title: S. aureus Exposure Cohort_1394_3687_18751_29

city: Durham

first: Hamza

last: Aziz

state: NC

address: 101 Science Drive

department: Institute of Genomic Science and Policy

institute: Duke University

description: S. aureus Exposure Cohort

hyb_protocol: Amplification and hybridization onto Affymetrix murine 430A2.0 microarrays were performed by Duke University Microarray Core.

scan_protocol: Probe intensities were detected using Axon Genepix 4000B Scanner (Molecular Devices, Union City, CA).  Image files were generated using Affymetrix® GeneChip® Command Console® Software (AGCC).

data_processing: Expression Console (Affymetrix, Santa Clara, CA) was used to ensure that microarray data intensity files met quality control parameters.  Next, expression data from samples that met the quality standards were used in MATLAB to develop predictive models.

source_name: BALB/c male mice, S. aureus Exposure Cohort

label_protocol: RNA from samples that met  quality checks [260/280 ratio >1.8, 260/230 ration > 1.8 and RNA Integrity Number (RIN) > 7] was amplified and biotin-labeled using MessageAmp Premier RNA Amplification Kit (Ambion, Valencia, CA) according to standard protocols at the Duke University Microarray Core facility.

growth_protocol:
For C.albicans:  C. albicans was grown in YPD broth for 12-17 hours at 25 °C and 225 rpm.  The fungal broth was washed with sterile phosphate buffered saline (PBS) and adjusted to a dose of 2×105cfu per 200µl of inoculum.
For S.aureus:  S. aureus was grown in trypticase soy broth (TSB) at 30°C and 225rpm with aeration overnight.  1-2 mL of overnight broth was suspended in 100mL of fresh TSB and shaken at 150rpm for 1-2 hours at 30°C. Once in log phase, the bacterial broth was then harvested by centrifugation, washed with sterile PBS and re-suspended in it to an OD600 of 0.20.

extract_protocol: Whole blood RNA isolation and beta-globin reduction was carried out using the manufacturer’s protocol (Mouse Ribopure and GlobinClear, Ambion Inc).

treatment_protocol: Infection protocol:  Mice were injected using a standard tail vein injection.  Daily weights and twice-daily activity levels were noted to assess the clinical status of the mice.    Mice were then sacrificed by CO2 asphyxiation at pre-determined time intervals of 24 (n=8 mice), 48 (n = 6 mice), 72 (n = 7 mice), and 96-hours (n = 7 mice) post injection.  Control mice were also sacrificed on day 1 and day 4 and processed identically to their experimental counterparts.

tag: cohort

value: S. aureus Exposure Cohort

value: Whole Blood

tag: genotype

value: BALB/c

value: 8 wk old

tag: infection status

value: healthy

tag: infection duration (days)


title: S. aureus Exposure Cohort_1394_3687_18747_20

status: Public on Feb 25 2010

type: RNA

country: USA

description: S. aureus Exposure Cohort

label: biotin

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: age

value: staph


title: S. aureus Exposure Cohort_1394_3687_18749_25

description: S. aureus Exposure Cohort


title: Daoy_Biologicalreplicate1_1

city: san antonio

first: raquel

last: abreu

state: TX

address: 8403 Floyd Curl Drive

institute: CCRI

description: Biological Replicate 1

hyb_protocol: Labeled products were precipitated with isopropanol and resuspended in water prior to hybridization, which was performed with the NimbleGen hybridization kit.

scan_protocol: Microarrays were scanned with the Agilent Microarray Scanner G2565AA.

data_processing: Gene expression values were generated using NimbleScan expression RMA (Robust Multi-array Analysis). Report files were further analyzed in the R Project for Statistical Computing using the Bioconductor package limma. First to assess quality control (one microarray was eliminated) and then to achieve the same empirical distribution on the single channel microarray intensities of the two biological replicates. Finally, we averaged gene expression values to obtain the final values.

organism: Homo sapiens

source_name: Daoy medulloblastoma cells

label_protocol: Samples were labeled with Cy3-9mer primers using Klenow enzyme.

growth_protocol: MEM Richter’s modification medium (Gibco), supplemented with 10% fetal bovine serum (Atlanta Biologicals Inc., Lawrenceville, GA), 100 units/ml penicillin, and 100microg/ml streptomycin (Herndon, VA).

extract_protocol: RNA was purified using TRIzol as recommended by Invitrogen and re-purified with the RNeasy kit from Qiagen.

tag: genotype/variation

value: WT

tag: cell line

value: Daoy medulloblastoma cell line


title: case 1 genotype

status: Public on Feb 26 2010

type: genomic

city: Taipei

first: Yu Hsuan

last: Wu

address: No.155, Sec.2, Linong Street

country: Taiwan

institute: National Yang-Ming University

description: Genomic DNA extracted from germ cell tumors was genotyped using Infinium Human610_Quad Genotyping BeadChips (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48ºC, 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 XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Genomic DNA extracted from breast tumors was genotyped using Infinium Human610_Quad Genotyping BeadChips (Illumina).

label: C-Bio and A-DNP

molecule: genomic DNA

source_name: GCT patient case

label_protocol: 200ng 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: Extraction of genomic DNA from fresh frozen tissue was performed using proteinase K and repeated phenol-chloroform extraction.

value: primary intracranial pediatric germ cell tumor (GCT)

tag: diagnosis

value: germinoma

value: 13.6 years


title: S. aureus Exposure Cohort_1394_3687_18752_c3

description: S. aureus Exposure Cohort


title: case 7 genotype

value: 15.9 years


title: RCC-JW_emetine_1 (GINI)

city: Groningen

first: Gerben

last: Duns

address: Oostersingel, ingang 47, 2nd floor, room E2.036

country: Netherlands

institute: Genetics Department, Groningen University

hyb_protocol: Transcript abundance in treated and untreated cells was measured using Human HT-12_V3_Beadchips (48K) (Ilumina)following the manufacturer's protocol

scan_protocol: Arrays were scanned using an Illumina scanner

data_processing: Microarray data normalization was performed using the Lumi package implemented in R. Data were transformed and normalized using variance-stabilizing transformation followed by robust spline normalization.

source_name: cell line derived from clear cell renal cell carcinoma tumor

label_protocol: Total RNA was labeled using the Illumina ® TotalPrep™-96 RNA amplification kit following the manufacturer's instructions.

growth_protocol: The cell lines were maintained in RPMI 1640 (Sigma) supplemented with 10 % fetal calf serum (Gibco), penicillin (1.0 U/l) (Gibco), streptomycin (1 μg/ul) (Gibco), glutamin (2.0 mM) (Gibco). Cells were grown in an incubator at 37˚C, 5% CO2.

extract_protocol: Total RNA was isolated using RNEasy miniKIT (Qiagen) following the manufacturer's protocol

treatment_protocol: Cells were grown to approximately 70 % confluence in 75 cm flasks, medium was refreshed, emetine dihydrochloride hydrate was added (100 μg/ml).Following 8 hrs of incubation (37 °C, 5% CO2), cells were trypsinized and harvested

value: RCC-JW (KTCTL-195)

tag: depositor

value: Cell Lines Service, www.cellbank.de

tag: gender

value: Male

tag: sample type

value: clear cell renal cell carcinoma primary tumour

tag: tumor stage

tag: age of diagnosis

tag: treatment

value: emetine


title: S. aureus Exposure Cohort_1394_3687_18748_22

description: S. aureus Exposure Cohort

value: S. aureus Exposure Cohort


title: case 2 genotype

value: 12 years


title: RCC-JF_emetine_2 (GINI)

value: RCC-JF (KTCTL-140 )

value: Female


title: RCC-JW_caffeine_1 (GINI)

treatment_protocol: Cells were grown to approximately 70 % confluence in 75 cm flasks, medium was refreshed, caffeine was added (10 mM).Following 8 hrs of incubation (37 °C, 5% CO2), cells were trypsinized and harvested

value: Caffeine


title: RCC-JF_caffeine_1 (GINI)


title: S. aureus Exposure Cohort_1394_3687_18745_14

description: S. aureus Exposure Cohort

value: Whole Blood

value: BALB/c

value: 8 wk old

value: staph


title: RCC-JW_not-treated_1 (GINI)

treatment_protocol: Cells were grown to approximately 70 % confluence in 75 cm flasks, medium was refreshed.Following 8 hrs of incubation (37 °C, 5% CO2), cells were trypsinized and harvested


title: RCC-JF_emetine_1 (GINI)


title: RCC-JF_not-treated_caffeine exp_2 (GINI)


title: RCC-JW_not-treated_2 (GINI)


title: RCC-JW_caffeine_2 (GINI)


title: RCC-JF_not-treated_emetine_2 (GINI)


title: S. aureus Exposure Cohort_1394_3687_18746_16

description: S. aureus Exposure Cohort


title: S. aureus Exposure Cohort_1394_3687_18750_28

description: S. aureus Exposure Cohort

value: healthy


title: RCC-JF_not-treated_caffeine exp_1 (GINI)


title: RCC-HS_emetine_1 (GINI)

value: RCC-HS (KTCTL-30)


title: S. aureus Exposure Cohort_1394_3687_18744_12

description: S. aureus Exposure Cohort


title: S. aureus Exposure Cohort_1394_3687_18742_1

description: S. aureus Exposure Cohort


title: RCC-HS_caffeine_2 (GINI)


title: RCC-FG2_emetine_2 (GINI)

value: RCC-FG2 (KTCTL-26A)


title: C. albicans Signature  Validation Cohort_1394_3120_15462_1461

description: C. albicans Signature  Validation Cohort

source_name: BALB/c male mice, C.albicans Signature  Validation Cohort

value: C.albicans Signature  Validation Cohort


title: C. albicans Signature  Validation Cohort_1394_3120_15463_1462


title: S. aureus Exposure Cohort_1394_3687_18743_2

description: S. aureus Exposure Cohort


title: RCC-HS_not-treated_1 (GINI)

value: Cell Lines Service, www.cellbank.de


title: S. aureus Exposure Cohort_1394_3687_18741_1549

description: S. aureus Exposure Cohort


title: RCC-JF_caffeine_2 (GINI)


title: RCC-HS_caffeine_1 (GINI)


title: RCC-HS_not-treated_2 (GINI)


title: RCC-HS_emetine_2 (GINI)


title: RCC-FG2_caffeine_1 (GINI)

value: Male


title: RCC-FG2_emetine_1 (GINI)

value: clear cell renal cell carcinoma primary tumour


title: RCC-FG2_caffeine_2 (GINI)


title: RCC-ER_emetine_1 (GINI)

value: RCC-ER (KTCTL-13)

value: pT3a, N1,Mx/GIII

value: emetine


title: RCC-JF_not-treated_emetine_1 (GINI)

value: RCC-JF (KTCTL-140 )


title: RCC-ER_emetine_2 (GINI)


title: RCC-FG2_not-treated_2 (GINI)


title: RCC-FG2_not-treated_1 (GINI)


title: RCC-ER_caffeine_1 (GINI)


title: 0 WT-E256X (A22366)

