title: 48_47.3B080905Slide92(normalized)

status: Public on May 31 2011

type: RNA

city: Vicksburg

first: Mitchell

last: Wilbanks

state: MS

address: 3909 Halls Ferry Road

department: Environmental Laboratory

country: USA

institute: US Army Engineer Research and Development Center

description: raw data file: 48_47.3vsCon1B080905Slide92.txt

hyb_protocol: cDNA from 1mg total RNA was synthesized, hybridized to arrays, and detected by secondary hybridization to Alex647 and Cy3 dendrimer oligonucleotides using an Array900 detection kit per manufacturers instruction. cDNA was hybridized to 8k Sigma/Compugen rat 70-mer oligonucleotide libraries arrayed on glass slides.

scan_protocol: After secondary hybridization, slides were scanned using a 5 micron ChipReader microarray reader (BioRad, Hercules).  Spots were identified and quantified using VersArray software (BioRad).

data_processing: Raw intensity data obtained from image analysis program GenePix was imported into R package “limma” and loess normalization was applied for each group.  Note: For each two color loop designed hybridization, each channel was separated, normalized and analyzed as single color data. Each time point was tested for significant differentially expressed (DE) genes by running 1-way ANOVA, followed by multiple pair-wise comparison between the control and the 4 dose treatments.

molecule: total RNA

organism: Rattus norvegicus

source_name: brain tissue

label_protocol: Total RNA from three out of five randomly selected biological replicates at each dose was compared using the two-color interwoven loop design microarray experiment [9]. cDNA from 1mg total RNA was synthesized, hybridized to arrays, and detected by secondary hybridization to Alex647 (reference) and Cy3 dendrimer oligonucleotides using an Array900 detection kit per manufacturer’s instruction. cDNA was hybridized to 8k Sigma/Compugen rat 70-mer oligonucleotide libraries arrayed on glass slides [http://www.cag.icph.or/].

growth_protocol: Female Sprague-Dawley rats (175-225 grams) were from the in-house breeding colony (College of Pharmacy, University of Louisiana at Monroe [ULM] and treated in accordance with the Guide for Use and Care of Animals.  Breeders were from Harlan-Sprague Dawley in Madison, WI.  Housing consisted of a 12 h light/dark cycle with ad libitum access to tap water and rodent chow (Harlan/Teklad 7012, Madison, WI).  Rats were housed individually in polycarbonate cages on hardwood bedding (Sani-chips, Harlan/Tekland, Madison, WI) one week prior to treatment.   Study protocols were preapproved by the ULM Animal Care and Use Committee.

extract_protocol: RNA was prepared using the RNeasy mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Food was withdrawn the night before treatments, which were administered by gavage between 8 and 10 AM.Groups of rats were weighed and randomly assigned to treatment (0,1.2, 12, 24, or 47 mg RDX/kg body weight. Rats were observed continuously for the first hour after dosing, hourly for 8 h and daily thereafter.  Moribund rats were euthanized with CO2.

tag: strain

value: Sprague-Dawley

tag: gender

value: female

tag: agent

value: RDX

tag: agent dose (mg rdx/kg body weight)

tag: time

value: 48 hr

tag: tissue

value: brain


title: 90_1.2-2B040606_Slide48(normalized)

description: raw data file: Con1vs1.2-2B040606_Slide48.txt

scan_protocol: An Axon GenePix® 4000B Microarray Scanner (Molecular Devices Inc.) was used to scan microarray images at 5 μm resolution.  Grids were manually fit to microarray spots using GenePix Software (Molecular Devices).  Data for which the spot intensity was less than the background intensity plus 2x the background standard deviation for ≥1 signal channel were excluded from analysis.

value: 90 days


title: 90_47-3B040606_Slide47(normalized)

description: raw data file: 47-3vsCon-1B040606_Slide47.txt


title: 90_1.2-3B040606_Slide43(normalized)

description: raw data file: Con-3vs1.2-3B040606_Slide43.txt


title: 90_Con-1B040606_Slide33(normalized)

description: raw data file: Con1vs1.2-1B040606_Slide33.txt

value: control


title: 90_1.2-2B040606_Slide38(normalized)

description: raw data file: Con-2vs1.2-2B040606_Slide38.txt


title: 90_47-3B040606_Slide57(normalized)

description: raw data file: 47-3vsCon-2B040606_Slide57.txt


title: 90_1.2-1B040606_Slide58(normalized)

description: raw data file: Con-3vs1.2-1B040606_Slide58.txt


title: 90_Con-3B040606_Slide43(normalized)


title: 90_Con-1B040606_Slide48(normalized)


title: 90_Con-1B040606_Slide47(normalized)


title: 90_47-2B040606_Slide42(normalized)

description: raw data file: 47-2vsCon-3B040606_Slide42.txt


title: 90_Con-3B040606_Slide42(normalized)


title: 90_Con-2B040606_Slide57(normalized)


title: 90_47-3B040606_Slide46(normalized)

description: raw data file: 24-3vs47-3B040606_Slide46.txt


title: 90_Con-1B040606_Slide52(normalized)

description: raw data file: 47-2vsCon-1B040606_Slide52.txt


title: 90_Con-2B040606_Slide38(normalized)


title: 90_Con-2B040606_Slide53(normalized)

description: raw data file: Con-2vs1.2-3B040606_Slide53.txt


title: 90_47-2B040606_Slide52(normalized)


title: 90_1.2-1B040606_Slide33(normalized)


title: 90_47-1B040606_Slide62(normalized)

description: raw data file: 47-1vsCon-3B040606_Slide62.txt


title: 90_Con-3B040606_Slide62(normalized)


title: 48_Con1B080905Slide92(normalized)


title: 90_Con-2B040606_Slide37(normalized)

description: raw data file: 47-1vsCon-2B040606_Slide37.txt


title: 90_47-1B040606_Slide37(normalized)


title: 90_1.2-3B040606_Slide53(normalized)


title: 90_Con-3B040606_Slide58(normalized)


title: 90_24-3B040606_Slide61(normalized)

description: raw data file: 24-3vs47-1B040606_Slide61.txt


title: 90_24-3B040606_Slide46(normalized)


title: 90_47-1B040606_Slide61(normalized)


title: 90_47-3B040606_Slide56(normalized)

description: raw data file: 24-2vs47-3B040606_Slide56.txt


title: 90_12-3B040606_Slide45(normalized)

description: raw data file: 12-3vs24-3B040606_Slide45.txt


title: 90_24-1B040606_Slide50(normalized)

description: raw data file: 12-3vs24-1B040606_Slide50.txt


title: 90_12-3B040606_Slide50(normalized)


title: 90_24-2B040606_Slide40(normalized)

description: raw data file: 12-2vs24-2B040606_Slide40.txt


title: 90_12-2B040606_Slide60(normalized)

description: raw data file: 12-2vs24-3B040606_Slide60.txt


title: 90_24-2B040606_Slide56(normalized)


title: 90_47-1B040606_Slide36(normalized)

description: raw data file: 24-1vs47-1B040606_Slide36.txt


title: 90_24-1B040606_Slide36(normalized)


title: 90_24-3B040606_Slide45(normalized)


title: 90_24-3B040606_Slide60(normalized)


title: 90_12-1B040606_Slide35(normalized)

description: raw data file: 12-1vs24-1B040606_Slide35.txt


title: 90_24-1B040606_Slide51(normalized)

description: raw data file: 24-1vs47-2B040606_Slide51.txt


title: 90_12-3B040606_Slide44(normalized)

description: raw data file: 1.2-3vs12-3B040606_Slide44.txt


title: 90_47-2B040606_Slide41(normalized)

description: raw data file: 24-2vs47-2B040606_Slide41.txt


title: 90_24-2B040606_Slide55(normalized)

description: raw data file: 12-1vs24-2B040606_Slide55.txt


title: 90_12-1B040606_Slide55(normalized)


title: 90_24-1B040606_Slide35(normalized)


title: 90_1.2-3B040606_Slide54(normalized)

description: raw data file: 1.2-3vs12-1B040606_Slide54.txt


title: 90_47-2B040606_Slide51(normalized)


title: 90_12-1B040606_Slide54(normalized)


title: 90_1.2-3B040606_Slide44(normalized)


title: 90_12-2B040606_Slide40(normalized)


title: 90_12-3B040606_Slide49(normalized)

description: raw data file: 1.2-2vs12-3B040606_Slide49.txt


title: 90_24-2B040606_Slide41(normalized)


title: 90_1.2-2B040606_Slide49(normalized)


title: 90_12-2B040606_Slide39(normalized)

description: raw data file: 1.2-2vs12-2B040606_Slide39.txt


title: 90_12-2B040606_Slide59(normalized)

description: raw data file: 1.2-1vs12-2B040606_Slide59.txt


title: 90_1.2-2B040606_Slide39(normalized)


title: 90_1.2-1B040606_Slide59(normalized)


title: 90_12-1B040606_Slide34(normalized)

description: raw data file: 1.2-1vs12-1B040606_Slide34.txt


title: 90_1.2-1B040606_Slide34(normalized)


title: 28_1.2-3B100605_Slide87(normalized)

description: raw data file: Con-2vs1.2-3B100605_Slide87.txt

value: 28 days


title: 28_47-2B100605_Slide58(normalized)

description: raw data file: 47-2vsCon3B100605_Slide58.txt


title: 28_47-1B100605_Slide78(normalized)

description: raw data file: 47-1vsCon-3B100605_Slide78.txt


title: 28_1.2-3B100605_Slide57(normalized)

description: raw data file: Con-3vs1.2-3B100605_Slide57.txt


title: 28_Con-3B100605_Slide58(normalized)


title: 28_Con-3B100605_Slide82(normalized)

description: raw data file: Con-3vs1.2-1B100605_Slide82.txt


title: 28_1.2-1B100605_Slide82(normalized)


title: 28_Con-2B100605_Slide87(normalized)


title: 28_Con-1B100605_Slide88(normalized)

description: raw data file: 47-2vsCon-1B100605_Slide88.txt


title: 28_Con-2B100605_Slide54(normalized)

description: raw data file: Con-2vs1.2-2B100605_Slide54.txt


title: 28_24-3B100605_Slide62(normalized)

description: raw data file: 24-3vs47-3B100605_Slide62.txt


title: 28_47-3B100605_Slide62(normalized)


title: 28_47-2B100605_Slide88(normalized)


title: 28_47-1B100605_Slide79(normalized)

description: raw data file: 24-3vs47-1B100605_Slide79.txt


title: 28_1.2-2B100605_Slide54(normalized)


title: 28_1.2-2B100605_Slide64(normalized)

description: raw data file: Con-1vs1.2-2B100605_Slide64.txt


title: 28_Con-1B100605_Slide64(normalized)


title: 28_1.2-1B100605_Slide47(normalized)

description: raw data file: Con-1vs1.2-1B100605_Slide47.txt


title: 28_Con-2B100605_Slide83(normalized)

description: raw data file: 47-3vsCon-2B100605_Slide83.txt


title: 28_47-3B100605_Slide61(normalized)

description: raw data file: 47-3vsCon-1B100605_Slide61.txt


title: 28_Con-1B100605_Slide47(normalized)


title: 28_Con-1B100605_Slide61(normalized)


title: 28_47-3B100605_Slide83(normalized)


title: 28_47-3B100605_Slide84(normalized)

description: raw data file: 24-2vs47-3B100605_Slide84.txt


title: 28_Con-2B100605_Slide51(normalized)

description: raw data file: 47-1vsCon-2B100605_Slide51.txt


title: 28_47-1B100605_Slide51(normalized)


title: 28_24-3B100605_Slide79(normalized)


title: 28_Con-3B100605_Slide78(normalized)


title: 28_Con-3B100605_Slide57(normalized)


title: 28_24-2B100605_Slide84(normalized)


title: 28_24-1B100605_Slide65(normalized)

description: raw data file: 24-1vs47-2B100605_Slide65.txt


title: 28_47-1B100605_Slide52(normalized)

description: raw data file: 24-1vs47-1B100605_Slide52.txt


title: 28_24-2B100605_Slide56(normalized)

description: raw data file: 24-2vs47-2B100605_Slide56.txt


title: 28_24-1B100605_Slide52(normalized)


title: 28_12-3B100605_Slide59(normalized)

description: raw data file: 12-3vs24-3B100605_Slide59.txt


title: 28_47-2B100605_Slide56(normalized)


title: 28_24-3B100605_Slide59(normalized)


title: 28_24-3B100605_Slide80(normalized)

description: raw data file: 12-2vs24-3B100605_Slide80.txt


title: 28_12-3B100605_Slide66(normalized)

description: raw data file: 12-3vs24-1B100605_Slide66.txt


title: 28_47-2B100605_Slide65(normalized)


title: 28_24-1B100605_Slide49(normalized)

description: raw data file: 12-1vs24-1B100605_Slide49.txt


title: 28_12-1B100605_Slide85(normalized)

description: raw data file: 12-1vs24-2B100605_Slide85.txt


title: 28_12-3B100605_Slide60(normalized)

description: raw data file: 1.2-3vs12-3B100605_Slide60.txt


title: 28_1.2-2B100605_Slide53(normalized)

