title: HGDP-644


title: HGDP-706

status: Public on Feb 08 2008

type: genomic

city: Bethesda

first: J Raphael

last: Gibbs

state: MD

address: 35 Convent Drive, Bldg 35/1A1015, MSC3707

department: Computational Biology Core

country: USA

institute: National Institutue on Aging, NIH

description: Genomic DNA extracted from lymphoblastoid cell lines from a ethnically diverse series was genotyped using Infinium HumanHap550 Genotyping BeadChips (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC3/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using Beadstudio 3.1.4 (Illumina).

label: C-Bio and A-DNP

molecule: genomic DNA

organism: Homo sapiens

source_name: lymphoblastoid cell lines

label_protocol: Genotyping was performed using Illumina Infinium HumanHap550 Genotyping BeadChips according to the manufacturerÕs protocol (Illumina Inc., San Diego, CA, www.illumina.com). 1000ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: DNA was extracted at the Foundation Jean Dausset (CEPH) in Paris using standard protocols.

tag: Population

value: Colombian

tag: Country

value: Colombia

tag: Region

value: AMERICA

tag: Gender

value: Female


title: HGDP-708


title: HGDP-664

value: Melanesian

value: Bougainville

value: OCEANIA


title: HGDP-656


title: HGDP-702


title: HGDP-655

value: Male


title: HGDP-591

value: Druze

value: Israel-Carmel


title: HGDP-662


title: HGDP-549

value: Papuan


title: HGDP-548


title: HGDP-553


title: HGDP-552


title: HGDP-551


title: HGDP-547


title: HGDP-579


title: HGDP-554


title: HGDP-544


title: HGDP-382

value: Burusho

value: Pakistan


title: HGDP-388


title: HGDP-372


title: Ref_vs_40_6wks_2

status: Public on Feb 13 2008

type: RNA

city: Rockville

first: Jia

last: Liu

address: 9712 Medical Center Drive

institute: Plant Genomics

description: This is a study to characterize gene expression profiles in stored Russet Burbank potato tubers. Tubers were harvested from commercial fields in the central sands region of Wisconsin in the fall of 2006. The tubers were put into storage at 55 degrees F for preconditioning and wound healing. Shortly after the temperature of the storage bin began to decrease, uniform, healthy tubers were selected for use in this microarray analysis. Tubers were at 53.6 degrees F at this time, and pieces of starch-storing tissue were collected for use as the reference sample. Other tubers were moved to temperature-controlled lockers and these were cooled gradually to either 48 or 40 degrees F following industry standard procedures. The expectation was that tubers held at 48 degrees would not have a significant accumulation of glucose and fructose, but that tubers cooled to 40 degrees would undergo low temperature sweetening and accumulate glucose and fructose to a degree that is unsuitable for processing. Three weeks later, when the locker temperatures were 48 degrees F and 41.5 degrees F, tissue samples were collected for RNA analysis. After another three weeks, samples were collected from tubers at 48 degrees F and 40 degrees F. At that time some tubers were moved from the 48 degree locker to the 40 degree locker in order to see if gene expression changes observed as a result of gradual cooling are similar to those that occur following a sudden decrease in temperature. Three weeks later, samples were collected from tubers held at 48 degrees F, tubers held at 40 degrees F, and from the tubers that were moved from 48 to 40 degrees F. At this time another set of tubers was transferred from 48 degrees to 40 degrees. Three weeks later the last samples were harvested from tubers held at 48 degrees F, from tubers held at 48 degrees F and from tubers that were transferred three weeks prior from 48 to 40 degrees. RNA was isolated from tissue extracted from three tubers.

hyb_protocol: Hybridization with indirectly labeled mRNA (SGED_SOP_6.1.1, SGED_SOP_6.2.1-4)

scan_protocol: Axon 4000B scanner. Both the 635nm (red, Cy5) and 532nm (green, Cy3) channels are scanned simultaneously at 100% laser power, the PMT set between 600 and 950. Slides are scanned at a resolution of 10micron

data_processing: The TIFF images were quantified using Genepix 5.0. Local background was subtracted from the signal value and the data was normalized using the quantile method in the limma package of bioconductor.

molecule: total RNA

organism: Solanum tuberosum

label_protocol: Amino allyl labeling and direct labeling (SGED_SOP_5.1.1 + SGED_SOP_6.1.1)

growth_protocol: Commercial field, central Wisconsin sumer 2006

extract_protocol: Phenol method with carbohydrate-enriched tissue such as tubers and trizol for other tissues such as leaves (SGED_SOP_3.1.1 + SGED_SOP_3.3.1)

treatment_protocol: Held at 40 F to 6 weeks

tag: Solanum tuberosum, Tuber, Abiotic stress

treatment_protocol: Held at 48 F to 9 weeks, transferred to 40 F for 3 weeks


title: HGDP-376


title: HGDP-330

value: Kalash


title: HGDP-328


title: HGDP-326


title: HGDP-346


title: HGDP-491


title: HGDP-351


title: HGDP-542


title: HGDP-356


title: HGDP-321


title: HGDP-78

value: Balochi


title: HGDP-333


title: HGDP-76


title: HGDP-74


title: HGDP-281


title: HGDP-72


title: HGDP-70


title: HGDP-68


title: HGDP-56


title: HGDP-66


title: HGDP-58


title: HGDP-62


title: HGDP-64


title: HGDP-54


title: HGDP-1417

value: Bantu

value: Kenya

value: AFRICA


title: HGDP-60


title: HGDP-57


title: HGDP-1411


title: HGDP-1415


title: HGDP-1412


title: HGDP-52


title: HGDP-1419


title: HGDP-1413


title: HGDP-1408


title: HGDP-1414


title: HGDP-1416


title: HGDP-1285

value: Mandenka

value: Senegal


title: HGDP-1406


title: HGDP-1286


title: HGDP-1405


title: HGDP-1284


title: HGDP-1282

value: Mozabite


title: HGDP-1283


title: HGDP-1281

value: Female


title: HGDP-1275


title: HGDP-1278


title: HGDP-1273


title: HGDP-1279


title: HGDP-1274


title: HGDP-1271


title: HGDP-1280


title: HGDP-1270


title: HGDP-1277


title: HGDP-1276


title: HGDP-1272


title: HGDP-1269


title: HGDP-1266


title: HGDP-1265


title: HGDP-1260


title: HGDP-1263


title: HGDP-1267


title: HGDP-1268


title: HGDP-1262


title: HGDP-1257


title: HGDP-1259


title: HGDP-1264


title: HGDP-1261


title: HGDP-1256


title: HGDP-1258


title: HGDP-1255


title: HGDP-1253


title: HGDP-1254


title: HGDP-1202


title: HGDP-1199


title: HGDP-1089


title: HGDP-1086


title: HGDP-1200


title: HGDP-1085


title: HGDP-1090


title: HGDP-1093


title: HGDP-1081


title: HGDP-1201


title: HGDP-1034


title: HGDP-1036

value: San

value: Namidia


title: HGDP-1088

value: Male


title: HGDP-1094


title: HGDP-1084


title: HGDP-1035


title: HGDP-1091


title: HGDP-1031


title: HGDP-1033


title: HGDP-1030


title: HGDP-1032


title: HGDP-1029


title: HGDP-992


title: HGDP-1027

value: Melanesian

value: Bougainville

value: OCEANIA


title: HGDP-993


title: HGDP-1028


title: HGDP-991


title: HGDP-988


title: HGDP-994


title: HGDP-987


title: HGDP-986


title: HGDP-984


title: HGDP-985


title: HGDP-944

value: Yoruba

value: Nigeria


title: HGDP-940


title: HGDP-939


title: HGDP-938


title: HGDP-978


title: HGDP-935


title: HGDP-942


title: HGDP-941


title: HGDP-934


title: HGDP-982


title: HGDP-931


title: HGDP-937


title: HGDP-983


title: HGDP-936


title: HGDP-930


title: HGDP-943


title: HGDP-928


title: HGDP-927


title: HGDP-932


title: HGDP-933


title: HGDP-926


title: HGDP-929


title: HGDP-924


title: HGDP-925


title: HGDP-922


title: HGDP-919


title: HGDP-923


title: HGDP-918


title: HGDP-920


title: HGDP-917


title: HGDP-913


title: HGDP-914


title: HGDP-921


title: HGDP-912


title: HGDP-908


title: HGDP-911


title: HGDP-909


title: HGDP-916


title: HGDP-915


title: HGDP-910


title: HGDP-905


title: HGDP-699

value: Palestinian

value: Israel-Central


title: HGDP-907


title: HGDP-789


title: HGDP-700


title: HGDP-824


title: HGDP-904


title: HGDP-825


title: HGDP-788


title: HGDP-722


title: HGDP-698


title: HGDP-697


title: HGDP-906


title: HGDP-696


title: HGDP-691


title: HGDP-694


title: HGDP-688


title: HGDP-695


title: HGDP-692


title: HGDP-686


title: HGDP-682


title: HGDP-690


title: HGDP-689


title: HGDP-681


title: HGDP-683


title: HGDP-684


title: HGDP-679


title: HGDP-660


title: HGDP-663


title: HGDP-675


title: HGDP-678


title: HGDP-654

value: Bedouin

value: Israel-Negev


title: HGDP-723


title: HGDP-658


title: HGDP-677


title: HGDP-653


title: HGDP-676


title: HGDP-661


title: HGDP-657


title: HGDP-651


title: HGDP-649


title: HGDP-648


title: HGDP-693


title: HGDP-647


title: HGDP-645


title: HGDP-646


title: HGDP-643


title: HGDP-641


title: HGDP-639


title: HGDP-642


title: HGDP-631


title: HGDP-635


title: HGDP-629


title: HGDP-637


title: HGDP-630


title: HGDP-636


title: HGDP-605

value: Druze

value: Israel-Carmel


title: HGDP-650


title: HGDP-638


title: HGDP-633


title: HGDP-632


title: HGDP-628


title: HGDP-627


title: HGDP-623


title: HGDP-680


title: HGDP-622


title: HGDP-626


title: HGDP-624


title: HGDP-619


title: HGDP-621


title: HGDP-640


title: HGDP-618


title: HGDP-616


title: HGDP-611


title: HGDP-613


title: HGDP-617


title: HGDP-610


title: HGDP-612


title: HGDP-615


title: HGDP-609


title: HGDP-614


title: HGDP-625


title: OVCAR-3

city: Burlingame

first: Douglas

last: Ross

state: CA

address: 863 Mitten Rd #103

institute: Applied-Genomics

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26853.gif

hyb_protocol: 65°C overnight in a water bath.

scan_protocol: All arrays were scanned using GenePix 4000A microarray scanner (Axon Instruments, Union City, CA) and initial data analysis was carried out using GenePix Pro 3.0

data_processing: Array elements were manually flaged to exclude apparent problematic spots. All non-flagged array elements for which the fluorescent intensity in each channel was at least 300 units and the regression correlation between the red and green channels was greater than 0.6 were considered well measured and included in the study. Inclusion of a gene in correlative studies required that greater than 80% of measurements across all the cell lines in the study were present.

molecule: polyA RNA

label_protocol: For each comparative array hybridization, labeled cDNA was synthesized by reverse transcription from test cell mRNA in the presence of Cy5-dUTP, and from the reference mRNA with Cy3-dUTP, using the Superscript II reverse-transcription kit (Gibco-BRL).