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 WT-E256X (A22366)

scan_protocol: Pixel Size : 5 Scan Date : 2008-11-05 Scan Time : 15:22:26 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : 9.1.3.1
Datafile type : Agilent result file
Normalizaton: Default settings of Agilent Feature Extractor

organism: Saccharomyces cerevisiae

source_name: wt

extract_protocol:
Extraction method: Hoffman-Winston prep:
http://dunham.gs.washington.edu/MDyeastDNAprep.pdf

tag: strain name

value: wt


title: C. albicans Signature  Validation Cohort_1394_3120_15459_1457

value: candida


title: C. albicans Signature  Validation Cohort_1394_3120_15460_1459

value: Whole Blood


title: 0 Dis XVI-rpn6

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XVI-rpn6

scan_protocol: Pixel Size : 5 Scan Date : 2010-01-29 Scan Time : 08:53:45 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Dis XVI-rpn6

value: Dis XVI-rpn6


title: C. albicans Signature  Validation Cohort_1394_3120_15457_1452

value: BALB/c

value: 8 wk old


title: RCC-ER_not-treated_emetine exp_1 (GINI)


title: RCC-ER_not-treated_emetine exp_2 (GINI)


title: RCC-ER_caffeine_2 (GINI)

value: Caffeine


title: C. albicans Signature  Validation Cohort_1394_3120_15456_1448


title: C. albicans Signature  Validation Cohort_1394_3120_15455_1446


title: RCC-ER_not-treated_caffeine exp_2 (GINI)


title: 0 Dis XVI-URA3 (A23517)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XVI-URA3 (A23517)

scan_protocol: Pixel Size : 5 Scan Date : 2008-09-18 Scan Time : 08:53:40 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Dis XVI-URA3 (A23517)

value: Dis XVI-URA3 (A23517)


title: RCC-AB_caffeine_1 (GINI)

value: RCC-AB (KTCTL-21)

value: pT2, N0, MX/GII


title: C. albicans Signature  Validation Cohort_1394_3120_15454_1445

value: C.albicans Signature  Validation Cohort


title: RCC-ER_not-treated_caffeine exp_1 (GINI)

value: Cell Lines Service, www.cellbank.de

value: Male


title: RCC-AB_emetine_1 (GINI)

value: clear cell renal cell carcinoma primary tumour


title: 0 Dis XV-E256X (A22394)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XV-E256X (A22394)

scan_protocol: Pixel Size : 5 Scan Date : 2008-11-21 Scan Time : 14:47:26 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: 0 Dis XV-URA3 (A23516)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XV-URA3 (A23516)

scan_protocol: Pixel Size : 5 Scan Date : 2009-04-24 Scan Time : 10:37:44 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Dis XV-URA3 (A23516)

value: Dis XV-URA3 (A23516)


title: RCC-AB_emetine_2 (GINI)

value: emetine


title: 0 Dis XIV-URA3 (A23515)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XIV-URA3 (A23515)

source_name: Dis XIV-URA3 (A23515)

value: Dis XIV-URA3 (A23515)


title: RCC-AB_not-treated_caffeine exp_2 (GINI)


title: RCC-AB_not-treated_emetine exp_2 (GINI)


title: RCC-AB_not-treated_emetine exp_1 (GINI)


title: RCC-AB_not-treated_caffeine exp_1 (GINI)


title: C. albicans Signature  Validation Cohort_1394_3120_15453_1444


title: RCC5_caffeine_2 (GINI)

value: Gerharz and Gabbert (Virchows Archiv (1994) 424:403-409)

value: clear cell renal cell carcinoma

value: unknown


title: C. albicans Signature  Validation Cohort_1394_3120_15451_1440

value: Whole Blood

value: candida


title: C. albicans Signature  Validation Cohort_1394_3120_15452_1443

value: BALB/c

value: 8 wk old


title: C. albicans Signature  Validation Cohort_1394_3120_15449_1436


title: RCC5_emetine_1 (GINI)


title: C. albicans Signature  Validation Cohort_1394_3120_15450_1439


title: RCC5_not-treated_2 (GINI)


title: RCC5_emetine_2 (GINI)


title: C. albicans Signature  Validation Cohort_1394_3120_15448_1433


title: 0 Dis XIV-E256X (A22393)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XIV-E256X (A22393)

scan_protocol: Pixel Size : 5 Scan Date : 2009-04-08 Scan Time : 11:38:00 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

value: wt


title: 0 Dis XIII-URA3 (A23514)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XIII-URA3 (A23514)

source_name: Dis XIII-URA3 (A23514)

value: Dis XIII-URA3 (A23514)


title: C. albicans Signature  Validation Cohort_1394_3120_15447_1432


title: RCC4_emetine_1 (GINI)


title: 0 Dis XIV-GFP (A21965)

description: Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.

scan_protocol: Pixel Size : 5 Scan Date : 2008-01-08 Scan Time : 15:33:21 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B

source_name: Dis XIV-GFP (A21965)

value: Dis XIV-GFP (A21965)


title: RCC5_not-treated_1 (GINI)


title: RCC4_emetine_2 (GINI)


title: 0 Dis XII-GFP (A21963)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XII-GFP (A21963)

source_name: Dis XII-GFP (A21963)

value: Dis XII-GFP (A21963)


title: RCC5_caffeine_1 (GINI)

value: Caffeine


title: 0 Dis XVI-GFP (A21967)

scan_protocol: Pixel Size : 5 Scan Date : 2008-03-27 Scan Time : 12:14:46 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B

source_name: Dis XVI-GFP (A21967)

value: Dis XVI-GFP (A21967)


title: RCC4_caffeine_2 (GINI)


title: 0 WT-GFP (A21954)

scan_protocol: Pixel Size : 5 Scan Date : 2008-03-27 Scan Time : 12:10:47 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B


title: C. albicans Signature  Validation Cohort_1394_3120_15446_1424

value: C.albicans Signature  Validation Cohort


title: 0 Dis XIII-GFP (A21964)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XIII-GFP (A21964)

scan_protocol: Pixel Size : 5 Scan Date : 2008-09-08 Scan Time : 13:17:05 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Dis XIII-GFP (A21964)

value: Dis XIII-GFP (A21964)


title: C. albicans Signature  Validation Cohort_1394_3120_15444_1429


title: 0 Dis XI-rpn6

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XI-rpn6

source_name: Dis XI-rpn6

value: Dis XI-rpn6


title: 0 Dis XI-GFP-cup1-UBI4 (A25129)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XI-GFP-cup1-UBI4 (A25129)

scan_protocol: Pixel Size : 5 Scan Date : 2009-10-29 Scan Time : 09:21:43 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Dis XI-GFP-cup1-UBI4 (A25129)

value: Dis XI-GFP-cup1-UBI4 (A25129)


title: RCC4_not-treated_caffeine exp_1 (GINI)

value: Gerharz and Gabbert (Virchows Archiv (1994) 424:403-409)


title: C.albicans Initial Signature Cohort_1394_2828_14438_1127

description: C.albicans Initial Signature Cohort

source_name: BALB/c male mice, C.albicans Initial Signature Cohort

value: C.albicans Initial Signature Cohort

value: healthy


title: 0 Dis XI-URA3 (A23512)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XI-URA3 (A23512)

scan_protocol: Pixel Size : 5 Scan Date : 2008-10-02 Scan Time : 16:30:59 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Dis XI-URA3 (A23512)

value: Dis XI-URA3 (A23512)


title: C. albicans Signature  Validation Cohort_1394_3120_15445_1423

value: Whole Blood

value: candida


title: C. albicans Signature  Validation Cohort_1394_3120_15443_1417

value: BALB/c

value: 8 wk old


title: RCC4_not-treated_emetine exp_1 (GINI)

value: clear cell renal cell carcinoma

value: unknown


title: C. albicans Signature  Validation Cohort_1394_3120_15442_1416


title: RCC4_caffeine_1 (GINI)


title: RCC4_not-treated_caffeine exp_2 (GINI)


title: RCC4_not-treated_emetine exp_2 (GINI)


title: 0 Dis XI-GFP (A21962)

scan_protocol: Pixel Size : 5 Scan Date : 2008-03-27 Scan Time : 12:13:11 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B

source_name: Dis XI-GFP (A21962)

value: Dis XI-GFP (A21962)

value: wt


title: 0 Dis XII-E256X (A22391)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XII-E256X (A22391)


title: 0 Dis XI-ubp6CA

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XI-ubp6CA

scan_protocol: Pixel Size : 5 Scan Date : 2009-07-09 Scan Time : 11:02:03 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Dis XI-ubp6CA

value: Dis XI-ubp6CA


title: 0 Dis XV-GFP (A21966)

scan_protocol: Pixel Size : 5 Scan Date : 2008-03-27 Scan Time : 12:14:31 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B

source_name: 0 Dis XV-GFP (A21966)

value: 0 Dis XV-GFP (A21966)


title: C.albicans Initial Signature Cohort_1394_2828_14437_1124

description: C.albicans Initial Signature Cohort

scan_protocol: Probe intensities were detected using Axon Genepix 4000B Scanner (Molecular Devices, Union City, CA).  Image files were generated using Affymetrix® GeneChip® Command Console® Software (AGCC).


