title: Cow 7251 -30d relative to parturition

value: Mammary biopsy of cow at -30 day relative to parturition

value: Bovine tissue reference (mammary, liver, muscle, adipsoe, and placenta)


title: serous ovarian cancer 499d

status: Public on Mar 01 2012

type: RNA

city: Niigata

first: Kosuke

last: Yoshihara

address: 1-757 Asahimachi-dori

department: Obstetrics and Gynecology

country: Japan

institute: Niigata University

hyb_protocol: Cy3-labeled cRNAs (1.65 µg) were hybridized for 17 hours at 65°C to an Agilent Whole Human Genome Oligo Microarray in a rotating Agilent hybridization oven.

scan_protocol: The hybridized microarray was washed and then scanned in Cy3 channel with the Agilent DNA Microarray Scanner (model G2565CA).

data_processing: Signal intensity per spot was generated from the scanned image with Feature Extraction Software ver.10.1 (Agilent Technologies) in the default settings.

molecule: total RNA

organism: Homo sapiens

source_name: high-grade serous ovarian cancer

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labering Kit, one-color (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).

extract_protocol: Total RNA was extracted from tissue samples using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's recommendations. RNA was examined with a 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA, USA) using an RNA 6000 Nano LabChip (Agilent Technologies)

tag: tissue

value: high-grade serous ovarian cancer tumor

tag: grading

tag: Stage

value: IIIc

tag: surgery status

value: suboptimal

tag: taxane

tag: platinum

tag: pfs (m)

tag: rec (1)

tag: os (m)

tag: death (1)


title: Cow 7136 300d relative to parturition

city: Corvallis

first: Massimo

last: Bionaz

state: OR

address: 316A Withycombe Hall

department: Animal and Rangeland Sciences

country: USA

institute: Oregon State University

description: A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipsoe, and placenta) were used as reference.

hyb_protocol: Labelled cDNA hybridised using 80 μL of the hybridization buffer #1 (Ambion).  Slides placed in humidified slide chambers (Corning) in water bath for 40 h at 42 °C. Prior scanning the microarray were washed for 5 min by agitation 3 times with wash buffers in the following order: 1×SSC and 0.2% SDS solution preheated at 42°C, 0.1×SSC and 0.2% SDS solution, and 0.1×SSC solution. Lastly, slides were inserted into a 50 mL tube, spin-dried and gassed with Argon to preserve dye from bleaching.

scan_protocol: Arrays were scanned with a ScanArray 4000 (GSI-Lumonics) dual-laser confocal scanner and images were processed and edited using GenePix 6.0 (Axon Instruments).

data_processing: Array quality was assessed using an in-house parser written in Perl language. Spots that received a -100 flag by GenePix 6.0 were removed from further analysis and background intensity was subtracted from the foreground intensity. Spots on the slide were considered “good” if the median intensity was ≥3 standard deviation above median background for each channel (i.e., dye). Spots were flagged “present” when both dyes passed the criteria, “marginal” if only one dye passed the criteria, or “absent” when both dyes failed to pass the criteria. Statistical analysis was conducted on oligos that were flagged as “present” and “marginal”. Data from a total of 124 microarrays were normalized for dye and array effects (i.e., Loess normalization and array centering and scaling) before statistical analysis.

organism: Bos taurus

label_protocol: Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using Superscript III Kit (Invitrogen) as manufacturers instructions.

growth_protocol: Cows were maintain in a normal farm management

extract_protocol: Biopsy tissue was weighted (~0.5-1.0 g) and immediately subjected to RNA extraction using ice-cold TRIZol. Genomic DNA was removed from RNA with DNAse (Qiagen) using RNeasy Mini Kit columns (Qiagen)

tag: breed

value: Holstein dairy cow

value: Mammary biopsy of cow at 300 day relative to parturition

value: Holstein dairy cows


title: Cingulate cortex_Vinclozolin_Female_biological rep6

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description:
Treatment-Sex Group: CngCTX-F-Vin
Marina-CngCTX-Vin-FM-6-121009-96.CEL
Cingulate cortex from F3-generation Vincozolin lineage female 11 months old rat brain

hyb_protocol: Following fragmentation, ssDNA were hybridized  on Affymetrix Rat Gene 1.0 ST Array according to standard Affymetrix protocol. Chips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip® Scanner 3000.

data_processing: The data for each of the 12 studied  male or female brain areas (F-Amy, F-CngCTX, F-EnCTX, F-Hipp, F-OlfB, F-POAH ,M-Amy, M-CngCTX, M-EnCTX, M-Hipp, M-OlfB, M-POAH) were pre-processed and analyzed as a separate group (12 groups,  9-12 chips per group) with Partek Genomic Suite 6.5 beta software (Partek Inc. St. Louis MO) in August-October of 2010 using RMA GC-content adjusted algorithm background correction, quintile normalization, median polish methods for probesets summarization, and log values of probes signals using base 2.

label: biotin

organism: Rattus norvegicus

source_name: Cingulate cortex from F3-generation Vincozolin lineage female rat brain

label_protocol: Biotin-labeled ssDNA were prepared according to the standard Affymetrix protocol from at least 300 ng total RNA (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual, 2005-2209, Affymetrix).

growth_protocol: Male and female rats of the F3 generation of Vinclozolin (Vinclozolin-Lineage) and DMSO Control (Control-Lineage) Lineages were selected out of litters from untreated F2 generation mothers at Washington State University according to established protocols (Anway et al., 2005).  On postnatal day (PND) 22, one day after weaning, animals were shipped to the University of Texas.  Upon arriving at the University of Texas, one animal from each Lineage (Control and Vinclozolin) was pair-housed (one control and one vinclozolin animal) and remained in these dyads throughout the duration of the behavioral study.  All rats were sacrificed at age of 11 months and certain brain areas samples were collected as 3 mm tissue punches and put into Trizol™ reagent (Invitrogen, USA) and kept at -20 degrees Celsius until RNA isolation.

extract_protocol: RNA was isolated from individual animal tissue homogenate in 750 ul Trizol™ reagent (Invitrogen, USA), according to manufacturer’s instructions.

treatment_protocol: Gestating outbred Sprague-Dawley mother rats were given intraperitoneal injections of Vinclozolin (100mg/kg/day) or vehicle (DMSO, Control) from embryonic day 8-14 (E8-E14) of gestation (i.e. F0 generation) [Cupp AS, et al., 2003].  Male and female rats of the F3 generation of Vinclozolin and Control lineages were selected out of litters from untreated F2 generation.  One animal from each lineage (Control and Vinclozolin) were pair-housed (one control and one vinclozolin animal) and remained in these dyads throughout the duration of the behavioral study until sacrifice at age of 11 months.

tag: rna prep date

tag: scan date

tag: animal id

tag: vin/con rats dyad group

tag: strain

value: Sprague-Dawley rat

tag: gender

value: Female

tag: generation

tag: lineage

value: Vincozolin

value: Cingulate cortex

tag: age

value: 11 months


title: serous ovarian cancer 497d

tag: tissue

tag: grading

tag: Stage

tag: surgery status


title: C. elegans_rep3_stage6

city: Haifa

first: Itai

last: Yanai

address: Technion City

department: Biology

country: Israel

institute: Technion - Israel Institute of Technology

description: C. elegans_rep3_stage6

hyb_protocol: The hybridization and washing of the microarrays were performed following the Agilent protocol for single-channel arrays.

scan_protocol: Agilent Microarray Scanner was used to scan the slides

data_processing: Feature Extraction was used for data processing with protocol GE1_105_Dec08

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: C. elegans, stage6

label_protocol: 6μg of RNA was labeled with Cy-3 and 1.65μg of labeled aRNA was incubated on each microarray. Each embryonic stage was measured in independent biological triplicates.

growth_protocol: Standard C. elegans techniques were followed to grow worms (Stiernagle 2006).

extract_protocol: RNA was extracted from embryos using Trizol. Each sample comprised 48 individually staged embryos. Total RNA was amplified by two round of in vitro transcription (IVT)and cy3 labeled using the MessageAmpII kit (Ambion). We also added to this reaction RNA from a Spike-in kit (Agilent) that included 10 different species of RNA at various concentrations.

treatment_protocol: For the embryo collection of all species adult hermaphrodites or females were collected and cut to obtain embryos. Embryos were washed with a bleach solution (70% DDW, 20% bleach, 10% 5M KOH) for 30 seconds and subsequently with a 5% BSA solution for 30 seconds. 4-cell embryos were collected,washed 4 times in clear DDW and incubated at 20°C for the appropriate time for each species to reach stages 1-10. After incubation embryos were frozen in liquid nitrogen and kept at -80°C until RNA extraction.

