title: SKOV3

description: Baseline profiling of SKOV3 cells

source_name: SKOV3 cells

tag: cell line


title: PEO4

status: Public on Jul 01 2012

type: RNA

city: Tampa

first: Steven

last: Eschrich

state: FL

address: 12902 Magnolia Drive

department: Biostatistics & Bioinformatics

country: USA

institute: Moffitt Cancer Center

description: Baseline profiling of PEO4 cells

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques.  Arrays are hybridized for 18 hours at 45C with vigorous mixing.   Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed.  Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Data were processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260).

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: PEO4 cells

label_protocol: The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin.  After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency.  The labeled molecules are biotinylated-cRNA.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation.  Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.

tag: cell type

value: ovarian cancer cells


title: Ejaculate resulting in oocyte fertilization, F43

city: 20246 Hamburg

first: Andrej-Nikolai

last: Spiess

address: Martinistr. 52

department: Andrology

country: Germany

institute: University Hospital Hamburg-Eppendorf

hyb_protocol: Hybridization was conducted for 20h at 37°C, and arrays were washed in 1x TNT (10 min, RT) and 1x TNT (60 min, 46°C). Staining with Cy5-Streptavidin was done for 30 min at RT. Then, arrays were washed 2 times with 1x TNT for 10 min and 0.2x SSPE for 30s. They were spin-dried in a centrifuge at 2000 rpm for 2 min.

scan_protocol: Scanning was done on a ScanArray Gx Scanner (Perkin Elmer) at PMT 70/LP 90% setting and 5um resolution. Images were acquired with the ScanArray Express 3.0 software (Perkin Elmer).

data_processing: Scan images were converted to raw values by the CodeLink Expression analysis software (GE Healthcare, USA). Genes with lower than 5th percentile expression values over all samples were removed. Normalization was by quantile normalization using the Bioconducter package 'affy'.

label: biotin

source_name: ejaculate after 30 min liquefaction

label_protocol: 50 - 500 ng total RNA were amplified with the MessageAmp III Kit (Ambion, USA), and Biotin-UTP was incorporated as a label.

extract_protocol: RNA was extracted from the ejaculates by a specially designed two-fold genomic DNA pre-elimination protocol (Rneasy Micro). Details are to be found under http://www.dr-spiess.de/supp/MHRCappallo2011/RNA.pdf.

treatment_protocol: Human ejaculates were liquefied for 30 min at 37°C, and an aliquot of 1 mL was washed once by centrifugation in PBS (500 g).

tag: tissue

value: ejaculate

tag: ivf outcome

value: oocyte fertilization

tag: motility (a+b) [%]

tag: ejaculate volume

tag: concentration [10e6/ml]

tag: oocytes in metaphase ii

tag: age of woman [years]

tag: fertilisation ratio [%] (2pn/mii)

tag: cumulative embryo score

tag: pregnancies


title: PEO1

description: Baseline profiling of PEO1 cells

source_name: PEO1 cells


title: Ejaculate resulting in oocyte fertilization, F44


title: 14269056 - Mock 12h RB2 vs prgh 12h RB2

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: What is the transcriptomic reprogramming after Salmonella infection, What is the importance of the T3SS in the plant infection, Are there differences in gene expression between the 2 bacterial strains? What are the functions of these genes,

hyb_protocol: prgh 12h RB2 Cy5 / Mock 12h RB2 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: Experiments were designed with the statistics group of the Unité de Recherche en Génomique Végétale. 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. Differential analysis was based on the log ratios averaged on the dye-swap: The technical replicates were averaged to get one log-ratio per biological replicat and these values were used to performed a paired t-test. A trimmed variance is calculated from spots which do not displaying extreme variance (see details in Gagnot  et al. 2008). The raw P-values were adjusted by the Bonferroni method, which controls the Family Wise Error Rate in order to keep a strong control of the false positives in a multiple-comparison context. We considered as being differentially expressed the probes with a Bonferroni P-value < 0.05.