title: C.albicans Initial Signature Cohort_1394_2828_14432_1112

description: C.albicans Initial Signature Cohort


title: 0 Dis XI-E256X-cup1-UBI4 (A25136)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XI-E256X-cup1-UBI4 (A25136)

source_name: wt


title: 0 Dis IX-GFP (A21960)

scan_protocol: Pixel Size : 5 Scan Date : 2008-03-27 Scan Time : 12:12:54 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B

source_name: Dis IX-GFP (A21960)

value: Dis IX-GFP (A21960)


title: 0 Dis XI-E256X-cup1-UBI4 (A25136)a

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XI-E256X-cup1-UBI4 (A25136)a

scan_protocol: Pixel Size : 5 Scan Date : 2009-12-04 Scan Time : 13:53:50 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Dis XI-E256X-cup1-UBI4 (A25136)a

value: Dis XI-E256X-cup1-UBI4 (A25136)a


title: C.albicans Initial Signature Cohort_1394_2828_14436_1123

description: C.albicans Initial Signature Cohort


title: C.albicans Initial Signature Cohort_1394_2828_14435_1116

description: C.albicans Initial Signature Cohort


title: 0 Dis VIII-ubp6CA

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis VIII-ubp6CA

source_name: Dis VIII-ubp6CA

value: Dis VIII-ubp6CA


title: 0 Dis II-GFP (A21956)

scan_protocol: Pixel Size : 5 Scan Date : 2008-03-27 Scan Time : 12:11:51 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B

source_name: Dis II-GFP (A21956)

value: Dis II-GFP (A21956)


title: 0 Dis VIII-rpn6

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis VIII-rpn6

scan_protocol: Pixel Size : 5 Scan Date : 2010-01-29 Scan Time : 08:53:45 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Dis VIII-rpn6

value: Dis VIII-rpn6


title: 0 Dis XVI-9.2 (A25059)

scan_protocol: Pixel Size : 5 Scan Date : 2007-12-05 Scan Time : 15:33:55 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B


title: RCC1_caffeine_2 (GINI)

scan_protocol: Arrays were scanned using an Illumina scanner

source_name: cell line derived from clear cell renal cell carcinoma tumor

value: Gerharz and Gabbert (Virchows Archiv (1994) 424:403-409)

value: Caffeine


title: C.albicans Initial Signature Cohort_1394_2828_14431_1057

description: C.albicans Initial Signature Cohort

value: C.albicans Initial Signature Cohort

value: Whole Blood


title: C.albicans Initial Signature Cohort_1394_2828_14433_1113

description: C.albicans Initial Signature Cohort

value: BALB/c

value: healthy


title: C.albicans Initial Signature Cohort_1394_2828_14434_1114

description: C.albicans Initial Signature Cohort

value: 8 wk old


title: 0 Dis VIII-URA3 (A23509)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis VIII-URA3 (A23509)

source_name: Dis VIII-URA3 (A23509)

value: Dis VIII-URA3 (A23509)


title: 0 Dis XI-E256X (A22390)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XI-E256X (A22390)

scan_protocol: Pixel Size : 5 Scan Date : 2008-11-05 Scan Time : 15:22:26 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: 0 Dis VIII-GFP-cup1-UBI4 (A25128)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis VIII-GFP-cup1-UBI4 (A25128)

source_name: Dis VIII-GFP-cup1-UBI4 (A25128)

value: Dis VIII-GFP-cup1-UBI4 (A25128)


title: 0 Dis I-GFP (A21955)

scan_protocol: Pixel Size : 5 Scan Date : 2008-03-27 Scan Time : 12:11:33 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B

source_name: Dis I-GFP (A21955)

value: Dis I-GFP (A21955)

value: wt


title: serous tumor (1198)

city: Houston

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: serous tumor (1198)

hyb_protocol: According to Illumina protocol.

scan_protocol: According to Illumina protocol.

data_processing: The image data were compiled into a project using  Beadstudio software gene expression module version 3.2.7.  No normalization was used. The data was exported as txt files using the build-in function of export to GeneSpring GX format. The option of sample probe profile was chosen. Data were subsequently quantile normalized for the analysis.

source_name: serous ovarian adenocarcinoma

label_protocol: According to Illumina protocol.

growth_protocol: Primary cultures of normal ovarian surface epithelium (NOSE) were performed as previously described. Briefly, brushings of the ovarian surface were performed in pre- and postmenopausal women undergoing clinically indicated surgery. NOSE cells were cultured in 1:1 MCDB105/M199 (Sigma). The epithelial origin of cultured cells was confirmed using immunohistochemistry to examine the expression of vimentin and cytokeratins, and only cultures containing >90% epithelial cells were used.  NOSE and cancer cell lines were cultured with 10% heat-inactivated fetal bovine serum and 1% penicillin-streptomycin solution (Invitrogen).

extract_protocol: Total RNA was extracted using the mirVana miRNA Isolation Kit (ABI). RNA quality were inspected on a 2100 Bioanalyzer (Agilent).

tag: disease state

value: Ovarian tumor (serous)


title: 0 Dis VIII-GFP (A21959)

scan_protocol: Pixel Size : 5 Scan Date : 2008-03-27 Scan Time : 12:12:36 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B

source_name: Dis VIII-GFP (A21959)

value: Dis VIII-GFP (A21959)


title: 0 Dis XVI-9.1 (A25058)

scan_protocol: Pixel Size : 5 Scan Date : 2007-12-05 Scan Time : 15:33:37 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B


title: 0 Dis XI-14.1 (A25074)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XI-14.1 (A25074)

scan_protocol: Pixel Size : 5 Scan Date : 2007-11-07 Scan Time : 10:50:50 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B


title: C.albicans Initial Signature Cohort_1394_2828_14429_1055

description: C.albicans Initial Signature Cohort

source_name: BALB/c male mice, C.albicans Initial Signature Cohort

tag: cohort

value: candida


title: RCC1_not-treated_2 (GINI)

value: clear cell renal cell carcinoma

value: unknown


title: RCC1_emetine_2 (GINI)

value: emetine


title: RCC1_not-treated_1 (GINI)

value: Gerharz and Gabbert (Virchows Archiv (1994) 424:403-409)


title: 0 Dis XIV-9.2 (A25055)

scan_protocol: Pixel Size : 5 Scan Date : 2007-12-05 Scan Time : 15:33:19 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B


title: RCC1_caffeine_1 (GINI)

value: Caffeine


title: 0 Dis XIII-9.2 (A25053)

scan_protocol: Pixel Size : 5 Scan Date : 2007-12-05 Scan Time : 15:32:13 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B


title: serous tumor (15989)

description: serous tumor (15989)


title: 0 Dis VIII-E256X (A22371)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis VIII-E256X (A22371)


title: serous tumor (21027)

description: serous tumor (21027)


title: C.albicans Initial Signature Cohort_1394_2828_14428_1053

description: C.albicans Initial Signature Cohort

value: C.albicans Initial Signature Cohort

tag: genotype


title: 0 Dis V-URA3 (A23508)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis V-URA3 (A23508)

scan_protocol: Pixel Size : 5 Scan Date : 2008-09-18 Scan Time : 08:53:40 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: C.albicans Initial Signature Cohort_1394_2828_14430_1056

description: C.albicans Initial Signature Cohort

value: Whole Blood

tag: infection status


title: C.albicans Initial Signature Cohort_1394_2828_14425_1048

description: C.albicans Initial Signature Cohort

value: BALB/c

tag: infection duration (days)


title: RCC1_emetine_1 (GINI)


title: C.albicans Initial Signature Cohort_1394_2828_14424_1046

description: C.albicans Initial Signature Cohort

tag: tissue


title: C.albicans Initial Signature Cohort_1394_2828_14427_1052

description: C.albicans Initial Signature Cohort

tag: age


title: 0 Dis V-rpn6

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis V-rpn6

source_name: Dis V-rpn6

value: Dis V-rpn6


title: 0 Dis XIV-9.1 (A25054)

description: Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.

scan_protocol: Pixel Size : 5 Scan Date : 2007-12-05 Scan Time : 15:33:04 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B


title: C.albicans Initial Signature Cohort_1394_2828_14426_1051

description: C.albicans Initial Signature Cohort

scan_protocol: Probe intensities were detected using Axon Genepix 4000B Scanner (Molecular Devices, Union City, CA).  Image files were generated using Affymetrix® GeneChip® Command Console® Software (AGCC).

value: 8 wk old


title: 0 Dis XIII-9.1 (A25052)

scan_protocol: Pixel Size : 5 Scan Date : 2007-12-05 Scan Time : 15:31:54 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B


title: 0 Dis V-GFP (A21958)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis V-GFP (A21958)

scan_protocol: Pixel Size : 5 Scan Date : 2009-06-18 Scan Time : 13:24:55 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Dis V-GFP (A21958)

value: Dis V-GFP (A21958)


title: serous tumor (2386)

description: serous tumor (2386)


title: 0 Dis XI-9.2 (A25049)

scan_protocol: Pixel Size : 5 Scan Date : 2007-12-05 Scan Time : 15:31:38 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B


title: serous tumor (18132)

description: serous tumor (18132)


title: 0 Dis V-lys2 (A23489)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis V-lys2 (A23489)

scan_protocol: Pixel Size : 5 Scan Date : 2008-11-07 Scan Time : 13:54:54 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: serous tumor (13396)

description: serous tumor (13396)


title: 0 Dis VIII-9.2 (A25043)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis VIII-9.2 (A25043)

scan_protocol: Pixel Size : 5 Scan Date : 2009-06-02 Scan Time : 13:00:44 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: 0 Dis IX-9.1 (A25044)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis IX-9.1 (A25044)


title: C.albicans Initial Signature Cohort_1394_2828_14422_1041

description: C.albicans Initial Signature Cohort


title: 0 Dis XI-9.1 (A25048)

scan_protocol: Pixel Size : 5 Scan Date : 2007-12-05 Scan Time : 15:31:25 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B


title: serous tumor (1459)

description: serous tumor (1459)


title: serous tumor (1576)

description: serous tumor (1576)


title: C.albicans Initial Signature Cohort_1394_2828_14423_1044

description: C.albicans Initial Signature Cohort


title: 0 Dis IX-9.2 (A25045)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis IX-9.2 (A25045)


title: C.albicans Initial Signature Cohort_1394_2828_14421_1039

description: C.albicans Initial Signature Cohort


title: 0 Dis V-E256X (A22370)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis V-E256X (A22370)

scan_protocol: Pixel Size : 5 Scan Date : 2008-11-05 Scan Time : 15:22:26 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: 0 Dis V-GFP-cup1-UBI4 (A25127)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis V-GFP-cup1-UBI4 (A25127)

scan_protocol: Pixel Size : 5 Scan Date : 2009-10-29 Scan Time : 09:21:43 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Dis V-GFP-cup1-UBI4 (A25127)

value: Dis V-GFP-cup1-UBI4 (A25127)


title: C.albicans Initial Signature Cohort_1394_2828_14419_1036

description: C.albicans Initial Signature Cohort


title: serous tumor (10367)

description: serous tumor (10367)

scan_protocol: According to Illumina protocol.