tag: developmental stage

value: 7th AB division


title: C. elegans_rep3_stage4

description: C. elegans_rep3_stage4

source_name: C. elegans, stage4

value: 5th AB division


title: C. elegans_rep3_stage8

description: C. elegans_rep3_stage8

source_name: C. elegans, stage8

value: Comma stage


title: Cingulate cortex_Control_Female_biological rep6

description:
Treatment-Sex Group: CngCTX-F-Con
Marina-CngCTX-Con-FM-6-121009-90.CEL
Cingulate cortex from F3-generation control lineage (vehicle) female 11 months old rat brain

source_name: Cingulate cortex from F3-generation control lineage (vehicle) female rat brain

value: control (vehicle)


title: C. elegans_rep3_stage5

description: C. elegans_rep3_stage5

source_name: C. elegans, stage5

value: 6th AB division


title: Cingulate cortex_Vinclozolin_Female_biological rep3

description:
Treatment-Sex Group: CngCTX-F-Vin
Marina-CngCTX-Vin-FM-3-121009-93.CEL
Cingulate cortex from F3-generation Vincozolin lineage female 11 months old rat brain


title: Cingulate cortex_Vinclozolin_Female_biological rep2

description:
Treatment-Sex Group: CngCTX-F-Vin
Marina-CngCTX-Vin-FM-2-121009-92.CEL
Cingulate cortex from F3-generation Vincozolin lineage female 11 months old rat brain


title: serous ovarian cancer 498d2

tag: taxane

tag: platinum

tag: pfs (m)

tag: rec (1)

tag: os (m)


title: serous ovarian cancer 493d

tag: death (1)


title: serous ovarian cancer 494d


title: serous ovarian cancer 496d


title: serous ovarian cancer 495d

value: optimal


title: serous ovarian cancer 491d

value: high-grade serous ovarian cancer tumor


title: C. elegans_rep3_stage7

description: C. elegans_rep3_stage7

source_name: C. elegans, stage7

value: Ventral enclosure stage


title: C. elegans_rep3_stage3

description: C. elegans_rep3_stage3

source_name: C. elegans, stage3

value: 4th AB division


title: Cow 7136 60d relative to parturition

treatment_protocol: Cows were maintain in a normal farm management

tag: breed

value: Holstein dairy cow

value: Mammary biopsy of cow at 60 day relative to parturition

value: Bovine tissue reference (mammary, liver, muscle, adipsoe, and placenta)


title: Cow 7136 30d relative to parturition

value: Mammary biopsy of cow at 30 day relative to parturition

value: Holstein dairy cows


title: Cow 7136 120d relative to parturition

value: Mammary biopsy of cow at 120 day relative to parturition


title: Cow 7136 240d relative to parturition

value: Mammary biopsy of cow at 240 day relative to parturition


title: Cingulate cortex_Control_Female_biological rep5

description:
Treatment-Sex Group: CngCTX-F-Con
Marina-CngCTX-Con-FM-5-121009-89.CEL
Cingulate cortex from F3-generation control lineage (vehicle) female 11 months old rat brain

tag: rna prep date

tag: scan date

tag: animal id

tag: vin/con rats dyad group

tag: strain

value: Sprague-Dawley rat

value: Female

value: Cingulate cortex

value: 11 months


title: Cow 7136 15d relative to parturition

value: Mammary biopsy of cow at 15 day relative to parturition


title: Cingulate cortex_Vinclozolin_Female_biological rep1

description:
Treatment-Sex Group: CngCTX-F-Vin
Marina-CngCTX-Vin-FM-1-121009-91.CEL
Cingulate cortex from F3-generation Vincozolin lineage female 11 months old rat brain

tag: gender

tag: generation

tag: lineage

value: Vincozolin

tag: tissue

tag: age


title: C. elegans_rep3_stage1

description: C. elegans_rep3_stage1

source_name: C. elegans, stage1

tag: developmental stage

value: 4-cell stage


title: Cingulate cortex_Control_Female_biological rep4

description:
Treatment-Sex Group: CngCTX-F-Con
Marina-CngCTX-Con-FM-4-121009-88.CEL
Cingulate cortex from F3-generation control lineage (vehicle) female 11 months old rat brain

value: control (vehicle)


title: serous ovarian cancer 490d

value: high-grade serous ovarian cancer tumor

tag: grading

tag: Stage

value: IIIc

tag: surgery status

value: suboptimal

tag: taxane

tag: platinum


title: C. elegans_rep3_stage2

description: C. elegans_rep3_stage2

source_name: C. elegans, stage2

value: E-cell division


title: C. elegans_rep2_stage9

description: C. elegans_rep2_stage9

source_name: C. elegans, stage9

value: Movement


title: Cingulate cortex_Control_Female_biological rep3

description:
Treatment-Sex Group: CngCTX-F-Con
Marina-CngCTX-Con-FM-3-121009-87.CEL
Cingulate cortex from F3-generation control lineage (vehicle) female 11 months old rat brain


title: Cow 7136 -15d relative to parturition

tag: breed

value: Holstein dairy cow

value: Mammary biopsy of cow at -15 day relative to parturition

value: Bovine tissue reference (mammary, liver, muscle, adipsoe, and placenta)


title: Cingulate cortex_Vinclozolin_Male_biological rep12

description:
Treatment-Sex Group: CngCTX-M-Vin
Marina-CngCTX-Vin-M-12-120909-84.CEL
Cingulate cortex from F3-generation Vincozolin lineage male 11 months old rat brain

source_name: Cingulate cortex from F3-generation Vincozolin lineage male rat brain

tag: rna prep date

value: Male


title: Cow 7136 1d relative to parturition

value: Mammary biopsy of cow at 1 day relative to parturition

value: Holstein dairy cows


title: Cingulate cortex_Vinclozolin_Male_biological rep10

description:
Treatment-Sex Group: CngCTX-M-Vin
Marina-CngCTX-Vin-M-10-120909-82.CEL
Cingulate cortex from F3-generation Vincozolin lineage male 11 months old rat brain

tag: scan date

value: Sprague-Dawley rat

value: Cingulate cortex


title: Cow 7136 -30d relative to parturition

value: Mammary biopsy of cow at -30 day relative to parturition


title: Cingulate cortex_Control_Female_biological rep2

description:
Treatment-Sex Group: CngCTX-F-Con
Marina-CngCTX-Con-FM-2-121009-86.CEL
Cingulate cortex from F3-generation control lineage (vehicle) female 11 months old rat brain

tag: animal id

value: Female

value: 11 months


title: serous ovarian cancer 487d

tag: pfs (m)

tag: rec (1)

tag: os (m)

tag: death (1)


title: serous ovarian cancer 49d


title: serous ovarian cancer 488d

value: IV


title: Cingulate cortex_Control_Female_biological rep1

description:
Treatment-Sex Group: CngCTX-F-Con
Marina-CngCTX-Con-FM-1-121009-85.CEL
Cingulate cortex from F3-generation control lineage (vehicle) female 11 months old rat brain

tag: vin/con rats dyad group

tag: strain

tag: gender

tag: generation

tag: lineage

value: control (vehicle)


title: C. elegans_rep2_stage10

description: C. elegans_rep2_stage10

source_name: C. elegans, stage10

tag: developmental stage

value: Juvenile L1 larvae


title: C. elegans_rep2_stage8

description: C. elegans_rep2_stage8

value: Comma stage


title: serous ovarian cancer 484d

tag: tissue

value: high-grade serous ovarian cancer tumor

tag: grading

tag: Stage

tag: surgery status

value: suboptimal


title: Cingulate cortex_Vinclozolin_Male_biological rep9

description:
Treatment-Sex Group: CngCTX-M-Vin
Marina-CngCTX-Vin-M-9-120909-81.CEL
Cingulate cortex from F3-generation Vincozolin lineage male 11 months old rat brain

tag: rna prep date

value: Vincozolin

tag: age


title: C. elegans_rep2_stage6

description: C. elegans_rep2_stage6

value: 7th AB division


title: C. elegans_rep2_stage5

description: C. elegans_rep2_stage5

value: 6th AB division


title: C. elegans_rep2_stage7

description: C. elegans_rep2_stage7

value: Ventral enclosure stage


title: C. elegans_rep2_stage3

description: C. elegans_rep2_stage3

value: 4th AB division


title: serous ovarian cancer 483d

value: IIIc

tag: taxane

tag: platinum


title: C. elegans_rep2_stage4

description: C. elegans_rep2_stage4

value: 5th AB division


title: serous ovarian cancer 486d

tag: pfs (m)

tag: rec (1)


title: serous ovarian cancer 481d

tag: os (m)

tag: death (1)


title: serous ovarian cancer 482d


title: Cingulate cortex_Vinclozolin_Male_biological rep7

description:
Treatment-Sex Group: CngCTX-M-Vin
Marina-CngCTX-Vin-M-7-120909-79.CEL
Cingulate cortex from F3-generation Vincozolin lineage male 11 months old rat brain

tag: scan date

tag: animal id

tag: vin/con rats dyad group

tag: strain

value: Sprague-Dawley rat

value: Male

value: Cingulate cortex


title: serous ovarian cancer 480d2


title: Cingulate cortex_Control_Male_biological rep12

description:
Treatment-Sex Group: CngCTX-M-Con
Marina-CngCTX-Con-M-12-120909-78.CEL
Cingulate cortex from F3-generation control lineage (vehicle) male 11 months old rat brain

source_name: Cingulate cortex from F3-generation control lineage (vehicle) male rat brain

tag: gender

tag: generation

tag: lineage

value: 11 months


title: Cingulate cortex_Control_Male_biological rep10

description:
Treatment-Sex Group: CngCTX-M-Con
Marina-CngCTX-Con-M-10-120909-76.CEL
Cingulate cortex from F3-generation control lineage (vehicle) male 11 months old rat brain