organism: Arabidopsis thaliana

source_name: prgh 12h RB2

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: whole plant - 14 days-old Arabidopsis seedlings grown in MS/2 agar + 1% sugar (pH 5,7) in long day at 22°C were transfered in liquid MS/2 (pH 5,7) without sugar a day before treatment. 3 seedlings / well in 6 well plates with 5 ml media. The treatment consists in the addition of Salmonella Typhimurium 14028 (wild type) and St 14028 prgH mutant. Bacterial solutions were prepared in 10 mM MgCl2 and added to the media to a final concentration of OD600=0,2. Mock treatment was done by adding equal volume of MgCl2. Treatments were started at 9 am, seedlings were placed back in the rotonde and samples were taken at 2,4 6,12, and 24 hours post inoculation. Three replicates per treatment were frozen in liquid nitrogen and kept at -80°C.

extract_protocol: prgh 12h RB2:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:Salmonella mutant 12h - pathogen - pathogen infection,salmonella typhimurium:time 12hour . addition of bacterial solution (in MgCl2 10 mM) at OD600 nm= 0,2 with salmonella WT 14028 or Salmonella mutant prgh or mock treatment (MgCl2 10 mM same volume) to liquid medium.

tag: cultivar/ecotype

value: columbia mutant (col0)

tag: harvest date

tag: treatment

value: Salmonella mutant 12h,salmonella typhimurium

tag: time

source_name: Mock 12h RB2

extract_protocol: Mock 12h RB2:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:control 12h - pathogen - pathogen infection,mgcl2 10mm:time 12hour . addition of bacterial solution (in MgCl2 10 mM) at OD600 nm= 0,2 with salmonella WT 14028 or Salmonella mutant prgh or mock treatment (MgCl2 10 mM same volume) to liquid medium.

value: control 12h,mgcl2 10mm


title: OVCAR8

description: Baseline profiling of OVCAR8 cells

source_name: OVCAR8 cells


title: OVCAR4

description: Baseline profiling of OVCAR4 cells

source_name: OVCAR4 cells


title: OVCAR5

description: Baseline profiling of OVCAR5 cells

source_name: OVCAR5 cells


title: OVCAR2

description: Baseline profiling of OVCAR2 cells

source_name: OVCAR2 cells


title: patient 22

city: angers

first: frederique

last: savagner

address: 4 rue larrey

institute: Inserm

description: paired control tissue

hyb_protocol: The microarrays were first incubated at 50°C in a 50mM Ethanolamine - 100mM Tris base – SDS 0.1% solution for 15 minutes, and in a SSC 4x – 0.1% SDS solution for 15 minutes. The microarrays were then pre-hybridized 1 hour at 42°C. For each test, 20 µg of Cy3 labelled fragmented and hybridization mix resuspended samples were mixed with 20 µg of Cy5 labelled fragmented and hybridization mix resuspended reference. These mixes were denatured 2 minutes at 100°C and incubated 10 minutes at 37°C before hybridization. The microarrays were hybridized overnight at 42°C.

scan_protocol: The microarrays were scanned at 10 µM /pixel resolution with the Perkin Scanner (Waltham, MS, USA).

data_processing:
The signal intensities were extracted with the Genepix Pro 5.1 image_analysis software (Axon Instruments, Sunnyvale, CA).
The Genespring GX software (version 7) was used to analyse the microarrays data. We first applied a “per spot and per chip” lowess normalisation on the data, normalising each chip to the median of the spots (50th percentile) and each gene to the median of the replicates (cut off in raw signal = 50).

source_name: thyroid tumor

label_protocol: The Cy3 (test) and Cy5 (reference) label were performed using the Amino Allyl MessageAmp™ II CyDye™ aRNA Amplification kit (Ambion, Cambridgeshire, UK) and the RNA fragmentation Reagents kit (Ambion).