title: C.albicans Initial Signature Cohort_1394_2828_14420_1037

description: C.albicans Initial Signature Cohort


title: 0 Dis IX-ubp6-CA

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis IX-ubp6-CA

scan_protocol: Pixel Size : 5 Scan Date : 2009-07-09 Scan Time : 11:02:03 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Dis IX-ubp6-CA

value: Dis IX-ubp6-CA


title: 0 Dis VIII-9.1 (A25042)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis VIII-9.1 (A25042)

source_name: wt

value: wt


title: C.albicans Initial Signature Cohort_1394_2828_14418_1035

description: C.albicans Initial Signature Cohort


title: 0 Dis IX-URA3 (A23510)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis IX-URA3 (A23510)

source_name: Dis IX-URA3 (A23510)

value: Dis IX-URA3 (A23510)


title: C.albicans Initial Signature Cohort_1394_2828_14417_1029

description: C.albicans Initial Signature Cohort


title: 0 Dis VIII-E256X-cup1-UBI4 (A25131)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis VIII-E256X-cup1-UBI4 (A25131)

scan_protocol: Pixel Size : 5 Scan Date : 2009-12-04 Scan Time : 13:53:50 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Dis VIII-E256X-cup1-UBI4 (A25131)

value: Dis VIII-E256X-cup1-UBI4 (A25131)


title: C.albicans Initial Signature Cohort_1394_2828_14416_1028

description: C.albicans Initial Signature Cohort

value: candida


description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
AA Evolved Disome 13.2 c1 P-lim Chemostat RNA 4x44k

scan_protocol: Pixel Size : 10 Scan Date : 2007-05-04 Scan Time : 10:45:59 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : 9.5.1.1
Datafile type : Agilent result file
Normalizaton: Default settings of Agilent Feature Extractor

growth_protocol: Media : phosphate-limited chemostat media

extract_protocol:
Extraction method: acid phenol prep:
http://dunham.gs.washington.edu/MDyeastRNA.pdf

value: Evolved Disome XIII 14.2


title: 0 Dis II-URA3 (A23506)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis II-URA3 (A23506)

scan_protocol: Pixel Size : 5 Scan Date : 2008-10-02 Scan Time : 16:30:59 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Dis II-URA3 (A23506)

value: Dis II-URA3 (A23506)


title: C.albicans Initial Signature Cohort_1394_2828_14415_1025

description: C.albicans Initial Signature Cohort


title: 0 Dis IX-E256X (A22387)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis IX-E256X (A22387)


title: 0 Dis IV-E256X (A22369)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis IV-E256X (A22369)

scan_protocol: Pixel Size : 5 Scan Date : 2008-11-21 Scan Time : 14:47:26 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: C.albicans Initial Signature Cohort_1394_2828_14413_1020

description: C.albicans Initial Signature Cohort


title: OVCAR-5 serous cell line culture, subconfluent

value: OVCAR-5 serous cell line culture


title: C.albicans Initial Signature Cohort_1394_2828_14412_1019

description: C.albicans Initial Signature Cohort


title: 0 Dis II-E256X (A22368)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis II-E256X (A22368)


title: OV-90 serous cell line culture, subconfluent

value: OV-90 serous cell line culture


description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
AA Evolved Disome 14.2 c1 P-lim Chemostat RNA 4x44k

value: Evolved Disome XIV 14.2


title: OVCAR-8 serous cell line culture, subconfluent

value: OVCAR-8 serous cell line culture


title: 0 Dis I-URA3 (A23505)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis I-URA3 (A23505)

scan_protocol: Pixel Size : 5 Scan Date : 2008-09-18 Scan Time : 08:53:40 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: HEY serous cell line culture, subconfluent

value: HEY serous cell line culture


title: C.albicans Initial Signature Cohort_1394_2828_14414_1021

description: C.albicans Initial Signature Cohort

value: C.albicans Initial Signature Cohort

value: Whole Blood

value: BALB/c


description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
AA Evolved Disome 11.2 c1 P-lim Chemostat RNA 4x44k

value: Evolved Disome XI 14.2


title: C.albicans Initial Signature Cohort_1394_2828_14409_1015

description: C.albicans Initial Signature Cohort

value: 8 wk old


description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
AA Evolved Disome 13.1 c1 P-lim Chemostat RNA 4x44k

value: Evolved Disome XIII 14.1


title: C.albicans Initial Signature Cohort_1394_2828_14410_1016

description: C.albicans Initial Signature Cohort


title: C.albicans Initial Signature Cohort_1394_2828_14411_1017

description: C.albicans Initial Signature Cohort


description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
AA Evolved Disome 5.2 c1 P-lim Chemostat RNA 4x44k

scan_protocol: Pixel Size : 5 Scan Date : 2007-05-25 Scan Time : 11:28:11 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

value: wt

value: Evolved Disome V 14.2


title: SKOV3 serous cell line culture, subconfluent

value: SKOV3 serous cell line culture


title: OVCAR-3 serous cell line culture, subconfluent

value: OVCAR-3 serous cell line culture


title: OVCA-433 serous cell line culture, subconfluent

value: OVCA-433 serous cell line culture


description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
AA Evolved Disome 8.2 c1 P-lim Chemostat RNA 4x44k

scan_protocol: Pixel Size : 5 Scan Date : 2007-05-25 Scan Time : 11:19:10 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

value: Evolved Disome VIII 14.2


description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
AA Evolved Disome 8.1 c1 P-lim Chemostat RNA 4x44k

value: Evolved Disome VIII 14.1


title: 0 Dis IV-GFP (A21957)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis IV-GFP (A21957)

source_name: Dis IV-GFP (A21957)

value: Dis IV-GFP (A21957)


description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
AA Evolved Disome 9.2 c1 P-lim Chemostat RNA 4x44k

value: Evolved Disome IX 14.2


description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
AA Evolved Disome 10.1 c1 P-lim Chemostat RNA 4x44k

value: Evolved Disome X 14.1


title: 0 Dis I-E256X (A22367)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis I-E256X (A22367)


description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
AA Evolved Disome 5.1 c1 P-lim Chemostat RNA 4x44k

value: Evolved Disome V 14.1


title: 0 Dis XV-9.1 (A25056)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XV-9.1 (A25056)

scan_protocol: Pixel Size : 5 Scan Date : 2009-04-24 Scan Time : 10:37:44 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: 0 Dis XV-9.2 (A25057)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XV-9.2 (A25057)


title: NOSE cell culture, biological rep8

description: NOSE cell culture, biological rep8

source_name: Normal ovarian surface epithelium (NOSE) cell culture


title: C.albicans Initial Signature Cohort_1394_2828_14408_1014

description: C.albicans Initial Signature Cohort

scan_protocol: Probe intensities were detected using Axon Genepix 4000B Scanner (Molecular Devices, Union City, CA).  Image files were generated using Affymetrix® GeneChip® Command Console® Software (AGCC).

value: C.albicans Initial Signature Cohort

value: candida


title: C.albicans Initial Signature Cohort_1394_2828_14407_1013

description: C.albicans Initial Signature Cohort

value: Whole Blood

value: BALB/c


title: C.albicans Initial Signature Cohort_1394_2828_14405_1011

description: C.albicans Initial Signature Cohort

value: 8 wk old


title: 0 Dis XII-9.2 (A25051)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XII-9.2 (A25051)


title: C.albicans Initial Signature Cohort_1394_2828_14406_1012

description: C.albicans Initial Signature Cohort


title: 0 Dis XII-9.1 (A25050)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XII-9.1 (A25050)


title: C.albicans Initial Signature Cohort_1394_2828_14404_1010

description: C.albicans Initial Signature Cohort


title: C.albicans Initial Signature Cohort_1394_2828_14403_1009

description: C.albicans Initial Signature Cohort

value: healthy


title: 0 Dis X-9.2 (25047)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis X-9.2 (25047)

scan_protocol: Pixel Size : 5 Scan Date : 2009-06-02 Scan Time : 12:51:28 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

value: wt


description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
AA Evolved Disome 9.1 c1 P-lim Chemostat RNA 4x44k

value: Evolved Disome IX 14.1


title: 0 Dis XII-14.2 (A25077)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XII-14.2 (A25077)


description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
AA Disome 5 (14479) P-lim Chemostat RNA 4x44k array

scan_protocol: Pixel Size : 5 Scan Date : 2007-06-15 Scan Time : 10:09:50 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

value: Disome V (14479)


title: T. atro (41471902)

city: Salamanca

first: Enrique

last: Monte

state: Salamanca

address: Rio Duero

department: Spanish-Portuguese Centre for Agricultural Research

country: Spain

institute: University of Salamanca

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Microarray scanning, data acquisition and identification of probe sets showing a significant difference (p=0.05) in expression level between the two culture conditions considered were performed by Roche-NimbleGen as in previous studies (Samolski et al., 2009). Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).Transcripts showing significantly up-regulated expression (2-fold and 5-fold changes) were annotated using Gene Ontology (GO) (Gotz et al., 2008) for TrichoEST derived transcripts and the eukaryotic orthologous groups (KOG) classification (Tatusov et al., 2003) for the genes indentified in the genomes of T. atroviride and T. virens. Considering a differential expression with a fold-change greater than 2.0, 2024 transcripts were identified (1051 up-regulated and 973 down-regulated). With a fold-change greater than 5.0, just 288 genes displayed differential expression (261 up-regulated and 27 down-regulated).

organism: Trichoderma atroviride

source_name: T. atro

label_protocol: High quality purified RNAs were submitted to Roche-NimbleGene (40 μg per 3-microarray set) where cDNAs were synthesized, amplified and labeled and then used for subsequent hybridization. Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Control: T. atroviride P1 mycelium grown (approximately for 24h) at 25ºC on a cellophane sheet in PDA (Difco) plates before contact (at a distance of 5 mm) a R. solani colony grown under identical conditions in the same plate. Test (mycoparasitic interaction): T. atroviride P1 mycelium after contact (5 mm) the above R. solani colony.

extract_protocol: Total RNAs were extracted using TRIzol® reagent (Invitrogen Life Technologies, Carlsbad, CA, USA), according to the manufacturer's instructions, and then purified using the RNeasy MinElute Cleanup Kit (Qiagen, Hilden, Germany). The RNA quality and quantity were determined using a Nanodrop spectrophotometer.

treatment_protocol: Freeze-dried mycelia from control and R. solani-interaction conditions were ground in liquid nitrogen using a mortar and pestle.

tag: strain

value: T. atroviride P1 wild type

value: mycelium


title: T. atro (41214002)


title: NOSE cell culture, biological rep6

description: NOSE cell culture, biological rep6

tag: cell line

value: Normal ovarian surface epithelium (NOSE)


title: NOSE cell culture, biological rep4

description: NOSE cell culture, biological rep4


title: 0 Dis X-9.1 (25046)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis X-9.1 (25046)


title: C.albicans Initial Signature Cohort_1394_2828_14402_1003

description: C.albicans Initial Signature Cohort


title: NOSE cell culture, biological rep7

description: NOSE cell culture, biological rep7


title: NOSE cell culture, biological rep5

description: NOSE cell culture, biological rep5


title: T. atro (40355602)


title: ALL8_33R_relapse

status: Public on Mar 01 2010

city: Nijmegen

first: Roland

middle: P.