tag: tissue


title: Cingulate cortex_Vinclozolin_Male_biological rep8

description:
Treatment-Sex Group: CngCTX-M-Vin
Marina-CngCTX-Vin-M-8-120909-80.CEL
Cingulate cortex from F3-generation Vincozolin lineage male 11 months old rat brain


title: C. elegans_rep2_stage2

description: C. elegans_rep2_stage2

tag: developmental stage

value: E-cell division


title: C. elegans_rep2_stage1

description: C. elegans_rep2_stage1

value: 4-cell stage


title: Cingulate cortex_Control_Male_biological rep11

description:
Treatment-Sex Group: CngCTX-M-Con
Marina-CngCTX-Con-M-11-120909-77.CEL
Cingulate cortex from F3-generation control lineage (vehicle) male 11 months old rat brain

tag: rna prep date

value: control (vehicle)


title: serous ovarian cancer 477d

tag: grading

tag: Stage

tag: surgery status


title: serous ovarian cancer 479d

value: IV

tag: taxane

tag: platinum

tag: pfs (m)


title: Cingulate cortex_Control_Male_biological rep9

description:
Treatment-Sex Group: CngCTX-M-Con
Marina-CngCTX-Con-M-9-120909-75.CEL
Cingulate cortex from F3-generation control lineage (vehicle) male 11 months old rat brain

tag: age


title: C. elegans_rep1_stage9

description: C. elegans_rep1_stage9

value: Movement


title: 14248989 - Control pool1 vs dic8-PA pool1

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Role of DGK in gene expression

hyb_protocol: dic8-PA pool1 Cy5 / Control pool1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

source_name: dic8-PA pool1

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: cell culture/primary cell - Media=Gamborg hygrometry Temperature=22°C Light=100 microE

extract_protocol: Pool of extract, dic8-PA RB1:1ug, dic8-PA RB2:1ug, dic8-PA RB3:1ug. (Amplification_Ambion.txt) Amplification of mRNA  (Kit AMBION MessageAmp aRNA Amplification #1750)

treatment_protocol: Name:diC8-PA 200 microM - compound based treatment - compound addition,pa:quantity 200uM time 4hour .

tag: ecotype

value: columbia

value: 5 day

tag: treatment

value: diC8-PA 200 microM

source_name: Control pool1

extract_protocol: Pool of extract, Control RB1:1ug, Control RB2:1ug, Control RB3:1ug. (Amplification_Ambion.txt) Amplification of mRNA  (Kit AMBION MessageAmp aRNA Amplification #1750)

treatment_protocol: Name:Control - compound based treatment - compound addition,gamborg,gaba:time 4hour .

value: gamborg,gaba


title: serous ovarian cancer 476d

source_name: high-grade serous ovarian cancer

value: high-grade serous ovarian cancer tumor

value: suboptimal

tag: rec (1)

tag: os (m)

tag: death (1)


title: 14248992 - Control pool2 vs dic8-PA pool2

description: Role of DGK in gene expression

hyb_protocol: dic8-PA pool2 Cy5 / Control pool2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: dic8-PA pool2

extract_protocol: Pool of extract, dic8-PA RB4:1ug, dic8-PA RB5:1ug, dic8-PA RB6:1ug. (Amplification_Ambion.txt) Amplification of mRNA  (Kit AMBION MessageAmp aRNA Amplification #1750)

source_name: Control pool2

extract_protocol: Pool of extract, Control RB4:1ug, Control RB5:1ug, Control RB6:1ug. (Amplification_Ambion.txt) Amplification of mRNA  (Kit AMBION MessageAmp aRNA Amplification #1750)


title: 14248994 - dic8-PA pool2 vs Control pool2

description: Role of DGK in gene expression

hyb_protocol: Control pool2 Cy5 / dic8-PA pool2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14248990 - dic8-PA pool1 vs Control pool1

description: Role of DGK in gene expression

hyb_protocol: Control pool1 Cy5 / dic8-PA pool1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: C. elegans_rep1_stage8

description: C. elegans_rep1_stage8

value: Comma stage


title: serous ovarian cancer 475d2


title: C. elegans_rep1_stage7

description: C. elegans_rep1_stage7

value: Ventral enclosure stage


title: C. elegans_rep1_stage10

description: C. elegans_rep1_stage10

value: Juvenile L1 larvae


title: Cingulate cortex_Control_Male_biological rep8

description:
Treatment-Sex Group: CngCTX-M-Con
Marina-CngCTX-Con-M-8-120909-74.CEL
Cingulate cortex from F3-generation control lineage (vehicle) male 11 months old rat brain

tag: scan date

tag: animal id

tag: vin/con rats dyad group

tag: strain

value: Sprague-Dawley rat

tag: gender

value: Male

tag: generation


title: 14227626 - ABA pool2 vs terBut pool2

description: Role of DGK in gene expression

hyb_protocol: terBut pool2 Cy5 / ABA pool2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: terBut pool2

extract_protocol: Pool of extract, terBut RB4:1ug, terBut RB5:1ug, terBut RB6:1ug. (Amplification_Ambion.txt) Amplification of mRNA  (Kit AMBION MessageAmp aRNA Amplification #1750)

treatment_protocol: Name:terBut - compound based treatment - compound addition,terbut:time 4hour .

value: terBut

source_name: ABA pool2

extract_protocol: Pool of extract, ABA RB4:1ug, ABA RB5:1ug, ABA RB6:1ug. (Amplification_Ambion.txt) Amplification of mRNA  (Kit AMBION MessageAmp aRNA Amplification #1750)

treatment_protocol: Name:ABA 10-5 M - compound based treatment - compound addition,aba:quantity 10nM time 4hour .

value: ABA 10-5 M


title: serous ovarian cancer 470d2

tag: tissue

tag: grading

tag: Stage

value: IIIc

value: optimal


title: Cingulate cortex_Control_Male_biological rep7

description:
Treatment-Sex Group: CngCTX-M-Con
Marina-CngCTX-Con-M-7-120909-73.CEL
Cingulate cortex from F3-generation control lineage (vehicle) male 11 months old rat brain

tag: rna prep date

tag: lineage

value: control (vehicle)

value: Cingulate cortex

value: 11 months


title: C. elegans_rep1_stage6

description: C. elegans_rep1_stage6

source_name: C. elegans, stage6

tag: developmental stage

value: 7th AB division


title: 14227625 - terBut pool2 vs ABA pool2

description: Role of DGK in gene expression

hyb_protocol: ABA pool2 Cy5 / terBut pool2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: ecotype

value: columbia

tag: age

value: 5 day


title: C. elegans_rep1_stage5

description: C. elegans_rep1_stage5

source_name: C. elegans, stage5

value: 6th AB division


title: serous ovarian cancer 469d

value: high-grade serous ovarian cancer tumor

value: IV

tag: surgery status

value: suboptimal

tag: taxane

tag: platinum

tag: pfs (m)

tag: rec (1)


title: Olfactory bulbs_Vinclozolin_Female_biological rep6

description:
Treatment-Sex Group: OlfB-F-Vin
Marina-OlfB-Vin-Fm-6-011310-72.CEL
Olfactory bulb from F3-generation Vincozolin lineage female 11 months old rat brain

source_name: Olfactory bulb from F3-generation Vincozolin lineage female rat brain

tag: scan date

tag: animal id

tag: vin/con rats dyad group

value: Female

value: Vincozolin

value: Olfactory bulbs


title: Olfactory bulbs_Vinclozolin_Female_biological rep4

description:
Treatment-Sex Group: OlfB-F-Vin
Marina-OlfB-Vin-Fm-4-011310-70.CEL
Olfactory bulb from F3-generation Vincozolin lineage female 11 months old rat brain

tag: strain

value: Sprague-Dawley rat

tag: gender

tag: generation


title: serous ovarian cancer 468d

tag: tissue

tag: grading

tag: Stage

tag: os (m)

tag: death (1)


title: Olfactory bulbs_Vinclozolin_Female_biological rep5

description:
Treatment-Sex Group: OlfB-F-Vin
Marina-OlfB-Vin-Fm-5-011310-71.CEL
Olfactory bulb from F3-generation Vincozolin lineage female 11 months old rat brain

tag: rna prep date

tag: lineage

tag: age


title: C. elegans_rep1_stage4

description: C. elegans_rep1_stage4

source_name: C. elegans, stage4

tag: developmental stage

value: 5th AB division


title: 14227621 - terBut pool1 vs R59022 pool1

description: Role of DGK in gene expression

hyb_protocol: R59022 pool1 Cy5 / terBut pool1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Pool of extract, R59022 RB1:1ug, R59022 RB2:1ug, R59022 RB3:1ug. (Amplification_Ambion.txt) Amplification of mRNA  (Kit AMBION MessageAmp aRNA Amplification #1750)

treatment_protocol: Name:R59022 - compound based treatment - compound addition,r59022:time 4hour .

