intestine 3 17 days old


title: Normal control serum (TraingSet_225)


title: Localized Prostate Cancer Serum (TrainSet_122)


title: Amoxicillin treated Proximal, Small Intestine 1 17 days old


title: Control Colon 3 21 days old


title: Localized Prostate Cancer Serum (TrainSet_130)


title: Normal control serum (TraingSet_103)


title: Localized Prostate Cancer Serum (TrainSet_119)


title: Normal control serum (TraingSet_170)


title: Amoxicillin treated Distal, Small Intestine 2 21 days old


title: Normal control serum (TraingSet_181)


title: Amoxicillin treated Distal, Small Intestine 1 21 days old


title: Amoxicillin treated Distal, Small Intestine 2 17 days old


title: Localized Prostate Cancer Serum (TrainSet_146)


title: Amoxicillin treated Distal, Small Intestine 1 17 days old


title: Amoxicillin treated Colon 3 17 days old


title: Localized Prostate Cancer Serum (TrainSet_163)


title: Normal control serum (TraingSet_207)


title: Localized Prostate Cancer Serum (TrainSet_191)


title: NF54-limb-14h-1

city: Baltimore

first: Minoru

last: Ko

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

hyb_protocol: Agilent 60-mer oligo microarray processing protocol (SSC Wash/SureHyb Chamber set-up) V4.1, April 2004.  Agilent Publication Number:  G4140-90030 V4.1 APRIL 2004.   The manual can be found at  https://www.chem.agilent.com/scripts/literaturePDF.asp?iWHID=34961,  or through a WEB search on the manual title.

data_processing: Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.

organism: Xenopus laevis

label_protocol: Agilent Low RNA Input Fluorescent Linear Amplification Protocol

extract_protocol: standard method using TRIZOL reagent

treatment_protocol: Xenopus tadpoles (NF54) were treated with 1 mM methimazole in 0.1 X MMR solution for 1 week to block the endogenous TH production and reduce the TH present in the system of the tadpole. They were then treated with 100 nM T3 in 1 mM methimazole and 0.1 x MMR for another 14h.

tag: N/A  unknown sex NF Stage 54 (premetamorphic)

organism: unidentified

source_name: Universal RNA

extract_protocol: mRNAs were extracted with QuickPrep Micro mRNA Purification Kit from Amersham

tag: Universal RNA


title: Normal control serum (TraingSet_165)


title: NF54-limb-untreated-3

treatment_protocol: Xenopus tadpoles (NF54) were treated with 1 mM methimazole in 0.1 X MMR solution for 1 week to block the endogenous TH production and reduce the TH present in the system of the tadpole. They were then treated with fresh 1 mM methimazole in 0.1 x MMR for another 48h.


title: Amoxicillin treated Colon 2 21 days old


title: Localized Prostate Cancer Serum (TrainSet_125)


title: Localized Prostate Cancer Serum (TrainSet_199)


title: Normal control serum (TraingSet_167)


title: Amoxicillin treated Colon 1 21 days old


title: NF54-limb-untreated-2


title: Amoxicillin treated Colon 2 17 days old


title: Localized Prostate Cancer Serum (TrainSet_150)


title: Amoxicillin treated Colon 1 17 days old


title: Amoxicillin treated Colon 3 21 days old


title: Normal control serum (TraingSet_166)


title: NF54-limb-48h-3

treatment_protocol: Xenopus tadpoles (NF54) were treated with 1 mM methimazole in 0.1 X MMR solution for 1 week to block the endogenous TH production and reduce the TH present in the system of the tadpole. They were then treated with 100 nM T3 in 1 mM methimazole and 0.1 x MMR for another 48h.


title: Amoxicillin treated Proximal, Small Intestine 3 21 days old


title: Localized Prostate Cancer Serum (TrainSet_223)


title: NF54-brain-24h-2

treatment_protocol: Xenopus tadpoles (NF54) were treated with 1 mM methimazole in 0.1 X MMR solution for 1 week to block the endogenous TH production and reduce the TH present in the system of the tadpole. They were then treated with 100 nM T3 in 1 mM methimazole and 0.1 x MMR for another 24h.