growth_protocol: Cell lines were grown from the publicly available NCI DTP frozen stocks in RPMI-1640 supplemented with phenol red, glutamine (2 mM) and 5% fetal calf serum. To minimize the contribution of variations in culture conditions or cell density to differential gene expression, we grew each cell line to 80% confluence and isolated mRNA 24 hours after transfer to fresh medium.

extract_protocol: To minimize the contribution of variations in culture conditions or cell density to differential gene expression, we grew each cell line to 80% confluence and isolated mRNA 24 hours after transfer to fresh medium. Cells were lysed in buffer containing Protein/Rnase Degrader (Invitrogen) and messenger RNA was purified with the FastTrack 2.0 purification kit (Invitrogen).

tag: tumor cell line

source_name: Reference Batch CRH

tag: Tumor cell line pool


title: HGDP-620


title: HGDP-604


title: MOLT-4

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26836.gif


title: HGDP-600


title: HGDP-602


title: HGDP-603


title: HGDP-606


title: IGROV1

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26837.gif


title: M14

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26851.gif


title: HGDP-598


title: UACC-62

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26852.gif


title: ACHN

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26763.gif

source_name: ACHN


title: HGDP-595


title: HGDP-599


title: EKVX

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26834.gif

source_name: EKVX


title: HGDP-588


title: HS-578T

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26819.gif


title: SK-MEL-5

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26850.gif


title: SW-620

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26818.gif


title: SK-OV-3

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26835.gif


title: NCI-H322M

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39410.gif


title: HCT-15

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26817.gif


title: HGDP-586


title: HGDP-585


title: HGDP-594


title: NCI-H460

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26831.gif


title: HGDP-592


title: HCC-2998

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26830.gif


title: SR

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26810.gif

source_name: SR


title: HGDP-582

description: Genomic DNA extracted from lymphoblastoid cell lines from a ethnically diverse series was genotyped using Infinium HumanHap550 Genotyping BeadChips (Illumina).


title: UACC-257

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26833.gif


title: HGDP-577


title: HGDP-590


title: K-562

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26813.gif


title: HGDP-581


title: HGDP-580


title: HGDP-587


title: SF-268

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26796.gif


title: HOP-92

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26847.gif


title: HGDP-583


title: DU-145

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26779.gif


title: HGDP-574


title: HGDP-575


title: NCI-H226

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26848.gif


title: MALME-3M

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26849.gif


title: HGDP-578


title: MDA-MB-435

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39409.gif


title: HGDP-584


title: HGDP-571


title: HGDP-572


title: HGDP-570


title: Arabidopsis thaliana grown under arsenate stress

city: Knoxville

first: Jason

last: Abercrombie

state: TN

address: 2431 Joe Johnson Blvd.

department: Plant Sciences

institute: University of Tennessee

description: condensed table of 6 hybridzations (slides 249, 247, 244, 250, 246, and 248)

hyb_protocol: Microarrays comprised of 70-mer oligonucleotides obtained from the University of Arizona (http://ag.arizona.edu/microarray/) were immobilized by rehydrating the slide over a 50ºC waterbath for 10 s and snap drying on a 65ºC heating block for 5 s for a total of four times.  Slides were UV-crosslinked at 180 mJ in a UV cross-linker (Stratagene, La Jolla, CA).  The slides were then washed in 1% SDS, dipped in 100% EtOH five times followed by 3 min shaking.  Slides were spun dry at 1000 rpm for 2 minutes and immediately placed in a light-proof box.  The 90 µl hybridization mix was pipetted onto a microarray slide underneath a lifterslip (Lifterslip, Portsmouth, NH) and placed in a hybridization chamber (Corning, Corning, NY) overnight at 55ºC.

scan_protocol: After hybridization, slides were washed in 2X SSC, 0.5% SDS for 5 minutes at 55ºC, 0.5X SSC for 5 minutes at room temperature, and 0.05X SSC for 5 minutes at room temperature.  Slides were then spun dry at 1000 rpm in a Sorvall centrifuge and scanned with a GenePix 4000B scanner (Axon Instruments, Inc., Union City, CA).

data_processing:
The intensity variation was removed by fitting a loess regression using SAS 9.1 (SAS, Cary, NC).  Data were log-2 transformed and statistically analyzed using rank product statistics to identify differentially expressed genes.  Bioconductor (www.bioconductor.org) Rank Prod package was used to perform the rank product analysis.
Significantly different genes reported in this study exhibited P <0.001, as designated by the rank product analysis. The false discovery rate value obtained was based on 10,000 random permutations. Since 10,000 random permutations was very computer intensive, 1000 random permutations were performed 10 different times each time starting with a different random seed number and the average FDR value calculated was used for further analysis. The genes that had FDR values less than or equal to 0.01 were considered as differentially expressed.

label: Cy3, Cy5

organism: Arabidopsis thaliana

source_name: whole plant, arsenate treated

label_protocol: Total RNA from six biological replicates were purified using RNeasy MiniElute columns (Qiagen, Valencia, CA).  A total of 1.25 µg of purified total RNA was subjected to Aminoallyl Message Amp II kit (Ambion, Austin, TX) first strand cDNA synthesis, second strand synthesis, and in vitro transcription for amplified RNA (aRNA) synthesis.  aRNA was purified according to manufacturers protocol (Ambion, Austin, TX) and quantified using a Nanodrop spectrophotometer.  Two 4 µg samples of aRNA were labeled with Cy3 and Cy5 monoreactive dyes (Amersham Pharmacia, Pittsburgh, PA) in order to conduct a dye swap technical replicate for each biological replicate.  Each aRNA sample was brought to dryness in a Speedvac and dissolved in 5 µL of 0.2 M NaHCO3 buffer.  Five microliters of Cy3 or Cy5 (in DMSO) was added to each sample and incubated for 2 hrs in the dark at RT.  Labeled aRNA was purified according to kit instructions (Ambion, Austin, TX) and quantified using the Nanodrop spectrophotometer. One-hundred pmol Cy3- and Cy5-labeled aRNA targets were denatured by incubating at 65°C for 5 min and added to a hybridization mix containing 9 µl 20X SSC, 5.4 µl Liquid Block (Amersham Pharmacia, Pittsburgh, PA), and 3.6 µl 2% SDS for a 90 µl total volume.

growth_protocol: Arabidopsis thaliana ecotype Columbia seeds were surface sterilized and plated on agar-solidified MS culture medium supplemented with B5 vitamins, 10% sucrose, 2% Gelrite ®, pH 5.8. Plants were grown aseptically in petri plates that were cold stratified at 4°C for 24 hrs and then placed in a growth chamber at 25°C under a 16 hr photoperiod.

extract_protocol: After 10 d, 2 g of whole plant material (shoots + roots) was harvested from each plate, frozen in liquid nitrogen, and subjected to RNA isolation using Trizol ® reagent (Invitrogen, Carlsbad, CA) according to manufacturer’s protocol.

treatment_protocol: Arsenic-treated plates were supplemented with 100 µM potassium arsenate (Sigma) according to a previously determined sub-lethal growth response curve.

tag: arsenate treated

label: Cy5, Cy3

source_name: whole plant, control, untreated

tag: untreated control


title: RPMI-8226_40k

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26845.gif


title: HGDP-573


title: NCI-H522

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26846.gif


title: NCI-H23

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26844.gif


title: DMS-114

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56328.gif


title: SF-539

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26829.gif


title: HL-60

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26843.gif


title: HOP-18

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56338.gif


title: HGDP-565

description: Genomic DNA extracted from lymphoblastoid cell lines from a ethnically diverse series was genotyped using Infinium HumanHap550 Genotyping BeadChips (Illumina).


title: XF-498

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56344.gif


title: HGDP-576


title: U-251

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26828.gif


title: RXF-393

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26772.gif


title: HGDP-564


title: HGDP-568


title: HGDP-569


title: COLO-205

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26842.gif


title: SNB-78

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56337.gif


title: RXF-631

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56341.gif


title: TK-10

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26827.gif


title: M19-Mel

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56335.gif


title: SNB-75

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26826.gif


title: HGDP-566


title: HGDP-560


title: KM-20L2

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56332.gif


title: HGDP-562


title: HCT-116

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26809.gif


title: HT29

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26841.gif


title: MCF-7

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26808.gif


title: UO-31

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26840.gif


title: NCI/ADR-RES

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26825.gif

source_name: NCI/ADR-RES


title: SN-12C

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26824.gif


title: CAKI-1

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26806.gif


title: LOX-IMVI

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26823.gif

source_name: LOX-IMVI


title: HGDP-558

description: Genomic DNA extracted from lymphoblastoid cell lines from a ethnically diverse series was genotyped using Infinium HumanHap550 Genotyping BeadChips (Illumina).


title: HGDP-550

value: Papuan


title: KM-12

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26807.gif


title: OVCAR-5

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26822.gif


title: HGDP-556


title: HGDP-557


title: HGDP-543


title: HGDP-545


title: SF-295

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26805.gif


title: HGDP-541


title: HGDP-478

value: AFRICA


title: HGDP-479


title: HGDP-476

value: Female


title: HGDP-559


title: SK-MEL-2

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26821.gif


title: HGDP-561


title: HGDP-474


title: HGDP-540


title: SK-MEL-28

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26820.gif


title: HGDP-546


title: A549/ATCC

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26804.gif


title: CCRF-CEM

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26803.gif

source_name: CCRF-CEM


title: HGDP-475


title: HGDP-477


title: 786-O

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26789.gif


title: HGDP-473


title: A-498

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26769.gif


title: HGDP-470


title: PC-3

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26858.gif


title: HGDP-472


title: HGDP-471


title: MDA-MB-231

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26855.gif


title: T-47D

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26785.gif


title: V2 cy5, O2 cy3

city: Tucson

first: David

middle: Richard

last: Holding

state: AZ

address: 303 Forbes Building

institute: University of Arizona

description: Compares vitreous and opaque kernel pools (biological replicates) two.

hyb_protocol: hybridization protocol can be found at http://www.maizearray.org/files/Hybridization_Protocol_For_cRNA_Targets.pdf

scan_protocol: Slides were scanned using a GenePix Autoloader 4200AL microarray scanner Images were quantified using Agilent Feature Extraction Software (version A.7.5).

data_processing: VSN (variance stabilized normalization) normalization, SAM (statistical analysis for microarrays, Microsoft Excel plugin) used applied for statistical analysis

organism: Zea mays

source_name: Vitrous endosperm pool 2 total RNA

label_protocol: 1 μg RNA samples were used to make Cy3- and Cy5-labeled targets with a three step protocol as follows: 1) cDNA was synthesized using an oligo-(d)T primer that incorporated the T7 promoter; 2) targets were amplified using in vitro transcription to produce aminoallyl-labeled cRNA; and 3) aminoallyl-labeled cRNA was coupled to Cy-labeled dyes.  Details of these protocols can be found at: http://www.maizearray.org/files/cRNA_Target_Production_Using_RNA_Amplification.pdf

growth_protocol: Plants grown and pollinated in greenhouse under controlled condtions (16 hour day, 70 °F night, 85 °F day

extract_protocol: Total RNA extracted according to Holding et al (2007) Plant Cell 19:2569-2582, and treated with DNAse1

treatment_protocol: Ears frozen in liquid N2, stored at -80 °C, pericarp and embryo removed prior to RNA extraction

tag: Pool representing five F4 true breeding 18 DAP vitreous endosperm ears derived from K0326Y (QPM; vitreous) by W64Ao2 (soft:opaque) cross

source_name: Opaque endosperm pool 2 total RNA

tag: Pool representing five F4 true breeding 18 DAP opaque endosperm ears derived from K0326Y (QPM; vitreous) by W64Ao2 (soft:opaque) cross


title: SNB-19

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26856.gif


title: HOP-62

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26857.gif


title: 1 hour biopsy sample of transplanted kidney from LD 14 donor

city: Toyoake

first: Mamoru

last: Kusaka

state: Aichi

address: 1-98 Kutsukake

department: Department of Urology

country: Japan

institute: Fujita-Health University

description: Kidney one hour biopsy from DCD donor or from living donor

hyb_protocol: The microarray experiments were then carried out using competitive hybridization experiments with Cy5-labeled kidney RNA asa a test RNA and with Cy3-labeled pooled normal kidney as a template control for normalization

scan_protocol: The glass slides were scanned using as an Agilent G2565BA microscanner.