tag: ecotype

tag: treatment

source_name: terBut pool1

extract_protocol: Pool of extract, terBut RB1:1ug, terBut RB2:1ug, terBut RB3:1ug. (Amplification_Ambion.txt) Amplification of mRNA  (Kit AMBION MessageAmp aRNA Amplification #1750)

value: terBut


title: 14227558 - R59022 pool2 vs terBut pool2

description: Role of DGK in gene expression

hyb_protocol: terBut pool2 Cy5 / R59022 pool2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Pool of extract, R59022 RB4:1ug, R59022 RB5:1ug, R59022 RB6:1ug. (Amplification_Ambion.txt) Amplification of mRNA  (Kit AMBION MessageAmp aRNA Amplification #1750)


title: C. elegans_rep1_stage3

description: C. elegans_rep1_stage3

source_name: C. elegans, stage3

value: 4th AB division


title: serous ovarian cancer 462d

value: IIIc

tag: surgery status

tag: taxane

tag: platinum

tag: pfs (m)

tag: rec (1)


title: Olfactory bulbs_Vinclozolin_Female_biological rep2

description:
Treatment-Sex Group: OlfB-F-Vin
Marina-OlfB-Vin-Fm-2-011310-68.CEL
Olfactory bulb from F3-generation Vincozolin lineage female 11 months old rat brain

tag: scan date

tag: animal id

tag: vin/con rats dyad group

tag: strain

tag: gender

tag: generation


title: Olfactory bulbs_Control_Female_biological rep6

description:
Treatment-Sex Group: OlfB-F-Con
Marina-OlfB-Con-Fm-6-011310-66.CEL
Olfactory bulb from F3-generation control lineage (vehicle) female 11 months old rat brain

source_name: Olfactory bulb from F3-generation control lineage (vehicle) female rat brain

tag: rna prep date

value: control (vehicle)

tag: tissue


title: Olfactory bulbs_Vinclozolin_Female_biological rep3

description:
Treatment-Sex Group: OlfB-F-Vin
Marina-OlfB-Vin-Fm-3-011310-69.CEL
Olfactory bulb from F3-generation Vincozolin lineage female 11 months old rat brain

tag: lineage

tag: age

value: 11 months


title: C. elegans_rep1_stage2

description: C. elegans_rep1_stage2

source_name: C. elegans, stage2

tag: developmental stage

value: E-cell division


title: Olfactory bulbs_Control_Female_biological rep5

description:
Treatment-Sex Group: OlfB-F-Con
Marina-OlfB-Con-Fm-5-011310-65.CEL
Olfactory bulb from F3-generation control lineage (vehicle) female 11 months old rat brain


title: 14227637 - ABA pool1 vs terBut pool1

description: Role of DGK in gene expression

hyb_protocol: terBut pool1 Cy5 / ABA pool1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: ecotype

value: columbia

tag: treatment

source_name: ABA pool1

extract_protocol: Pool of extract, ABA RB1:1ug, ABA RB2:1ug, ABA RB3:1ug. (Amplification_Ambion.txt) Amplification of mRNA  (Kit AMBION MessageAmp aRNA Amplification #1750)

value: ABA 10-5 M


title: 14227622 - R59022 pool1 vs terBut pool1

description: Role of DGK in gene expression

hyb_protocol: terBut pool1 Cy5 / R59022 pool1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: 5 day


title: serous ovarian cancer 467d

value: high-grade serous ovarian cancer tumor

tag: grading

tag: Stage

tag: surgery status

tag: taxane

tag: os (m)

tag: death (1)


title: serous ovarian cancer 464d

value: Optimal

tag: platinum

tag: pfs (m)

tag: rec (1)


title: serous ovarian cancer 456d

value: optimal


title: 14227557 - terBut pool2 vs R59022 pool2

description: Role of DGK in gene expression

hyb_protocol: R59022 pool2 Cy5 / terBut pool2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14227732 - clca2 repet3 vs ws repet3

description: What are the transcriptional adaptations induced by genetically modifying vacuolar nitrate transport

hyb_protocol: ws repet3 Cy5 / clca2 repet3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: ws repet3

growth_protocol: roots - Media=2 mM nitrate (adapted minimum media from Armengaud et al, Plant Phys 2004)  hygrometry=In vitro plant:98%  Temperature=18-22 (Night-Day)  Light=65 µE for 16h/day

extract_protocol: ws repet3:10ug. (Qiagen_RNeasy.pdf)

value: wassilewskija

tag: genotype/variation

value: normal

tag: dev.stage (boyes et al. plant cell 2001)

source_name: clca2 repet3

extract_protocol: clca2 repet3:10ug. (Qiagen_RNeasy.pdf)

value: mutant (ws)


title: 14227554 - terBut pool1 vs ABA pool1

description: Role of DGK in gene expression

hyb_protocol: ABA pool1 Cy5 / terBut pool1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: serous ovarian cancer 461d

hyb_protocol: Cy3-labeled cRNAs (1.65 µg) were hybridized for 17 hours at 65°C to an Agilent Whole Human Genome Oligo Microarray in a rotating Agilent hybridization oven.

tag: tissue

value: IV

value: suboptimal


title: C. briggsae_rep3_stage10

description: C. briggsae_rep3_stage10

organism: Caenorhabditis briggsae

source_name: C. briggsae, stage10

value: Juvenile L1 larvae


title: C. briggsae_rep3_stage9

description: C. briggsae_rep3_stage9

source_name: C. briggsae, stage9

value: Movement


title: 14227735 - ws repet4 vs clca2 repet4

hyb_protocol: clca2 repet4 Cy5 / ws repet4 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: clca2 repet4

extract_protocol: clca2 repet4:10ug. (Qiagen_RNeasy.pdf)

source_name: ws repet4

extract_protocol: ws repet4:10ug. (Qiagen_RNeasy.pdf)


title: serous ovarian cancer 45d

source_name: high-grade serous ovarian cancer

extract_protocol: Total RNA was extracted from tissue samples using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's recommendations. RNA was examined with a 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA, USA) using an RNA 6000 Nano LabChip (Agilent Technologies)

value: IIIc


title: C. briggsae_rep3_stage8

description: C. briggsae_rep3_stage8

source_name: C. briggsae, stage8

value: Comma stage


title: C. elegans_rep1_stage1

description: C. elegans_rep1_stage1

source_name: C. elegans, stage1

value: 4-cell stage


title: Olfactory bulbs_Control_Female_biological rep3

description:
Treatment-Sex Group: OlfB-F-Con
Marina-OlfB-Con-Fm-3-011310-63.CEL
Olfactory bulb from F3-generation control lineage (vehicle) female 11 months old rat brain

hyb_protocol: Following fragmentation, ssDNA were hybridized  on Affymetrix Rat Gene 1.0 ST Array according to standard Affymetrix protocol. Chips were washed and stained in the Affymetrix Fluidics Station 450.

extract_protocol: RNA was isolated from individual animal tissue homogenate in 750 ul Trizol™ reagent (Invitrogen, USA), according to manufacturer’s instructions.

tag: rna prep date

tag: scan date

tag: animal id

tag: vin/con rats dyad group

tag: strain

value: Sprague-Dawley rat

tag: gender

value: Female

tag: generation

tag: lineage

value: control (vehicle)

value: Olfactory bulbs

value: 11 months


title: Olfactory bulbs_Vinclozolin_Male_biological rep12

description:
Treatment-Sex Group: OlfB-M-Vin
Marina-OlfB-Vin-M-12-011210-60.CEL
Olfactory bulb from F3-generation Vincozolin lineage male 11 months old rat brain

source_name: Olfactory bulb from F3-generation Vincozolin lineage male rat brain

value: Male

value: Vincozolin

tag: age


title: Olfactory bulbs_Control_Female_biological rep1

description:
Treatment-Sex Group: OlfB-F-Con
Marina-OlfB-Con-Fm-1-011310-61.CEL
Olfactory bulb from F3-generation control lineage (vehicle) female 11 months old rat brain


title: 14227630 - 35A2 repet1 vs ws repet1

hyb_protocol: ws repet1 Cy5 / 35A2 repet1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: ws repet1

extract_protocol: ws repet1:10ug. (Qiagen_RNeasy.pdf)

tag: ecotype

value: wassilewskija

source_name: 35A2 repet1

extract_protocol: 35A2 repet1:10ug. (Qiagen_RNeasy.pdf)


title: 14227733 - 35A2 repet3 vs ws repet3

hyb_protocol: ws repet3 Cy5 / 35A2 repet3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: normal

source_name: 35A2 repet3

extract_protocol: 35A2 repet3:10ug. (Qiagen_RNeasy.pdf)


title: 14227629 - clca2 repet1 vs ws repet1

hyb_protocol: ws repet1 Cy5 / clca2 repet1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: clca2 repet1

extract_protocol: clca2 repet1:10ug. (Qiagen_RNeasy.pdf)

value: mutant (ws)


title: 14227634 - ws repet2 vs clca2 repet2

hyb_protocol: clca2 repet2 Cy5 / ws repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: clca2 repet2

extract_protocol: clca2 repet2:10ug. (Qiagen_RNeasy.pdf)

source_name: ws repet2

extract_protocol: ws repet2:10ug. (Qiagen_RNeasy.pdf)


title: serous ovarian cancer 42d

value: high-grade serous ovarian cancer tumor

tag: grading

tag: Stage

tag: surgery status

tag: taxane

tag: os (m)

tag: death (1)


title: Olfactory bulbs_Vinclozolin_Male_biological rep10

description:
Treatment-Sex Group: OlfB-M-Vin
Marina-OlfB-Vin-M-10-011210-58.CEL
Olfactory bulb from F3-generation Vincozolin lineage male 11 months old rat brain

tag: tissue


title: serous ovarian cancer 43d

value: suboptimal

tag: platinum

tag: pfs (m)

tag: rec (1)


title: C. briggsae_rep3_stage5

description: C. briggsae_rep3_stage5

hyb_protocol: The hybridization and washing of the microarrays were performed following the Agilent protocol for single-channel arrays.