title: NF54-brain-48h-3


title: Normal control serum (TraingSet_107)


title: Normal control serum (TraingSet_113)


title: Localized Prostate Cancer Serum (TrainSet_144)


title: Localized Prostate Cancer Serum (TrainSet_128)


title: Normal control serum (TraingSet_112)


title: NF54-limb-48h-2


title: Localized Prostate Cancer Serum (TrainSet_141)


title: Localized Prostate Cancer Serum (TrainSet_194)


title: Localized Prostate Cancer Serum (TrainSet_124)


title: Localized Prostate Cancer Serum (TrainSet_151)


title: Localized Prostate Cancer Serum (TrainSet_126)


title: NF54-brain-48h-2


title: Normal control serum (TraingSet_109)


title: Localized Prostate Cancer Serum (TrainSet_137)


title: NF54-brain-untreated-3


title: NF54-brain-24h-1


title: Localized Prostate Cancer Serum (TrainSet_138)


title: NF54-brain-24h-3


title: Localized Prostate Cancer Serum (TrainSet_120)


title: NF54-brain-untreated-2


title: Localized Prostate Cancer Serum (TrainSet_129)


title: NF54-brain-untreated-1


title: NF54-brain-48h-1


title: NF54-Tail-48h-3

treatment_protocol: Xenopus tadpole (NF54) were treated with 100 nM T3 for 48h in 0.1 X MMR solution.

tag: unknown sex NF Stage 54 (premetamorphic)


title: NF54-limb-untreated-1


title: Normal control serum (TraingSet_174)


title: Localized Prostate Cancer Serum (TrainSet_152)


title: Normal control serum (TraingSet_184)


title: Localized Prostate Cancer Serum (TrainSet_195)


title: NF54-Tail-24h-2

treatment_protocol: Xenopus tadpole (NF54) were treated with 100 nM T3 for 24h in 0.1 X MMR solution.


title: NF54-Tail-48h-1


title: Localized Prostate Cancer Serum (TrainSet_200)


title: Normal control serum (TraingSet_214)


title: Normal control serum (TraingSet_164)


title: NF54-Tail-24h-1


title: Normal control serum (TraingSet_108)


title: NF62-Tail-1

treatment_protocol: Xenopus tadpoles (NF61) were in 0.1 X MMR solution till they reached NF62 stage (about 48h).

tag: unknown sex NF Stage 62 (metamorphic climax)


title: NF54-Tail-untreated-3

treatment_protocol: Xenopus tadpole (NF54) were in 0.1 X MMR solution for 48 hours


title: NF54-Tail-48h-2


title: Localized Prostate Cancer Serum (TrainSet_145)


title: NF54-Tail-untreated-2


title: Localized Prostate Cancer Serum (TrainSet_192)


title: Normal control serum (TraingSet_219)


title: Localized Prostate Cancer Serum (TrainSet_142)


title: Localized Prostate Cancer Serum (TrainSet_149)


title: Normal control serum (TraingSet_189)


title: Localized Prostate Cancer Serum (TrainSet_197)


title: Normal control serum (TraingSet_117)


title: Localized Prostate Cancer Serum (TrainSet_123)


title: Localized Prostate Cancer Serum (TrainSet_153)


title: Normal control serum (TraingSet_179)


title: Normal control serum (TraingSet_114)


title: Localized Prostate Cancer Serum (TrainSet_158)


title: Normal control serum (TraingSet_203)


title: Brain_cumulus_clone_2

city: Tokyo

first: Takashi

last: Kohda

address: 1-5-45 Yushima, Bunko-ku

department: Medical Research Institute

institute: Tokyo Medical and Dental University

description: Neonatal brain from cumulus clone mouse.

data_processing: Intensity is normalized to the mean raw intensity value

source_name: Neonatal brain from cumulus clone sample 2.

value: C57BL/6 x DBA/2.

tag: Gender

value: female

value: neonate

value: brain


title: Normal control serum (TraingSet_190)


title: Localized Prostate Cancer Serum (TrainSet_121)


title: Normal control serum (TraingSet_115)


title: Localized Prostate Cancer Serum (TrainSet_134)


title: Localized Prostate Cancer Serum (TrainSet_104)


title: Normal control serum (TraingSet_208)


title: Localized Prostate Cancer Serum (TrainSet_132)


title: Localized Prostate Cancer Serum (TrainSet_155)


title: Localized Prostate Cancer Serum (TrainSet_118)


title: Normal control serum (TraingSet_187)


title: Localized Prostate Cancer Serum (TrainSet_148)


title: Localized Prostate Cancer Serum (TrainSet_127)


title: Normal control serum (TraingSet_182)


title: Brain_cumulus_clone_4

source_name: Neonatal brain from cumulus clone sample 4.


title: Normal control serum (TraingSet_111)


title: Localized Prostate Cancer Serum (TrainSet_147)


title: Normal control serum (TraingSet_168)


title: Normal control serum (TraingSet_178)


title: Localized Prostate Cancer Serum (TrainSet_154)


title: Normal control serum (TrainSet_215)


title: Normal control serum (TraingSet_175)


title: Normal control serum (TraingSet_116)


title: Localized Prostate Cancer Serum (TrainSet_139)


title: Localized Prostate Cancer Serum 20 (PCA-120)