data_processing: Data processed with FeautureExtraction v7.1

source_name: 1 hour biopsy sample of transplanted kidney LD 14 with Cy5

label_protocol: 200ng of total RNA was used for T7 RNA polymerase-based cDNA labeling

extract_protocol: Total RNA was extracted from transplanted using RNeasy (Qiagen, Valencia, CA, USA)

tag: kidney sample from LD donor (1 hr after reperfusion)

source_name: normal control with Cy3

extract_protocol: Total RNA was extracted from using RNeasy (Qiagen, Valencia, CA, USA)

tag: normal kidney sample commercially


title: V3 cy3, O2 cy5

description: Compares vitreous and opaque kernel pools (biological replicates) V3 and O3

source_name: Opaque endosperm pool 3 total RNA

source_name: Vitreous endosperm pool 3 total RNA

tag: Ears frozen in liquid N2, stored at -80 °C, pericarp and embryo removed prior to RNA extraction

tag: Plants grown and pollinated in greenhouse under controlled condtions (16 hour day, 70 °F night, 85 °F day


title: HGDP-466

description: Genomic DNA extracted from lymphoblastoid cell lines from a ethnically diverse series was genotyped using Infinium HumanHap550 Genotyping BeadChips (Illumina).


title: 1 hour biopsy sample of transplanted kidney from LD 15 donor

source_name: 1 hour biopsy sample of transplanted kidney LD 15 with Cy5


title: 1 hour biopsy sample of transplanted kidney from LD 13 donor

source_name: 1 hour biopsy sample of transplanted kidney LD 13 with Cy5


title: OVCAR-8

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26838.gif

source_name: Reference Batch CRH


title: V1 cy5, O1 cy3

description: Compares vitreous and opaque kernel pools (biological replicates) one.

source_name: Vitrous endosperm pool 1 total RNA

source_name: Opaque endosperm pool 1 total RNA


title: OVCAR-4

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26839.gif


title: HGDP-469

source_name: lymphoblastoid cell lines


title: 1 hour biopsy sample of transplanted kidney from LD 10 donor

source_name: 1 hour biopsy sample of transplanted kidney LD 10 with Cy5


title: V4 cy3, O4 cy5

description: Compares vitreous and opaque kernel pools (biological replicates) V4 and O4.

source_name: Opaque endosperm pool 4 total RNA

source_name: Vitreous endosperm pool 4 total RNA


title: HGDP-468


title: 1 hour biopsy sample of transplanted kidney from LD 12 donor

source_name: 1 hour biopsy sample of transplanted kidney LD 12 with Cy5


title: HGDP-467


title: 1 hour biopsy sample of transplanted kidney from LD 11 donor

source_name: 1 hour biopsy sample of transplanted kidney LD 11 with Cy5


title: HGDP-463


title: Very-late luteal phase CL, biological rep 3

city: Beaverton

first: Randy

middle: Lloyd

last: Bogan

state: OR

address: 505 NW 185th Ave

department: Reproductive Sciences

institute: Oregon National Primate Research Center

description: Gene expression data from CL that are undergoing structural regression. These CL have already undergone functional regression (cessation of progesterone production), and menses has occurred. This stage represents the remnants of the CL during structural regression (the second phase of luteolysis).

hyb_protocol: Labeled target is fragmented at 95C in the presence of high magnesium concentration.  The fragmented material is combined with biotinylated hybridization control oligomer and biotinylated control cRNAs for BioB, BioC, BioD and CreX (Affymetrix) in hybridization buffer.  Ten micrograms of target is hybridized for 16 hours at 45C to the GeneChip Rhesus Macaque Genome array (Affymetrix), followed by washing, staining with streptavidin-phycoerythrin (Molecular Probes), signal amplification with biotinylated anti-streptavidin antibody (Vector Labs), and a final staining step on the Fluidics Station 450 (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 with the 7G upgrade (Affymetrix) and GCOS version 1.4.0 software (Affymetrix), yielding cell fluorescence intensity (.CEL files).  Image inspection was performed manually immediately following each scan.

data_processing: The processed image files (.CEL) were normalized across arrays using the robust multichip average (RMA) algorithm and log-transformed (base 2).After normalization, GeneSifter (VizX Labs) microarray expression analysis software was used to analyze the resultant data.

label: Biotin

organism: Macaca mulatta

source_name: Corpus luteum collected between days 18-19 after the midcycle LH surge (menses)

label_protocol: Messenger RNA is amplified and labeled from 2 micrograms of total RNA in two steps according to the standard Affymetrix one-cycle cDNA protocol (Expression Analysis Technical Manual Rev.4). In the first step, mRNA is converted to double-stranded cDNA using Superscript Reverse Transcriptase (Invitrogen) and an oligo-dT primer linked to a T7 RNA polymerase binding site sequence (Affymetrix).  In the second step, amplified and labeled cRNA (the target) is produced in an in vitro transcription reaction using T7 RNA polymerase and biotin-UTP (Affymetrix). Following removal of free nucleotides, target yield is measured by UV260 absorbance.

extract_protocol: Trizol (Invitrogen) extraction of total RNA was performed according to the manufacturer's instructions, and total RNA obtained by Trizol extraction was further purified using RNeasy spin columns (Qiagen) following manufacturer instructions.

treatment_protocol: Blood samples were collected daily by saphenous venipuncture starting six days after onset of menses. Serum was separated and samples were assayed daily for estradiol concentrations. Following the midcycle estradiol surge, the first day of low serum estradiol (< 100pg/ml) corresponds with the day after the LH surge (LH surge = day 0). On the appropriate day following the midcycle LH surge, the CL was collected during aseptic midline laparotomy, immediately flash frozen in liquid nitrogen, and stored at -80°C until total RNA was extracted.

tag: Gender:female, Tissue

value: Corpus luteum, reproductive state:normal menstrual cyclicity


title: 1 hour biopsy sample of transplanted kidney from LD 8 donor

source_name: 1 hour biopsy sample of transplanted kidney LD 8 with Cy5


title: HGDP-462


title: 1 hour biopsy sample of transplanted kidney from LD 7 donor

source_name: 1 hour biopsy sample of transplanted kidney LD 7 with Cy5


title: BT549

description:
Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26854.gif


title: 1 hour biopsy sample of transplanted kidney from LD 9 donor

source_name: 1 hour biopsy sample of transplanted kidney LD 9 with Cy5

source_name: normal control with Cy3


title: HGDP-465


title: Very-late luteal phase CL, biological rep 1


title: Very-late luteal phase CL, biological rep 2


title: Very-late luteal phase CL, biological rep 4


title: HGDP-461


title: Late luteal phase CL, biological rep 4

description: Gene expression data from CL that are undergoing functional regression. Luteolysis (CL death) is subdivided into two steps: 1) a decrease in progesterone secretion (functional regression), and 2) apoptosis and structural remodeling of luteal tissue (structural regression). This stage corresponds to CL in the first stage of luteolysis (functional regression). They have, or are about to, quit producing progesterone, but the tissue has not yet started to degenerate.

source_name: Corpus luteum collected between days 14-16 after the midcycle LH surge


title: Late luteal phase CL, biological rep 3


title: HGDP-459


title: 1 hour biopsy sample of transplanted kidney from LD 5 donor

source_name: 1 hour biopsy sample of transplanted kidney LD 5 with Cy5


title: HGDP-460


title: Late luteal phase CL, biological rep 2


title: HGDP-457


title: Late luteal phase CL, biological rep 1


title: 1 hour biopsy sample of transplanted kidney from LD 4 donor

source_name: 1 hour biopsy sample of transplanted kidney LD 4 with Cy5


title: 1 hour biopsy sample of transplanted kidney from LD 3 donor

source_name: 1 hour biopsy sample of transplanted kidney LD 3 with Cy5


title: 1 hour biopsy sample of transplanted kidney from LD 6 donor

source_name: 1 hour biopsy sample of transplanted kidney LD 6 with Cy5


title: 1 hour biopsy sample of transplanted kidney from LD 2 donor

source_name: 1 hour biopsy sample of transplanted kidney LD 2 with Cy5


title: Mid-late luteal phase CL, biological rep 4

description: Gene expression data from CL that are still functional (i.e. producing progesterone) but are just prior to the time when CL regression (luteolysis) is initiated, i.e. this is a transitionary period from a functional CL to a regressing CL

source_name: Corpus luteum collected between days 10-12 after the midcycle LH surge


title: Mid-late luteal phase CL, biological rep 3


title: Mid-late luteal phase CL, biological rep 2


title: HGDP-456

source_name: lymphoblastoid cell lines


title: HGDP-464


title: HGDP-458


title: 1 hour biopsy sample of transplanted kidney from LD 1 donor

source_name: 1 hour biopsy sample of transplanted kidney LD 1 with Cy5


title: Mid-late luteal phase CL, biological rep 1


title: human control for DCD study

description: human control for DCD study

source_name: commerical normal kidney, control with Cy5

extract_protocol: Total RNA was extracted from normal using RNeasy (Qiagen, Valencia, CA, USA)

source_name: commerical normal kidney, control with Cy3


title: HGDP-454


title: HGDP-455


title: 1 hour biopsy sample of transplanted kidney from DCD 11 donor

source_name: 1 hour biopsy sample of transplanted kidney DCD 11 with Cy5

tag: kidney sample from DCD donor (1 hr after reperfusion)


title: 1 hour biopsy sample of transplanted kidney from DCD 14 donor

source_name: 1 hour biopsy sample of transplanted kidney DCD 14 with Cy5


title: Mid luteal phase CL, biological rep 4

description: Gene expression data from CL during luteal maintenance, i.e. once luteinization is complete and the CL is fully formed, this is the period of peak production of progesterone.

source_name: Corpus luteum collected between days 7-8 after the midcycle LH surge


title: HGDP-453

tag: Population


title: Mid luteal phase CL, biological rep 3


title: 1 hour biopsy sample of transplanted kidney from DCD 10 donor

source_name: 1 hour biopsy sample of transplanted kidney DCD 10 with Cy5


title: 1 hour biopsy sample of transplanted kidney from DCD 12 donor

source_name: 1 hour biopsy sample of transplanted kidney DCD 12 with Cy5


title: Mid luteal phase CL, biological rep 1


title: 1 hour biopsy sample of transplanted kidney from DCD 13 donor

source_name: 1 hour biopsy sample of transplanted kidney DCD 13 with Cy5

source_name: normal control with Cy3


title: 1 hour biopsy sample of transplanted kidney from DCD 9 donor

source_name: 1 hour biopsy sample of transplanted kidney DCD 9 with Cy5


title: HGDP-452

tag: Country


title: Early luteal phase CL, biological rep 3

description: Gene expression data from CL during luteal development (luteinization), i.e. just after ovulation when the cellular constituents remaining from the preovulatory follicle are transformed into the CL.