description: raw data file: 1.2-2vs12-2B100605_Slide53.txt


title: 28_12-1B100605_Slide49(normalized)


title: 28_12-2B100605_Slide55(normalized)

description: raw data file: 12-2vs24-2B100605_Slide55.txt


title: 28_12-2B100605_Slide53(normalized)


title: 28_12-1B100605_Slide86(normalized)

description: raw data file: 1.2-3vs12-1B100605_Slide86.txt


title: 28_12-2B100605_Slide81(normalized)

description: raw data file: 1.2-1vs12-2B100605_Slide81.txt


title: 28_1.2-2B100605_Slide63(normalized)

description: raw data file: 1.2-2vs12-3B100605_Slide63.txt


title: 28_1.2-1B100605_Slide81(normalized)


title: 28_12-2B100605_Slide80(normalized)


title: 28_12-3B100605_Slide63(normalized)


title: 28_24-1B100605_Slide66(normalized)


title: 28_12-1B100605_Slide50(normalized)

description: raw data file: 1.2-1vs12-1B100605_Slide50.txt


title: 28_1.2-3B100605_Slide60(normalized)


title: 28_24-2B100605_Slide85(normalized)


title: 28_1.2-1B100605_Slide50(normalized)


title: 14_1.2-3B011106_Slide41(normalized)

description: raw data file: Con-3vs1.2-3B011106_Slide41.txt

value: 14 days


title: 14_Con-3B011106_Slide41(normalized)


title: 14_1.2-1B011106_Slide70(normalized)

description: raw data file: Con-3vs1.2-1B011106_Slide70.txt


title: 14_Con-2B011106_Slide51(normalized)

description: raw data file: Con-2vs1.2-3B011106_Slide51.txt


title: 14_1.2-2B011106_Slide36(normalized)

description: raw data file: Con-2vs1.2-2B011106_Slide36.txt


title: 14_Con-2B011106_Slide36(normalized)


title: 14_1.2-3B011106_Slide51(normalized)


title: 14_Con-3B011106_Slide70(normalized)


title: 14_1.2-2B011106_Slide46(normalized)

description: raw data file: Con-1vs1.2-2B011106_Slide46.txt


title: 14_47-3B011106_Slide55(normalized)

description: raw data file: 47-3vsCon2B011106_Slide55.txt


title: 14_Con-2B011106_Slide55(normalized)


title: 14_Con-1B011106_Slide45(normalized)

description: raw data file: 47-3vsCon-1B011106_Slide45.txt


title: 14_47-2B011106_Slide50(normalized)

description: raw data file: 47-2vsCon-1B011106_Slide50.txt


title: 14_Con-1B011106_Slide31(normalized)

description: raw data file: Con-1vs1.2-1B011106_Slide31.txt


title: 14_Con-1B011106_Slide50(normalized)


title: 14_47-1B011106_Slide74(normalized)

description: raw data file: 47-1vsCon3B011106_Slide74.txt


title: 14_Con-3B011106_Slide74(normalized)


title: 14_Con-2B011106_Slide35(normalized)

description: raw data file: 47-1vsCon-2B011106_Slide35.txt


title: 14_47-2B011106_Slide40(normalized)

description: raw data file: 47-2vsCon-3B011106_Slide40.txt


title: 14_Con-3B011106_Slide40(normalized)


title: 14_Con-1B011106_Slide46(normalized)


title: 14_47-1B011106_Slide73(normalized)

description: raw data file: 24-3vs47-1B011106_Slide73.txt


title: 14_24-3B011106_Slide44(normalized)

description: raw data file: 24-3vs47-3B011106_Slide44.txt


title: 14_1.2-1B011106_Slide31(normalized)


title: 14_47-1B011106_Slide35(normalized)


title: 14_47-3B011106_Slide45(normalized)


title: 14_24-3B011106_Slide73(normalized)


title: 14_47-2B011106_Slide39(normalized)

description: raw data file: 24-2vs47-2B011106_Slide39.txt


title: 14_24-2B011106_Slide39(normalized)


title: 14_12-1B011106_Slide33(normalized)

description: raw data file: 12-1vs24-3B011106_Slide33.txt


title: 14_24-2B011106_Slide53(normalized)

description: raw data file: 12-1vs24-2B011106_Slide53.txt


title: 14_24-1B011106_Slide34(normalized)

description: raw data file: 24-1vs47-1B011106_Slide34.txt


title: 14_12-1B011106_Slide53(normalized)


title: 14_24-3B011106_Slide33(normalized)


title: 14_47-3B011106_Slide54(normalized)

description: raw data file: 24-2vs47-3B011106_Slide54.txt


title: 14_47-3B011106_Slide44(normalized)


title: 14_12-3B011106_Slide42(normalized)

description: raw data file: 1.2-3vs12-3B011106_Slide42.txt


title: 14_24-3B011106_Slide72(normalized)

description: raw data file: 12-2vs24-3B011106_Slide72.txt


title: 14_12-3B011106_Slide48(normalized)

description: raw data file: 12-3vs24-1B011106_Slide48.txt


title: 14_24-1B011106_Slide49(normalized)

description: raw data file: 24-1vs47-2B011106_Slide49.txt


title: 14_24-1B011106_Slide48(normalized)


title: 14_12-3B011106_Slide43(normalized)

description: raw data file: 12-3vs24-3B011106_Slide43.txt


title: 14_47-1B011106_Slide34(normalized)


title: 14_12-2B040606_Slide07(normalized)

description: raw data file: 12-2vs24-2B040606_Slide07Repeat.txt


title: 14_12-2B011106_Slide72(normalized)


title: 14_24-2B040606_Slide07Repeat(normalized)


title: 14_24-3B011106_Slide43(normalized)


title: 14_1.2-3B011106_Slide42(normalized)


title: 14_12-3B011106_Slide47(normalized)

description: raw data file: 1.2-2vs12-3B011106_Slide47.txt


title: 14_1.2-3B011106_Slide52(normalized)

description: raw data file: 1.2-3vs12-1B011106_Slide52.txt


title: 14_12-1B011106_Slide52(normalized)


title: 14_1.2-2B011106_Slide47(normalized)


title: 14_12-2B011106_Slide37(normalized)

description: raw data file: 1.2-2vs12-2B011106_Slide37.txt


title: 28_1.2-3B100605_Slide86(normalized)

description: raw data file: 1.2-3vs12-1B100605_Slide86.txt


title: 28_24-2B100605_Slide55(normalized)

description: raw data file: 12-2vs24-2B100605_Slide55.txt


title: 14_47-2B011106_Slide49(normalized)


title: 14_12-1B011106_Slide32(normalized)

description: raw data file: 1.2-1vs12-1B011106_Slide32.txt


title: 14_1.2-1B011106_Slide71(normalized)

description: raw data file: 1.2-1vs12-2B011106_Slide71.txt


title: 7_1.2mg-3B032207Slide33(normalized)

description: raw data file: Con-3vs1.2mg-3B032207Slide33.txt

value: 7 days


title: 14_1.2-1B011106_Slide32(normalized)


title: 7_1.2mg-2B032207Slide28(normalized)

description: raw data file: Con-1vs1.2mg-2B032207Slide28.txt


title: 7_Con-2B032207Slide02(normalized)

description: raw data file: Con-2vs1.2mg-2B032207Slide02RE.txt


title: 7_Con-3B032207Slide18(normalized)

description: raw data file: Con-3vs1.2mg-1B032207Slide18.txt


title: 7_1.2mg-3B032207Slide23(normalized)

description: raw data file: Con-2vs1.2mg-3B032207Slide23.txt


title: 7_1.2mg-1B032207Slide18(normalized)


title: 7_Con-3B032207Slide33(normalized)


title: 14_12-2B011106_Slide71(normalized)


title: 7_Con-3B032207Slide09RE(normalized)

description: raw data file: 47mg-2vsCon-3B032207Slide09RE.txt


title: 14_1.2-2B011106_Slide37(normalized)


title: 7_1.2mg-2B032207Slide02RE(normalized)


title: 7_47mg-2B032207Slide09(normalized)


title: 7_Con-1B032207Slide28(normalized)


title: 7_47mg-2B032207Slide24(normalized)

description: raw data file: 47mg-2vsCon-1B032207Slide24.txt


title: 7_Con-1B032207Slide24(normalized)


title: 7_Con-1B032207Slide29(normalized)

description: raw data file: 47mg-3vsCon-1B032207Slide29.txt


title: 7_47mg-3B032207Slide29(normalized)


title: 7_47mg-1B032207Slide14(normalized)

description: raw data file: 47mg-1vsCon-3B032207Slide14.txt


title: 7_47mg-3B032207Slide45(normalized)

description: raw data file: 47mg-3vsCon-2B032207Slide45RE.txt


title: 7_Con-1B032207Slide44(normalized)

description: raw data file: Con-1vs1.2mg-1B032207Slide44.txt


title: 7_Con-2B032207Slide23(normalized)


title: 7_Con-2B032207Slide45RE(normalized)


title: 7_Con-2B032207Slide12RE(normalized)

description: raw data file: 47mg-1vsCon-2B032207Slide12RE.txt


title: 7_1.2mg-1B032207Slide44(normalized)


title: 7_47mg-1B032207Slide12(normalized)


title: 7_Con-3B032207Slide14(normalized)


title: 7_47mg-1B032207Slide15(normalized)

description: raw data file: 24mg-3vs47mg-1B032207Slide15.txt


title: 7_47mg-2B032207Slide35(normalized)

description: raw data file: 24mg-2vs47mg-2B032207Slide35.txt


title: 7_24mg-1B032207Slide26(normalized)

description: raw data file: 12mg-3vs24mg-1B032207Slide26.txt


title: 7_12mg-1B032207Slide42(normalized)

description: raw data file: 12mg-1vs24mg-1B032207Slide42.txt


title: 7_12mg-2B032207Slide36(normalized)

description: raw data file: 12mg-2vs24mg-2B032207Slide36.txt


title: 7_47mg-3B032207Slide30(normalized)

description: raw data file: 24mg-3vs47mg-3B032207Slide30.txt


title: 7_24mg-3B032207Slide30(normalized)


title: 7_24mg-1B032207Slide41(normalized)

description: raw data file: 24mg-1vs47mg-1B032207Slide41.txt


title: 7_47mg-1B032207Slide41(normalized)


title: 7_24mg-2B032207Slide04RE(normalized)

description: raw data file: 12mg-1vs24mg-2B032207Slide04RE.txt


title: 7_47mg-3B032207Slide20(normalized)

description: raw data file: 24mg-2vs47mg-3B032207Slide20.txt


title: 7_1.2mg-3B032207Slide08(normalized)

description: raw data file: 1.2mg-3vs12mg-3B032207Slide08RE.txt


title: 7_24mg-2B032207Slide35(normalized)


title: 7_47mg-2B032207Slide05RE(normalized)

description: raw data file: 24mg-1vs47mg-2B032207Slide05RE.txt


title: 7_24mg-3B032207Slide15(normalized)


title: 7_12mg-3B032207Slide26(normalized)


title: 7_24mg-2B032207Slide20(normalized)


title: 7_12mg-3B032207Slide07(normalized)

description: raw data file: 12mg-3vs24mg-3B032207Slide07RE.txt


title: 7_12mg-2B032207Slide16(normalized)

description: raw data file: 12mg-2vs24mg-3B032207Slide16.txt


title: 7_24mg-2B032207Slide36(normalized)


title: 7_24mg-3B032207Slide07RE(normalized)


title: 7_24mg-1B032207Slide05(normalized)


title: 7_12mg-3B032207Slide08RE(normalized)


title: 7_12mg-1B032207Slide04(normalized)


title: 7_12mg-3B032207Slide27(normalized)

description: raw data file: 1.2mg-2vs12mg-3B032207Slide27.txt


title: 7_24mg-3B032207Slide16(normalized)


title: 7_24mg-1B032207Slide42(normalized)


title: 7_1.2mg-2B032207Slide27(normalized)


title: 7_1.2mg-3B032207Slide22(normalized)

description: raw data file: 1.2mg-3vs12mg-1B032207Slide22.txt


title: 7_12mg-1B032207Slide22(normalized)


title: 14_24-2B011106_Slide54(normalized)

description: raw data file: 24-2vs47-3B011106_Slide54.txt


title: 7_12mg-1B032207Slide43(normalized)

description: raw data file: 1.2mg-1vs12mg-1B032207Slide43.txt


title: 7_1.2mg-1B032207Slide43(normalized)


title: 7_12mg-2B032207Slide17(normalized)

description: raw data file: 1.2mg-1vs12mg-2B032207Slide17.txt


title: 48_1.2.3B080905Slide62(normalized)

description: raw data file: Con2vs1.2.3B080905Slide62.txt


title: 48_Con3B080905Slide63(normalized)

description: raw data file: Con3vs1.2.1B080905Slide63.txt


title: 48_1.2.1B080905Slide63(normalized)


title: 48_Con2B080905Slide09(normalized)

description: raw data file: Con2vs1.2.2B080905Slide09.txt


title: 7_12mg-2B032207Slide10RE(normalized)

description: raw data file: 1.2mg-2vs12mg-2B032207Slide10RE.txt


title: 48_1.2.2B080905Slide28(normalized)