source_name: C. briggsae, stage5

extract_protocol: RNA was extracted from embryos using Trizol. Each sample comprised 48 individually staged embryos. Total RNA was amplified by two round of in vitro transcription (IVT)and cy3 labeled using the MessageAmpII kit (Ambion). We also added to this reaction RNA from a Spike-in kit (Agilent) that included 10 different species of RNA at various concentrations.

tag: developmental stage

value: 6th AB division


title: 14227635 - ws repet2 vs 35A2 repet2

hyb_protocol: 35A2 repet2 Cy5 / ws repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 35A2 repet2

extract_protocol: 35A2 repet2:10ug. (Qiagen_RNeasy.pdf)

tag: genotype/variation

tag: dev.stage (boyes et al. plant cell 2001)


title: serous ovarian cancer 44d


title: Olfactory bulbs_Vinclozolin_Male_biological rep9

description:
Treatment-Sex Group: OlfB-M-Vin
Marina-OlfB-Vin-M-9-011210-57.CEL
Olfactory bulb from F3-generation Vincozolin lineage male 11 months old rat brain

tag: rna prep date

tag: scan date

tag: animal id

tag: vin/con rats dyad group

tag: strain

tag: gender

tag: generation


title: serous ovarian cancer 41d2R

tag: grading

tag: Stage

value: IIIb

tag: surgery status

value: optimal

tag: taxane


title: Olfactory bulbs_Control_Female_biological rep4

description:
Treatment-Sex Group: OlfB-F-Con
Marina-OlfB-Con-Fm-4-011310-64.CEL
Olfactory bulb from F3-generation control lineage (vehicle) female 11 months old rat brain

source_name: Olfactory bulb from F3-generation control lineage (vehicle) female rat brain

tag: lineage

tag: tissue

tag: age


title: 14227627 - ws repet4 vs 35A2 repet4

hyb_protocol: 35A2 repet4 Cy5 / ws repet4 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 35A2 repet4

extract_protocol: 35A2 repet4:10ug. (Qiagen_RNeasy.pdf)

tag: ecotype


title: Olfactory bulbs_Vinclozolin_Male_biological rep11

description:
Treatment-Sex Group: OlfB-M-Vin
Marina-OlfB-Vin-M-11-011210-59.CEL
Olfactory bulb from F3-generation Vincozolin lineage male 11 months old rat brain


title: C. briggsae_rep3_stage7

description: C. briggsae_rep3_stage7

source_name: C. briggsae, stage7

tag: developmental stage

value: Ventral enclosure stage


title: C. briggsae_rep3_stage2

description: C. briggsae_rep3_stage2

source_name: C. briggsae, stage2

value: E-cell division


title: C. briggsae_rep3_stage6

description: C. briggsae_rep3_stage6

source_name: C. briggsae, stage6

value: 7th AB division


title: C. briggsae_rep3_stage1

description: C. briggsae_rep3_stage1

source_name: C. briggsae, stage1

value: 4-cell stage


title: C. briggsae_rep2_stage10

description: C. briggsae_rep2_stage10

source_name: C. briggsae, stage10

value: Juvenile L1 larvae


title: C. briggsae_rep3_stage4

description: C. briggsae_rep3_stage4

source_name: C. briggsae, stage4

value: 5th AB division


title: 14227632 - 352.7 repet1 vs ws repet1

hyb_protocol: ws repet1 Cy5 / 352.7 repet1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: genotype/variation

tag: dev.stage (boyes et al. plant cell 2001)

extract_protocol: 352.7 repet1:10ug. (Qiagen_RNeasy.pdf)


title: serous ovarian cancer 4d

source_name: high-grade serous ovarian cancer

value: IIIc

tag: platinum

tag: pfs (m)

tag: rec (1)

tag: os (m)

tag: death (1)


title: serous ovarian cancer 38d


title: serous ovarian cancer 368d2

value: IV


title: 14227636 - ws repet2 vs 352.7 repet2

hyb_protocol: 352.7 repet2 Cy5 / ws repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 352.7 repet2:10ug. (Qiagen_RNeasy.pdf)


title: serous ovarian cancer 367d


title: Olfactory bulbs_Vinclozolin_Male_biological rep8

description:
Treatment-Sex Group: OlfB-M-Vin
Marina-OlfB-Vin-M-8-011210-56.CEL
Olfactory bulb from F3-generation Vincozolin lineage male 11 months old rat brain

source_name: Olfactory bulb from F3-generation Vincozolin lineage male rat brain

tag: rna prep date

tag: scan date

tag: animal id

tag: vin/con rats dyad group

tag: strain

value: Sprague-Dawley rat

tag: gender

value: Male

tag: generation

value: Vincozolin

value: Olfactory bulbs

value: 11 months


title: Olfactory bulbs_Vinclozolin_Male_biological rep7

description:
Treatment-Sex Group: OlfB-M-Vin
Marina-OlfB-Vin-M-7-011210-55.CEL
Olfactory bulb from F3-generation Vincozolin lineage male 11 months old rat brain

tag: lineage

tag: tissue

tag: age


title: Olfactory bulbs_Control_Male_biological rep12

description:
Treatment-Sex Group: OlfB-M-Con
Marina-OlfB-Con-M-12-011210-54.CEL
Olfactory bulb from F3-generation control lineage (vehicle) male 11 months old rat brain

source_name: Olfactory bulb from F3-generation control lineage (vehicle) male rat brain

value: control (vehicle)


title: lymphoma metastasis 4

city: Changsha

first: luo

last: zhaohui

state: Hunan

address: 110 Xiangya Road

country: China

institute: Cancer  Research  Institute

description:
lymphoma metastasis of nasopharyngeal carcinoma
SAMPLE 22

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: lymphoma metastasis 4

label_protocol: Standard Illumina label protocol

extract_protocol: the sanple were RNA was extracted with Trizol reagent

treatment_protocol: the Nasopharyngeal carcinoma samples and the normal sanmples were  protected in the Liquid nitrogen. Laser capture microdissection was used to separate the cancer tissues from the normal tissues. Samples were first frozen-sectioned by using LEICA CM 1900 cryomicrotome. Phase contrast images were acquired using LEICA CTR 6500.

tag: disease state


title: lymphoma metastasis 3

description:
lymphoma metastasis of nasopharyngeal carcinoma
SAMPLE 21

source_name: lymphoma metastasis 3


title: lymphoma metastasis 1

description:
lymphoma metastasis of nasopharyngeal carcinoma
SAMPLE 19

source_name: lymphoma metastasis 1


title: serous ovarian cancer 365d

value: high-grade serous ovarian cancer tumor

tag: grading

tag: Stage

tag: surgery status

tag: taxane


title: lymphoma metastasis 2

description:
lymphoma metastasis of nasopharyngeal carcinoma
SAMPLE 20

source_name: lymphoma metastasis 2


title: 14227734 - 352.7 repet3 vs ws repet3

hyb_protocol: ws repet3 Cy5 / 352.7 repet3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: ws repet3

extract_protocol: ws repet3:10ug. (Qiagen_RNeasy.pdf)

tag: ecotype

value: wassilewskija

tag: genotype/variation

value: normal

tag: dev.stage (boyes et al. plant cell 2001)

extract_protocol: 352.7 repet3:10ug. (Qiagen_RNeasy.pdf)

value: mutant (ws)


title: Olfactory bulbs_Control_Male_biological rep10

description:
Treatment-Sex Group: OlfB-M-Con
Marina-OlfB-Con-M-10-011210-52.CEL
Olfactory bulb from F3-generation control lineage (vehicle) male 11 months old rat brain

tag: rna prep date

tag: scan date


title: serous ovarian cancer 366d

value: suboptimal

tag: platinum

tag: pfs (m)

tag: rec (1)

tag: os (m)

tag: death (1)


title: C. briggsae_rep2_stage9

description: C. briggsae_rep2_stage9

source_name: C. briggsae, stage9

tag: developmental stage

value: Movement


title: Olfactory bulbs_Control_Male_biological rep9

description:
Treatment-Sex Group: OlfB-M-Con
Marina-OlfB-Con-M-9-011210-51.CEL
Olfactory bulb from F3-generation control lineage (vehicle) male 11 months old rat brain

tag: animal id

tag: vin/con rats dyad group

tag: strain

tag: gender

tag: generation

tag: lineage

tag: tissue

tag: age


title: serous ovarian cancer 362d

tag: grading

tag: Stage

tag: surgery status

tag: taxane


title: C. briggsae_rep2_stage6

description: C. briggsae_rep2_stage6

value: 7th AB division


title: serous ovarian cancer 360d

tag: platinum

tag: pfs (m)