source_name: Corpus luteum collected between days 3-5 after the midcycle LH surge


title: Mid luteal phase CL, biological rep 2


title: Early luteal phase CL, biological rep 4


title: HGDP-450

tag: Region


title: Early luteal phase CL, biological rep 2


title: 1 hour biopsy sample of transplanted kidney from DCD 7 donor

source_name: 1 hour biopsy sample of transplanted kidney DCD 7 with Cy5


title: HGDP-451

tag: Gender


title: HGDP-449


title: 1 hour biopsy sample of transplanted kidney from DCD 8 donor

source_name: 1 hour biopsy sample of transplanted kidney DCD 8 with Cy5


title: 1 hour biopsy sample of transplanted kidney from DCD 5 donor

source_name: 1 hour biopsy sample of transplanted kidney DCD 5 with Cy5


title: 1 hour biopsy sample of transplanted kidney from DCD 4 donor

source_name: 1 hour biopsy sample of transplanted kidney DCD 4 with Cy5


title: HGDP-307

source_name: lymphoblastoid cell lines

value: Kalash

value: Pakistan


title: NF1_RNAi_r3

city: London

first: Luke

middle: Adam

last: Noon

address: Gower Street

department: LMCB

country: United Kingdom

institute: MRC

description: NF1 RNAi

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Affymetrix CEL files were processed using RMA

label: biotin

organism: Rattus norvegicus

source_name: Primary Rat Schwann cells, NF1 RNAi

label_protocol: standard Affymetrix protocol

extract_protocol: QIagen RNeasy plus

tag: Tissue

value: sciatic nerve


title: NF1_RNAi+UO126_r1

description: NF1 RNAi +UO126

source_name: Primary Rat Schwann cells, NF1 RNAi +UO126


title: NF1_RNAi+UO126_r3

description: NF1 RNAi +UO126


title: Control_r3

description: Control RNAi

source_name: Primary Rat Schwann cells, Control RNAi


title: HGDP-448

value: Male


title: HGDP-315


title: 1 hour biopsy sample of transplanted kidney from DCD 2 donor

source_name: 1 hour biopsy sample of transplanted kidney DCD 2 with Cy5


title: Control_r1

description: Control RNAi


title: 2688 Triadimefon 1800ppm Testis

status: Public on Feb 07 2008

city: Research Triangle Park

last: Dix

state: NC

address: 109 TW Alexander Drive

department: ORD/NCCT

institute: US EPA

description:
T1800_01

Processed data not available because this sample was not included in the final analysis.

hyb_protocol: cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20).  GeneChips were hybridized at 45ºC for 16 h.  After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.

scan_protocol: Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.

data_processing: To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500.  Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA.  For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics.  Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate (FDR) of 25% for testis (p<0.000229), and an absolute difference of |1.2| or greater.  Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.

source_name: 2688 Triadimefon 1800ppm Testis

label_protocol: Five micrograms or purified total RNA from each liver or testis of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com).  Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer.  Biotinylated RNA (labeled cRNA) served as the microarray target.  cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.

extract_protocol: Total RNA was extracted from PND92 testis of individual Wistar Han IGS rats of the mid dose (M500, P500, T500 ppm) and high dose (M2000, P2500, T1800 ppm) treatment groups using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays.  For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE).  RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA).  Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays.  RNA was stored at -80ºC until labeling for microarray hybridization.

treatment_protocol: Feeding study, exposure from gestation day 6 through to post natal day 92

tag: testis

tag: Wistar Han Rat

tag: PND92 adult


title: NF1_RNAi_r2

description: NF1 RNAi


title: NF1_RNAi_r1

description: NF1 RNAi


title: HGDP-304


title: NF1_RNAi+UO126_r2

description: NF1 RNAi +UO126


title: 3170 Triadimefon 1800ppm Testis

source_name: 3170 Triadimefon 1800ppm Testis


title: 2678 Triadimefon 500ppm Testis

source_name: 2678 Triadimefon 500ppm Testis


title: 1 hour biopsy sample of transplanted kidney from DCD 3 donor

source_name: 1 hour biopsy sample of transplanted kidney DCD 3 with Cy5


title: HGDP-313


title: 1 hour biopsy sample of transplanted kidney from DCD 6 donor

source_name: 1 hour biopsy sample of transplanted kidney DCD 6 with Cy5


title: 2675 Triadimefon 500ppm Testis

source_name: 2675 Triadimefon 500ppm Testis


title: 2681 Triadimefon 500ppm Testis

source_name: 2681 Triadimefon 500ppm Testis


title: Early luteal phase CL, biological rep 1

source_name: Corpus luteum collected between days 3-5 after the midcycle LH surge


title: 3154 Triadimefon 1800ppm Testis

source_name: 3154 Triadimefon 1800ppm Testis


title: 2645 Propiconazole 2500ppm Testis

source_name: 2645 Propiconazole 2500ppm Testis


title: 2648 Propiconazole 2500ppm Testis

source_name: 2648 Propiconazole 2500ppm Testis


title: Control_r2

description: Control RNAi


title: HGDP-298


title: 2598 Myclobutanil 2000ppm Testis

source_name: 2598 Myclobutanil 2000ppm Testis


title: 2628 Propiconazole 500ppm Testis

source_name: 2628 Propiconazole 500ppm Testis


title: HGDP-302

source_name: lymphoblastoid cell lines


title: 1 hour biopsy sample of transplanted kidney from DCD 1 donor

source_name: 1 hour biopsy sample of transplanted kidney DCD 1 with Cy5

source_name: normal control with Cy3


title: 2600 Myclobutanil 2000ppm Testis

source_name: 2600 Myclobutanil 2000ppm Testis


title: 2630 Propiconazole 500ppm Testis

source_name: 2630 Propiconazole 500ppm Testis


title: 2642 Propiconazole 2500ppm Testis

source_name: 2642 Propiconazole 2500ppm Testis


title: 2588 Myclobutanil 500ppm Testis

description:
M500_03

Processed data not available because this sample was not included in the final analysis.

source_name: 2588 Myclobutanil 500ppm Testis


title: 2654 Propiconazole 2500ppm Testis

source_name: 2654 Propiconazole 2500ppm Testis


title: 2643 Propiconazole 2500ppm Testis

source_name: 2643 Propiconazole 2500ppm Testis


title: 2603 Myclobutanil 2000ppm Testis

source_name: 2603 Myclobutanil 2000ppm Testis


title: 2633 Propiconazole 500ppm Testis

source_name: 2633 Propiconazole 500ppm Testis


title: 2552 Control 0ppm Testis

description:
Control_01

Processed data not available because this sample was not included in the final analysis.

source_name: 2552 Control 0ppm Testis


title: 2585 Myclobutanil 500ppm Testis

source_name: 2585 Myclobutanil 500ppm Testis


title: 2696 Triadimefon 1800ppm Testis

source_name: 2696 Triadimefon 1800ppm Testis


title: 2553 Control 0ppm Testis

source_name: 2553 Control 0ppm Testis


title: 3156 Control 0ppm Testis

source_name: 3156 Control 0ppm Testis


title: 2558 Control 0ppm Testis

source_name: 2558 Control 0ppm Testis


title: 2627 Propiconazole 500ppm Testis

source_name: 2627 Propiconazole 500ppm Testis


title: 2597 Myclobutanil 2000ppm Testis

source_name: 2597 Myclobutanil 2000ppm Testis


title: 2561 Control 0ppm Testis

source_name: 2561 Control 0ppm Testis


title: HGDP-290

source_name: lymphoblastoid cell lines


title: 2591 Myclobutanil 500ppm Testis

source_name: 2591 Myclobutanil 500ppm Testis


title: 2606 Myclobutanil 2000ppm Testis

source_name: 2606 Myclobutanil 2000ppm Testis


title: 2672 Triadimefon 500ppm Testis

source_name: 2672 Triadimefon 500ppm Testis


title: HGDP-286


title: 2633 Propiconazole 500ppm Liver

description:
P500_04

Processed data not available because this sample was not included in the final analysis.

source_name: 2633 Propiconazole 500ppm Liver

label_protocol: Five micrograms or purified total RNA from each liver of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com).  Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer.  Biotinylated RNA (labeled cRNA) served as the microarray target.  cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.

tag: liver

tag: Wistar Han rat, PND92 adult


title: 2630 Propiconazole 500ppm Liver

description:
P500_03

Processed data not available because this sample was not included in the final analysis.

source_name: 2630 Propiconazole 500ppm Liver


title: HGDP-292


title: 2597 Myclobutanil 2000ppm Liver

description:
M2000_01

Processed data not available because this sample was not included in the final analysis.

source_name: 2597 Myclobutanil 2000ppm Liver


title: 3144 Control 0ppm Testis

source_name: 3144 Control 0ppm Testis


title: 2696 Triadimefon 1800ppm Liver

source_name: 2696 Triadimefon 1800ppm Liver


title: 3154 Triadimefon 1800ppm Liver

source_name: 3154 Triadimefon 1800ppm Liver


title: 2678 Triadimefon 500ppm Liver

source_name: 2678 Triadimefon 500ppm Liver


title: 3153 Triadimefon 1800ppm Liver

source_name: 3153 Triadimefon 1800ppm Liver


title: 2583 Myclobutanil 500ppm Testis

source_name: 2583 Myclobutanil 500ppm Testis


title: 3170 Triadimefon 1800ppm Liver

source_name: 3170 Triadimefon 1800ppm Liver


title: 3145 Control 0ppm Testis

source_name: 3145 Control 0ppm Testis


title: 2627 Propiconazole 500ppm Liver

source_name: 2627 Propiconazole 500ppm Liver


title: 2645 Propiconazole 2500ppm Liver

source_name: 2645 Propiconazole 2500ppm Liver


title: 2606 Myclobutanil 2000ppm Liver

source_name: 2606 Myclobutanil 2000ppm Liver


title: 2643 Propiconazole 2500ppm Liver

source_name: 2643 Propiconazole 2500ppm Liver


title: 2588 Myclobutanil 500ppm Liver

source_name: 2588 Myclobutanil 500ppm Liver


title: 2673 Triadimefon 500ppm Liver

source_name: 2673 Triadimefon 500ppm Liver


title: 2675 Triadimefon 500ppm Liver

source_name: 2675 Triadimefon 500ppm Liver


title: 2591 Myclobutanil 500ppm Liver

source_name: 2591 Myclobutanil 500ppm Liver


title: 2628 Propiconazole 500ppm Liver

source_name: 2628 Propiconazole 500ppm Liver


title: HGDP-1418

description: Genomic DNA extracted from lymphoblastoid cell lines from a ethnically diverse series was genotyped using Infinium HumanHap550 Genotyping BeadChips (Illumina).