description: raw data file: Con1vs1.2.2B080905Slide28.txt


title: 48_Con1B080905Slide28(normalized)


title: 48_47.3B080905Slide64(normalized)

description: raw data file: 47.3vsCon2B080905Slide64.txt


title: 48_1.2.2B080905Slide09(normalized)


title: 48_Con1B080905Slide57(normalized)

description: raw data file: 47.2vsCon1B080905Slide57.txt


title: 48_Con2B080905Slide64(normalized)


title: 48_47.2B080905Slide57(normalized)


title: 48_Con2B080905Slide04(normalized)

description: raw data file: 47.1vsCon2B080905Slide04.txt


title: 48_47.1B080905Slide03(normalized)

description: raw data file: 47.1vsCon3B080905Slide03.txt


title: 48_Con3B080905Slide03(normalized)


title: 48_Con1B080905Slide02(normalized)

description: raw data file: Con1vs1.2.1B080905Slide02.txt


title: 7_1.2mg-2B032207Slide10(normalized)


title: 48_47.1B080905Slide04(normalized)


title: 7_1.2mg-1B032207Slide17(normalized)


title: 48_1.2.3B080905Slide69(normalized)

description: raw data file: Con3vs1.2.3B080905Slide69.txt


title: 48_Con3B080905Slide69(normalized)


title: 48_24.3B080905Slide91(normalized)

description: raw data file: 24.3vs47.3B080905Slide91.txt


title: 48_47.1B080905Slide66(normalized)

description: raw data file: 24.3vs47.1B080905Slide66.txt


title: 48_47.3B080905Slide91(normalized)


title: 48_24.2B080905Slide65(normalized)

description: raw data file: 24.2vs47.3B080905Slide65.txt


title: 48_47.3B080905Slide65(normalized)


title: 48_24.3B080905Slide66(normalized)


title: 48_47.2B080905Slide71(normalized)

description: raw data file: 24.2vs47.2B080905Slide71.txt


title: 48_47.2B080905Slide29(normalized)

description: raw data file: 24.1vs47.2B080905Slide29.txt


title: 48_47.1B080905Slide05(normalized)

description: raw data file: 24.1vs47.1B080905Slide05.txt


title: 48_24.1B080905Slide30(normalized)

description: raw data file: 12.3vs24.1B080905Slide30.txt


title: 48_12.3B080905Slide90(normalized)

description: raw data file: 12.3vs24.3B080905Slide90.txt


title: 48_24.2B080905Slide07(normalized)

description: raw data file: 12.2vs24.2B080905Slide07.txt


title: 48_24.1B080905Slide05(normalized)


title: 48_24.3B080905Slide67(normalized)

description: raw data file: 12.2vs24.3B080905Slide67.txt


title: 48_24.1B080905Slide06(normalized)

description: raw data file: 12.1vs24.1B080905Slide06.txt


title: 48_24.3B080905Slide90(normalized)


title: 48_12.3B080905Slide30(normalized)


title: 48_24.2B080905Slide60(normalized)

description: raw data file: 12.1vs24.2B080905Slide60.txt


title: 48_24.2B080905Slide71(normalized)


title: 48_12.1B080905Slide60(normalized)


title: 48_12.2B080905Slide07(normalized)


title: 48_24.1B080905Slide29(normalized)


title: 48_12.3B080905Slide93(normalized)

description: raw data file: 1.2.3vs12.3B080905Slide93.txt


title: 48_12.1B080905Slide06(normalized)


title: 48_12.2B080905Slide67(normalized)


title: 48_12.2B080905Slide08(normalized)

description: raw data file: 1.2.2vs12.2B080905Slide08.txt


title: 48_1.2.3B080905Slide61(normalized)

description: raw data file: 1.2.3vs12.1B080905Slide61.txt


title: 48_1.2.3B080905Slide93(normalized)


title: 48_12.1B080905Slide61(normalized)


title: 48_12.3B080905Slide31(normalized)

description: raw data file: 1.2.2vs12.3B080905Slide31.txt


title: 48_1.2.2B080905Slide08(normalized)


title: 48_1.2.2B080905Slide31(normalized)


title: 48_12.2B080905Slide68(normalized)

description: raw data file: 1.2.1vs12.2B080905Slide68.txt


title: 24_Con3B08905Slide23(normalized)

description: raw data file: Con3vs1.2.3B08905Slide23.txt

value: 24 hr


title: 24_1.2.3B08905Slide23(normalized)


title: 24_1.2.3B08905Slide46(normalized)

description: raw data file: Con2vs1.2.3B08905Slide46.txt


title: 24_Con2B08905Slide18(normalized)

description: raw data file: Con2vs1.2.2B08905Slide18.txt


title: 24_Con2B08905Slide46(normalized)


title: 24_1.2.2B08905Slide18(normalized)


title: 24_Con1B08905Slide42(normalized)

description: raw data file: Con1vs1.2.2B08905Slide42.txt


title: 48_1.2.1B080905Slide68(normalized)


title: 24_1.2.1B08905Slide13(normalized)

description: raw data file: Con1vs1.2.1B08905Slide13.txt


title: 24_1.2.2B08905Slide42(normalized)


title: 24_47.3B08905Slide50(normalized)

description: raw data file: 47.3vsCon2B08905Slide50.txt


title: 24_47.3B08905Slide27(normalized)

description: raw data file: 47.3vsCon1B08905Slide27.txt


title: 24_Con1B08905Slide13(normalized)


title: 24_Con2B08905Slide50(normalized)


title: 24_Con2B08905Slide51(normalized)

description: raw data file: Con2vs1.2.1B08905Slide51.txt


title: 24_1.2.1B08905Slide51(normalized)


title: 24_Con1B08905Slide45(normalized)

description: raw data file: 47.2vsCon1B08905Slide45.txt


title: 24_47.2B08905Slide45(normalized)


title: 24_47.2B08905Slide22(normalized)

description: raw data file: 47.2vsCon3B08905Slide22.txt


title: 24_Con3B08905Slide22(normalized)


title: 24_Con3B08905Slide12(normalized)

description: raw data file: 47.1vsCon3B08905Slide12.txt


title: 24_47.1B08905Slide17(normalized)

description: raw data file: 47.1vsCon2B08905Slide17.txt


title: 24_Con1B08905Slide27 Red Twice(normalized)

description: raw data file: 47.3vsCon1B08905Slide27 Red Twice.txt


title: 24_47.1B08905Slide12(normalized)


title: 24_Con2B08905Slide17(normalized)


title: 24_47.3B08905Slide26(normalized)

description: raw data file: 24.3vs47.3B08905Slide26.txt


title: 24_47.1B08905Slide11(normalized)

description: raw data file: 24.3vs47.1B08905Slide11.txt


title: 24_24.3B08905Slide26(normalized)


title: 24_24.3B08905Slide11(normalized)


title: 24_47.3B08905Slide53(normalized)

description: raw data file: 24.2vs47.3B08905Slide53.txt


title: 24_24.2B08905Slide53(normalized)


title: 24_47.2B08905Slide21(normalized)

description: raw data file: 24.2vs47.2B08905Slide21.txt


title: 24_24.2B08905Slide21(normalized)


title: 24_47.2B08905Slide47(normalized)

description: raw data file: 24.1vs47.2B08905Slide47.txt


title: 24_24.1B08905Slide47(normalized)


title: 24_12.3B08905Slide25(normalized)

description: raw data file: 12.3vs24.3B08905Slide25.txt


title: 24_12.2B08905Slide20(normalized)

description: raw data file: 12.2vs24.2B08905Slide20.txt


title: 24_12.1B08905Slide15(normalized)

description: raw data file: 12.1vs24.1B08905Slide15.txt


title: 24_24.3B08905Slide25(normalized)


title: 24_24.1B08905Slide15(normalized)


title: 24_24.1B08905Slide16(normalized)

description: raw data file: 24.1vs47.1B08905Slide16.txt


title: 24_24.2B08905Slide20(normalized)


title: 24_12.1B08905Slide49(normalized)

description: raw data file: 12.1vs24.2B08905Slide49.txt


title: 24_24.3B08905Slide10(normalized)

description: raw data file: 12.2vs24.3B08905Slide10.txt


title: 24_47.1B08905Slide16(normalized)


title: 24_12.2B08905Slide10(normalized)


title: 24_12.3B08905Slide44(normalized)

description: raw data file: 12.3vs24.1B08905Slide44.txt


title: 24_24.1B08905Slide44(normalized)


title: 24_12.2B08905Slide19(normalized)

description: raw data file: 1.2.2vs12.2B08905Slide19.txt


title: 24_1.2.2B08905Slide43(normalized)

description: raw data file: 1.2.2vs12.3B08905Slide43.txt


title: 24_12.3B08905Slide43(normalized)


title: 24_1.2.2B08905Slide19(normalized)


title: 24_12.3B08905Slide24(normalized)

description: raw data file: 1.2.3vs12.3B08905Slide24.txt


title: 24_1.2.3B08905Slide24(normalized)


title: 24_12.1B08905Slide52(normalized)

description: raw data file: 1.2.1vs12.1B08905Slide52.txt


title: 24_24.2B08905Slide49(normalized)


title: 24_1.2.1B08905Slide52(normalized)


title: 24_12.1B08905Slide14(normalized)

description: raw data file: 1.2.1vs12.1B08905Slide14.txt


title: 24_1.2.1B08905Slide14(normalized)


title: 48_1.2.1B080905Slide02(normalized)

description: raw data file: Con1vs1.2.1B080905Slide02.txt


title: genomic DNA from gastric cancer tissue_GC626T

type: genomic

city: Daejeon

first: Han-Chul

last: Lee

address: 111 Gwahangno, Yuseong-gu

department: Medical Genome Research Center

country: South Korea

institute: KRIBB

description: tumor stomach sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Stomach

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

value: Female

tag: tissue type

value: gastric cancer tissue

tag: disease state

value: tumor


title: genomic DNA from gastric cancer cell line_SNU-484

description: tumor stomach sample

tag: cell line


title: genomic DNA from gastric cancer cell line_SNU-719

description: tumor stomach sample


title: genomic DNA from gastric cancer cell line_SNU-601

description: tumor stomach sample


title: genomic DNA from gastric cancer cell line_Az-521

description: tumor stomach sample


title: genomic DNA from gastric cancer tissue_GC607T

description: tumor stomach sample

value: Male


title: genomic DNA from gastric cancer cell line_NUGC-3

description: tumor stomach sample


title: genomic DNA from gastric cancer cell line_SNU-638

description: tumor stomach sample


title: genomic DNA from gastric cancer tissue_GC623T

description: tumor stomach sample


title: genomic DNA from gastric cancer cell line_SNU-005

description: tumor stomach sample


title: genomic DNA from gastric cancer tissue_GC316T

description: tumor stomach sample


title: genomic DNA from gastric cancer cell line_SNU-016

description: tumor stomach sample


title: genomic DNA from gastric cancer cell line_SNU-520

description: tumor stomach sample


title: genomic DNA from gastric cancer adjacent normal tissue_GC625N

description: normal stomach sample

value: gastric cancer adjacent normal tissue

value: normal


title: genomic DNA from gastric cancer adjacent normal tissue_GC607N

description: normal stomach sample


title: genomic DNA from gastric cancer adjacent normal tissue_GC055N

description: normal stomach sample


title: genomic DNA from gastric cancer adjacent normal tissue_GC316N

description: normal stomach sample


title: genomic DNA from gastric cancer adjacent normal tissue_GC623N

description: normal stomach sample


title: genomic DNA from gastric cancer tissue_GC055T

description: tumor stomach sample


title: genomic DNA from gastric cancer tissue_GC0316T

description: tumor stomach sample


title: genomic DNA from gastric cancer tissue_GC027T

description: tumor stomach sample


title: genomic DNA from gastric cancer adjacent normal tissue_GC027N

description: normal stomach sample


title: genomic DNA from gastric cancer adjacent normal tissue_GC0316N

description: normal stomach sample


title: genomic DNA from gastric cancer tissue_GC617T

description: tumor stomach sample


title: genomic DNA from gastric cancer tissue_GC625T

description: tumor stomach sample


title: genomic DNA from gastric cancer cell line_MKN74

description: tumor stomach sample


title: genomic DNA from gastric cancer adjacent normal tissue_GC626N

description: normal stomach sample


title: genomic DNA from gastric cancer adjacent normal tissue_GC617N

description: normal stomach sample


title: genomic DNA from gastric cancer tissue_GC610T

description: tumor stomach sample


title: genomic DNA from gastric cancer adjacent normal tissue_GC615N

description: normal stomach sample


title: genomic DNA from gastric cancer tissue_GC615T

description: tumor stomach sample


title: 48_Con2B080905Slide62(normalized)