last: Kuiper

address: Geert Grooteplein 10

department: Human Genetics

institute: Radboud University Nijmegen Medical Centre

description: ALL relapse sample

hyb_protocol: Hybridizations were performed according to the standard Affymetrix protocol from 250 ng genomic DNA (Genechip Mapping 500k assay manual 701930 Rev.3, Affymetrix) using an Affymetrix hybridisation oven 640 and an Affymetrix Fluidic station 450.

scan_protocol: Scanning performed according to the standard Affymetrix protocol from 250 ng genomic DNA (Genechip Mapping 500k assay manual 701930 Rev.3, Affymetrix) using an Affymetrix scanner 3000.

data_processing: copy number detection using CNAG2.0 software (http://www.genome.umin.jp/)

source_name: Bone marrow

label_protocol: Biotinylated DNA was prepared according to the standard Affymetrix protocol from 250 ng genomic DNA (Genechip Mapping 500k assay manual 701930 Rev.3, Affymetrix).

extract_protocol: QiaAmp purification kit (Qiagen)

value: male

value: Bone marrow

value: ALL relapse sample


title: NOSE cell culture, biological rep3

description: NOSE cell culture, biological rep3


title: T. atro-Rs (41179202)

organism:
Trichoderma atroviride
Rhizoctonia solani

source_name: T. atro-Rs


title: 0 Dis II-9.2 (A25037)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis II-9.2 (A25037)

scan_protocol: Pixel Size : 5 Scan Date : 2009-06-18 Scan Time : 13:24:55 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
AA Evolved Disome 10.2 c1 P-lim Chemostat RNA

value: Evolved Disome X 14.2


title: C.albicans Initial Signature Cohort_1394_2828_14401_1002

description: C.albicans Initial Signature Cohort


title: NOSE cell culture, biological rep2

description: NOSE cell culture, biological rep2


title: 0 Dis II-9.1 (A25036)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis II-9.1 (A25036)


title: T. atro-Rs (40161202)


title: C.albicans Initial Signature Cohort_1394_2828_14400_1001

description: C.albicans Initial Signature Cohort


title: 0 Dis I-9.2 (A25035)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis I-9.2 (A25035)

scan_protocol: Pixel Size : 5 Scan Date : 2010-01-29 Scan Time : 08:53:45 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: 0 Dis I-9.1 (A25034)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis I-9.1 (A25034)


title: NOSE cell culture, biological rep1

description: NOSE cell culture, biological rep1

scan_protocol: According to Illumina protocol.


title: T. atro-Rs (40155702)


title: negative control mimic (NTC2)_31_NEG_5

description: negative control mimic (mir-31 knockup control, OVCAR-8), biological rep3

source_name: OVCAR-8 ovarian cancer cell line

growth_protocol: OVCAR-8 cells were cultured in RPMI 1640 (Invitrogen), with 10% heat-inactivated fetal bovine serum and 1% penicillin-streptomycin solution (Invitrogen).

extract_protocol: Cells were harvested 48 hours after transfection. Total RNA was extracted using the mirVana miRNA Isolation Kit (ABI). RNA quality were inspected on a 2100 Bioanalyzer (Agilent).

treatment_protocol: Transfection conditions for each cell line were optimized for maximum efficiency in preliminary experiments using Dy547-labeled miRIDIAN hairpin inhibitor and mimic transfection controls (Dharmacon). OVSAYO cells were transfected in 6-well plates (3.0 x 105 cells/well) using 3 μl Invitrogen Lipofectamine 2000 and 3 μg total hairpin inhibitor (66 nM). Control groups were cells treated with transfection reagent alone (mock transfection), and cells transfected with miRIDIAN hairpin inhibitor negative control #1 or mimic negative control #2, which are based on C. elegans miRNAs that have minimal sequence identity to human miRNAs (Dharmacon).

tag: protocol

value: control


title: negative control mimic (NTC2)_31_NEG_1

description: negative control mimic (mir-31 knockup control, OVCAR-8), biological rep1


title: FC-1801 cells infected with lentiviral vectors encoding a control sh-RNA, biological rep3

city: New York

first: Wei

last: Li

state: NY

address: 430 East 67th street

department: Cell Biology

institute: Memorial Sloan-Kettering Cancer Center

description: Gene expression data from primary mouse Schwann cell cultures from E12.5 Nf2flox/flox embryos infected with adenoviral Cre and immortalized in vitro

hyb_protocol: 15ug of labeled cRNA were hybridized on the MOE 430A2.0 arrays

scan_protocol: according to manufacturer

data_processing: Overall intensity was targetted to 500. Signal intensities were generated using GCOS1.4

label: Biotin

source_name: Primary mouse Schwann cell cultures

label_protocol: 1ug total RNA was labeled using the Magascript Ambion kit (cat#AM1334)

extract_protocol: Trizol

tag: cell type

value: FC-1801 parental cells


title: KO_0525-3

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description: SPC(+)Cre(-), Dox E6.5-12.5, PN15; knockout

hyb_protocol: The cRNA was then hybridized to the murine genome MOE430 (consists of ≈ 45000 gene entries) chips (Affymetrix, Santa Clara, CA) according to the manufacturer’s protocol.

scan_protocol: Affymetrix Microarray Suite 5.0 was used to scan and quantitate the gene chips under default scan settings.

data_processing: data processed/normalized by algorithm:RMA

label_protocol: based on Affymetrix protocols

extract_protocol: Whole lung total RNA was purified by RNeasy Mini Kit according to the manufacturers protocol (Cat. 74104, Qiagen, Valencia, CA).

value: whole lung

tag: genotype/variation


title: 0 Dis XVI-14.2 batch RNA

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XVI-14.2 batch RNA

scan_protocol: Pixel Size : 5 Scan Date : 2009-06-26 Scan Time : 08:32:41 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: disome

growth_protocol: Media : minus His plus G418

value: Dis XVI-14.2


title: C.albicans Initial Signature Cohort_1394_2828_14399_1000

description: C.albicans Initial Signature Cohort

source_name: BALB/c male mice, C.albicans Initial Signature Cohort

value: C.albicans Initial Signature Cohort

value: Whole Blood

value: BALB/c


title: control_0530-1

description: SPC(+)Cre(-), Dox E6.5-12.5, PN15; control

value: wildtype, control


title: KO_0525-2

source_name: SPC(+)Cre(-), Dox E6.5-12.5, PN15; knockout


title: 0 Dis XVI-14.1 batch RNA

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XVI-14.1 batch RNA

value: wt

source_name: Dis XVI-14.1

value: Dis XVI-14.1


title: negative control mimic (NTC2)_31_NEG_3

description: negative control mimic (mir-31 knockup control, OVCAR-8), biological rep2


title: KO_0424-2


title: FC-1801 cells infected with lentiviral vectors encoding Merlin-L64P, biological rep2

treatment_protocol: primary mouse Schwann cell cultures from E12.5 Nf2flox/flox embryos infected with adenoviral Cre and immortalized in vitro


title: hsa-mir-31 mimic_31#2

description: hsa-mir-31 mimic (mir-31 knockup in OVCAR-8), biological rep2

value: hsa-mir-31 overexpression


title: hsa-mir-31 mimic_31#3

description: hsa-mir-31 mimic (mir-31 knockup in OVCAR-8), biological rep3


title: P19-day4b

city: Stratford

first: Eric

last: Moss

state: NJ

address: 2 Medical Center Dr.

department: Molecular Biology

institute: UMDNJ

description: biological replicate 2 of 2

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA array version 11.0 (Exiqon, Denmark), which contains capture probes targeting all miRNAs for human, mouse or rat registered in the miRBASE version 13.0 at the Sanger Institute. The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria).

scan_protocol: The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 7.0 software (BioDiscovery, Inc., USA)

data_processing: The quantified signals were background corrected (Normexp with offset value 10 – Ritchie et al., 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.

source_name: P19 EC cells

label_protocol: One µg total RNA from sample and reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labeling kit (Exiqon, Denmark) following the procedure described by the manufacturer.

growth_protocol: P19 cells were grown in maintained in alpha-MEM  supplemented with 2.5% fetal bovine serum, 7.5% bovine serum, and 50 units/mL of penicillin/streptomycin. P19_Lin28 cells were maintained in the same medium with 2 microg/mL puromycin .

extract_protocol: Total RNA was purified using the miRNA isolation kit (Ambion, Austin, TX, USA).

treatment_protocol: P19 and P19+Lin28A cells differentiated to 5 days with Retinoic acid/aggregation to induce neurogenesis by standard methods.

value: mouse P19 cells

source_name: common reference pool


title: P19(Lin28)-day4b

description: biological replicate 2 of 2

source_name: transfected P19 EC cells

value: mouse P19 cells, stably transfected with plasmid constitutively expressing human LIN28


title: FC-1801 cells infected with lentiviral vectors encoding a control sh-RNA, biological rep1


title: Turkey 3-4

city: Mississippi State

first: Chinling

last: Wang

state: MS

address: College of Veterinary Medicine P.O. box 6100

department: Basic Sciences

institute: Missippi State University

description: Data were obtained from three biological and four technical replicates (n = 12). For each biological replicate, flip dye analysis was performed. The expression level of genes obtained from the mean of each gene on the twelve slides was considered significantly different over 1.5 fold changes. The difference was presented at a significant level (P < 0.05).

hyb_protocol: About 5.8 ug of each labelled cDNA were hybridized, resuspended in 50 ml hybridization buffer (40% formamide, 5X sodium chloride/sodium citrate buffer, 0.1% SDS, and 0.6 ug/ul salmon sperm DNA) and loaded on a microarray slide. The slide was incubated for 16h at 42 °C, and then washed with low, medium, and high stringency buffer containing 0.1 mM DTT.

scan_protocol: The hybridized slides were scanned at 10 um resolutions within the range of photomultiplier tube between 650 and 750 on two channels (cy3 and cy5) using a GenePix 4000B microarray scanner (Axon Instruments, Union City, CA).

data_processing: The signal intensity of spots on the slides was adjusted and quantified by background subtraction using Spotfinder software. Data LOWESS normalization was performed using Ginkgo software. The data from the normalized ratio of query to reference signal for each spot were transformed using a log2 scale.