source_name: lymphoblastoid cell lines

value: Bantu

value: Kenya


title: 2598 Myclobutanil 2000ppm Liver

source_name: 2598 Myclobutanil 2000ppm Liver


title: 2654 Propiconazole 2500ppm Liver

source_name: 2654 Propiconazole 2500ppm Liver


title: 3153 Triadimefon 1800ppm Testis

source_name: 3153 Triadimefon 1800ppm Testis


title: 2681 Triadimefon 500ppm Liver

source_name: 2681 Triadimefon 500ppm Liver


title: 2585 Myclobutanil 500ppm Liver

source_name: 2585 Myclobutanil 500ppm Liver


title: 2603 Myclobutanil 2000ppm Liver

source_name: 2603 Myclobutanil 2000ppm Liver


title: 2582 Myclobutanil 500ppm Liver

source_name: 2582 Myclobutanil 500ppm Liver


title: 2642 Propiconazole 2500ppm Liver

source_name: 2642 Propiconazole 2500ppm Liver


title: HGDP-288


title: 3156 Control 0ppm Liver

source_name: 3156 Control 0ppm Liver


title: 2672 Triadimefon 500ppm Liver

source_name: 2672 Triadimefon 500ppm Liver


title: HGDP-285


title: 2558 Control 0ppm Liver

source_name: 2558 Control 0ppm Liver


title: 2583 Myclobutanil 500ppm Liver

source_name: 2583 Myclobutanil 500ppm Liver


title: 2600 Myclobutanil 2000ppm Liver

source_name: 2600 Myclobutanil 2000ppm Liver


title: 2561 Control 0ppm Liver

source_name: 2561 Control 0ppm Liver


title: 2553 Control 0ppm Liver

source_name: 2553 Control 0ppm Liver


title: 2636 Propiconazole 500ppm Liver

source_name: 2636 Propiconazole 500ppm Liver


title: 3145 Control 0ppm Liver

source_name: 3145 Control 0ppm Liver


title: Tri_03

data_processing: To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500.  Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA.  For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics.  Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate and an absolute difference of |1.2| or greater.  Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.

label_protocol: Five micrograms or purified total RNA from each liver of 3 individual rats per treatment group was hybridized to individual Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com).  Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer.  Biotinylated RNA (labeled cRNA) served as the microarray target.  cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.

extract_protocol: Total RNA was extracted from liver using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays.  For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE).  RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA).  Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays.  RNA was stored at -80ºC until labeling for microarray hybridization.

treatment_protocol: Seveny-two hour exposure, 10 week old adult male Srpague-Dawley rats dosed every 24 hours by gavage.

tag: Sprague Dawley 10 wk old males


title: Myclo336_03

treatment_protocol: Three hundred thirty-six hour exposure, 10 week old adult male Srpague-Dawley rats dosed by gavage.


title: Tri336_03


title: Propi_01


title: 3144 Control 0ppm Liver

source_name: 3144 Control 0ppm Liver


title: Propi_02


title: Tri_01


title: Myclo_02


title: Control_03


title: Myclo336_02


title: Tri336_02


title: 2552 Control 0ppm Liver

source_name: 2552 Control 0ppm Liver


title: Myclo_01


title: Propi_03


title: Tri336_04


title: Control_02


title: Myclo336_04


title: Myclo336_05


title: Tri336_05


title: Control336_02


title: Myclo024_03

treatment_protocol: Twenty-four hour exposure, 10 week old adult male Srpague-Dawley rats dosed by gavage.


title: Control336_03


title: Tri024_03


title: Tri_02


title: Tri336_01


title: Control_01


title: Myclo_03


title: Control336_04


title: Tri024_04


title: Control024_04


title: Myclo336_01


title: Tri024_02


title: Myclo024_02


title: Control336_05


title: Control336_01


title: Control024_05


title: Tri024_01


title: Myclo024_05


title: Tri024_05


title: Tri006_05

treatment_protocol: Six hour exposure, 10 week old adult male Srpague-Dawley rats dosed by gavage.


title: Tri006_04


title: Control024_02


title: Myclo024_04


title: Tri006_03


title: Control024_03


title: Control024_01


title: Myclo024_01


title: Myclo006_01


title: Control006_04


title: Tri006_01


title: Myclo006_04


title: AdERb+E2 for 24h, biological rep5

city: Santa Monica

first: Edmund

middle: C

last: Chang

state: California

address: 2225 Colorado Ave

institute: Kite Pharma

description: AdERb+E2 for 24h, biological rep5

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human-U133A. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Affymetrix protocol

data_processing: The data were analyzed with GCRMA in R/Bioconductor using default analysis settings.

source_name: MCF-7 breast cancer cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA.

growth_protocol: MCF-7 cells expressing endogenous ERalpha were plated in 100mm dish in 5% CD-stripped calf serum.

extract_protocol: Total RNA was extracted using 1mL of TRIzol (Invitrogen) per 100mm dish.

treatment_protocol: Cells were infected with adenovirus carrying either estrogen receptor beta (AdERb) or no insert (Ad) at multiplicity of infection (moi) of 20.  Cells were infected with adenovirus for a period of 48hr before treatment with either vehicle control (veh), 6nM 17beta-estradiol (E2), 6nM genistein (LG), 300nM genistein (HG), 300nM S-Equol(EQ), HG+3uM ICI182,780 (IG), EQ+3uM ICI 182,780(IE) for a additional periods of 4h or 24hr before harvest.

tag: infected with adenovirus carrying estrogen receptor beta

tag: treated with vehicle control


title: Myclo006_03


title: AdERb+LG for 24h, biological rep7

description: AdERb+LG for 24h, biological rep7

tag: treated with 6nM genistein


title: AdERb+veh for 24h, biological rep4

description: AdERb+veh for 24h, biological rep4


title: AdERb+HG for 24h, biological rep4

description: AdERb+HG for 24h, biological rep4

tag: treated with 300nM genistein


title: Control006_05


title: Control006_03


title: Myclo006_05


title: Control006_02


title: AdERb+LG for 24h, biological rep9

description: AdERb+LG for 24h, biological rep9


title: AdERb+E2 for 24h, biological rep4

description: AdERb+E2 for 24h, biological rep4


title: Myclo006_02


title: AdERb+E2 for 24h, biological rep6

description: AdERb+E2 for 24h, biological rep6


title: Tri006_02


title: AdERb+veh for 24h, biological rep5

description: AdERb+veh for 24h, biological rep5


title: AdERb+LG for 24h, biological rep8

description: AdERb+LG for 24h, biological rep8


title: Ad+IE for 24h, biological rep5

description: Ad+IE for 24h, biological rep5

tag: infected with adenovirus carrying no insert

tag: treated with 300nM S-Equol and 3uM ICI 182,780


title: Ad+EQ for 24h, biological rep4

description: Ad+EQ for 24h, biological rep4

tag: treated with 300nM S-Equol


title: Ad+EQ for 24h, biological rep6

description: Ad+EQ for 24h, biological rep6


title: Ad+IE for 24h, biological rep4

description: Ad+IE for 24h, biological rep4


title: Control006_01


title: Ad+E2 for 24h, biological rep5

description: Ad+E2 for 24h, biological rep5

tag: treated with 6nM 17beta-estradiol


title: AdERb+EQ for 24h, biological rep4

description: AdERb+EQ for 24h, biological rep4

tag: treated with 300nM genistein and 3uM ICI182,780


title: Ad+HG for 24h, biological rep5

description: Ad+HG for 24h, biological rep5


title: AdERb+LG for 24h, biological rep5

description: AdERb+LG for 24h, biological rep5


title: AdERb+IG for 24h, biological rep1

description: AdERb+IG for 24h, biological rep1


title: Ad+IG for 24h, biological rep5

description: Ad+IG for 24h, biological rep5


title: Ad+IG for 24h, biological rep4

description: Ad+IG for 24h, biological rep4


title: Ad+EQ for 24h, biological rep5

description: Ad+EQ for 24h, biological rep5


title: Ad+HG for 24h, biological rep6

description: Ad+HG for 24h, biological rep6


title: Ad+E2 for 24h, biological rep4

description: Ad+E2 for 24h, biological rep4


title: AdERb+LG for 24h, biological rep4

description: AdERb+LG for 24h, biological rep4


title: AdERb+veh for 24h, biological rep6

description: AdERb+veh for 24h, biological rep6


title: AdERb+EQ for 24h, biological rep1

description: AdERb+EQ for 24h, biological rep1


title: Ad+veh for 24h, biological rep5

description: Ad+veh for 24h, biological rep5


title: AdERb+HG for 24h, biological rep3

description: AdERb+HG for 24h, biological rep3


title: AdERb+LG for 24h, biological rep6

description: AdERb+LG for 24h, biological rep6


title: AdERb+HG for 24h, biological rep2

description: AdERb+HG for 24h, biological rep2


title: Ad+IG for 24h, biological rep6

description: Ad+IG for 24h, biological rep6


title: AdERb+EQ for 24h, biological rep3

description: AdERb+EQ for 24h, biological rep3


title: AdERb+IG for 24h, biological rep2

description: AdERb+IG for 24h, biological rep2


title: Ad+HG for 24h, biological rep4

description: Ad+HG for 24h, biological rep4


title: AdERb+LG for 24h, biological rep1

description: AdERb+LG for 24h, biological rep1


title: AdERb+EQ for 24h, biological rep2

description: AdERb+EQ for 24h, biological rep2


title: AdERb+LG for 24h, biological rep2

description: AdERb+LG for 24h, biological rep2


title: Ad+veh for 24h, biological rep6

description: Ad+veh for 24h, biological rep6


title: Ad+veh for 24h, biological rep4

description: Ad+veh for 24h, biological rep4


title: AdERb+E2 for 24h, biological rep2

description: AdERb+E2 for 24h, biological rep2


title: Ad+IG for 24h, biological rep1

description: Ad+IG for 24h, biological rep1


title: Ad+IG for 24h, biological rep3

description: Ad+IG for 24h, biological rep3


title: AdERb+LG for 24h, biological rep3

description: AdERb+LG for 24h, biological rep3


title: AdERb+veh for 24h, biological rep1

description: AdERb+veh for 24h, biological rep1


title: AdERb+veh for 24h, biological rep3

description: AdERb+veh for 24h, biological rep3


title: AdERb+veh for 24h, biological rep2

description: AdERb+veh for 24h, biological rep2


title: Ad+EQ for 24h, biological rep2

description: Ad+EQ for 24h, biological rep2


title: Ad+IG for 24h, biological rep2

description: Ad+IG for 24h, biological rep2


title: Ad+EQ for 24h, biological rep1

description: Ad+EQ for 24h, biological rep1


title: AdERb+E2 for 24h, biological rep3

description: AdERb+E2 for 24h, biological rep3


title: AdERb+E2 for 24h, biological rep1

description: AdERb+E2 for 24h, biological rep1


title: parental Lovo colorectal cancer cells

city: Pamplona

first: Eva

last: Bandres

address: Avda Pio XII, 55

department: Cancer Research Program

country: Spain

institute: Center for Applied Medical Research (CIMA), University of Navarra

description: Each cell line was analyzed in duplicate, with RNA reference (Stratagene) as reference sample and labeled each biological condition once by Cy3 and once by Cy5. Taking the average of two arrays thus labeled, cancel the dye effect on any particular gene. In total we used 16 slides.