description: raw data file: Con2vs1.2.3B080905Slide62.txt

value: Sprague-Dawley


title: genomic DNA from gastric cancer tissue_GC518T

description: tumor stomach sample


title: genomic DNA from gastric cancer adjacent normal tissue_GC528N

description: normal stomach sample


title: genomic DNA from gastric cancer adjacent normal tissue_GC518N

description: normal stomach sample


title: genomic DNA from gastric cancer tissue_GC407T

description: tumor stomach sample


title: genomic DNA from gastric cancer tissue_GC438T

description: tumor stomach sample


title: genomic DNA from gastric cancer cell line

description: tumor stomach sample


title: genomic DNA from gastric cancer adjacent normal tissue_GC438N

description: normal stomach sample


title: genomic DNA from gastric cancer tissue_GC528T

description: tumor stomach sample


title: genomic DNA from gastric cancer adjacent normal tissue_GC330N

description: normal stomach sample


title: genomic DNA from gastric cancer adjacent normal tissue_GC610N

description: normal stomach sample


title: genomic DNA from gastric cancer tissue_GC603T

description: tumor stomach sample


title: genomic DNA from gastric cancer tissue_GC330T

description: tumor stomach sample


title: genomic DNA from gastric cancer adjacent normal tissue_GC407N

description: normal stomach sample


title: genomic DNA from gastric cancer adjacent normal tissue_GC327N

description: normal stomach sample


title: genomic DNA from gastric cancer tissue_GC327T

description: tumor stomach sample


title: genomic DNA from gastric cancer adjacent normal tissue_GC412N

description: normal stomach sample


title: genomic DNA from gastric cancer tissue_GC326T

description: tumor stomach sample


title: genomic DNA from gastric cancer adjacent normal tissue_GC603N

description: normal stomach sample


title: genomic DNA from gastric cancer adjacent normal tissue_GC406N

description: normal stomach sample


title: genomic DNA from gastric cancer tissue_GC412T

description: tumor stomach sample


title: genomic DNA from gastric cancer adjacent normal tissue_GC317N

description: normal stomach sample


title: genomic DNA from gastric cancer tissue_GC317T

description: tumor stomach sample


title: genomic DNA from gastric cancer tissue_GC306T

description: tumor stomach sample


title: genomic DNA from gastric cancer tissue_GC406T

description: tumor stomach sample


title: genomic DNA from gastric cancer adjacent normal tissue_GC306N

description: normal stomach sample


title: genomic DNA from gastric cancer adjacent normal tissue_GC326N

description: normal stomach sample


title: genomic DNA from gastric cancer tissue_GC125T

description: tumor stomach sample


title: genomic DNA from gastric cancer adjacent normal tissue_GC125N

description: normal stomach sample


title: genomic DNA from gastric cancer adjacent normal tissue_GC126N

description: normal stomach sample


title: genomic DNA from gastric cancer tissue_GC037T

description: tumor stomach sample


title: genomic DNA from gastric cancer tissue_GC126T

description: tumor stomach sample


title: genomic DNA from gastric cancer tissue_GC057T

description: tumor stomach sample


title: genomic DNA from gastric cancer tissue_GC007T

description: tumor stomach sample


title: genomic DNA from gastric cancer tissue_GC222T

description: tumor stomach sample


title: genomic DNA from gastric cancer adjacent normal tissue_GC222N

description: normal stomach sample


title: genomic DNA from gastric cancer tissue_GC212T

description: tumor stomach sample


title: genomic DNA from gastric cancer adjacent normal tissue_GC037N

description: normal stomach sample


title: genomic DNA from gastric cancer tissue_GC021T

description: tumor stomach sample


title: genomic DNA from gastric cancer adjacent normal tissue_GC007N

description: normal stomach sample


title: genomic DNA from gastric cancer adjacent normal tissue_GC013N

description: normal stomach sample


title: genomic DNA from gastric cancer adjacent normal tissue_GC212N

description: normal stomach sample


title: genomic DNA from gastric cancer adjacent normal tissue_GC021N

description: normal stomach sample


title: white_pre-adipocyte_post-differentiation_replicate3

city: Stirling

first: Iain

last: Gallagher

address: Room 4B133 Cottrell Building, University of Stirling, Airthrey Road

department: Faculty of Health Sciences and Sport

country: United Kingdom

institute: University of Stirling

hyb_protocol: The arrays were incubated at 60°C for 16 hours in a hybridisation oven.

scan_protocol: After hybridisation the slides were manually washed for 2 minutes in Buffer A at 60oC, rinsed in Buffer B followed by a 2-minute wash in buffer B at RT and 2 minutes in Buffer C at RT. All buffers were supplied by EXIQON. After washing the slides were dried by centrifugation for 2 minutes at 1000rpm. The slides were immediately scanned using an Agilent G2565BA scanner with a spot size of 10um and 100% PMT gain.

data_processing: QuantArray software was used to quantify the signals from the Agilent scanner using the fixed circle approach. Background subtracted signal intensities were normalized in R using quantile normalization.

organism: Mus musculus

source_name: White adipocytes post differentiation

label_protocol: Samples were labelled using Exiqon’s miRCURY LNA array labelling kit (Vedbæk, Denmark): 2ug total RNA was incubated with labelling buffer, the Hy3 dye, labelling enzyme and spike-in microRNAs for 1 hour at 37°C. The enzyme was then heat-inactivated at 65°C for 15 minutes, followed by addition of 2 x hybridisation buffer. The samples were incubated at 95°C for 5 minutes while protected from light. The samples were then briefly spun down and filtered through a 0.45-micron durapore filter (Millipore), and 40 ul sample was loaded to the arrays by capillary force using a cover slip (Erie Scientific).

growth_protocol: Brown adipocytes we harvested from male NMRI mice housed under standard conditions. At the age of 4 weeks, the mice were killed and cells from pooled interscapular, cervical and axillary brown adipose tissue depots. Epididymal white adipose tissue were isolated from the same mice.

extract_protocol: Total RNA was extracted from cultured cells with Ultraspec (Biotecx, Houston, TX) according to the manufacturer’s protocol

treatment_protocol: The cells were cultured in 10 cm2 6-well plates in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% newborn calf serum (NCS) (Hyclone, Erembodegem, Belgium, or Invitrogen, Carlsbad, CA), 0.17 mM insulin, 25 g/ml sodium ascorbate, 10 mM Hepes (pH 7.4), 4 mM glutamine, 50 units/ml penicillin and 50 g/ml streptomycin, supplemented or not with 1 mM rosiglitazone maleate (Alexis Biochemicals, Lausen, Switzerland). The media were changed on day-1, day-3, and day-5 of culture. Some of the cell cultures, grown in absence of rosiglitazone, were treated with 1 mM norepinephrine (Sigma–Aldrich, Stockholm, Sweden) 2 h prior to harvest

value: White adipocytes

tag: differentiation status

value: post

value: NMRI


title: genomic DNA from gastric cancer tissue_GC013T

description: tumor stomach sample


title: genomic DNA from gastric cancer adjacent normal tissue_GC057N

description: normal stomach sample


title: white_pre-adipocyte_pre-differentiation_replicate3

source_name: White adipocytes pre differentiation

value: pre


title: adipose_tissue_IGT (16722)

hyb_protocol: As per Affymetrix directions

scan_protocol: As per Affymetrix directions

data_processing: All array data were normalized using the Microarray Suite version 5.0 (MAS 5.0) algorithm to a global scaling intensity of 100. Data were filtered using present/absent calls. Probes called absent by MAS 5.0 across all arrays were discarded. Further data processing were performed by RMA.

label: biotin

source_name: subcutaneous adipose tissue

label_protocol: As per Affymetrix directions

extract_protocol: Frozen tissue was homogenised in Trizol (Invitrogen) using a motor-driven homogenizer (Polytron, Kinematica, Newark, NY, USA). RNA was extracted according to manufacturer’s protocol.

treatment_protocol: Adipose tissue biopsies were obtained from the subcutaneous abdominal region (from the area below the umbilicus in a 4-cm range on either side) using the percutaneous needle biopsy technique with suction. Biopsies were quickly dissected free from visible blood and connective tissue and frozen in liquid nitrogen. To avoid interference of circadian rhythms and post-prandial responses, biopsies were obtained between 8 am and 10 am following an overnight fast.

tag: clinical status

value: IGT

tag: bmi

tag: age

tag: fasting insulin

tag: fasting glucose

tag: vo2max ffm


title: adipose_tissue_NGT (16707)

value: NGT


title: white_pre-adipocyte_pre-differentiation_replicate2


title: white_pre-adipocyte_post-differentiation_replicate2


title: white_pre-adipocyte_post-differentiation_replicate1


title: adipose_tissue_NGT (16467)


title: adipose_tissue_IGT (16728)


title: AGS cells_galectin-3 silenced

city: Goyang-si

first: Kyung-Hee

last: Chun

state: Gyeonggi-do

address: 323 ilsan-ro

department: Division of Translational & Clinical Research I

institute: National Cancer Center

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Genechip® Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: AGS cells_galectin-3 silenced

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

value: gastric cancer cell line AGS

tag: genotype/variation

value: galectin-3 silenced


title: adipose_tissue_IGT (16616)


title: adipose_tissue_DM (16470)

value: DM


title: adipose_tissue_NGT (17197)


title: adipose_tissue_IGT (16443)


title: white_pre-adipocyte_pre-differentiation_replicate1

tag: strain


title: adipose_tissue_IGT (16437)


title: adipose_tissue_NGT (16762)


title: brown_pre-adipocyte_post-differentiation_replicate3

source_name: Brown adipocytes post differentiation

value: Brown adipocytes


title: AGS cells_control

source_name: AGS cells_control

value: control


title: brown_pre-adipocyte_pre-differentiation_replicate3

source_name: Brown adipocytes pre differentiation


title: brown_pre-adipocyte_post-differentiation_replicate2


title: adipose_tissue_DM (16431)


title: brown_pre-adipocyte_pre-differentiation_replicate2


title: brown_pre-adipocyte_post-differentiation_replicate1


title: brown_pre-adipocyte_pre-differentiation_replicate1


title: adipose_tissue_IGT (16155)


title: adipose_tissue_DM (16167)


title: adipose_tissue_NGT (16191)


title: adipose_tissue_DM (15667)


title: adipose_tissue_NGT (15661)


title: adipose_tissue_DM (16107)


title: adipose_tissue_DM (16140)


title: adipose_tissue_DM (16173)


title: adipose_tissue_DM (16122)


title: adipose_tissue_DM (15640)


title: adipose_tissue_NGT (15594)


title: adipose_tissue_IGT (15558)


title: adipose_tissue_IGT (15637)


title: adipose_tissue_NGT (15655)


title: adipose_tissue_DM (15570)


title: adipose_tissue_NGT (15625)


title: DvuA0137-II

city: Berkeley

first: Lara

last: Rajeev

state: CA

address: 1 Cyclotron Road

institute: Lawrence Berkeley Lab

description:
DvuA0137-high
DAP-chip of DvuA0137 bound DNA / input DNA

hyb_protocol: 6 µg of the Cy3- and Cy5- labeled DNA were pooled together and hybridized to a 385k custom tiling array according to the manufacturer's instructions (Roche-Nimblegen)

scan_protocol: The arrays were scanned on a GenePix 4200A scanner according to Nimblegen's protocol

data_processing: The array data was processed using the Nimblescan software (v 2.4) following the manufacturer's guidelines for processing Chip-chip data

organism: Nitratidesulfovibrio vulgaris

source_name: RR DvuA0137 bound enriched DNA

label_protocol: The input and enriched samples were whole genome amplified using Sigma WGA2 kit. One µg of input and enriched WGA samples were labeled with Cy3 and Cy5-nonamers respectively using Klenow Polyermase (3'-5' exo-), and the labeled DNA was precipitated with isopropanol and NaCl.

extract_protocol: D. vulgaris Hildenborough genomic DNA was sheared by sonication to an average length of 500 bp.Binding reactions were set up 2-3 µg of sheared genomic DNA, and purified His-tagged response regulator, in 10 mM Tris HCl, pH 7.5, 1 mM DTT, 5 mM MgCl2, 50 mM acetyl phosphate and 25% glycerol. The amount of protein used in the binding reactions was determined based on activity of protein in EMSAs. The reactions were incubated at 25C in a thermal cycler for 30 minutes. 10 µl of the reaction was saved as input DNA. The rest was allowed to bind to 30 µl of Ni-NTA resin that had been washed in the binding/wash buffer (10 mM Tris-HCl, pH 7.5, 5 mM MgCl2, 50 mM KCl, 25% glycerol). After 30 min of binding, the tubes were spun down to remove the unbound DNA. The resin was washed three times in 100 µl of the wash buffer, and then the bound DNA was eluted with 35 µl of elution buffer (20 mM sodium phosphate buffer pH 8, 500 mM NaCl, and 500 mM imidazole). 35 µl of this elution buffer was also added to the input DNA. The input and the enriched DNA fractions were cleaned up using Qiagen PCR purification columns.