growth_protocol: Human thyroid tissues.

extract_protocol: The total RNA were extracted using a trizol® Reagent extraction procedure. RNA quality was checked on a bionalyzer and considered when RIN> 8

treatment_protocol: Human tumoral and paired control tissues.

value: Oncocytic tumor

tag: individual

value: patient 22

source_name: normal thyroid tissue

value: pool of paired control normal thyroid tissue


title: Ejaculate resulting in oocyte fertilization, F15


title: Ejaculate resulting in oocyte fertilization, F6


title: Ejaculate resulting in oocyte fertilization, F36


title: patient 21

description: paired control tissue

value: patient 21


title: 14268895 - Mock 12h RB1 vs prgh 12h RB1

hyb_protocol: prgh 12h RB1 Cy5 / Mock 12h RB1 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: prgh 12h RB1

extract_protocol: prgh 12h RB1:5ug. (Qiagen_RNeasy.pdf)

source_name: Mock 12h RB1

extract_protocol: Mock 12h RB1:5ug. (Qiagen_RNeasy.pdf)


title: 14268896 - prgh 12h RB1 vs Mock 12h RB1

hyb_protocol: Mock 12h RB1 Cy5 / prgh 12h RB1 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: OVCAR3

description: Baseline profiling of OVCAR3 cells

source_name: OVCAR3 cells

tag: cell line


title: Ejaculate resulting in oocyte fertilization, F42


title: 14269060 - Mock 6h RB2 vs prgh 6h RB2

hyb_protocol: prgh 6h RB2 Cy5 / Mock 6h RB2 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: prgh 6h RB2

extract_protocol: prgh 6h RB2:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:Salmonella mutant 6h - pathogen - pathogen infection,salmonella typhimurium:time 6hour . addition of bacterial solution (in MgCl2 10 mM) at OD600 nm= 0,2 with salmonella WT 14028 or Salmonella mutant prgh or mock treatment (MgCl2 10 mM same volume) to liquid medium.

value: Salmonella mutant 6h,salmonella typhimurium

source_name: Mock 6h RB2

extract_protocol: Mock 6h RB2:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:control 6h - pathogen - pathogen infection,mgcl2 10mm:time 6hour . addition of bacterial solution (in MgCl2 10 mM) at OD600 nm= 0,2 with salmonella WT 14028 or Salmonella mutant prgh or mock treatment (MgCl2 10 mM same volume) to liquid medium.

value: control 6h,mgcl2 10mm


title: patient 20

description: paired control tissue

value: patient 20


title: OVCAR10

description: Baseline profiling of OVCAR10 cells

source_name: OVCAR10 cells

tag: cell type


title: Ejaculate resulting in biochemical pregnancy, F13

tag: tissue

value: biochemical pregnancy


title: 14269055 - prgh 6h RB2 vs Mock 6h RB2

hyb_protocol: Mock 6h RB2 Cy5 / prgh 6h RB2 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: patient 19

description: paired control tissue

value: patient 19


title: patient 18

description: paired control tissue

value: patient 18


title: patient 17

description: paired control tissue

value: patient 17


title: 14268892 - 14028 12h RB1 vs Mock 12h RB1

hyb_protocol: Mock 12h RB1 Cy5 / 14028 12h RB1 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: 14028 12h RB1:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:Salmonella WT 12h - pathogen - pathogen infection,salmonella typhimurium:time 12hour . addition of bacterial solution (in MgCl2 10 mM) at OD600 nm= 0,2 with salmonella WT 14028 or Salmonella mutant prgh or mock treatment (MgCl2 10 mM same volume) to liquid medium.