organism: Listeria monocytogenes

source_name: Total RNA from Listeria monocytogenes F2365 labeled with cy3.

label_protocol: To synthesize cDNA, 2.5 ug of total RNA was reversely transcribed. cDNA was synthesized using 2 ul of Smart® reverse transcriptase (Clontech, Palo Alto, CA) and 1 ul of random hexamers in the presence of 0.1 M dithiothreitol (DTT) [Invitrogen], 25 mM dNTP with 3:2 ratio of aminoallyl (aa)-dUTP and dTTP (Ambion, Austin, TX). After cDNA synthesis, the cDNA was purified and unincorpotated aa-dUTP was removed using a MinElute® PCR purification kit (Qiagen). The purified cDNA resuspended in 0.1 M sodium carbonate buffer (pH 9.3) was labelled with cy3.

growth_protocol: About 2.3 x 10^8 CFU/ml was inoculated aseptically in BHI agar plates and incubated at 15 °C for 5 days in a BOD10 refrigerated incubator.

extract_protocol: RNA Protect® (Qiagen, Valencia, CA) was added in bacterial culture at a ratio of 2:1 before collecting cells. Total RNA was extracted from the bacterial pellet, and purified using Trizol® (Invitrogen, Carlsbad, CA) and the RNeasy® Mini Kit (Qiagen), respectively.

treatment_protocol:
hybridization:
image_acquisition:
labeling:
reverse_transcription:
spin:
wash:

tag: media

value: agar

source_name: Total RNA from Listeria monocytogenes F2365 labeled with cy5.

label_protocol: To synthesize cDNA, 2.5 ug of total RNA was reversely transcribed. cDNA was synthesized using 2 ul of Smart® reverse transcriptase (Clontech, Palo Alto, CA) and 1 ul of random hexamers in the presence of 0.1 M dithiothreitol (DTT) [Invitrogen], 25 mM dNTP with 3:2 ratio of aminoallyl (aa)-dUTP and dTTP (Ambion, Austin, TX). After cDNA synthesis, the cDNA was purified and unincorpotated aa-dUTP was removed using a MinElute® PCR purification kit (Qiagen). The purified cDNA resuspended in 0.1 M sodium carbonate buffer (pH 9.3) was labelled with cy5.

growth_protocol: About 2.3 x 10^8 CFU/ml was inoculated aseptically on a turkey meat slice in a sterile stomacher bag and incubated at 15 °C for 5 days in a BOD10 refrigerated incubator.

tag: nutrients

value: turkey matrix


title: FC-1801 cells infected with lentiviral vectors encoding a control sh-RNA, biological rep2


title: P19-day4a

description: biological replicate 1 of 2


title: P19(Lin28)-day4a

description: biological replicate 1 of 2

value: mouse P19 cells stably transfected with plasmid constitutively expressing human LIN28


title: 0 Dis XIV batch RNA

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XIV batch RNA

source_name: wt

source_name: Dis XIV

value: Dis XIV


title: control_0525-1

source_name: SPC(+)Cre(-), Dox E6.5-12.5, PN15; control


title: FC-1801 cells infected with lentiviral vectors encoding a sh-RNA targeting DCAF1, biological rep3


title: hsa-mir-31 mimic_31#1

description: hsa-mir-31 mimic (mir-31 knockup in OVCAR-8), biological rep1


title: Turkey 3-2

growth_protocol: About 2.3 x 10^8 CFU/ml was inoculated aseptically in BHI agar plate and incubated at 15 °C for 5 days in a BOD10 refrigerated incubator.


title: FC-1801 cells infected with lentiviral vectors encoding Merlin-L64P, biological rep3


title: control_0412-7


title: 0 Dis XI-14.1 batch RNA

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XI-14.1 batch RNA

source_name: Dis XI-14.1

value: Dis XI-14.1


title: FC-1801 cells infected with lentiviral vectors encoding Merlin-L64P, biological rep1

value: FC-1801 parental cells


title: FC-1801 cells infected with lentiviral vectors encoding sh-DCAF1 in combination with wild type Merlin, biological rep3


title: Turkey 3-3


title: 0 Dis XI-14.2 batch RNA

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XI-14.2 batch RNA

source_name: Dis XI-14.2

value: Dis XI-14.2


title: FC-1801 cells infected with lentiviral vectors encoding a sh-RNA targeting DCAF1, biological rep2


title: 0 Dis XVI batch RNA

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XVI batch RNA

source_name: Dis XVI

value: Dis XVI


title: FC-1801 cells infected with lentiviral vectors encoding a sh-RNA targeting DCAF1, biological rep1


title: 0 Dis XIV-14.2 batch RNA

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XIV-14.2 batch RNA

source_name: Dis XIV-14.2

value: Dis XIV-14.2


title: 0 Dis XI batch RNA

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XI batch RNA

source_name: Dis XI

value: Dis XI


title: Turkey 3-1


title: NOSE cell culture, biological rep9

description: NOSE cell culture, biological rep9

source_name: Normal ovarian surface epithelium (NOSE) cell culture


title: Turkey 2-4


title: 0 Dis IX-14.1 batch RNA

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis IX-14.1 batch RNA

scan_protocol: Pixel Size : 5 Scan Date : 2009-06-19 Scan Time : 09:27:51 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Dis IX-14.1

value: Dis IX-14.1


title: Turkey 2-2


title: Turkey 1-4


title: FC-1801 cells infected with lentiviral vectors encoding sh-DCAF1 in combination with wild type Merlin, biological rep2

description: Gene expression data from primary mouse Schwann cell cultures from E12.5 Nf2flox/flox embryos infected with adenoviral Cre and immortalized in vitro

source_name: Primary mouse Schwann cell cultures


title: Turkey 2-1


title: Turkey 1-3

growth_protocol: About 2.3 x 10^8 CFU/ml was inoculated aseptically on each turkey meat slice in a sterile stomacher bag and incubated at 15 °C for 5 days in a BOD10 refrigerated incubator.


title: 0 Dis VIII-14.1 batch RNA

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis VIII-14.1 batch RNA

source_name: Dis VIII-14.1

value: Dis VIII-14.1


title: Turkey 2-3


title: 0 Dis IX batch RNA

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis IX batch RNA

value: wt

source_name: Dis IX

value: Dis IX


title: 0 Dis V-14.2 batch RNA

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis V-14.2 batch RNA


title: alg-3; alg-4 double mutant

status: Public on Feb 24 2010

city: Worcester

first: Craig

last: Mello

state: MA

address: 368 Plantatoin Street, Suite AS5-2047

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

description: no additional information

hyb_protocol: Hybridization to the arrays was made using standard Affymetrix protocols and reagents

scan_protocol: Scanning was done with GeneChip Scanner 3000 7G at the University Massachusetts Medical School’s Genomics Core Facility

data_processing:
Signal values for each array probe were calculated using Affymetrix Tiling Analysis Software 1.1.2 (bandwidth: 30; intensities: PM/MM) with three alg-3/4(tm1155; ok1041) replicates as the experimental datasets and three wild type replicates as the controls. Probe overlap with annotations was assessed using the Affymerix-provided ce4 coordinate, which indicates the genomic position matching the center of the array probe. Only genes with signal for at least 10 different probes in either the wild type or alg-3/4(tm1155; ok1041) samples were included for analysis.
Results file descriptions:
Affymetrix probe coordinates (release WS170) were converted to release WS192 coordinates using a Perl script. Gene expression values were defined as the geometric mean of all probe signals within a gene that had a P-value of <0.1. Actin was used to normalize expression values prior to comparison. Additional results file array_data_alg3alg4.txt is linked as supplementary file on the Series GSE18719 record.

organism: Caenorhabditis elegans

source_name: total RNA from alg-3;alg-4

label_protocol: Reverse transcritption was performed on 7µg of each sample using the GeneChip WT Double-Stranded cDNA Synthesis Kit.  The dsDNA was then purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified.  7.5µg of each dsDNA sample were used for the subsequent fragmentation and labeling reactions, using the GeneChip WT Double Stranded DNA Terminal Labeling Kit (Affymetrix).

growth_protocol: Synchronous populations of wild type and alg-3(tm1155);alg-4(ok1041) animals were grown for 54 hours post-hatching at 20 C on OP50 E. coli at a density of approximately 50000 animals per 15cm Petri dish.

extract_protocol: RNA extraction was performed using TRI-Reagent (MRC Laboratories).  Instead of pelleting and resuspending the RNA (as described in the TRI Reagent protocol), RNA was recovered, washed and eluted using the RiboPure total RNA isolation kit (Ambion).

value: alg-3;alg-4 double mutant


title: N2 wild type

description: no additional information

source_name: total RNA from wild type

value: wild type N2


title: 0 Dis VIII batch RNA

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis VIII batch RNA

source_name: Dis VIII

value: Dis VIII


title: FC-1801 cells infected with lentiviral vectors encoding sh-DCAF1 in combination with wild type Merlin, biological rep1


title: FC-1801 cells infected with lentiviral vectors encoding wild type Merlin, biological rep3


title: 0 WT batch RNA

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 WT batch RNA

extract_protocol:
Extraction method:acid phenol prep:
http://dunham.gs.washington.edu/MDyeastRNA.pdf


title: FC-1801 cells infected with lentiviral vectors encoding wild type Merlin, biological rep2


title: Turkey 1-2

source_name: Total RNA from Listeria monocytogenes F2365 labeled with cy5.

value: agar

source_name: Total RNA from Listeria monocytogenes F2365 labeled with cy3.


title: 0 Dis V batch RNA

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis V batch RNA

source_name: wt

source_name: Dis V

value: Dis V


title: Turkey 1-1

hyb_protocol: About 5.8 ug of each labelled cDNA were hybridized, resuspended in 50 ml hybridization buffer (40% formamide, 5X sodium chloride/sodium citrate buffer, 0.1% SDS, and 0.6 ug/ul salmon sperm DNA), and loaded on a microarray slide. The slide was incubated for 16 h at 42 C, and then washed with low, medium, and high stringency buffer containing 0.1 mM DTT.

scan_protocol: The hybridized slides were scanned at 10 um resolutions within the range of photomultiplier tube between 650 and 750 on two channels, cy3 and cy5 dyes using a GenePix 4000B microarray scanner (Axon Instruments, Union City, CA).

extract_protocol: RNA Protect® (Qiagen, Valencia, CA) was added in bacterial culture at a ratio of 2:1 before collecting cells. Total RNA from the bacterial cell pellet was extracted and purified using Trizol® (Invitrogen, Carlsbad, CA) and the RNeasy® Mini Kit (Qiagen), respectively.