tag: protein

value: 6X His-tagged DvuA0137

tag: sample type

value: enriched fraction

source_name: Input DNA from RR DvuA0137 binding reaction

value: input fraction


title: DvuA0137-I

description:
DvuA0137-low
DAP-chip of DvuA0137 bound DNA / input DNA


title: adipose_tissue_IGT (15537)


title: adipose_tissue_IGT (15552)


title: DvuA0057

description:
DvuA0057
DAP-chip of DvuA0057 bound DNA / input DNA

source_name: RR DvuA0057bound enriched DNA

value: 6X His-tagged DvuA0057

source_name: Input DNA from RR DvuA0057 binding reaction


title: Dvu3381

description:
Dvu3381
DAP-chip of Dvu3381 bound DNA / input DNA

source_name: RR Dvu3381 bound enriched DNA

value: 6X His-tagged Dvu3381

source_name: Input DNA from RR Dvu3381 binding reaction


title: Dvu3023

description:
Dvu3023
DAP-chip of Dvu3023 bound DNA / input DNA

source_name: RR Dvu3023 bound enriched DNA

value: 6X His-tagged Dvu3023

source_name: Input DNA from RR Dvu3023 binding reaction


title: Dvu3334

description:
Dvu3334
DAP-chip of Dvu3334 bound DNA / input DNA

source_name: RR Dvu3334 bound enriched DNA

value: 6X His-tagged Dvu3334

source_name: Input DNA from RR Dvu3334 binding reaction


title: adipose_tissue_DM (15516)


title: Dvu2675-I

description:
Dvu2675-low
DAP-chip of Dvu2675 bound DNA / input DNA

source_name: RR Dvu2675 bound enriched DNA

value: 6X His-tagged Dvu2675

source_name: Input DNA from RR Dvu2675 binding reaction


title: adipose_tissue_NGT (15501)

source_name: subcutaneous adipose tissue


title: Dvu1083-III

description:
Dvu1083-III
DAP-chip of Dvu1083 bound DNA / input DNA

source_name: RR Dvu1083 bound enriched DNA

value: 6X His-tagged Dvu1083

source_name: Input DNA from RR Dvu1083 binding reaction


title: Dvu2675-II

description:
Dvu2675-medium
DAP-chip of Dvu2675 bound DNA / input DNA


title: Dvu2675-III

description:
Dvu2675-high
DAP-chip of Dvu2675 bound DNA / input DNA


title: Dvu3305

description:
Dvu3305
DAP-chip of Dvu3305 bound DNA / input DNA

source_name: RR Dvu3305 bound enriched DNA

value: 6X His-tagged Dvu3305

source_name: Input DNA from RR Dvu3305 binding reaction


title: Dvu1156

description:
Dvu1156
DAP-chip of Dvu1156 bound DNA / input DNA

source_name: RR Dvu1156 bound enriched DNA

value: 6X His-tagged Dvu1156

source_name: Input DNA from RR Dvu1156 binding reaction


title: adipose_tissue_NGT (15497)

value: NGT


title: Dvu2394

description:
Dvu2394
DAP-chip of Dvu2394 bound DNA / input DNA

source_name: RR Dvu2394 bound enriched DNA

value: 6X His-tagged Dvu2394

source_name: Input DNA from RR Dvu2394 binding reaction


title: Dvu2114

description:
Dvu2114
DAP-chip of Dvu2114 bound DNA / input DNA

source_name: RR Dvu2114 bound enriched DNA

value: 6X His-tagged Dvu2114

source_name: Input DNA from RR Dvu2114 binding reaction


title: Dvu2588

description:
Dvu2588
DAP-chip of Dvu2588 bound DNA / input DNA

source_name: RR Dvu2588 bound enriched DNA

value: 6X His-tagged Dvu2588

source_name: Input DNA from RR Dvu2588 binding reaction


title: Dvu1083-I

description:
Dvu1083-I
DAP-chip of Dvu1083 bound DNA / input DNA


title: adipose_tissue_NGT (15495)


title: Dvu2934

description:
Dvu2934
DAP-chip of Dvu2934 bound DNA / input DNA

source_name: RR Dvu2934 bound enriched DNA

value: 6X His-tagged Dvu2934

source_name: Input DNA from RR Dvu2934 binding reaction


title: Dvu1083-II

description:
Dvu1083-II
DAP-chip of Dvu1083 bound DNA / input DNA


title: Dvu1063

description:
Dvu1063
DAP-chip of Dvu1063 bound DNA / input DNA

source_name: RR Dvu1063 bound enriched DNA

value: 6X His-tagged Dvu1063

source_name: Input DNA from RR Dvu1063 binding reaction


title: Dvu0804

description:
Dvu0804
DAP-chip of Dvu0804 bound DNA / input DNA

source_name: RR Dvu0804 bound enriched DNA

value: 6X His-tagged Dvu0804

source_name: Input DNA from RR Dvu0804 binding reaction


title: iPS from WT fibroblast - cell line 1

city: Jerusalem

first: Yonatan

last: Stelzer

address: Givat-Ram

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem

description:
WT-HiPSC(1)
Gene expression data from iPS cell line 1 derived normal fibroblast

hyb_protocol: Affymetrix protocol, 11ug cRNA

scan_protocol: GeneChip scanner 3000 7G, GeneChip Operating Software v1.4

data_processing: Affymetrix Expression Console RMA

source_name: iPS cell line 1 derived from healthy individual

label_protocol: 200ng total RNA, Affymetrix protocol

growth_protocol: Cells were maintained on mitomycin C (MMC)-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium [DMEM/F12 (Invitrogen)

extract_protocol: total RNA from the parthenogenetic fibroblast and undifferentiated samples was isolated using RNA Extraction kit (RBC),  RNA from both normal iPS and HESCs was isolated using Qiagen Rneasy mini kit

treatment_protocol: total RNA was isolated from undifferentiated pluripotent stem cells grown in standard HESC growth conditions on mouse embryonic fibroblast feeder layer.

tag: gender

value: Male

value: undifferentiated induced pluripotent stem cell

value: wild type


title: H9 embryonic stem cell - biological replicate 3

description:
WT-HESC(3)
Gene expression data from H9 embryonic stem cells - biological replicate 3

value: Female

value: undifferentiated embryonic stem cell


title: Dvu0679

description:
Dvu0679
DAP-chip of Dvu0679 bound DNA / input DNA

source_name: RR Dvu0679 bound enriched DNA

value: 6X His-tagged Dvu0679

value: enriched fraction

source_name: Input DNA from RR Dvu0679 binding reaction

value: input fraction


title: ESC, biological rep3

city: Shanghai

first: Guohui

last: Ding

address: 320 Yueyang Road

country: China

institute: Shanghai Institutes for Biological Sciences

description:
Gene expression data from ES cells cell line E14
CB2009511_E14_3

hyb_protocol: 15 μg of aRNA were hybridized for 16 hr at 45℃ on the GeneChip Mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner GCS3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Mouse embryonic stem cells

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 2 μg total RNA (Affymetrix GeneChip® 3’ IVT Express Kit User Manual)

growth_protocol: ntESCs, iPSCs and iPSC-nt-ESCs were cultured on irradiated MEFs, in mESC medium containing leukaemia inhibitory factor (LIF), 15% FBS, nonessential amino acids, L-glutamine, Nucleosides, 2-mercaptoethanol and penicillin/streptomycin.

treatment_protocol: Cells were collected and pelleted before Trizol was added and stored in -80℃ before extraction.

value: male

value: ES cells cell line E14

tag: cell type

value: embryonic stem cells


title: normal fibroblast

description:
WT-Fib
Gene expression data from normal fibroblast

source_name: fibroblast from healthy individual

value: fibroblast


title: Dvu0946

description:
Dvu0946
DAP-chip of Dvu0946 bound DNA / input DNA

source_name: RR Dvu0946 bound enriched DNA

value: 6X His-tagged Dvu0946

source_name: Input DNA from RR Dvu0946 binding reaction


title: Dvu0744-I

description:
Dvu0744-low
DAP-chip of Dvu0744 bound DNA / input DNA

source_name: RR Dvu0744 bound enriched DNA

value: 6X His-tagged Dvu0744

source_name: Input DNA from RR Dvu0744 binding reaction


title: ESC, biological rep2

description:
Gene expression data from ES cells cell line E14
CB2009511_E14_2


title: H9 embryonic stem cell - biological replicate 1

description:
WT-HESC(1)
Gene expression data from H9 embryonic stem cells - biological replicate 1


title: iPS from WT fibroblast - cell line 2

description:
WT-HiPSC(2)
Gene expression data from iPS cell line2 derived normal fibroblast

source_name: iPS cell line 2 derived from healthy individual


title: Dvu0744-II

description:
Dvu0744-high
DAP-chip of Dvu0744 bound DNA / input DNA


title: Dvu0653-I

description:
Dvu0653-low
DAP-chip of Dvu0653 bound DNA / input DNA

source_name: RR Dvu0653 bound enriched DNA

value: 6X His-tagged Dvu0653

source_name: Input DNA from RR Dvu0653 binding reaction


title: H9 embryonic stem cell - biological replicate 2

description:
WT-HESC(2)
Gene expression data from H9 embryonic stem cells - biological replicate 2


title: iPS from fibroblast B - cell line 34

description:
PgHiPSC-B-34
Gene expression data from iPS cell line 41 derived from patient B

source_name: iPS cell line 34 derived from patient B

value: parthenogenetic


title: Dvu0621

description:
Dvu0621
DAP-chip of Dvu0621 bound DNA / input DNA

source_name: RR Dvu0621 bound enriched DNA

value: 6X His-tagged Dvu0621

source_name: Input DNA from RR Dvu0621 binding reaction


title: ESC, biological rep1

description:
Gene expression data from ES cells cell line E14
CB2009511_E14_1


title: iPS from fibroblast A - cell line 11

description:
PgHiPSC-A-11
Gene expression data from iPS cell line 11 derived from patient A

source_name: iPS cell line 11 derived from patient A


title: Dvu0749

description:
Dvu0749
DAP-chip of Dvu0749 bound DNA / input DNA

source_name: RR Dvu0749 bound enriched DNA

value: 6X His-tagged Dvu0749

source_name: Input DNA from RR Dvu0749 binding reaction


title: Fibroblast B

description:
Pg-Fib-B
Gene expression data from fibroblast - B

source_name: fibroblast derived from patient B


title: Dvu0596

description:
Dvu0596
DAP-chip of Dvu0596 bound DNA / input DNA

source_name: RR Dvu0596 bound enriched DNA

value: 6X His-tagged Dvu0596

source_name: Input DNA from RR Dvu0596 binding reaction


title: Dvu0653-II

description:
Dvu0653-high
DAP-chip of Dvu0653 bound DNA / input DNA


title: Dvu2577

description:
Dvu2577
DAP-chip of Dvu2577 bound DNA / input DNA

source_name: RR Dvu2577 bound enriched DNA

value: 6X His-tagged Dvu2577

source_name: Input DNA from RR Dvu2577 binding reaction


title: Dvu0539

description:
Dvu0539
DAP-chip of Dvu0539 bound DNA / input DNA

source_name: RR Dvu0539 bound enriched DNA

value: 6X His-tagged Dvu0539

source_name: Input DNA from RR Dvu0539 binding reaction


title: Dvu1419

description:
Dvu1419
DAP-chip of Dvu1419 bound DNA / input DNA

source_name: RR Dvu1419 bound enriched DNA

value: 6X His-tagged Dvu1419

source_name: Input DNA from RR Dvu1419 binding reaction


title: iPS from fibroblast B - cell line 36

description:
PgHiPSC-B-36
Gene expression data from iPS cell line 36 derived from patient B

source_name: iPS cell line 36 derived from patient B

value: Female

value: undifferentiated induced pluripotent stem cell


title: Fibroblast A

description:
Pg-Fib-A
Gene expression data from fibroblast - A

source_name: fibroblast derived from patient A


title: Dvu0118

description:
Dvu0118
DAP-chip of Dvu0118 bound DNA / input DNA

source_name: RR Dvu0118 bound enriched DNA

value: 6X His-tagged Dvu0118

value: enriched fraction

source_name: Input DNA from RR Dvu0118 binding reaction

value: input fraction


title: Dvu0110

description:
Dvu0110
DAP-chip of Dvu0110 bound DNA / input DNA

source_name: RR Dvu0110 bound enriched DNA

value: 6X His-tagged Dvu0110

source_name: Input DNA from RR Dvu0110 binding reaction


title: iPS from fibroblast B - cell line 41

description:
PgHiPSC-B-41
Gene expression data from iPS cell line 41 derived from patient B

source_name: iPS cell line 41 derived from patient B


title: TG, mouse2

city: San Francisco

first: Joseph

last: Shieh

address: 533 Parnassus Ave

institute: University of California San Francisco

hyb_protocol: Following fragmentation, samples were hybridized in a Genechip hybridization oven 640 using standard Affymetrix protocol

scan_protocol: Scanning was performed using a Genechip Scanner 3000

data_processing: RMA normalized signal

source_name: cardiac ventricle

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol

extract_protocol: Total RNA was isolated using guanidine thiocyanate and phenol extraction.

tag: genotype

value: miR-499 transgenic

tag: tissue

value: cardiac ventricle


title: E.coli_IVT-RNA_sigmaS

city: Segrate, Milano

first: Clelia

last: Peano

address: Via Fratelli Cervi 93

department: Institute of Biomedical Technologies

country: Italy

institute: National Research Council

hyb_protocol: The fragmented and labeled cDNAs were then hybridized for 16 h at 45°C on individual E.coli Genome 2.0 arrays.