hyb_protocol: The microarrays used in our study were the Human 19K Oligo Array from Center for Applied Genomics (University of Medicine of New Jersey). Microarray slides were prehybridized in buffer containing 5x SSC, 25% formamide and 0.1% SDS at 42 °C for 45min and washed by dipping in isopropanol. The slides were then dipped in distilled water and dried with compressed air.  The Final Hybridization Mix was added to the prehybridized slide. A 22 x 60 mm coverslip was cleaned with compressed air and then gradually placed on the slide to form a thin layer of labeled targets. To maintain humidity inside the chamber, 20 l 2x SSC was added to the two reservoir wells. The chamber was then tightly sealed and incubated at 55 °C water bath overnight for 16-20 h. Slide was then removed from the chamber, washed for 10 min sequentially at 42 ºC in 2x SSC/0.2% SDS buffer, at room temperature in 2x SSC buffer and at room temperature in 0.2x SSC buffer, rinsed in distilled water for 5 s, and dried by compressed air.  Then, we prepare the 3DNA Array 350 Capture Reagent (Vial 1) by thawing the vial in the dark at room temperature for 20 minutes, vortexing at the maximum setting for 3 seconds and microfuge briefly and incubating at 50-55°C for 10 minutes. Simultaneously we resuspended the 2X Hybridization Buffer (Vial 6) by heating to 70°C for at least 10 minutes. For each array, we prepare a 3DNA Hybridization Mix containing 2.5ul of 3DNA Array 350 Capture Reagent-1 (Vial 1),  2.5ul of 3DNA Array 350 Capture Reagent-2 (Vial 1) , 25ul of 2X Hybridization Buffer (Vial 6) and 20 ul of water. Gently vortex and briefly microfuge the 3DNA Hybridization Mix. We incubate the 3DNA Hybridization Mix first at 75-80°C for 10 minutes, and then we add the 3DNA Hybridization Mix to a prewarmed microarray, taking care to leave behind any precipitate at the bottom of the tube. To maintain humidity inside the chamber, 20 l 2x SSC was added to the two reservoir wells. The chamber was then tightly sealed and incubated at 60 °C water bath for 4 h.   Slide was then removed from the chamber, washed for 10 min sequentially at 65 ºC in 2x SSC/0.2% SDS buffer, at room temperature in 2x SSC buffer and at room temperature in 0.2x SSC buffer, rinsed in distilled water for 5 s, and dried by compressed air.

scan_protocol: All slides were scanned immediately with an Affymetrix GMS 418 Array Scanner using appropriate gains on the photomultiplier tube to obtain the highest intensity without saturation. A 16 bit TIFF image was generated for each channel, Cy3 and Cy5. The image analysis was performed with Imagene 4.1 software (BioDiscovery) to quantify the signal intensities. Data from spots not recognized by the Imagene analysis software were excluded from further considerations (empty, poor and negative spots). Data from the spots visually identified as flawed (<15% in all arrays) were also removed. Only the spots with flag value equal to 0 were included in the analysis.

data_processing: The data sets were imported into Microsoft Excel in order to analyze the quality for each feature. Two parameters were used to asses the data filtration: difference between median and mean under 20% for each feature and intensity feature median greater than background mean plus 2 standard deviation. Normalization data was performed with ArrayNorm 1.7.2 software by using Lowess and Dye Swap Sim Fix Filter methods. Visualization of results was performed with the normalized data using average linkage and Euclidean distance as a measurement of similarity using GENESIS 1.5.0 Software (Alexander Sturn, Institute for Genomics and Bioinformatics, Graz University of Technology). ANOVA was used as statistical function to determine gene expression differences between resistant (cluster R) and sensitive (cluster S) cell groups. The differences were considered statistically significant when two-sided p-values were less than 0.01.

source_name: Total RNA from human parental Lovo colorectal cancer cells

label_protocol: Labeling of total RNA was performed using 3DNA Array-350 Detection kit according to manufacturer's protocol (Genisphere, Hatfield, PA). Total RNA was reverse transcribed using reverse transcription (RT) primers. Briefly, 5 µg of total RNA and 1 µl of Cy3 or Cy5 capture sequence were brought to 11 µl with RNase free water and incubated for 10 min at 80°C. In a separate microtube 4 µl of 5x RT buffer, 1 µl dNTP mix, 2 µl 0.1M DTT, 1 l of Superase In TM Rnase inhibitor and 1µl of Superscript II reverse transcriptase were combined and the reaction was incubated 2 h at 42°C. The reaction was terminated by adding 3.5 µl of 0.5 M NaOH/50 mM EDTA and incubating it at 65°C for 10 min. The reaction was neutralized with 5 µl 1 M Tris-Cl, pH 7.5. The Cy3 and Cy5 reactions were then combined and precipitated with 15 µg of linear acrylamide, 250 µl 3 M ammonium acetate, and 875 µl 100% ethanol at -20 °C for 1 hour. Following precipitation the pellet was dried with speed-vac. In preparation for hybridization the cDNA pellet was resuspended in 29 µl RNase free water deionized distilled water. Then, 29 µl hybridization buffer (vial 12) were added to the mix and incubated at 80 °C for 10 min, followed by 55 °C for 45 min. This is the Final Hybridization Mix for loading on the array.

growth_protocol: After selection of Oxa-resistant cell lines, the analysis of resistance degree and cross resistance to other drugs was assessed by using MTT colorimetric assay. All cell lines were grown in P60 dishes and total RNA from each sample isolated by using the RNeasy Mini kit (Qiagen) and were exhaustively treated with RNase-free DNAse I. RNA quantification were performed using NanoDrop spectophotometer (Nucliber).

tag: parental Lovo colorectal cancer cells

source_name: reference RNA (Human Reference RNA, Stratagene)

tag: Human Reference RNA from Stragene


source_name: Total RNA from human LS513-Oxaplatin-resistant colorectal cancer cells

extract_protocol: All cell lines were grown in P60 dishes and total RNA from each sample isolated by using the RNeasy Mini kit (Qiagen) and were exhaustively treated with RNase-free DNAse I. RNA quantification were performed using NanoDrop spectophotometer (Nucliber).


title: AdERb+HG for 24h, biological rep1

description: AdERb+HG for 24h, biological rep1


source_name: Total RNA from human Lovo-Oxaplatin-resistant colorectal cancer cells


title: LS513 colorectal cancer cells

source_name: Total RNA from human parental LS513 colorectal cancer cells

tag: LS513 colorectal cancer cells


title: Ad+HG for 24h, biological rep1

description: Ad+HG for 24h, biological rep1


title: Ad+LG for 24h, biological rep2

description: Ad+LG for 24h, biological rep2


source_name: Total RNA from human  HT29-Oxaplatin-resistant colorectal cancer cells


title: Ad+HG for 24h, biological rep2

description: Ad+HG for 24h, biological rep2


title: Ad+LG for 24h, biological rep1

description: Ad+LG for 24h, biological rep1


title: parental DLD1 colorectal cancer cells

source_name: Total RNA from human parental DLD1 colorectal cancer cells

tag: parental DLD1 colorectal cancer cells


title: Ad+E2 for 24h, biological rep2

description: Ad+E2 for 24h, biological rep2


source_name: Total RNA from human  DLD1-Oxaplatin-resistant colorectal cancer cells


title: Ad+HG for 24h, biological rep3

description: Ad+HG for 24h, biological rep3


title: Ad+EQ for 24h, biological rep3

description: Ad+EQ for 24h, biological rep3


title: Ad+E2 for 24h, biological rep3

description: Ad+E2 for 24h, biological rep3


title: Ad+E2 for 24h, biological rep1

description: Ad+E2 for 24h, biological rep1


title: parental HT29 colorectal cancer cells

source_name: Total RNA from human parental HT29 colorectal cancer cells

tag: parental HT29 colorectal cells


title: AdERb+IE for 4h, biological rep3

description: AdERb+IE for 4h, biological rep4


title: Ad+LG for 24h, biological rep3

description: Ad+LG for 24h, biological rep3


title: Ad+veh for 24h, biological rep3

description: Ad+veh for 24h, biological rep3


title: Ad+veh for 24h, biological rep1

description: Ad+veh for 24h, biological rep1


title: Ad+veh for 24h, biological rep2

description: Ad+veh for 24h, biological rep2


title: AdERb+EQ for 4h, biological rep2

description: AdERb+EQ for 4h, biological rep2


title: AdERb+EQ for 4h, biological rep1

description: AdERb+EQ for 4h, biological rep1


title: AdERb+EQ for 4h, biological rep3

description: AdERb+IE for 4h, biological rep3


title: AdERb+IG for 4h, biological rep2

description: AdERb+IG for 4h, biological rep2


title: AdERb+HG for 4h, biological rep2

description: AdERb+HG for 4h, biological rep2


title: AdERb+IG for 4h, biological rep3

description: AdERb+IG for 4h, biological rep3


title: AdERb+HG for 4h, biological rep1

description: AdERb+HG for 4h, biological rep1


title: AdERb+LG for 4h, biological rep2

description: AdERb+LG for 4h, biological rep2


title: AdERb+LG for 4h, biological rep3

description: AdERb+LG for 4h, biological rep3


title: AdERb+IE for 4h, biological rep1

description: AdERb+IE for 4h, biological rep1


title: AdERb+IE for 4h, biological rep2

description: AdERb+IE for 4h, biological rep2


title: AdERb+veh for 4h, biological rep3

description: AdERb+veh for 4h, biological rep3


title: AdERb+IG for 4h, biological rep1

description: AdERb+IG for 4h, biological rep1


title: AdERb+LG for 4h, biological rep1

description: AdERb+LG for 4h, biological rep1


title: AdERb+veh for 4h, biological rep2

description: AdERb+veh for 4h, biological rep2


title: AdERb+E2 for 4h, biological rep3

description: AdERb+E2 for 4h, biological rep3


title: Ad+IE for 4h, biological rep3

description: Ad+IE for 4h, biological rep3


title: AdERb+HG for 4h, biological rep3

description: AdERb+HG for 4h, biological rep3


title: Ad+IE for 4h, biological rep2

description: Ad+IE for 4h, biological rep2


title: AdERb+E2 for 4h, biological rep2

description: AdERb+E2 for 4h, biological rep2


title: AdERb+E2 for 4h, biological rep1

description: AdERb+E2 for 4h, biological rep1


title: Ad+IG for 4h, biological rep1

description: Ad+IG for 4h, biological rep1


title: Ad+IG for 4h, biological rep2

description: Ad+IG for 4h, biological rep2


title: Ad+EQ for 4h, biological rep3

description: Ad+EQ for 4h, biological rep3


title: LPS 24h Direct

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

description: To assess differential expression of genes, the normalized log intensity ratios were analyzed with Student’s t-test (p<0.01). The Bayesian modification to the false discovery rate (FDR) was used to correct for multiple comparison tests, estimating the q-value for the set of differentially expressed genes .

hyb_protocol: We used a dye swap experimental design and each sample was hybridized to two microarrays. For the first slide, test and control cDNA were labeled with Cy5 and Cy3 respectively, and for the second array dye assignment was reversed. All head kidney samples were analyses using the dye swap protocol. The slides were pre-treated with 1% BSA, fraction V, 5 x SSC, 0.1% SDS (30 min at 50ºC) and washed with 2 x SSC (3 min) and 0.2 x SSC (3 min) and hybridized overnight in cocktail containing 1.3 x Denhardt’s, 3 x SSC 0.3% SDS, 2.1 μg/μl polyadenylate and 1 μg/μl yeast tRNA.

scan_protocol: Scanning was performed with ScanArray 5000 and images were processed with QuantArray (GSI Luminomics).  The measurements in spots were filtered by criteria I/B ≥ 3 and (I-B)/(SI+SB) ≥ 0.6, where I and B are the mean signal and background intensities and SI, SB are the standard deviations.

data_processing: After subtraction of mean background, locally weighted non-linear regression (Lowess) normalization was performed separately for each slide

organism: Oncorhynchus mykiss

source_name: LPS head kidney 24h (test)

label_protocol: cDNA Cy3 Labelling with Cy3- and Cy5-dCTP (Amersham Pharmacia) was completed using SuperScript III reverse transcriptase (Invitrogen) and oligo(dT) primer, and cDNA was purified with Microcon YM30 (Millipore).