value: turkey matrix


title: 0 Dis V-14.1 batch RNA

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis V-14.1 batch RNA


title: FC-1801 cells infected with lentiviral vectors encoding wild type Merlin, biological rep1


title: FC-1801 parental cells uninfected, biological rep2

description: FC-1801 parental cells uninfected


title: FC-1801 parental cells uninfected, biological rep1

description: FC-1801 parental cells uninfected


title: Female Bull 1 sample 2

city: Madrid

first: Pablo

last: Bermejo-Álvarez

state: Madrid

address: Ctra La Coruña Km 5,9

department: Reproducción Animal

institute: INIA

description: Gene expression data from female Day 7 blastocysts produced with sorted semen from Bull1

hyb_protocol: Labelled cRNA was fragmented in fragmentation buffer (5× buffer: 200 mM Tris-acetate (pH 8.1)/500 mM KOAc/150 mM MgOAc) and hybridised to the microarrays in 200µl of hybridization solution containing 15µg labelled target in 1× Mes buffer (0.1 M Mes/1.0 M NaCl/20 mM EDTA 0.01%/Tween20) and 0.1mg/ml herring sperm DNA, 10% DMSO, 0.5mg/ml BSA, 50 pM control oligonucleotide B2 and 1x eukaryotic hybridization controls (bioB, bioC, bioD, cre). Both control oligonucleotide B2 and eukaryotic hybridisation controls were purchased from Affymetrix. Hybridization mix was applied to Bovine Genome array (Affymetrix), and arrays were placed on a rotisserie and rotated at 60 rpm for 16h at 45°C. Following hybridization, the arrays were washed and stained with a streptavidin-phycoerythrin conjugate (Molecular Probes).

scan_protocol: The arrays were scanned using a confocal scanner (GC3000_Affymetrix). The image data were analysed by GeneChip Operating Software (GCOS 1.4, Affymetrix)

data_processing: For the Bioinformatic analysis dChip (www.dchip.org) and Affy/AffyPLM (Bioconductor) software were used to look for samples acting as outliers and Partek Genomics Suite 6.4 (Partek® software, Copyright © 2008 Partek Inc., St. Louis, MO, USA.Partek) to perform gene expression analysis. RMA processing was used for normalizing the data as well as a global median normalisation. The change in each gene expression was calculated by determining the fold change (ratio) of the mean intensity of each group.

organism: Bos taurus

source_name: Female blastocysts from Bull 1

label_protocol: Labelled cRNA was synthesized with a linear RNA amplification method (Message Amp Premier kit, Ambion) following provider´s instructions and using 50 ng of total RNA as template for reverse transcription.

growth_protocol: Details for embryo production are provided in Biology of Reproduction 2008; 79:594-597.

extract_protocol: Total RNA was isolated and purified using RNaeasy Micro kit (Qiagen).

treatment_protocol: Blastocysts were snap frozen on Day 7 post-insemination and kept at -80 ºC until analysis.

value: blastocyst

value: Mixed breed

value: Day 7 post insemination

tag: gender

value: Female


title: FC-1801 parental cells uninfected, biological rep3

description: FC-1801 parental cells uninfected

value: FC-1801 parental cells


title: Gene expression profiles of HL-60 cells exposed to dichloromethane (IC50) [sample 2]

city: Seoul

first: Sailendra

middle: Nath

last: Sarma

address: P.O. Box 131, Cheongryang

country: South Korea

institute: Korea Institute of Science and Technology

description: HL-60 cells were treated with 53.86 mM dichloromethane for 3 h, and the RNA was subjected to microarray analysis.

hyb_protocol: Labeling and hybridization were performed by instruction of Platinum Biochip Reagent Kit (GenoCheck Co. Ltd., Korea). This was followed by the coupling of the Cy3 dye for the controls (DMSO) or Cy5 dye for the treated samples. Hybridization was performed in a hybridization oven at 62℃ for 12 h. After washing (2× SSC/0.1% SDS for 2 min at 58℃, 1× SSC for 2 min at RT and 0.2× SSC for 3 min at RT), the slide was dried by centrifugation at 800 rpm for 3 min at RT.

scan_protocol: Hybridization images on the slides were scanned by ScanArray Lite (PerkinElmer Life Sciences, USA). Scanned images were analyzed with GenePix 3.0 software (Axon Instruments, USA) to obtain gene expression ratios.

data_processing: The fluorescent intensity of each spot was calculated by local median background subtraction. The robust scatter-plot smoother LOWESS function was used to perform intensity dependent normalization for the gene expression. Scatter plot analysis was made by Microsoft Excel 2003. Significance Analysis of Microarray (SAM) was performed for the selection of the genes with significant gene expression changes (Tusher et al., 2001). Computing a p-value for each gene assessed the statistical significance of the differential expression of genes. To determine the p-value, a permutation procedure was used and for each permutation, two-sample t statistics were computed for each gene. Genes were considered differentially expressed when logarithmic gene expression ratios in three independent hybridizations were more than 1.5 or less than 0.66, i.e., 1.5-fold difference in expression level, and when the p-values were less than 5.

source_name: HL-60 cells treated with DMSO for 3 h

label_protocol: Gene expression analysis was conducted on the RNA samples using 35 K whole human genome microarray (Operon Biotechnologies, Inc. Germany). Triplicate analysis was performed for each chemical, simultaneously. Labeling and hybridization were performed by instruction of Platinum Biochip Reagent Kit (GenoCheck Co. Ltd., Korea). Cy3 dye for the controls (DMSO).

extract_protocol: Total RNA was extracted from the HL-60 cells treated to DMSO for 3 h using the Trizol reagent (Invitrogen, USA) and purified using RNeasy mini kit (Qiagen, USA) according to the manufacturer's instructions. Genomic DNA was removed using RNase-free DNase set (Qiagen, USA) during RNA purification. RNA quality were assessed with the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, USA) (260/280 nm ratios) and only samples with an A260/A280 ratio between 1.9 and 2.2 were considered for suitable use. The RNA quality was checked with the Experion automated electrophoresis station (Bio-Rad Laboratories, USA) (28S/18S ratio).

value: human promyelocytic leukemia cells

tag: treatment

value: DMSO

tag: treatment time

value: 3 h

source_name: HL-60 cells treated with dichloromethane (IC50) for 3 h

label_protocol: Gene expression analysis was conducted on the RNA samples using 35 K whole human genome microarray (Operon Biotechnologies, Inc. Germany). Triplicate analysis was performed for each chemical, simultaneously. Labeling and hybridization were performed by instruction of Platinum Biochip Reagent Kit (GenoCheck Co. Ltd., Korea). Cy5 dye for the treated samples.

extract_protocol: Total RNA was extracted from the HL-60 cells treated to IC50 dose of dichloromethane for 3 h, using the Trizol reagent (Invitrogen, USA) and purified using RNeasy mini kit (Qiagen, USA) according to the manufacturer's instructions. Genomic DNA was removed using RNase-free DNase set (Qiagen, USA) during RNA purification. RNA quality were assessed with the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, USA) (260/280 nm ratios) and only samples with an A260/A280 ratio between 1.9 and 2.2 were considered for suitable use. The RNA quality was checked with the Experion automated electrophoresis station (Bio-Rad Laboratories, USA) (28S/18S ratio).

tag: treament

value: dichloromethane

tag: treament dose

tag: treament time

value: 3 hr


title: Gene expression profiles of HL-60 cells exposed to trichloroethylene (IC20) [sample 3]

description: HL-60 cells were treated with 1.78 mM trichloroethylene for 3 h, and the RNA was subjected to microarray analysis.

source_name: HL-60 cells treated with trichloroethylene (IC20) for 3 h

extract_protocol: Total RNA was extracted from the HL-60 cells treated to IC20 dose of trichloroethylene for 3 h, using the Trizol reagent (Invitrogen, USA) and purified using RNeasy mini kit (Qiagen, USA) according to the manufacturer's instructions. Genomic DNA was removed using RNase-free DNase set (Qiagen, USA) during RNA purification. RNA quality were assessed with the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, USA) (260/280 nm ratios) and only samples with an A260/A280 ratio between 1.9 and 2.2 were considered for suitable use. The RNA quality was checked with the Experion automated electrophoresis station (Bio-Rad Laboratories, USA) (28S/18S ratio).

value: trichloroethylene


title: Gene expression profiles of HL-60 cells exposed to ethylbenzene (IC50) [sample 3]

description: HL-60 cells were treated with 0.99 mM ethylbenzene for 3 h, and the RNA was subjected to microarray analysis.

source_name: HL-60 cells treated with ethylbenzene (IC50) for 3 h

extract_protocol: Total RNA was extracted from the HL-60 cells treated to IC50 dose of ethylbenzene for 3 h, using the Trizol reagent (Invitrogen, USA) and purified using RNeasy mini kit (Qiagen, USA) according to the manufacturer's instructions. Genomic DNA was removed using RNase-free DNase set (Qiagen, USA) during RNA purification. RNA quality were assessed with the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, USA) (260/280 nm ratios) and only samples with an A260/A280 ratio between 1.9 and 2.2 were considered for suitable use. The RNA quality was checked with the Experion automated electrophoresis station (Bio-Rad Laboratories, USA) (28S/18S ratio).

value: ethylbenzene


title: Female Bull 3 sample 3

description: Gene expression data from female Day 7 blastocysts produced with sorted semen from Bull3

source_name: Female blastocysts from Bull 3

tag: genotype


title: Male Bull 1 sample 3

description: Gene expression data from male Day 7 blastocysts produced with sorted semen from Bull1

source_name: Male blastocysts from Bull 1

value: Male


title: Gene expression profiles of HL-60 cells exposed to trichloroethylene (IC50) [sample 3]

description: HL-60 cells were treated with 4.11 mM trichloroethylene for 3 h, and the RNA was subjected to microarray analysis.

source_name: HL-60 cells treated with trichloroethylene (IC50) for 3 h

extract_protocol: Total RNA was extracted from the HL-60 cells treated to IC50 dose of trichloroethylene for 3 h, using the Trizol reagent (Invitrogen, USA) and purified using RNeasy mini kit (Qiagen, USA) according to the manufacturer's instructions. Genomic DNA was removed using RNase-free DNase set (Qiagen, USA) during RNA purification. RNA quality were assessed with the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, USA) (260/280 nm ratios) and only samples with an A260/A280 ratio between 1.9 and 2.2 were considered for suitable use. The RNA quality was checked with the Experion automated electrophoresis station (Bio-Rad Laboratories, USA) (28S/18S ratio).