scan_protocol: After hybridization, GeneChips were washed and stained with streptavidin-conjugated phycoerythrin by using the Fluidic Station FS450 (Affymetrix) according to the FS450_0006 Protocol. Fluorescent images of the arrays were acquired using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: After quality controls of data distribution the raw data (CEL files) were used to perform, normalization and probe set summarization through RMA algorithm (Robust Multiarray Analysis) by using the Affymetrix Gene Expression Console Software (www.affymetrix.com).   Normalized data were then uploaded into OneChannelGUI Software (http://www.bioinformatica.unito.it/oneChannelGUI/)  to perform a differential expression analysis. As the dataset is limited in number of samples and replicates (4 GeneChips hybridized, 2 replicates for each condition) we decided to apply a  simple non-parametric statistical method based on ranks of fold changes to perform a two-class paired differential analysis. To select only significatively differentially expressed genes we set the following parameters for the Rank Product analysis: 100 permutations and 0.1 cut-off percentage of false positives (pfp) which corresponds to a p-value<0.01.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: RNA produced by in vitro transcription, with RNA polymerase E σS, of 2 ug of genomic DNA from E. coli MG1655 digested with EcoRI

label_protocol: The RNA samples were processed for microarray hybridization, following the instructions of the GeneChip® Expression Analysis Technical Manual (Chapter 5,6 and 7, Prokaryotic target Preparation, Hybridization, Washing, Staining and Scanning). The protocol consists in cDNA synthesis by reverse transcription (starting in this case with 1 ug RNA), followed by cDNA fragmentation with DNase I and labeling with Terminal Deoxynucleotidyl Transferase.

extract_protocol: E. coli RNA polymerase core enzyme was purchased from Epicentre (Madison, WI, USA). Histidine-tagged σ factors were produced and purified as described (Lacour et al., 2003; Checroun et al., 2004); proteins appeared pure from contaminants as determined by denaturing protein gel electrophoresis (data not shown). For reconstitution of RNA polymerase holoenzymes, the core enzyme was incubated for 10 minutes at 37 °C with either σS or σ70 at a 1:10 ratio. For calculation of RNA polymerase concentrations in transcription assays, it was assumed that, after reconstitution, core enzyme would be 100% active and fully saturated by either σ factor. 2 ug of genomic DNA from E. coli MG1655 digested with EcoRI were used in transcription assays for ROMA experiments. RNA polymerase holoenzyme concentrations were 100 nM in 50 ul reaction mixture. Ten independent run-off transcription assays were performed, and transcripts were pooled together (ca. 1 ug total RNA).

value: cDNA produced by RT of RNA deriving from vitro transcription, with RNA polymerase E σS, of 2 ug of genomic DNA from E. coli MG1655 digested with EcoRI


title: iPS from fibroblast A - cell line 26

description:
PgHiPSC-A-26
Gene expression data from iPS cell line 26 derived from patient A

source_name: iPS cell line 26 derived from patient A


title: iPS from fibroblast A - cell line 20

description:
PgHiPSC-A-20
Gene expression data from iPS cell line 20 derived from patient A

source_name: iPS cell line 20 derived from patient A


title: E.coli_IVT-RNA_sigmaS-2


title: ntESC-1, biological rep3

description:
Gene expression data from ntES cells cell line NTM1_7
CB2009511_NT_m1_7_3

source_name: Mouse nuclear transfer ES cells

value: C57BL/6×129sv/Jae F1 ×129sv/Jae

value: male

value: ntES cells cell line NTM1_7

value: nuclear transfer ES cells


title: WT, mouse2

value: wild-type


title: TG, mouse1


title: ntESC-2, biological rep3

description:
Gene expression data from ntES cells cell line NTM2_4
CB2009511_NT_m2_4_3

value: ntES cells cell line NTM2_4


title: WT, mouse3


title: ntESC-2, biological rep2

description:
Gene expression data from ntES cells cell line NTM2_4
CB2009511_NT_m2_4_2


title: TG, mouse3


title: ntESC-2, biological rep1

description:
Gene expression data from ntES cells cell line NTM2_4
CB2009511_NT_m2_4_1


title: WT, mouse1


title: ntESC-1, biological rep2

description:
Gene expression data from ntES cells cell line NTM1_7
CB2009511_NT_m1_7_2


title: E.coli_IVT-RNA_sigma70-1

source_name: RNA produced by in vitro transcription, with RNA polymerase E σ70, of 2 ug of genomic DNA from E. coli MG1655 digested with EcoRI

value: cDNA produced by RT of RNA deriving from vitro transcription, with RNA polymerase E σ70, of 2 ug of genomic DNA from E. coli MG1655 digested with EcoRI


title: ntESC-1, biological rep1

description:
Gene expression data from ntES cells cell line NTM1_7
CB2009511_NT_m1_7_1


title: control culture 20 hr, biological rep 2

city: Galveston

first: Sarah

middle: L

last: Castro

state: TX

address: 301 University Blvd

institute: University of Texas Medical Branch

description: Gene expression data from S. aureus cultured in control orientated RWV bioreactor

hyb_protocol: 2 mg of labeled cDNA product was hybridizied for 16 hours at 45°C to the S. aureus Genome Array.  GeneChips were washed and stained on the GeneChip Fluidics Station 450.

scan_protocol: Fluorescence was detected with an Affymetrix-GS3000 Gene Array scanner. The arrays were hybridized, washed, stained, and scanned according to the directions detailed in the Affymetrix GeneChip Expression Analysis Technical Manual (http://www.affymetrix.com/support/support_result.affx.).

data_processing: The data were analyzed by GeneChip Operating Software (GCOS) version 1.4 using a global scaling strategy and running a comparison analysis.

organism: Staphylococcus aureus subsp. aureus N315

source_name: S. aureus control culture 20 hrs

label_protocol: cDNA were prepared according to the Affymetrix Prokaryotic Target Preparation protocol from 10µg of total RNA (Expression Analysis Technical Manual). Following cDNA fragmentation, the products were terminally labeled using the biotinylated GeneChip DNA Labeling Reagent.

growth_protocol: S. aureus was cultured in RWV bioreactors in tryptic soy broth growth media for 20 hours at 37 degrees C.  Rotation of RWVs was maintained at 25 rev/min.

extract_protocol: Total RNA was extracted using Rneasy mini kit (Qiagen) per manufacturer’s instructions.

treatment_protocol: Staphylococcal cells were removed from vessels at 20 hours and placed into RNAprotect (Qiagen).

tag: growth phase

value: stationary

tag: treatment

value: control


title: low-shear culture 20 hr, biological rep 1

description: Gene expression data from S. aureus cultured in low-shear orientated RWV bioreactor

source_name: S. aureus low-shear culture 20 hrs

value: low shear


title: low-shear culture 20 hr, biological rep 2


title: iPSC-4, biological rep2

description:
Gene expression data from iPS cell line iPSM2_4
CB2009511_ips_m2_4_2

source_name: Mouse induced pluripotent stem cells

tag: cell line

value: iPS cell line iPSM2_4

value: induced pluripotent stem cells


title: iPSC-4, biological rep3

description:
Gene expression data from iPS cell line iPSM2_4
CB2009511_ips_m2_4_3


title: E.coli_IVT-RNA_sigma70-2


title: iPSC-4, biological rep1

description:
Gene expression data from iPS cell line iPSM2_4
CB2009511_ips_m2_4_1


title: control culture 20 hr, biological rep 1


title: iPSC-3, biological rep2

description:
Gene expression data from iPS cell line iPSM2_3
CB2009511_ips_m2_3_2

value: iPS cell line iPSM2_3


title: iPSC-3, biological rep3

description:
Gene expression data from iPS cell line iPSM2_3
CB2009511_ips_m2_3_3


title: HK-2 cells, 0hrs_rep2

city: Belfast

first: Derek

middle: P

last: Brazil

address: Grosvenor Road

institute: Queen's University

description:
Gene expression data from hk-2 cells treated with TGFß1, t=0hrs.
SR4

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized on the Affymetrix GeneChip HGU133A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station according to the EukGE-WS2 protocol.

scan_protocol: GeneChips were scanned twice at 3m resolution using the Affymetrix GeneChip System confocal scanner.

data_processing: The data were quality checked and analyzed using the R programming language.  The GCRMA algorithm was used for background correction and normalization.

source_name: HK-2 cells

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

growth_protocol: HK-2 cells were cultured at 37 °C in a humidified atmosphere of 95% air/5% CO2, and maintained in DMEM-F12 supplemented with 2 mM L-glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin, 10 ng/ml EGF, 36 ng/ml hydrocortisone, 4 pg/ml triiodothyronine and 5 μg/ml insulin–transferrin–selenium solution. Cells were subcultured using trypsin–EDTA at a ratio of 1:5.

extract_protocol: Total RNA was isolated using the Trizol method and purified on Qiagen RNeasy columns

treatment_protocol: HK-2 cells were plated in triplicate for stimulation with TGFβ1 for 0, 24 or 48 h.  This experiment was carried out three times on different days, with triplicate samples for each time point being pooled on each occasion.

value: human kidney proximal tubule epithelial cell line HK-2

tag: agent

value: untreated

tag: time


title: iPSC-3, biological rep1

description:
Gene expression data from iPS cell line iPSM2_3
CB2009511_ips_m2_3_1


title: HK-2 cells, 24hrs_rep2

description:
Gene expression data from hk-2 cells treated with TGFß1, t=24hrs.
SR5


title: HK-2 cells, 48hrs_rep3

description:
Gene expression data from hk-2 cells treated with TGFß1, t=48hrs.
SR9


title: HK-2 cells, 48hrs_rep1

description:
Gene expression data from hk-2 cells treated with TGFß1, t=48hrs.
SR3


title: iPSC-2, biological rep2

description:
Gene expression data from iPS cell line iPSM1_8
CB2009511_ips_m1_8_2

value: iPS cell line iPSM1_8


title: pre-treatment tumor biopsy HSP_01B13442

city: Barcelona

first: MIGUEL ANGEL

last: PAVON

state: Barcelona

address: Sant Antoni Maria Claret, 167

department: INSTITUT INVESTIGACIÓ BIOMÉDICA SANT PAU

country: Spain

institute: HOSPITAL DE LA SANTA CREU I SANT PAU

description:
Gene expression data from a pre-treatment tumor biopsy
Patients included in our microarray study (n=63) were treated from 1999 to 2007 at Hospital de la Santa Creu i Sant Pau (HSCSP). All had a pathologically confirmed, untreated, locally advanced (stage III, IVA & IVB) HNSCC. Patients defined as not operable at diagnosis were treated with concomitant CRT (stage IVB), whereas operable patients (stage III or IVA) were treated with IC followed by CRT/RT or surgery.  Induction Chemotherapy consisted on the administration of cisplatin at a dose of 100 mg/m2 on day 1, and 5-FU at a dose of 1,000 mg/m2/day by continuous intravenous infusion on days 2 to 6 every 3 weeks, per three courses.   After IC, patients whose tumour showed a complete response or a partial response above 50% received radiotherapy (IC+RT) or chemo radiotherapy (IC+CRT). Patients with stable or progressive disease after IC were treated with surgery (IC+SURGERY). Radiotherapy, at a total dose of 70 Gy, was administered to the primary tumor and clinically positive nodes, in 35 fractions of 2 Gy each, over a 7-week period. Nodal areas not clinically involved by tumor received a total dose of 50 Gy. Concomitant chemo radiotherapy (cCRT) consisted in RT at the same doses plus 3 cycles of cisplatin at a dose of 100mg/m2 on day 1 every 3 weeks.
Probe microarray washing and staining was performed in a Fluidics Station 450 applying the midi_euk2v3_450 protocol.

hyb_protocol: Ten micrograms of biotinylated cRNA, previously fragmented, were hybridized to the Affymetrix HG-U133A 2.0 microarray at 45ºC for 16 hours in the Affymetrix hybridization oven.

scan_protocol: Microarrays were scanned using a Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA, USA).The acquisition of microarray images was performed using GCOS software

data_processing: All the microarrays “.CEL” files included in the study were pre-processed applying the Robust Multi-array Average (RMA) algorithm (Irizarry, Hobbs et al. 2003) implemented in the Bioconductor statistical affy package  (http://www.bioconductor.org).

source_name: pre-treatment tumor biopsy

label_protocol: cDNA and cRNA synthesis were performed using 2μg of total RNA from each biopsy as starting material and the GeneChip One-Cycle Target Labelling and Control Reagents Kit, following the instructions described in the Affymetrix user’s manual (Affymetrix, Santa Clara, CA, USA). After “in vitro” transcription, we obtained biotinylated cRNA. cRNA quality was checked using the Agilent 2100 Bioanalyzer.

extract_protocol: The study was performed using 63 fresh pre-treatment primary tumor biopsies and five normal mucosa samples obtained from HNSCC patients. A sample aliquot was used for pathological diagnosis of the malignancy and another aliquot was immersed in RNAlater (Applied Biosystems Incorp, Foster City, CA), frozen in cold isopentane and kept in liquid nitrogen until RNA processing. Total RNA was extracted with Trizol (Invitrogen Ltd, Paisley, UK) and the phenol-chloroform method as previously described (Pavon, Parreno et al. 2008). Samples were, then, cleaned-up using RNeasy® Spin columns (Qiagen Incorp, Valencia, CA). Total RNA was quantified spectrophotometrically. The Agilent 2100 Bioanalyzer and the RNA Nano 6000 kit (Agilent Technologies, Santa Clara, USA) were used to determine the integrity of total RNA samples. Only samples with an RNA integrity number (RIN) higher than seven were included.