title: C. briggsae_rep2_stage7

description: C. briggsae_rep2_stage7

value: Ventral enclosure stage


title: IV stage 4

description:
nasopharyngeal carcinoma of IV stage
SAMPLE 18

source_name: IV stage 4

tag: disease state

value: nasopharyngeal carcinoma


title: Olfactory bulbs_Control_Male_biological rep11

description:
Treatment-Sex Group: OlfB-M-Con
Marina-OlfB-Con-M-11-011210-53.CEL
Olfactory bulb from F3-generation control lineage (vehicle) male 11 months old rat brain

tag: rna prep date

tag: scan date


title: C. briggsae_rep2_stage3

description: C. briggsae_rep2_stage3

source_name: C. briggsae, stage3

tag: developmental stage

value: 4th AB division


title: 14227628 - ws repet4 vs 352.7 repet4

description: What are the transcriptional adaptations induced by genetically modifying vacuolar nitrate transport

hyb_protocol: 352.7 repet4 Cy5 / ws repet4 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 352.7 repet4:10ug. (Qiagen_RNeasy.pdf)

tag: ecotype

tag: genotype/variation

tag: dev.stage (boyes et al. plant cell 2001)

source_name: ws repet4

extract_protocol: ws repet4:10ug. (Qiagen_RNeasy.pdf)


title: serous ovarian cancer 36d

extract_protocol: Total RNA was extracted from tissue samples using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's recommendations. RNA was examined with a 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA, USA) using an RNA 6000 Nano LabChip (Agilent Technologies)

value: IV

value: optimal

tag: rec (1)

tag: os (m)

tag: death (1)


title: IV stage 3

description:
nasopharyngeal carcinoma of IV stage
SAMPLE 17

source_name: IV stage 3


title: serous ovarian cancer 363d

tag: tissue

value: IIIc


title: C. briggsae_rep2_stage5

description: C. briggsae_rep2_stage5

source_name: C. briggsae, stage5

value: 6th AB division


title: IV stage 2

description:
nasopharyngeal carcinoma of IV stage
SAMPLE16

source_name: IV stage 2


title: C. briggsae_rep2_stage4

description: C. briggsae_rep2_stage4

value: 5th AB division


title: Olfactory bulbs_Control_Male_biological rep8

description:
Treatment-Sex Group: OlfB-M-Con
Marina-OlfB-Con-M-8-011210-50.CEL
Olfactory bulb from F3-generation control lineage (vehicle) male 11 months old rat brain

extract_protocol: RNA was isolated from individual animal tissue homogenate in 750 ul Trizol™ reagent (Invitrogen, USA), according to manufacturer’s instructions.

tag: animal id

tag: vin/con rats dyad group

tag: strain

value: Sprague-Dawley rat

tag: gender

value: Male

tag: generation

tag: lineage

value: Olfactory bulbs

tag: age

value: 11 months


title: IV stage 1

description:
nasopharyngeal carcinoma of IV stage
SAMPLE 15

source_name: IV stage 1

tag: disease state

tag: Stage


title: Olfactory bulbs_Control_Male_biological rep7

description:
Treatment-Sex Group: OlfB-M-Con
Marina-OlfB-Con-M-7-011210-49.CEL
Olfactory bulb from F3-generation control lineage (vehicle) male 11 months old rat brain

tag: rna prep date

tag: scan date

value: control (vehicle)


title: serous ovarian cancer 358d

value: high-grade serous ovarian cancer tumor

tag: grading

tag: surgery status

tag: taxane

tag: platinum

tag: pfs (m)


title: III stage 4

description:
nasopharyngeal carcinoma of III stage
SAMPLE 14

source_name: III stage 4

value: III


title: Hippocampus_Vinclozolin_Female_biological rep5

description:
Treatment-Sex Group: Hip-F-Vin
Marina-Hipp-Vin-FM-5-112509-47.CEL
Hippocampus from F3-generation Vincozolin lineage female 11 months old rat brain

source_name: Hippocampus from F3-generation Vincozolin lineage female rat brain

value: Female

value: Vincozolin

tag: tissue

value: Hippocampus


title: Hippocampus_Vinclozolin_Female_biological rep4

description:
Treatment-Sex Group: Hip-F-Vin
Marina-Hipp-Vin-FM-4-112509-46.CEL
Hippocampus from F3-generation Vincozolin lineage female 11 months old rat brain

tag: animal id


title: Hippocampus_Vinclozolin_Female_biological rep3

description:
Treatment-Sex Group: Hip-F-Vin
Marina-Hipp-Vin-FM-3-112509-45.CEL
Hippocampus from F3-generation Vincozolin lineage female 11 months old rat brain

tag: vin/con rats dyad group


title: C. briggsae_rep1_stage10

description: C. briggsae_rep1_stage10

source_name: C. briggsae, stage10

tag: developmental stage

value: Juvenile L1 larvae


title: serous ovarian cancer 357d

source_name: high-grade serous ovarian cancer

value: suboptimal

tag: rec (1)

tag: os (m)

tag: death (1)


title: serous ovarian cancer 356d

value: IV


title: serous ovarian cancer 355d

value: optimal


title: C. briggsae_rep2_stage1

description: C. briggsae_rep2_stage1

source_name: C. briggsae, stage1

value: 4-cell stage


title: Hippocampus_Vinclozolin_Female_biological rep2

description:
Treatment-Sex Group: Hip-F-Vin
Marina-Hipp-Vin-FM-2-112509-44.CEL
Hippocampus from F3-generation Vincozolin lineage female 11 months old rat brain

tag: strain

tag: gender

tag: generation

tag: lineage

tag: age


title: C. briggsae_rep2_stage2

description: C. briggsae_rep2_stage2

source_name: C. briggsae, stage2

value: E-cell division


title: III stage 3

description:
nasopharyngeal carcinoma of III stage
SAMPLE 13

source_name: III stage 3

tag: disease state

value: nasopharyngeal carcinoma

tag: Stage


title: C. briggsae_rep1_stage9

description: C. briggsae_rep1_stage9

value: Movement


title: Hippocampus_Vinclozolin_Female_biological rep1

description:
Treatment-Sex Group: Hip-F-Vin
Marina-Hipp-Vin-FM-1-112509-43.CEL
Hippocampus from F3-generation Vincozolin lineage female 11 months old rat brain

tag: rna prep date

tag: scan date

value: Sprague-Dawley rat


title: C. briggsae_rep1_stage8

description: C. briggsae_rep1_stage8

source_name: C. briggsae, stage8

value: Comma stage


title: III stage 1

description:
nasopharyngeal carcinoma of III stage
SAMPLE 11

source_name: III stage 1


title: Hippocampus_Control_Female_biological rep6

description:
Treatment-Sex Group: Hip-F-Con
Marina-Hipp-Con-FM-6-112509-42.CEL
Hippocampus from F3-generation control lineage (vehicle) female 11 months old rat brain

source_name: Hippocampus from F3-generation control lineage (vehicle) female rat brain

value: 11 months


title: III stage 2

description:
nasopharyngeal carcinoma of III stage
SAMPLE12

source_name: III stage 2


title: I-II stage 4

description: SAMPLE 10

source_name: I-II stage 4

value: I-II


title: C. briggsae_rep1_stage7

description: C. briggsae_rep1_stage7

source_name: C. briggsae, stage7

value: Ventral enclosure stage


title: Hippocampus_Control_Female_biological rep5

description:
Treatment-Sex Group: Hip-F-Con
Marina-Hipp-Con-FM-5-112509-41.CEL
Hippocampus from F3-generation control lineage (vehicle) female 11 months old rat brain

value: control (vehicle)


title: serous ovarian cancer 353d

value: high-grade serous ovarian cancer tumor

tag: grading

tag: surgery status

tag: taxane

tag: platinum

tag: pfs (m)


title: Olfactory bulbs_Control_Female_biological rep2

description:
Treatment-Sex Group: OlfB-F-Con
Marina-OlfB-Con-Fm-2-011310-62.CEL
Olfactory bulb from F3-generation control lineage (vehicle) female 11 months old rat brain

source_name: Olfactory bulb from F3-generation control lineage (vehicle) female rat brain

tag: animal id

tag: vin/con rats dyad group

value: Female

tag: tissue

value: Olfactory bulbs


title: I-II stage 2

description: SAMPLE 8

source_name: I-II stage 2


title: serous ovarian cancer 352d

value: IIIc

tag: rec (1)

tag: os (m)

tag: death (1)


title: serous ovarian cancer 347d

value: suboptimal


title: Hippocampus_Control_Female_biological rep4

description:
Treatment-Sex Group: Hip-F-Con
Marina-Hipp-Con-FM-4-112509-40.CEL
Hippocampus from F3-generation control lineage (vehicle) female 11 months old rat brain