title: Gene expression profiles of HL-60 cells exposed to dichloromethane (IC50) [sample 1]


title: Female Bull 1 sample 1


title: Gene expression profiles of HL-60 cells exposed to trichloroethylene (IC50) [sample 1]


title: Female Bull 3 sample 1


title: Gene expression profiles of HL-60 cells exposed to ethylbenzene (IC50) [sample 1]


title: Gene expression profiles of HL-60 cells exposed to ethylbenzene (IC50) [sample 2]


title: Gene expression profiles of HL-60 cells exposed to dichloromethane (IC50) [sample 3]


title: Gene expression profiles of HL-60 cells exposed to trichloroethylene (IC20) [sample 2]


title: Female Bull 3 sample 2


title: Male Bull 1 sample 1


title: Female Bull 1 sample 3


title: Gene expression profiles of HL-60 cells exposed to trichloroethylene (IC50) [sample 2]


title: Gene expression profiles of HL-60 cells exposed to ethylbenzene (IC20) [sample 3]

description: HL-60 cells were treated with 0.36 mM ethylbenzene for 3 h, and the RNA was subjected to microarray analysis.

source_name: HL-60 cells treated with ethylbenzene (IC20) for 3 h

extract_protocol: Total RNA was extracted from the HL-60 cells treated to IC20 dose of ethylbenzene for 3 h, using the Trizol reagent (Invitrogen, USA) and purified using RNeasy mini kit (Qiagen, USA) according to the manufacturer's instructions. Genomic DNA was removed using RNase-free DNase set (Qiagen, USA) during RNA purification. RNA quality were assessed with the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, USA) (260/280 nm ratios) and only samples with an A260/A280 ratio between 1.9 and 2.2 were considered for suitable use. The RNA quality was checked with the Experion automated electrophoresis station (Bio-Rad Laboratories, USA) (28S/18S ratio).


title: Male Bull 3 sample 2

description: Gene expression data from male Day 7 blastocysts produced with sorted semen from Bull3

source_name: Male blastocysts from Bull 3


title: Gene expression profiles of HL-60 cells exposed to ethylbenzene (IC20) [sample 2]


title: Male Bull 3 sample 1


title: Male Bull 1 sample 2


title: Gene expression profiles of HL-60 cells exposed to trichloroethylene (IC20) [sample 1]


title: Gene expression profiles of HL-60 cells exposed to dichloromethane (IC20) [sample 3]

description: HL-60 cells were treated with 16.54 mM dichloromethane for 3 h, and the RNA was subjected to microarray analysis.

source_name: HL-60 cells treated with dichloromethane (IC20) for 3 h

extract_protocol: Total RNA was extracted from the HL-60 cells treated to IC20 dose of dichloromethane for 3 h, using the Trizol reagent (Invitrogen, USA) and purified using RNeasy mini kit (Qiagen, USA) according to the manufacturer's instructions. Genomic DNA was removed using RNase-free DNase set (Qiagen, USA) during RNA purification. RNA quality were assessed with the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, USA) (260/280 nm ratios) and only samples with an A260/A280 ratio between 1.9 and 2.2 were considered for suitable use. The RNA quality was checked with the Experion automated electrophoresis station (Bio-Rad Laboratories, USA) (28S/18S ratio).


title: Gene expression profiles of HL-60 cells exposed to dichloromethane (IC20) [sample 2]


title: Gene expression profiles of HL-60 cells exposed to ethylbenzene (IC20) [sample 1]


title: Male Bull 3 sample 3


title: Gene expression profiles of HL-60 cells exposed to dichloromethane (IC20) [sample 1]


title: Vehicle control, 6 hr, bile duct, biological replicate 1

city: Research Triangle Park

first: Neal

middle: F

last: Cariello

address: 5 Moore Drive, Bldg 9, Rom 2011

department: Safety Assessment

institute: GlaxoSmithKline

description:
Gene expression data
56_0mg_6hr_Bileduct.CEL

hyb_protocol: Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.

organism: Rattus norvegicus

source_name: Rat bile ducts from animal 6 hr after dosing with the vehicle, 10 ml/kg corn oil

label_protocol: Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies

growth_protocol: Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.

extract_protocol: RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.

treatment_protocol: Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.

value: Sprague Dawley

value: 8 weeks old

value: bile duct

tag: isolation method

value: Laser Capture Microdissection


title: 50 mg/kg ANIT, 6 hr, bile duct, biological replicate 4

description:
Gene expression data
84_50mg_6hr_Bileduct.CEL

source_name: Rat bile ducts from animal 6 hr after dosing with ANIT in the vehicle

tag: tissue


title: Vehicle control, 6 hr, bile duct, biological replicate 2

description:
Gene expression data
57_0mg_6hr_Bileduct.CEL

tag: age


title: Vehicle control, 6 hr, bile duct, biological replicate 3

description:
Gene expression data
58_0mg_6hr_Bileduct.CEL

tag: strain


title: 50 mg/kg ANIT, 6 hr, bile duct, biological replicate 2

description:
Gene expression data
82_50mg_6hr_Bileduct.CEL


title: Female Bull 2 sample 1

description: Gene expression data from female Day 7 blastocysts produced with sorted semen from Bull2

source_name: Female blastocysts from Bull 2

value: blastocyst


title: 50 mg/kg ANIT, 6 hr, bile duct, biological replicate 3

description:
Gene expression data
83_50mg_6hr_Bileduct.CEL


title: Selected Individual 20

city: Québec

first: Christopher

last: Sauvage

state: QC

address: 1030 Avenue de la médecine - Pavillon Marchand

department: Biology

country: Canada

institute: University Laval

description: Selected Individual 20

hyb_protocol: Microarray were hybridized using Cy3/Cy5 dyes (Genisphere) as detailed in St-Cyr et al. (2008)

scan_protocol: Transcription profiles from selected and control lines were measured using the Scanarray laser instrument (Packard Bioscience). Pictures were analysed and gene expression levels quantified using the Quantarray software with the histogram quantification method.

data_processing: Data from the two life stages were exported in text format and were separately analysed using a mixed model ANOVA and the R/MAANOVA package (Kerr and Churchill 2000; Wu et al. 2002). Normalization algorithm: Lowess

organism: Salvelinus fontinalis

source_name: Liver and caecum pyloric tissue mixed

label_protocol: Messenger RNA from each sample was reverse-transcribed and labelled using the Genisphere 3DNA Array 50 kit provided by Invitrogen, using the Superscript II retro-transcriptase enzyme and Cy3/Cy5 dyes (Genisphere), according to the manufacturer’s recommendations (Invitrogen protocol: http://web.uvic.ca/cbr/grasp/). Then, cDNA was purified using Microcon YM30 (Millipore, Beford, MA, USA)

extract_protocol:
Whole individuals were stored at -80°C prior to any sampling
All RNA extractions were performed on ice (4°C) and following the same protocol to reduce technical biases in genes expression measures. Entire “control” and “selected” fry were individually homogenised in a mixture composed of 4ml Trizol® reagent (Sigma) and 20 µL isopropanol (Sigma), using a Qiagen homogenizer, whereas approximately 150 mg of liver and pyloric caeca of individual juveniles were treated in the same way. Total RNA was extracted using the Purelink Micro to midi total RNA purification system kit (Invitrogen), according to the manufacturer’s recommendations. Subsequently, RNA integrity and quantity was controlled using a Nanodrop instrument (ND-1000, Nanodrop).

treatment_protocol: Samples were treated with DNAse enzyme prior to labeling

tag: fish line

value: selected

tag: tissue type

value: mixed liver and caecum pyloric tissue

value: 16 weeks old juveniles fish


title: Control Individual 15

description: Control Individual 15

value: control


title: Selected Individual 16

description: Selected Individual 16


title: Selected Individual 15

description: Selected Individual 15


title: Control Individual 14

description: Control Individual 14


title: Selected Individual 18

description: Selected Individual 18


title: Vehicle control, 6 hr, bile duct, biological replicate 4

description:
Gene expression data
59_0mg_6hr_Bileduct.CEL


title: Female Bull 2 sample 2

tag: cell type

value: Mixed breed

value: Day 7 post insemination

value: Female


title: 50 mg/kg ANIT, 6 hr, hepatocyte, biological replicate 5

description:
Gene expression data
185_50mg_6hr_Hep.CEL

source_name: Rat hepatocytes from animal 6 hr after dosing with ANIT in the vehicle

value: liver

value: hepatocyes


title: 50 mg/kg ANIT, 6 hr, bile duct, biological replicate 1

description:
Gene expression data
81_50mg_6hr_Bileduct.CEL


title: 50 mg/kg ANIT, 6 hr, hepatocyte, biological replicate 4

description:
Gene expression data
184_50mg_6hr_Hep.CEL


title: Female Bull 2 sample 3


title: Control Individual 13

description: Control Individual 13


title: Male Bull 2 sample 2

description: Gene expression data from male Day 7 blastocysts produced with sorted semen from Bull2

source_name: Male blastocysts from Bull 2


title: Control Individual 19

description: Control Individual 19


title: Selected Individual 19

description: Selected Individual 19


title: Selected Individual 13

description: Selected Individual 13


title: Male Bull 2 sample 1


title: 50 mg/kg ANIT, 6 hr, hepatocyte, biological replicate 1

description:
Gene expression data
181_50mg_6hr_Hep.CEL


title: Vehicle control, 6 hr, hepatocyte, biological replicate 5

description:
Gene expression data
160_0mg_6hr_Hep.CEL

source_name: Rat hepatocytes from animal 6 hr after dosing with the vehicle, 10 ml/kg corn oil


title: Control Individual 10

description: Control Individual 10


title: Control Individual 16

description: Control Individual 16


title: 50 mg/kg ANIT, 6 hr, hepatocyte, biological replicate 2

description:
Gene expression data
182_50mg_6hr_Hep.CEL


title: Vehicle control, 6 hr, hepatocyte, biological replicate 4

description:
Gene expression data
159_0mg_6hr_Hep.CEL


title: Selected Individual 12

description: Selected Individual 12


title: Selected Individual 11

description: Selected Individual 11


title: Vehicle control, 6 hr, hepatocyte, biological replicate 2

description:
Gene expression data
156_0mg_6hr_Hep.CEL


title: 50 mg/kg ANIT, 6 hr, bile duct, biological replicate 5

description:
Gene expression data
85_50mg_6hr_Bileduct.CEL


title: Control Individual 17

description: Control Individual 17


title: Selected Individual 10

description: Selected Individual 10


title: Vehicle control, 6 hr, hepatocyte, biological replicate 3

description:
Gene expression data
158_0mg_6hr_Hep.CEL


title: Control Individual 11

description: Control Individual 11