tag: sex

tag: tumor size (t)

tag: node involvement (n)

value: POSITIVE

tag: distant metastasis (m)

value: NEGATIVE

tag: patient treatment plan

value: IC+SURGERY

value: HNSCC tumor


title: HK-2 cells, 0hrs_rep3

description:
Gene expression data from hk-2 cells treated with TGFß1, t=0hrs.
SR7


title: HK-2 cells, 48hrs_rep2

description:
Gene expression data from hk-2 cells treated with TGFß1, t=48hrs.
SR6


title: normal mucosa HSP_M6

description:
Gene expression data from a normal mucosa biopsy
Patients included in our microarray study (n=63) were treated from 1999 to 2007 at Hospital de la Santa Creu i Sant Pau (HSCSP). All had a pathologically confirmed, untreated, locally advanced (stage III, IVA & IVB) HNSCC. Patients defined as not operable at diagnosis were treated with concomitant CRT (stage IVB), whereas operable patients (stage III or IVA) were treated with IC followed by CRT/RT or surgery.  Induction Chemotherapy consisted on the administration of cisplatin at a dose of 100 mg/m2 on day 1, and 5-FU at a dose of 1,000 mg/m2/day by continuous intravenous infusion on days 2 to 6 every 3 weeks, per three courses.   After IC, patients whose tumour showed a complete response or a partial response above 50% received radiotherapy (IC+RT) or chemo radiotherapy (IC+CRT). Patients with stable or progressive disease after IC were treated with surgery (IC+SURGERY). Radiotherapy, at a total dose of 70 Gy, was administered to the primary tumor and clinically positive nodes, in 35 fractions of 2 Gy each, over a 7-week period. Nodal areas not clinically involved by tumor received a total dose of 50 Gy. Concomitant chemo radiotherapy (cCRT) consisted in RT at the same doses plus 3 cycles of cisplatin at a dose of 100mg/m2 on day 1 every 3 weeks.
Probe microarray washing and staining was performed in a Fluidics Station 450 applying the midi_euk2v3_450 protocol.

source_name: normal mucosa biopsy

value: normal mucosa


title: normal mucosa HSP_M19


title: normal mucosa HSP_M4


title: MOLM-14 SAHA, biological rep1

city: Singapore

first: Jianbiao

last: Zhou

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute Singapore

description: MOLM-14 cells were treated with SAHA.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the affymetrix scanner

data_processing: The data were analyzed with Genespring GX7.3.1

source_name: MOLM-14 SAHA treated

extract_protocol: RNeasy Midi Kit (Qiagen)

treatment_protocol: DMSO, ABT-869, SAHA or Combinaiton (ABT-869 + SAHA)

value: AML cells


title: MOLM-14 Combination, biological rep3

description: MOLM-14 cells were treated with ABT-869 and SAHA.

source_name: MOLM-14 Combination treatment


title: HK-2 cells, 24hrs_rep1

description:
Gene expression data from hk-2 cells treated with TGFß1, t=24hrs.
SR2


title: HK-2 cells, 24hrs_rep3

description:
Gene expression data from hk-2 cells treated with TGFß1, t=24hrs.
SR8


title: MOLM-14 Combination, biological rep2


title: HK-2 cells, 0hrs_rep1

description:
Gene expression data from hk-2 cells treated with TGFß1, t=0hrs.
SR1


title: iPSC-1, biological rep2

description:
Gene expression data from iPS cell line iPSM1_6
CB2009511_ips_m1_6_2

tag: strain

value: C57BL/6×129sv/Jae F1 ×129sv/Jae

value: male

value: iPS cell line iPSM1_6


title: MOLM-14 SAHA, biological rep3

description: MOLM-14 cells were treated with SAHA.


title: MOLM-14 Combination, biological rep1


title: pre-treatment tumor biopsy HSP_99B12984


title: iPSC-2, biological rep3

description:
Gene expression data from iPS cell line iPSM1_8
CB2009511_ips_m1_8_3


title: normal mucosa HSP_M12


title: normal mucosa HSP_M5


title: iPSC-1, biological rep3

description:
Gene expression data from iPS cell line iPSM1_6
CB2009511_ips_m1_6_3


title: MOLM-14 SAHA, biological rep2

description: MOLM-14 cells were treated with SAHA.


title: iPSC-2, biological rep1

description:
Gene expression data from iPS cell line iPSM1_8
CB2009511_ips_m1_8_1


title: pre-treatment tumor biopsy HSP_01B10919

value: IC+RT


title: MOLM-14 ABT-869, biological rep3

description: MOLM-14 cells were treated with ABT-869.

source_name: MOLM-14 ABT-869 treated


title: pre-treatment tumor biopsy HSP_00B218


title: MOLM-14 ABT-869, biological rep2


title: pre-treatment tumor biopsy HSP_481

value: CRT


title: pre-treatment tumor biopsy HSP_479


title: pre-treatment tumor biopsy HSP_463


title: pre-treatment tumor biopsy HSP_461

value: female


title: pre-treatment tumor biopsy HSP_01B8875


title: iPSC-nt-ESC-3, biological rep3

description:
Gene expression data from ntiPS cell line ntiPSM2_3_3
BH2010115_NTipsm2_3_3_3

source_name: Mouse nuclear transfer ES cells from induced pluripotent stem cells

value: ntiPS cell line ntiPSM2_3_3


title: MOLM-14 ABT-869, biological rep1


title: pre-treatment tumor biopsy HSP_456


title: pre-treatment tumor biopsy HSP_438

value: IC+CRT


title: pre-treatment tumor biopsy HSP_445


title: pre-treatment tumor biopsy HSP_441


title: pre-treatment tumor biopsy HSP_444


title: iPSC-nt-ESC-3, biological rep1

description:
Gene expression data from ntiPS cell line ntiPSM2_3_3
BH2010115_NTipsm2_3_3_1

value: nuclear transfer ES cells from induced pluripotent stem cells


title: iPSC-nt-ESC-4, biological rep1

description:
Gene expression data from ntiPS cell line ntiPSM2_4_3
BH2010115_NTipsm2_4_3_1

value: ntiPS cell line ntiPSM2_4_3


title: MV4-11 Combination, biological rep2

description: MV4-11 cells were treated with ABT-869 and SAHA.

source_name: MV4-11 Combination treatment


title: pre-treatment tumor biopsy HSP_433

description:
Gene expression data from a pre-treatment tumor biopsy
Patients included in our microarray study (n=63) were treated from 1999 to 2007 at Hospital de la Santa Creu i Sant Pau (HSCSP). All had a pathologically confirmed, untreated, locally advanced (stage III, IVA & IVB) HNSCC. Patients defined as not operable at diagnosis were treated with concomitant CRT (stage IVB), whereas operable patients (stage III or IVA) were treated with IC followed by CRT/RT or surgery.  Induction Chemotherapy consisted on the administration of cisplatin at a dose of 100 mg/m2 on day 1, and 5-FU at a dose of 1,000 mg/m2/day by continuous intravenous infusion on days 2 to 6 every 3 weeks, per three courses.   After IC, patients whose tumour showed a complete response or a partial response above 50% received radiotherapy (IC+RT) or chemo radiotherapy (IC+CRT). Patients with stable or progressive disease after IC were treated with surgery (IC+SURGERY). Radiotherapy, at a total dose of 70 Gy, was administered to the primary tumor and clinically positive nodes, in 35 fractions of 2 Gy each, over a 7-week period. Nodal areas not clinically involved by tumor received a total dose of 50 Gy. Concomitant chemo radiotherapy (cCRT) consisted in RT at the same doses plus 3 cycles of cisplatin at a dose of 100mg/m2 on day 1 every 3 weeks.
Probe microarray washing and staining was performed in a Fluidics Station 450 applying the midi_euk2v3_450 protocol.


title: iPSC-nt-ESC-3, biological rep2

description:
Gene expression data from ntiPS cell line ntiPSM2_3_3
BH2010115_NTipsm2_3_3_2


title: MOLM-14 Control, biological rep2

description: MOLM-14 cells were treated with DMSO as control.

source_name: MOLM-14 DMSO treated


title: iPSC-1, biological rep1

description:
Gene expression data from iPS cell line iPSM1_6
CB2009511_ips_m1_6_1

value: induced pluripotent stem cells


title: MOLM-14 Control, biological rep3


title: pre-treatment tumor biopsy HSP_431

value: POSITIVE


title: pre-treatment tumor biopsy HSP_454

value: NEGATIVE


title: pre-treatment tumor biopsy HSP_439


title: MOLM-14 Control, biological rep1


title: iPSC-nt-ESC-2, biological rep3

description:
Gene expression data from ntiPS cell line ntiPSM1_8_3
BH2010115_NTipsm1_8_3_3

value: ntiPS cell line ntiPSM1_8_3


title: MV4-11 Combination, biological rep3


title: iPSC-nt-ESC-4, biological rep3

description:
Gene expression data from ntiPS cell line ntiPSM2_4_3
BH2010115_NTipsm2_4_3_3


title: iPSC-nt-ESC-4, biological rep2

description:
Gene expression data from ntiPS cell line ntiPSM2_4_3
BH2010115_NTipsm2_4_3_2


title: iPSC-nt-ESC-2, biological rep2

description:
Gene expression data from ntiPS cell line ntiPSM1_8_3
BH2010115_NTipsm1_8_3_2


title: pre-treatment tumor biopsy HSP_417

value: HNSCC tumor


title: pre-treatment tumor biopsy HSP_389


title: pre-treatment tumor biopsy HSP_390


title: pre-treatment tumor biopsy HSP_391


title: MV4-11 SAHA, biological rep3

description: MV4-11 cells were treated with SAHA.

source_name: MV4-11 SAHA treated


title: pre-treatment tumor biopsy HSP_370


title: MV4-11 ABT-869, biological rep2

description: MV4-11 cells were treated with ABT-869.

source_name: MV4-11 ABT-869 treated


title: pre-treatment tumor biopsy HSP_414

value: IC+SURGERY


title: pre-treatment tumor biopsy HSP_383


title: pre-treatment tumor biopsy HSP_397


title: iPSC-nt-ESC-2, biological rep1

description:
Gene expression data from ntiPS cell line ntiPSM1_8_3
BH2010115_NTipsm1_8_3_1


title: MV4-11 ABT-869, biological rep3

description: MV4-11 cells were treated with ABT-869.

value: AML cells


title: MV4-11 SAHA, biological rep2

description: MV4-11 cells were treated with SAHA.


title: pre-treatment tumor biopsy HSP_386


title: pre-treatment tumor biopsy HSP_357


title: iPSC-nt-ESC-1, biological rep1

description:
Gene expression data from ntiPS cell line ntiPSM1_6_5
BH2010115_NTipsm1_6_5_1

value: C57BL/6×129sv/Jae F1 ×129sv/Jae

value: ntiPS cell line ntiPSM1_6_5


title: MV4-11 SAHA, biological rep1

description: MV4-11 cells were treated with SAHA.


title: iPSC-nt-ESC-1, biological rep3

description:
Gene expression data from ntiPS cell line ntiPSM1_6_5
BH2010115_NTipsm1_6_5_3

value: male


title: pre-treatment tumor biopsy HSP_382


title: pre-treatment tumor biopsy HSP_377


title: pre-treatment tumor biopsy HSP_379


title: MV4-11 ABT-869, biological rep1

description: MV4-11 cells were treated with ABT-869.


title: MV4-11 Control, biological rep3

description: MV4-11 cells were treated with DMSO as control.

source_name: MV4-11 DMSO treated


title: iPSC-nt-ESC-1, biological rep2

description:
Gene expression data from ntiPS cell line ntiPSM1_6_5
BH2010115_NTipsm1_6_5_2


title: Blast-infected BC10, 48 hours, replicate3

city: Sapporo

first: Kouji

last: Satoh

state: Hokkaido

address: Hitsujigaoka 1

country: Japan

institute: NARO/HARC

description: Biological replicate 3 of 3, Blast-infected BC10 after 48 hours.