tag: strain

tag: gender

tag: generation

tag: lineage

value: Hippocampus


title: serous ovarian cancer 350d

tag: Stage


title: C. briggsae_rep1_stage5

description: C. briggsae_rep1_stage5

source_name: C. briggsae, stage5

tag: developmental stage

value: 6th AB division


title: C. briggsae_rep1_stage6

description: C. briggsae_rep1_stage6

source_name: C. briggsae, stage6

value: 7th AB division


title: I-II stage 3

description: SAMPLE 9

source_name: I-II stage 3

tag: disease state


title: serous ovarian cancer 348d2

tag: grading

tag: surgery status

value: optimal


title: serous ovarian cancer 346d

tag: taxane

tag: platinum


title: C. briggsae_rep1_stage3

description: C. briggsae_rep1_stage3

source_name: C. briggsae, stage3

value: 4th AB division


title: C. briggsae_rep1_stage2

description: C. briggsae_rep1_stage2

value: E-cell division


title: serous ovarian cancer 342d

tag: pfs (m)


title: I-II stage 1

description: SAMPLE 7

source_name: I-II stage 1

value: nasopharyngeal carcinoma


title: Hippocampus_Control_Female_biological rep3

description:
Treatment-Sex Group: Hip-F-Con
Marina-Hipp-Con-FM-3-112509-39.CEL
Hippocampus from F3-generation control lineage (vehicle) female 11 months old rat brain

tag: rna prep date

tag: scan date

tag: animal id

tag: vin/con rats dyad group

value: Sprague-Dawley rat

tag: age


title: C. briggsae_rep1_stage4

description: C. briggsae_rep1_stage4

source_name: C. briggsae, stage4

value: 5th AB division


title: Hippocampus_Vinclozolin_Male_biological rep12

description:
Treatment-Sex Group: Hip-M-Vin
Marina-Hipp-Vin-M-12-112409-36.CEL
Hippocampus from F3-generation Vincozolin lineage male 11 months old rat brain

source_name: Hippocampus from F3-generation Vincozolin lineage male rat brain

tag: strain

value: Male

value: Vincozolin

tag: tissue

value: 11 months


title: C. briggsae_rep1_stage1

description: C. briggsae_rep1_stage1

source_name: C. briggsae, stage1

value: 4-cell stage


title: normal 5

description:
normal healthy nasopharyngeal epithelial
SAMPLE 5

source_name: normal 5


title: C. briggsae_rep3_stage3

description: C. briggsae_rep3_stage3


title: normal 4

description:
normal healthy nasopharyngeal epithelial
SAMPLE 4

source_name: normal 4


title: Hippocampus_Vinclozolin_Male_biological rep11

description:
Treatment-Sex Group: Hip-M-Vin
Marina-Hipp-Vin-M-11-112409-35.CEL
Hippocampus from F3-generation Vincozolin lineage male 11 months old rat brain

tag: gender

tag: generation


title: normal 6

description:
normal healthy nasopharyngeal epithelial
SAMPLE 6

source_name: normal 6


title: Hippocampus_Vinclozolin_Male_biological rep10

description:
Treatment-Sex Group: Hip-M-Vin
Marina-Hipp-Vin-M-10-112409-34.CEL
Hippocampus from F3-generation Vincozolin lineage male 11 months old rat brain

tag: lineage


title: 144 hr Biofilm 3

city: Leeds

first: Victoria

last: Ryder

state: West Yorkshire

address: Clarendon way

department: Faculty of Biological Sciences

country: United Kingdom

institute: University of Leeds

description:
61978405_532
144B3
This is a S. aureus SH1000 sample grown as a biofilm for 144 hrs, this is the third of 3 biological replicates

hyb_protocol: Performed by Roche Nimblegen (Madison, WI, USA) as standard

data_processing: The normalized data are processed using quantile normalization (Bolstad et al., 2003, Bioinformatics, 19:185), and the Robust Multichip Average (RMA) algorithm (Irizarry et al., 2003, Nucleic Acids Res. 31: e15 and Irizarry et al., 2003, Biostatistics 4:249).

organism: Staphylococcus aureus

source_name: Biofilm growth for 144 hours

growth_protocol: Planktonic cultures were grown for 18 hrs at 37°C with shaking. Biofilm cultures were grown on mixed cellulose-ester membrane filter disks (25 mm diameter, 0.22 μm pore size) To promote biofilm formation, disks were immersed in 4% v/v normal pooled human plasma diluted in 0.05 M carbonate buffer and incubated at 4°C overnight prior to use. Plasma-soaked disks were inoculated with bacteria, placed on brain heart infusion agar, and incubated at 37°C. Once biofilms were established, loosely associated cells were removed from the disks by gentle agitation in sterile saline. Adherent cells were harvested from the biofilm by incubation of the disks for 30 mins at 37°C in the presence of cellulase (1 mg/ml in 0.05 M citrate buffer). In both cases, detached cells were then washed in sterile saline, harvested by centrifugation for 10 mins at 5000 x g, and resuspended in sterile saline.

extract_protocol: Planktonic cultures of SH1000 were combined with 2 volumes of RNAprotect Bacteria Reagent and the cells harvested by centrifugation at 5000 x g. Biofilm cultures of SH1000 were submerged in RNAprotect, detached with buffered cellulase and then centrifuged at 5000 x g to pellet the cells. Biofilm cell pellets were washed in RNAprotect and re-centrifuged. Cell pellets were stored at -80°C until required. Pellets were thawed at room temperature, washed in 10 ml of TE buffer, and resuspended in 1 ml of TE buffer containing 200 µg lysostaphin/ ml and incubated at 37°C for 60 90 mins. Proteinase K (40 µg/ml) was then added to the mixture and incubated for 10 mins at room temperature. Total RNA was purified from these samples using the RNeasy Midi kit (Qiagen) following the manufacturer’s instructions, including an on-column DNase digestion using the RNase-free DNase kit (Qiagen). cDNA synthesis, cDNA labelling, hybridisation and quantification of gene expression were performed by Roche Nimblegen (Madison, USA) using 4x72K multiplex microarrays. Of the 2892 predicted protein coding open reading frames of the S. aureus NCTC8325 genome, 2887 were represented on the microarrays. Data were analysed using ArrayStar™ (DNASTAR, Madison, USA), and genes were considered differentially regulated if they exhibited ≥2-fold up- or down-regulation. Transcriptional profiling was performed for 3 biological replicates.

tag: growth condition

value: Biofilm_144 hrs


title: serous ovarian cancer 335d

source_name: high-grade serous ovarian cancer

value: high-grade serous ovarian cancer tumor

tag: Stage

tag: rec (1)

tag: os (m)

tag: death (1)


title: Hippocampus_Vinclozolin_Male_biological rep9

description:
Treatment-Sex Group: Hip-M-Vin
Marina-Hipp-Vin-M-9-112409-33.CEL
Hippocampus from F3-generation Vincozolin lineage male 11 months old rat brain


title: normal 3

description:
normal healthy nasopharyngeal epithelial
SAMPLE 3

source_name: normal 3

tag: disease state


title: normal 2

description:
normal healthy nasopharyngeal epithelial
SAMPLE 2

source_name: normal 2


title: 144 hr Biofilm 2

description:
61994905_532
144B2
This is a S. aureus SH1000 sample grown as a biofilm for 144 hrs, this is the second of 3 biological replicates

scan_protocol: Performed by Roche Nimblegen (Madison, WI, USA) as standard


title: normal 1

description:
normal healthy nasopharyngeal epithelial
SAMPLE 1

source_name: normal 1


title: 144 hr Biofilm 1

description:
61995005_532
144B1
This is a S. aureus SH1000 sample grown as a biofilm for 144 hrs, this is the first of 3 biological replicates

label_protocol: Performed by Roche Nimblegen (Madison, WI, USA) as standard


title: 48 hr Biofilm 3

description:
61994805_532
48B3
This is a S. aureus SH1000 sample grown as a biofilm for 48 hrs, this is the third of 3 biological replicates

source_name: Biofilm growth for 48 hours

value: Biofilm_48 hrs


title: Hippocampus_Vinclozolin_Male_biological rep8

description:
Treatment-Sex Group: Hip-M-Vin
Marina-Hipp-Vin-M-8-112409-32.CEL
Hippocampus from F3-generation Vincozolin lineage male 11 months old rat brain


title: serous ovarian cancer 337d

tag: grading

value: IV

tag: surgery status

value: suboptimal

tag: taxane

tag: platinum

tag: pfs (m)


title: serous ovarian cancer 333d2

value: IIIc


title: 48 hr Biofilm 2

description:
61979405_532
48B2
This is a S. aureus SH1000 sample grown as a biofilm for 48 hrs, this is the second of 3 biological replicates


title: serous ovarian cancer 331d


title: C. briggsae_rep2_stage8

description: C. briggsae_rep2_stage8

source_name: C. briggsae, stage8

tag: developmental stage

value: Comma stage


title: Hippocampus_Control_Male_biological rep12

description:
Treatment-Sex Group: Hip-M-Con
Marina-Hipp-Con-M-12-112409-30.CEL
Hippocampus from F3-generation control lineage (vehicle) male 11 months old rat brain

source_name: Hippocampus from F3-generation control lineage (vehicle) male rat brain

tag: rna prep date

tag: scan date

tag: animal id

tag: vin/con rats dyad group

tag: strain

value: control (vehicle)