value: Salmonella WT 12h,salmonella typhimurium


title: Ejaculate resulting in biochemical pregnancy, F33

value: ejaculate

tag: ivf outcome


title: Ejaculate resulting in pregnancy, F57

value: pregnancy

tag: motility (a+b) [%]


title: OVCA432

description: Baseline profiling of OVCA432 cells

source_name: OVCA432 cells

value: ovarian cancer cells


title: Ejaculate resulting in biochemical pregnancy, F4

source_name: ejaculate after 30 min liquefaction

tag: ejaculate volume


title: 14268893 - Mock 6h RB1 vs prgh 6h RB1

hyb_protocol: prgh 6h RB1 Cy5 / Mock 6h RB1 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: prgh 6h RB1

extract_protocol: prgh 6h RB1:5ug. (Qiagen_RNeasy.pdf)

value: columbia mutant (col0)

source_name: Mock 6h RB1

extract_protocol: Mock 6h RB1:5ug. (Qiagen_RNeasy.pdf)


title: OVCA433

description: Baseline profiling of OVCA433 cells

source_name: OVCA433 cells


title: patient 16

description: paired control tissue

value: patient 16


title: OVCA420

description: Baseline profiling of OVCA420 cells

source_name: OVCA420 cells


title: Ejaculate resulting in pregnancy, F20

tag: concentration [10e6/ml]


title: patient 15

description: paired control tissue

value: macrofollicular adenoma

value: patient 15


title: 14268714 - Mock 12h RB1 vs 14028 12h RB1

hyb_protocol: 14028 12h RB1 Cy5 / Mock 12h RB1 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: control 12h,mgcl2 10mm


title: OVCA429

description: Baseline profiling of OVCA429 cells

source_name: OVCA429 cells


title: Leaf Biological Replicate 3

type: genomic

city: Hangzhou

first: Ping

last: Yu

state: Zhejiang Province

address: 359 Tiyuchang Road

department: Rice Germplasm Evaluation

country: China

institute: China National Rice Research Institute

description: Leaf Biological replicate 3 of 3,Guang-lu-ai 4(test) vsNipponbare(control)

hyb_protocol: labeled samples were co-hybridized with hybridization system(NimbleGen) according to the NimbleGen`s CGH user`s guide(see manufacture`s user guide)

scan_protocol: The arrays were scanned using MS200 scanner(NimbleGen) with 2µm resolution according to the NimbleGen`s CGH user`s guide(see manufacture`s user guide)

data_processing:
Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.5 CGH data extraction and analysis.
Fluorescence intensity data were normalized with qspline algorithm and ratio data were analyzed with the circular binary segmentation algorithm. Copy number variation calls were made if the averaged Log2 ratio of a segment was shifted by 1.0 from the baseline.

molecule: genomic DNA

organism: Oryza sativa

source_name: Nipponbare-leaf [reference]

label_protocol: pairs of genomic DNA (1µg) was labeled with fluorescent dyes Cy3 (test samples) or Cy5(reference DNA) according to the NimbleGen`s CGH user`s guide(see manufacture`s user guide)

extract_protocol: Genomic DNA was extracted and purified from fresh young leaves using a Promega kit (Wizard® Genomic DNA Purification Kit).

value: leaf

tag: subspecies

value: Japonica

tag: cultivar

value: Nipponbare

source_name: Guang-lu-ai 4-leaf [test]

value: Indica

value: Guang-lu-ai 4


title: patient 14

description: paired control tissue

source_name: thyroid tumor

value: patient 14

value: pool of paired control normal thyroid tissue


title: 14268712 - Mock 6h RB1 vs 14028 6h RB1

hyb_protocol: 14028 6h RB1 Cy5 / Mock 6h RB1 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: 14028 6h RB1:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:Salmonella WT 6h - pathogen - pathogen infection,salmonella typhimurium:time 6hour . addition of bacterial solution (in MgCl2 10 mM) at OD600 nm= 0,2 with salmonella WT 14028 or Salmonella mutant prgh or mock treatment (MgCl2 10 mM same volume) to liquid medium.