extract_protocol: TriReagent manufacturer's protocolRNA from infected and control kidneys was extracted with the Trizol reagent (Life Technologies) or Tri Reagent (Molecular Research Center, Cincinnati, OH, USA) according to the manufacturer’s instructions. DNase treatment was performed to remove contaminating DNA from preparations. RNA was precipitated using ethanol 100% and ammonium acetate (pH 5.2). The RNA was stored at -80 ºC in ethanol 70% until use.

tag: RNA from wild-type trout

source_name: LPS head kidney 24h (control)


title: Ad+EQ for 4h, biological rep1

description: Ad+EQ for 4h, biological rep1


title: Ad+EQ for 4h, biological rep2

description: Ad+EQ for 4h, biological rep2


title: AdERb+veh for 4h, biological rep1

description: AdERb+veh for 4h, biological rep1


title: IHNV 72h Direct

scan_protocol: Scanning was performed with ScanArray 5000 and images were processed with QuantArray (GSI Luminomics). The measurements in spots were filtered by criteria I/B ≥ 3 and (I-B)/(SI+SB) ≥ 0.6, where I and B are the mean signal and background intensities and SI, SB are the standard deviations.

source_name: IHNV head kidney 72h (test)

source_name: IHNV head kidney 72h (control)

label_protocol: Labelling with Cy3- and Cy5-dCTP (Amersham Pharmacia) was completed using SuperScript III reverse transcriptase (Invitrogen) and oligo(dT) primer, and cDNA was purified with Microcon YM30 (Millipore).

extract_protocol: RNA from infected and control kidneys was extracted with the Trizol reagent (Life Technologies) or Tri Reagent (Molecular Research Center, Cincinnati, OH, USA) according to the manufacturer’s instructions. DNase treatment was performed to remove contaminating DNA from preparations. RNA was precipitated using ethanol 100% and ammonium acetate (pH 5.2). The RNA was stored at -80 ºC in ethanol 70% until use.


title: Ad+IE for 4h, biological rep1

description: Ad+IE for 4h, biological rep1


title: Ad+HG for 4h, biological rep1

description: Ad+HG for 4h, biological rep1


title: IHNV 72h Reverse


title: IHNV 24h Reverse

source_name: IHNV head kidney 24h (control)

source_name: IHNV head kidney 24h (test)


title: Ad+LG for 4h, biological rep3

description: Ad+LG for 4h, biological rep3


title: IHNV 24h Direct


title: attenuatedIHNV 72h Direct

source_name: attIHNV head kidney 72h (test)

source_name: attIHNV head kidney 72h (control)


title: Ad+HG for 4h, biological rep2

description: Ad+HG for 4h, biological rep2

source_name: MCF-7 breast cancer cells


title: Ad+LG for 4h, biological rep1

description: Ad+LG for 4h, biological rep1


title: Ad+LG for 4h, biological rep2

description: Ad+LG for 4h, biological rep2


title: T-cell prolymphocytic leukemia, inv(14)(q11q32), case 12

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

country: Germany

institute: Institut fuer Zellbiologie

description: High-resolution copy-number determination using single nucleotide polymorphism chip technology in 11 inv(14)/t(14;14)-positive T-PLL Samples and 1 without the inversion.

hyb_protocol: Following fragmentation, labelled DNA was hybridized to GeneChips. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The Arrays were then  scanned using the Gene Chip Scanner 3000

data_processing: CEL files were generated using GeneChip Operating Software v 3.0 and SNP calls generated using GeneChip DNA Analysis Software (GDAS) v 3.0

source_name: Mononulear cells from T-PLL peripheral blood sample

label_protocol: DNA was restriction digested, PCR amplified, fragmented and labeled according to the manufacturer's instructions.

extract_protocol: Genomic DNA was extracted with QIAamp DNA Blood Midi Kit, Qiagen, Hilden, Germany

tag: Karyotype

tag: Age

value: 55 years

tag: Gender

value: male


title: T-cell prolymphocytic leukemia, inv(14)(q11q32), case 11

value: 68 years

value: female


title: Ad+E2 for 4h, biological rep2

description: Ad+E2 for 4h, biological rep2


title: Ad+E2 for 4h, biological rep1

description: Ad+E2 for 4h, biological rep1


title: attenuatedIHNV 72h Reverse


title: Ad+E2 for 4h, biological rep3

description: Ad+E2 for 4h, biological rep3


title: T-cell prolymphocytic leukemia without inv(14)(q11q32), case A

value: 67 years


title: attenuatedIHNV 24h Reverse

source_name: attIHNV head kidney 24h (control)

source_name: attIHNV head kidney 24h (test)


title: T-cell prolymphocytic leukemia, inv(14)(q11q32), case 10

value: 76 years


title: attenuatedIHNV 24h Direct


title: LPS 72h Direct

source_name: LPS head kidney 72h (test)

source_name: LPS head kidney 72h (control)


title: T-cell prolymphocytic leukemia, inv(14)(q11q32), case 6

value: 59 years


title: T-cell prolymphocytic leukemia, inv(14)(q11q32), case 9

value: 51 years


title: T-cell prolymphocytic leukemia, inv(14)(q11q32), case 7

value: 70 years


title: LPS 72h Reverse


title: LPS 24h Reverse


title: Ad+veh for 4h, biological rep2

description: Ad+veh for 4h, biological rep2

tag: treated with vehicle control


title: Ad+veh for 4h, biological rep3

description: Ad+veh for 4h, biological rep3


title: T-cell prolymphocytic leukemia, inv(14)(q11q32), case 4

value: 90 years


title: T-cell prolymphocytic leukemia, inv(14)(q11q32), case 5

value: 74 years


title: Ad+veh for 4h, biological rep1

description: Ad+veh for 4h, biological rep1


title: T4 mock_vs_T4 inoc rep4 KB

status: Public on Feb 05 2008

city: Urbana

first: min

last: li

state: IL

address: Rm230 1101 W peabody Dr

institute: University of Illinois at Urbana-Champaign

description: Replicate 4

hyb_protocol: Hegde et al 2000 Biotechniques 29:548-56

scan_protocol: Scanner: Perkin-Elmer ScanArray Express Software: ScanArray Express v2.1

data_processing:
Spot raw data from GenePix4.1
data cleaned and formatted with in-house PERL scripts
log2 transformed using R/MAANOVA
glowess normalization using R/MAANOVA
statistically analyzed by ANOVA in SAS to calculate p-values and fold-changes

organism: Glycine max

source_name: Pooled roots from 4-6 plants 4 days post mock inoc

label_protocol: Indirect incorporation using aa-dUTP, detailed in Zou et al 2005 MPMI 18:1161-1174

growth_protocol:
Growth Chamber (30C)
16 hour daylength: 60% humidity

extract_protocol: Trizol Phase Lock Gel RNA Extraction

treatment_protocol: water

tag: Cultivar

value: Supernodulating GmNARKmutant SS2-2

tag: 4 days post mock inoculation

value: 6 days

source_name: Pooled roots from 4-6 plants 4 days post inoc

treatment_protocol:
Bradyrhizobium japonicum strain USDA110
OD600: 0.01 in water
1 ml pipetted over 1:3 perlite:vermiculite growth medium
4 days post inoculation

tag: 4 days post inoculation


title: T-cell prolymphocytic leukemia, inv(14)(q11q32), case 3

value: 72 years


title: T4 mock_vs_T4 inoc rep3 KA

description: Replicate 3


title: T4 mock_vs_T4 inoc rep3 KB

description: Replicate 3


title: T-cell prolymphocytic leukemia, inv(14)(q11q32), case 2

value: 54 years


title: T4 mock_vs_T4 inoc rep2 KB

description: Replicate 2


title: T4 mock_vs_T4 inoc rep1 KB

description: Replicate 1


title: T4 mock_vs_T4 inoc rep1 KA

description: Replicate 1


title: T8 mock_vs_T4 mock rep1 KA

description: Replicate 1

source_name: Pooled roots from 4-6 plants 8 days post mock inoc

tag: 8 days post mock inoculation

value: 10 days


title: T4 mock_vs_T4 inoc rep4 KA

description: Replicate 4


title: T8 mock_vs_T4 mock rep3 KB

description: Replicate 3


title: T8 mock_vs_T4 mock rep4 KB

description: Replicate 4


title: T8 inoc_vs_T8 mock rep3 KA

description: Replicate 3

source_name: Pooled roots from 4-6 plants 8 days post inoc

treatment_protocol:
Bradyrhizobium japonicum strain USDA110
OD600: 0.01 in water
1 ml pipetted over 1:3 perlite:vermiculite growth medium
8 days post inoculation

tag: 8 days post inoculation


title: T8 mock_vs_T4 mock rep3 KA

description: Replicate 3


title: T4 mock_vs_T4 inoc rep2 KA

description: Replicate 2


title: T8 mock_vs_T4 mock rep2 KB

description: Replicate 2


title: T8 mock_vs_T4 mock rep2 KA

description: Replicate 2


title: T8 inoc_vs_T8 mock rep3 KB

description: Replicate 3


title: T8 inoc_vs_T8 mock rep4 KB

description: Replicate 4


title: T8 mock_vs_T4 mock rep4 KA

description: Replicate 4


title: T8 mock_vs_T4 mock rep1 KB

description: Replicate 1


title: T8 inoc_vs_T8 mock rep2 KB

description: Replicate 2


title: T8 inoc_vs_T8 mock rep1 KB

description: Replicate 1


title: L. reuteri_resumed growth during bile exposure_rep5B

city: East Lansing

first: Robert

last: Britton

state: MI

address: 6144 BPS Building  Michigan State University

department: Microbiology and Molecular Genetics

institute: Michigan State University

description: Dye-swap with samples used in biological replicate 5 of 5.  Comparison of L. reuteri ATCC 55730 cultures before bile treatment and after the resumption of growth in the presence of bile (0.5% oxgall).

hyb_protocol: For hybridization, yeast tRNA and salmon testes DNA were added to labeled cDNA along with a formamide hybridization buffer.  Samples were applied to slides, and hybridization was carried out at 42 degrees Celsius in Corning microarray hybridization chambers overnight. Slides were then washed sequentially for four minutes in each of the following buffers: 1X SSC and 0.2% SDS, 0.1X SSC and 0.2% SDS, and 0.1X SSC.

scan_protocol: Arrays were scanned on a Axon instruments GenePix 4000B scanner. Images were processed using GenePix Pro software (version 4.1)

data_processing: Normalization was performed by making the total intensity from both channels equal.  Spots that did not have at least 80% of pixels two standard deviations above the mean were exluded from anaysis.  Statistically significant changes in gene expression were deteremined by iterative outlier analysis, with three iterations performed (Britton, R.A., P. Eichenberger, J.E. Gonzalez-Pastor, P. Fawcett, R. Monson, R. Losick, and A.D. Grossman.  2002.  Genome-wide analysis of the stationary-phase sigma factor (sigma-H) regulon of Bacillus subtilis.  J. Bacteriol. 184:4881-90.).

organism: Limosilactobacillus reuteri

source_name: Total RNA from treated L. reuteri cells labeled with Cyanine-5 (red)

label_protocol: 10 ug of total RNA were primed with 2.5 ug of random hexamers (Qiagen) at 70 degrees Celsius for 10 minutes.  Reverse transcription was then carried out using Superscript III (Invitrogen) with 500 uM each dATP, dCTP, and dGTP, 300 uM dTTP, and 200 uM aminoallyl dUTP.  After reverse transcription, RNA was removed by hydrolysis and cDNA was cleaned.  cDNA was then labeled using CyDye Post-labeling reactive dye packs (Amersham).