value: Hippocampus

tag: age


title: Hippocampus_Vinclozolin_Male_biological rep7

description:
Treatment-Sex Group: Hip-M-Vin
Marina-Hipp-Vin-M-7-112409-31.CEL
Hippocampus from F3-generation Vincozolin lineage male 11 months old rat brain

tag: gender

tag: generation

tag: lineage

tag: tissue


title: serous ovarian cancer 330d

tag: Stage

tag: rec (1)

tag: os (m)

tag: death (1)


title: 48 hr Biofilm 1

description:
61979205_532
48B1
This is a S. aureus SH1000 sample grown as a biofilm for 48 hrs, this is the first of 3 biological replicates

tag: growth condition


title: Hippocampus_Control_Male_biological rep11

description:
Treatment-Sex Group: Hip-M-Con
Marina-Hipp-Con-M-11-112409-29.CEL
Hippocampus from F3-generation control lineage (vehicle) male 11 months old rat brain


title: E_faecalis_OG1RF_wild-type_N+Fe_medium_rep2

city: Rancagua

first: Mauricio

middle: Alejandro

last: Latorre

state: VI

address: Av. Libertador Bernardo OHiggins 611

department: ICI

country: Chile

institute: Universidad de OHiggins

description:
GEO_GLOPEZ2011_Efae_V583_EXP_growth_medium_N_Fe_strain_E_faecalis_OG1RF_wild-type_rep2
This sample is of wild-type Enterococcus faecalis OG1RF exposed to Fe treatment, correspond to the second of two biological replicates used in this experiment, each from separate cultures.
The Nimblegen platform is based on Enterococcus faecalis V583 (wild type strain). We made a cross hybridation.
SAMPLE 4

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

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

data_processing: All data was processes automatically using DNASTAR software Array star 3.0. See www.dnastar.com.

organism: Enterococcus faecalis OG1RF

source_name: iron sample_N medium gowth with 0.5 mM Fe-NTA

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

growth_protocol: Enterococcus faeclis OG1RF wild-type was grown to mid-log phase (O.D600nm 1.0), aerobically estandar condition at 37°C in N medium (Peptone 1 % (Difco), yeast extract 0.5 % (Difco), Na2HPO4 1 % (Merck) and glucose 1 % (Oxoid), Odermatt A, Solioz M. J Biol Chem 1995, 270(9).  In treatment cultures, strain was gowth at the same condition by adding Fe (Fe-NTA 0.5 mM) to the control medium.

extract_protocol: The RNA was extracted using a Qiagen RNeasy mini kit (Qiagen). Residual contaminating genomic DNA was removed with RQ1 RNase-free DNase (Promega) treatment according to the manufacturer’s protocol. The integrity of the RNA was assessed by gel electrophoresis.

treatment_protocol: All Fe-treated cells were exposed for 6 hours prior to harvesting (at mid-log phase, OD600nm 1.0); the untreated cells were collected simultaneously.

tag: genotype

value: wild type

tag: phenotype

value: normal


title: Planktonic 3

description:
61978305_532
P3
This is a S. aureus SH1000 sample grown planktonically for 18 hrs, this is the third of 3 biological replicates

source_name: Planktonic growth for 18 hours

value: Planktonic_18 hrs


title: E_faecalis_OG1RF_wild-type_N+Fe_medium_rep1

description:
GEO_GLOPEZ2011_Efae_V583_EXP_growth_medium_N_Fe_strain_E_faecalis_OG1RF_wild-type_rep1
This sample is of wild-type Enterococcus faecalis OG1RF exposed to Fe treatment, correspond to the first of two biological replicates used in this experiment, each from separate cultures.
The Nimblegen platform is based on Enterococcus faecalis V583 (wild type strain). We made a cross hybridation.
SAMPLE 3


title: E_faecalis_OG1RF_wild-type_N_medium_rep2

description:
GEO_GLOPEZ2011_Efae_V583_EXP_growth_medium_N_strain_E_faecalis_OG1RF_wild-type_rep2
This sample is of wild-type Enterococcus faecalis OG1RF, correspond to the second of two biological replicates used in this experiment, each from separate cultures.
The Nimblegen platform is based on Enterococcus faecalis V583 (wild type strain). We made a cross hybridation.
SAMPLE 2

source_name: controls sample_N medium growth


title: serous ovarian cancer 340d

hyb_protocol: Cy3-labeled cRNAs (1.65 µg) were hybridized for 17 hours at 65°C to an Agilent Whole Human Genome Oligo Microarray in a rotating Agilent hybridization oven.

tag: grading

tag: surgery status

tag: taxane

tag: platinum

tag: pfs (m)


title: serous ovarian cancer 323d

value: optimal


title: serous ovarian cancer 327d


title: Hippocampus_Control_Male_biological rep9

description:
Treatment-Sex Group: Hip-M-Con
Marina-Hipp-Con-M-9-120909-27.CEL
Hippocampus from F3-generation control lineage (vehicle) male 11 months old rat brain

tag: rna prep date

tag: scan date

tag: animal id

tag: vin/con rats dyad group

tag: strain

value: Sprague-Dawley rat

value: Male

tag: age


title: Planktonic 2

description:
61979505_532
P2
This is a S. aureus SH1000 sample grown planktonically for 18 hrs, this is the second of 3 biological replicates


title: Planktonic 1

description:
61978205_532
P1
This is a S. aureus SH1000 sample grown planktonically for 18 hrs, this is the first of 3 biological replicates


title: serous ovarian cancer 320d2

tag: tissue

tag: Stage

value: IIIb

tag: rec (1)


title: Hippocampus_Control_Male_biological rep10

description:
Treatment-Sex Group: Hip-M-Con
Marina-Hipp-Con-M-10-112409-28.CEL
Hippocampus from F3-generation control lineage (vehicle) male 11 months old rat brain

tag: gender

tag: generation

tag: lineage

value: 11 months


title: serous ovarian cancer 310d

tag: grading

tag: os (m)

tag: death (1)


title: serous ovarian cancer 318d

tag: surgery status

tag: taxane

tag: platinum


title: Amygdaloid nuclei_Vinclozolin_Female_biological rep5

description:
Treatment-Sex Group: Amy-F-Vin
Marina-Amy-Vin-Fm-5_111709-23(1D).CEL
Amygdaloid nuclei from F3-generation Vincozolin lineage female 11 months old rat brain

source_name: Amygdaloid nuclei from F3-generation Vincozolin lineage female rat brain

tag: rna prep date

tag: scan date

value: Female

value: Vincozolin

value: Amygdaloid nuclei


title: PA01_cell_37℃_rep3

city: Shanghai

first: daqiang

last: wu

address: 800 Dongchuan Road

department: School of life science and biotechnology

institute: Shanghaijiaotong University

description: gene expression at 37℃

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Agilent technologies, Santa Clara, CA, US)Hybridization Oven (Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes with Gene Expression Wash Buffer Kit( Agilent technologies, Santa Clara, CA, US), Stabilization and Drying Solution (Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions。

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent technologies, Santa Clara, CA, US) using default parameters.

organism: Pseudomonas aeruginosa

source_name: Cells, 37℃,replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using the  Low RNA Input Linear Amplification  kit (Agilent technologies, Santa Clara, CA, US) according to the manufacturer's instructions,and purified by RNeasy mini kit ( QIAGEN, GmBH, Germany).

growth_protocol: Cells were grown to OD600=5.0-6.0 (late exponential phase) in LB medium at 28℃ and 37℃, respectively.

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen,Carlsbad, CA, USA).

tag: growth phase

value: late exponential phase

tag: temperature


title: Hippocampus_Control_Male_biological rep7

description:
Treatment-Sex Group: Hip-M-Con
Marina-Hipp-Con-M-7-112409-25.CEL
Hippocampus from F3-generation control lineage (vehicle) male 11 months old rat brain

hyb_protocol: Following fragmentation, ssDNA were hybridized  on Affymetrix Rat Gene 1.0 ST Array according to standard Affymetrix protocol. Chips were washed and stained in the Affymetrix Fluidics Station 450.

tag: animal id

tag: vin/con rats dyad group

tag: strain

tag: age


title: serous ovarian cancer 319d

tag: tissue

value: high-grade serous ovarian cancer tumor

tag: Stage

value: suboptimal

tag: pfs (m)

tag: rec (1)


title: PA01_cell_37℃_rep2

description: gene expression at 37℃

source_name: Cells, 37℃,replicate 2


title: Amygdaloid nuclei_Vinclozolin_Female_biological rep6

description:
Treatment-Sex Group: Amy-F-Vin
Marina-Amy-Vin-Fm-6_111709-24(2A).CEL
Amygdaloid nuclei from F3-generation Vincozolin lineage female 11 months old rat brain

tag: gender

tag: generation

tag: lineage


title: Amygdaloid nuclei_Vinclozolin_Female_biological rep4

description:
Treatment-Sex Group: Amy-F-Vin
Marina-Amy-Vin-Fm-4_111709-22(3A).CEL
Amygdaloid nuclei from F3-generation Vincozolin lineage female 11 months old rat brain


title: PA01_cell_37℃_rep1

description: gene expression at 37℃

source_name: Cells, 37℃,replicate 1


title: serous ovarian cancer 307d

tag: grading

value: IIIc

tag: surgery status

tag: taxane

tag: os (m)

tag: death (1)