hyb_protocol: hybridization_Kit: in situ hybridization plus hybridization_Manufacturer: Agilent Technologies hybridization_Manual: Agilent Technologies

scan_protocol: Scanner: Agilent DNA microarray Scaner Manufacturer: Agilent Technologies Software: Scanner Control software Manual: Agilent Technologies

data_processing:
Software: Feature Extraction ver 9.5
Manufacturer: Agilent Technologies
Manual: Agilent Technologies

organism: Oryza sativa Indica Group

source_name: Blast-infected BC10, 48hours

label_protocol:
Kit: Low RNA Input Linear Amplification kit
Manufacturer: Agilent Technologies
Manual: Low RNA Input Linear Amplification kit standard protocol

growth_protocol:
Growth environment: greenhouse
Growth: pot culture (W:21.59cm ×D:11.43cm × H:8.89cm)
Growth media: Soil collected fielf of International Rice Research Institute, Philippines. Autoclaved prior to use
No of seedlings per pot : 15
Light condition: Natural conditions
Temperature: 28±3℃
Growth time (before treatment): 21 days after sowing
Growth time (after treatment): 24 hours

extract_protocol:
separation: trimming
extraction source: frozen
extraction source: shoots pooled from 5 individual plants
kit: TRIzol
manual: Invitrogen

treatment_protocol:
Treatment method: spray inoculation
Growth environment: greenhouse
Growth stage:  21-day-old plant
Light condition: Continuous dark
Temperature: 25℃
Humidity: 100%
Fungus inoculation: Magnaporthe oryzae, strain PO6-6
Fungus inoculation: spraying water suspended of 7 ×10e5 spores/ml
Fungus inoculation: 24hours

tag: cultivar

value: indica

value: whole plant

tag: plant height

value: 5 cm above ground

source_name: Mock inoculation BC10, 48hours

growth_protocol:
Growth environment: greenhouse
Growth: pot culture (W:21.59cm ×D:11.43cm × H:8.89cm)
Growth media: Soil collected fielf of InternationAu Rice Research Institute, Philippines. Auutoclaved prior to use
No of seedlings per pot : 15
Light condition: Natural conditions
Temperature: 28±3℃
Growth time (before treatment): 21 days after sowing
Growth time (after treatment): 24 hours

treatment_protocol:
Treatment method: spray inoculation
Growth environment: greenhouse
Growth stage:  21-day-old plant
Light condition: Continuous dark
Temperature: 25℃
Humidity: 100%
Mock inoculation: sterile distilled water
Mock inoculation: spraying water
Mock inoculation: 24hours


title: EC1118 Second-fermentation sample point 3_1

city: LOGROÑO

first: Vanessa

last: Penacho

state: LA RIOJA

address: c/ Madre de Dios, 51

department: Oenology & Viticulture

institute: ICVV/CSIC

hyb_protocol: 15 μg of cRNA were fragmented and hybridized to the Affymetrix GeneChip® Yeast Genome 2.0. Array in GeneChip® Hybridization Oven 640 for 16 h at 45°C. Hybridized microarrays were washed and stained with a streptavidin-phycoerythrin conjugate (SAPE) in a GeneChip® Fluidics Station 450.

scan_protocol: Hybridized cRNA was finally identified by the fluorescence signal in a GeneChip® 3000 scanner.

data_processing: The .CEL files generated from the scanning were converted to gene expression signals using the RMA software (Irizarry et al., 2003).

label: Biotin

organism: Saccharomyces cerevisiae

label_protocol: Double stranded cDNA was synthesized from 5 μg of total RNA using Onecycle cDNA Synthesis Kit (Affymetrix). After cDNA purification using the GeneChip Sample Cleanup Module (Affymetrix), this DNA was used as template for the in vitro transcription using the 3' IVT Express Labeling Kit (Affymetrix) to obtain the biotin labelled cRNA. Its size profile is evaluated with Bioanalyzer 6000.

growth_protocol: Second-fermentation assays were performed as described by Cebollero and Gonzalez (2006). 100 mL of YPD were inoculated to obtain a concentration of 10^5 cells/mL using an overnight S. cerevisiae EC1118 culture. After 48 h of incubation at 28 ºC and 150 rpm, cells were inoculated into fresh adaptation medium (0.08 g/L diammonium phosphate, 2.4 g/L tartaric acid, 20 g/L sucrose, 482 mL/L base wine from Cavas Freixenet, Sant Sadurní D’Anoia, Spain) to obtain a concentration of 10^6 cells/mL. The cells were incubated for 4 to 5 days at 28 ºC and 150 rpm, and base wine with sucrose (20 g/L) was subsequently inoculated at a concentration of 10^6 cells/mL with cells adapted to ethanol. Twenty litres of the base wine were bottled with 350 mL each one. All were sealed and incubated in static conditions at 16 ºC for approximately 40 days after tirage. Fermentation time course was monitored by weight loss evolution and ethanol increase.

extract_protocol: RNA was extracted from yeast cells exactly as previously described in Chomczynski and Sacchi (1987). Total RNA was then purified using the RNeasy Mini Kit-RNA Cleanup (Qiagen) according to the manufacturer's instructions. Concentration of total RNA was measured at 260 nm in a ND-1000 Spectrophotometer (Nanodrop, Thermo Fisher Scientific Inc.) and sample quality was checked using RNA Nano Labchips in a Bioanalyzer 6000 (Agilent Technologies).

value: EC1118 (Lallemand Inc.)

tag: sampling

value: second-fermentation sample obtained from an independant tirage assay at 19th day, with an ethanol increase of 1.27%

tag: sampling point

tag: biological replicate


title: EC1118 Second-fermentation sample point 3_2


title: EC1118 Second-fermentation sample point 3_3


title: MV4-11 Combination, biological rep1

tag: cell type


title: pre-treatment tumor biopsy HSP_343

value: female

value: IC+CRT

tag: tissue


title: pre-treatment tumor biopsy HSP_338


title: EC1118 Second-fermentation sample point 2_3

value: second-fermentation sample obtained from an independant tirage assay at 15th day, with an ethanol increase of 0.89%


title: EC1118 Second-fermentation sample point 1_3

value: second-fermentation sample obtained from an independant tirage assay at 7th day, with an ethanol increase of 0.26%


title: pre-treatment tumor biopsy HSP_477

value: POSITIVE

value: NEGATIVE


title: Blast-infected BC10, 48 hours, replicate2

description: Biological replicate 2 of 3, Blast-infected BC10 after 48 hours.


title: EC1118 Second-fermentation sample point 1_2


title: EC1118 Second-fermentation sample point 2_1


title: EC1118 Second-fermentation sample point 2_2


title: pre-treatment tumor biopsy HSP_327

value: IC+RT

value: HNSCC tumor


title: MV4-11 Control, biological rep2

value: AML cells


title: Day14_infected_rep1 _Dchip

city: South Bend

first: Kasturi

last: Haldar

email: khaldar@nd.edu, ptamez@nd.edu

state: IN

address: 107 Galvin Life Sciences

department: Biology

institute: University of Notre Dame

description: Gene expression data from differentiating hematopoietic stem cells that are preparing to extrude the nucleus and infected

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 plus 2.0 Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with 2 programs, GenePattern and Dchip. For GenePattern, Data were normalized with RMA using the “ExpressionFileCreator” module and filtered using the default settings of “PreprocessDataset” module. Dchip data were normalized using model-based expression and default settings.

source_name: CD34+-derived Hematopoietic stem cells in vitro differentiated to day 14, infected with Plasmodium falciparum for 24 h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA.

growth_protocol: Human primary erythroblasts were generated by culturing CD34 early hematopoietic progenitors initially isolated from growth factor-mobilized peripheral blood (purchased from ALL Cells, Inc.) using an Isolex 300i cell selection device. The culture contained 15% fetal bovine serum, 15% human serum, Isocove’s modified Dulbecco’s medium (IMDM), 10 ng/ml interleukin-3, 2 units/ml EPO, and 50 ng/ml SCF. During the  initial 8 days of culture, cells were fed on days 3 and 6 by adding equal volumes of fresh culture media supplemented with growth factors. However, no new interleukin-3 was added after the initial addition on day 0, and the amount of SCF added to the fresh media was gradually decreased at each feeding (day 3, 25 ng/ml; day 6, 10 ng/ml; day 8, 2 ng/ml). The amount of EPO added was 2 units/ml during each feeding. On day 8 of culture, cells were further purified by flow cytometry sorting for GlyA/CD71 or CD71 cells using a MoFlo high speed flow cytometer.  The purity of the population isolated by this method was 98–99%. Sorted cells were cultured in the same media as before with EPO and SCF, except the concentration of SCF was reduced to 2 ng/ml. Cells were fed one more time on day 10 of culture by adding equal volumes of fresh media with only EPO (2 units/ml) during this final feeding.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was purified over Qiagen columns (Rneasy) according to manufacturer's recommendations

treatment_protocol: Plasmodium falciparum 3D7 was synchronized by successive rounds of Percoll and sorbitol. Late stage schizonts were used to initiate infection of 2x10^6 erythroblasts at a multiplicity of infection =5. Erythroblasts were infected on day 10 (polychromatic stage) and day 14 (orthochromatic) of culture. Cells were resuspended at 1x10^6/ml in Iscove’s Modified Dulbecco’s Medium supplemented with 30% human serum and 2 units/ml EPO and incubated in 5% CO2-humidified chamber at 37ºC. Cells were harvested after 24 hr for RNA isolation.

value: growth factor-mobilized CD34+ hematopoietic stem cells

tag: developmental stage

value: differentiated to day 14 (orthochromatic stage)


title: pre-treatment tumor biopsy HSP_319

value: CRT


title: EC1118 Second-fermentation sample point 1_1


title: pre-treatment tumor biopsy HSP_323

value: male


title: Blast-infected BC10, 24 hours, replicate3

description: Biological replicate 3 of 3, Blast-infected BC10 after 24 hours.

source_name: Blast-infected BC10, 24hours

growth_protocol:
Growth environment: greenhouse
Growth: pot culture (W:21.59cm ×D:11.43cm × H:8.89cm)
Growth media: Soil collected fielf of International Rice Research Institute, Philippines. Autoclaved prior to use
No of seedlings per pot : 15
Light condition: Natural conditions
Temperature: 28±3℃
Growth time (before treatment): 21 days after sowing
Growth time (after treatment): 0 hour

value: indica

value: whole plant

source_name: Mock inoculation BC10, 24hours

growth_protocol:
Growth environment: greenhouse
Growth: pot culture (W:21.59cm ×D:11.43cm × H:8.89cm)
Growth media: Soil collected fielf of InternationAu Rice Research Institute, Philippines. Auutoclaved prior to use
No of seedlings per pot : 15
Light condition: Natural conditions
Temperature: 28±3℃
Growth time (before treatment): 21 days after sowing
Growth time (after treatment): 0 hour


title: pre-treatment tumor biopsy HSP_312

description:
Gene expression data from a pre-treatment tumor biopsy
Patients included in our microarray study (n=63) were treated from 1999 to 2007 at Hospital de la Santa Creu i Sant Pau (HSCSP). All had a pathologically confirmed, untreated, locally advanced (stage III, IVA & IVB) HNSCC. Patients defined as not operable at diagnosis were treated with concomitant CRT (stage IVB), whereas operable patients (stage III or IVA) were treated with IC followed by CRT/RT or surgery.  Induction Chemotherapy consisted on the administration of cisplatin at a dose of 100 mg/m2 on day 1, and 5-FU at a dose of 1,000 mg/m2/day by continuous intravenous infusion on days 2 to 6 every 3 weeks, per three courses.   After IC, patients whose tumour showed a complete response or a partial response above 50% received radiotherapy (IC+RT) or chemo radiotherapy (IC+CRT). Patients with stable or progressive disease after IC were treated with surgery (IC+SURGERY). Radiotherapy, at a total dose of 70 Gy, was administered to the primary tumor and clinically positive nodes, in 35 fractions of 2 Gy each, over a 7-week period. Nodal areas not clinically involved by tumor received a total dose of 50 Gy. Concomitant chemo radiotherapy (cCRT) consisted in RT at the same doses plus 3 cycles of cisplatin at a dose of 100mg/m2 on day 1 every 3 weeks.
Probe microarray washing and staining was performed in a Fluidics Station 450 applying the midi_euk2v3_450 protocol.


title: Day14_infected_rep2 _Dchip


title: Blast-infected BC10, 24 hours, replicate2

description: Biological replicate 2 of 3, Blast-infected BC10 after 24 hours.

value: 5 cm above ground


title: Blast-infected BC10, 48 hours, replicate1

description: Biological replicate 1 of 3, Blast-infected BC10 after 48 hours.


title: Day14_infected_rep3 _Dchip


title: MV4-11 Control, biological rep1

tag: cell line


title: Blast-infected SHZ-2, 48 hours, replicate3

description: Biological replicate 3 of 3, Blast-infected SHZ-2 after 48 hours.

source_name: Blast-infected SHZ, 48hours

source_name: Mock inoculation SHZ, 48hours


title: pre-treatment tumor biopsy HSP_330

source_name: pre-treatment tumor biopsy


title: Blast-infected BC10, 24 hours, replicate1

description: Biological replicate 1 of 3, Blast-infected BC10 after 24 hours.


title: Day14_uninfected_rep2 _Dchip

description: Gene expression data from differentiating hematopoietic stem cells that are preparing to extrude the nucleus

source_name: CD34+-derived Hematopoietic stem cells in vitro differentiated to day 14, uninfected


title: Day14_uninfected_rep3 _Dchip


title: pre-treatment tumor biopsy HSP_309


title: pre-treatment tumor biopsy HSP_293


title: Blast-infected SHZ-2, 48 hours, replicate2

description: Biological replicate 2 of 3, Blast-infected SHZ-2 after 48 hours.


title: pre-treatment tumor biopsy HSP_283


title: Day10_infected_rep2 _Dchip

description: Gene expression data from differentiating hematopoietic stem cells that are mitotic and infected

source_name: CD34+-derived Hematopoietic stem cells in vitro differentiated to day 10, infected with Plasmodium falciparum for 24 h

value: differentiated to day 10 (polychromatophilic stage)


title: Day10_infected_rep1 _Dchip


title: Day10_infected_rep3 _Dchip


title: pre-treatment tumor biopsy HSP_267