growth_protocol: Bacterial cells were grown under microaerobic conditions (2% oxygen) in MRS broth at 37 degrees Celsius.

extract_protocol: At the specified times, 5 ml of bacterial were collected and mixed with an equal part of ice-cold methanol.  Cell pellets were centrifuged, washed, and resuspended in 0.25 units/ul mutanolysin.  After incubation at 37 degrees Celsius for 20 minutes, total RNA was collected according to the manufacturer's instructions with the Qiagen RNeasy Kit.

treatment_protocol: Cells were collected after the resumption of growth in the presence of 0.5% oxgall (bile).

tag: Strain

source_name: Total RNA from untreated L. reuteri cells labeled with Cyanine-3 (green)

treatment_protocol: Cells were collected at mid-log phase of growth, immediately before the addition of bile at an optical density (wavelength 600nm) of 0.5.


title: L. reuteri_resumed growth during bile exposure_rep5A

description: Biological replicate 5 of 5.  Comparison of L. reuteri ATCC 55730 cultures before bile treatment and after the resumption of growth in the presence of bile (0.5% oxgall).

source_name: Total RNA from untreated L. reuteri cells labeled with Cyanine-5 (red)

source_name: Total RNA from treated L. reuteri cells labeled with Cyanine-3 (green)


title: T8 inoc_vs_T8 mock rep4 KA

description: Replicate 4


title: L. reuteri_resumed growth during bile exposure_rep4B

description: Dye-swap with samples used in biological replicate 4 of 5.  Comparison of L. reuteri ATCC 55730 cultures before bile treatment and after the resumption of growth in the presence of bile (0.5% oxgall).


title: L. reuteri_resumed growth during bile exposure_rep4A

description: Biological replicate 4 of 5.  Comparison of L. reuteri ATCC 55730 cultures before bile treatment and after the resumption of growth in the presence of bile (0.5% oxgall).


title: T-cell prolymphocytic leukemia, inv(14)(q11q32), case 1

value: 49 years


title: L. reuteri_resumed growth during bile exposure_rep3B

description: Dye-swap with samples used in biological replicate 3 of 5.  Comparison of L. reuteri ATCC 55730 cultures before bile treatment and after the resumption of growth in the presence of bile (0.5% oxgall).


title: T16 inoc_vs_T8 inoc rep4 KB

description: Replicate 4

source_name: Pooled roots from 4-6 plants 16 days post inoc

treatment_protocol:
Bradyrhizobium japonicum strain USDA110
OD600: 0.01 in water
1 ml pipetted over 1:3 perlite:vermiculite growth medium
16 days post inoculation

tag: 16 days post inoculation

value: 18 days


title: L. reuteri_resumed growth during bile exposure_rep3A

description: Biological replicate 3 of 5.  Comparison of L. reuteri ATCC 55730 cultures before bile treatment and after the resumption of growth in the presence of bile (0.5% oxgall).


title: L. reuteri_resumed growth during bile exposure_rep2B

description: Dye-swap with samples used in biological replicate 2 of 5.  Comparison of L. reuteri ATCC 55730 cultures before bile treatment and after the resumption of growth in the presence of bile (0.5% oxgall).


title: L. reuteri_resumed growth during bile exposure_rep2A

description: Biological replicate 2 of 5.  Comparison of L. reuteri ATCC 55730 cultures before bile treatment and after the resumption of growth in the presence of bile (0.5% oxgall).


title: T8 inoc_vs_T8 mock rep1 KA

description: Replicate 1


title: T16 inoc_vs_T8 inoc rep3 KA

description: Replicate 3


title: T16 inoc_vs_T8 inoc rep4 KA

description: Replicate 4


title: L. reuteri_resumed growth during bile exposure_rep1B

description: Dye-swap with samples used in biological replicate 1 of 5.  Comparison of L. reuteri ATCC 55730 cultures before bile treatment and after the resumption of growth in the presence of bile (0.5% oxgall).


title: T16 inoc_vs_T8 inoc rep3 KB

description: Replicate 3


title: T16 inoc_vs_T8 inoc rep1 KB

description: Replicate 1


title: T16 inoc_vs_T8 inoc rep2 KB

description: Replicate 2


title: T16 mock_vs_T16 inoc rep4 KB

description: Replicate 4

source_name: Pooled roots from 4-6 plants 16 days post mock inoc

tag: 16 days post mock inoculation


title: T16 inoc_vs_T8 inoc rep2 KA

description: Replicate 2


title: T16 mock_vs_T16 inoc rep3 KA

description: Replicate 3


title: T16 inoc_vs_T8 inoc rep1 KA

description: Replicate 1


title: L. reuteri_15 minutes bile exposure_rep5A

description: Biological replicate 5 of 5.  Comparison of L. reuteri ATCC 55730 culture before and after 15 minutes of exposure to 0.5% oxgall (bile).

treatment_protocol: Cells were collected 15 minutes after the addition of 0.5% oxgall (bile) to the mid-log phase culture.


title: L. reuteri_resumed growth during bile exposure_rep1A

description: Biological replicate 1 of 5.  Comparison of L. reuteri ATCC 55730 cultures before bile treatment and after the resumption of growth in the presence of bile (0.5% oxgall).


title: T16 mock_vs_T16 inoc rep4 KA

description: Replicate 4


title: T8 inoc_vs_T8 mock rep2 KA

description: Replicate 2


title: L. reuteri_15 minutes bile exposure_rep3A

description: Biological replicate 3 of 5.  Comparison of L. reuteri ATCC 55730 culture before and after 15 minutes of exposure to 0.5% oxgall (bile).


title: L. reuteri_15 minutes bile exposure_rep4A

description: Biological replicate 4 of 5.  Comparison of L. reuteri ATCC 55730 culture before and after 15 minutes of exposure to 0.5% oxgall (bile).


title: L. reuteri_15 minutes bile exposure_rep4B

description: Dye-swap with samples used in biological replicate 4 of 5.  Comparison of L. reuteri ATCC 55730 culture before and after 15 minutes of exposure to 0.5% oxgall (bile).


title: L. reuteri_15 minutes bile exposure_rep2B

description: Dye-swap with samples used in biological replicate 2 of 5.  Comparison of L. reuteri ATCC 55730 culture before and after 15 minutes of exposure to 0.5% oxgall (bile).


title: L. reuteri_15 minutes bile exposure_rep5B

description: Dye-swap with samples used in biological replicate 5 of 5.  Comparison of L. reuteri ATCC 55730 culture before and after 15 minutes of exposure to 0.5% oxgall (bile).


title: T16 mock_vs_T16 inoc rep2 KB

description: Replicate 2


title: T16 mock_vs_T16 inoc rep2 KA

description: Replicate 2


title: T0_vs_T16 mock rep3 KB

description: Replicate 3

source_name: Pooled roots from 4-6 plants T0

treatment_protocol:
Bradyrhizobium japonicum strain USDA110
OD600: 0.01 in water
sprayed over roots
then immediately collected

value: 2 days

growth_protocol: 16 hour daylength: 60% humidity


title: T16 mock_vs_T16 inoc rep3 KB

description: Replicate 3


title: L. reuteri_15 minutes bile exposure_rep1A

description: Biological replicate 1 of 5.  Comparison of L. reuteri ATCC 55730 culture before and after 15 minutes of exposure to 0.5% oxgall (bile).


title: T0_vs_T16 mock rep4 KB

description: Replicate 4


title: T16 mock_vs_T16 inoc rep1 KB

description: Replicate 1


title: T0_vs_T16 mock rep4 KA

description: Replicate 4


title: T0_vs_T16 mock rep2 KB

description: Replicate 2


title: L. reuteri_15 minutes bile exposure_rep3B

description: Dye-swap with samples used in biological replicate 3 of 5.  Comparison of L. reuteri ATCC 55730 culture before and after 15 minutes of exposure to 0.5% oxgall (bile).


title: L. reuteri_15 minutes bile exposure_rep2A

description: Biological replicate 2 of 5.  Comparison of L. reuteri ATCC 55730 culture before and after 15 minutes of exposure to 0.5% oxgall (bile).


title: L. reuteri_15 minutes bile exposure_rep1B

description: Dye-swap with samples used in biological replicate 1 of 5.  Comparison of L. reuteri ATCC 55730 culture before and after 15 minutes of exposure to 0.5% oxgall (bile).


title: G1E-ER4_E2-24hr_rep3

city: Chicago

first: Louis

last: Dore

address: 303 E Superior St., Lurie Bldg 5-250D

department: Feinberg School of Medicine

institute: Northwestern University

description: G1E-ER4 cells, induced with estradiol, 24hrs

hyb_protocol: Labeled RNA samples were hybridized on the miRCURY LNA Array (v8.0) along with a Hy5-labeled common reference, composed of a pool of equal quantities of all 6 samples.

scan_protocol: Scans were performed and quantified by Exiqon A/S using GenePix software (Molecular Devices) and the resultant gpr files were imported into GeneSpring software (Agilent).

data_processing: Probe signals that were present in at least two of the six samples were analyzed.  The data were exported to Microsoft Excel worksheets, log2-transformed, and analyzed for differentially expressed miRNAs using SAM (v3.01, Significance Analysis of Microarrays, Stanford University) in a two class unpaired design.  From SAM, we determined the fold change for each microRNA.

organism: Mus musculus

label_protocol: RNA samples were sent to Exiwon A/S (Vedbaek, Denmark) where they were labeled using the miRCURY Hy3/Hy5 labeling kit.

growth_protocol: G1E-ER4 cells were cultured in Iscove’s modified Dulbecco’s medium with 15% fetal calf serum, 4.5 x 10-5 M monothioglycerol, 2 U of Epo per ml, and 50 ng of stem cell factor per ml.

extract_protocol: Total cellular RNA was isolated from G1E-ER4 cells using TRIzol (Invitrogen) followed by purification over a glass fiber filter column (mirVana; Ambion), according to manufacturers' instructions.  RNA quality was assessed using an Agilent BioAnalyzer 2100.

treatment_protocol: G1E-ER4 cells were treated with 10-7 M b-estradiol for 24 hours where indicated.

tag: G1E-ER4 cells {Weiss et al., (1997) Mol Cell Biol 17:1642-1651} are derived from male GATA-1-null ES cells {Pevny et al., (1991) Nature 349:257-260}

source_name: Common reference

tag: common reference sample contains equal mixture of all 6 experimental samples


title: T16 mock_vs_T16 inoc rep1 KA

description: Replicate 1


title: G1E-ER4_E2-24hr_rep2

source_name: G1E-ER4 cells, induced with estradiol, 24hrs


title: G1E-ER4_E2-24hr_rep1


title: G1E-ER4_0hr_rep2

description: G1E-ER4 cells, untreated

source_name: G1E-ER4 cells, untreated


title: G1E-ER4_0hr_rep3

description: G1E-ER4 cells, untreated


title: G1E-ER4_0hr_rep1

description: G1E-ER4 cells, untreated


title: Inoc-T4_vs_T0 rep2 KB

description: Replicate 2


title: T0_vs_T16 mock rep1 KB

description: Replicate 1


title: Inoc-T4_vs_T0 rep4 KB

description: Replicate 4


title: Inoc-T4_vs_T0 rep1 KB

description: Replicate 1


title: Inoc-T4_vs_T0 rep1 KA

description: Replicate 1


title: Inoc-T4_vs_T0 rep3 KB

description: Replicate 3