value: Salmonella WT 6h,salmonella typhimurium

value: control 6h,mgcl2 10mm


title: 14268894 - prgh 6h RB1 vs Mock 6h RB1

hyb_protocol: Mock 6h RB1 Cy5 / prgh 6h RB1 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: Salmonella mutant 6h,salmonella typhimurium


title: 14268711 - prgh 12h RB1 vs Mock 12h RB1

value: Salmonella mutant 12h,salmonella typhimurium


title: Ejaculate resulting in pregnancy, F10

value: ejaculate

value: pregnancy

tag: oocytes in metaphase ii

tag: age of woman [years]

tag: fertilisation ratio [%] (2pn/mii)


title: Ejaculate resulting in pregnancy, F48

tag: cumulative embryo score

tag: pregnancies


title: 14268713 - 14028 6h RB1 vs Mock 6h RB1

hyb_protocol: Mock 6h RB1 Cy5 / 14028 6h RB1 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: cultivar/ecotype

value: columbia mutant (col0)

tag: harvest date

tag: treatment


title: patient 13

description: paired control tissue

value: macrofollicular adenoma

tag: individual

value: patient 13

source_name: normal thyroid tissue


title: OVARY1847

description: Baseline profiling of OVARY1847 cells

source_name: OVARY1847 cells

tag: cell line

tag: cell type

value: ovarian cancer cells


title: Leaf Biological Replicate 1

description: Leaf Biological replicate 1 of 3,Guang-lu-ai 4(test) vsNipponbare(control)

tag: tissue

value: leaf


title: OV90

description: Baseline profiling of OV90 cells

source_name: OV90 cells


title: patient 10

description: paired control tissue

value: patient 10


title: patient 12

description: paired control tissue

value: patient 12


title: OV2008

description: Baseline profiling of OV2008 cells

source_name: OV2008 cells


title: Ejaculate resulting in pregnancy, F39

tag: ivf outcome

tag: motility (a+b) [%]


title: 14268708 - prgh 6h RB1 vs Mock 6h RB1

tag: time


title: MCAS

description: Baseline profiling of MCAS cells

source_name: MCAS cells

value: MCAS


title: 14268709 - Mock 12h RB1 vs prgh 12h RB1

source_name: prgh 12h RB1

source_name: Mock 12h RB1

value: control 12h,mgcl2 10mm


title: patient 09

description: paired control tissue

value: patient 09


title: Ejaculate resulting in pregnancy, F31

tag: ejaculate volume

tag: concentration [10e6/ml]


title: patient 08

description: paired control tissue

value: patient 08

value: pool of paired control normal thyroid tissue


title: 14268706 - Mock 6h RB1 vs prgh 6h RB1

value: control 6h,mgcl2 10mm


title: Ejaculate resulting in pregnancy, F22

tag: oocytes in metaphase ii


title: patient 11

description: paired control tissue

value: patient 11


title: M41

description: Baseline profiling of M41 cells

source_name: M41 cells


title: Ejaculate resulting in pregnancy, F23

source_name: ejaculate after 30 min liquefaction

tag: age of woman [years]


title: patient 07

description: paired control tissue

value: patient 07


title: 14268705 - 14028 12h RB1 vs Mock 12h RB1

value: Salmonella WT 12h,salmonella typhimurium


title: M41CisR

description: Baseline profiling of M41CisR cells

source_name: M41CisR cells


title: 14268704 - Mock 12h RB1 vs 14028 12h RB1


title: IMCC5

description: Baseline profiling of IMCC5 cells

source_name: IMCC5 cells


title: Ejaculate resulting in pregnancy, F45

value: ejaculate

value: pregnancy

tag: fertilisation ratio [%] (2pn/mii)


title: Ejaculate resulting in pregnancy, F5

tag: cumulative embryo score


title: patient 06

description: paired control tissue

value: macrofollicular adenoma

value: patient 06


title: IMCC3

description: Baseline profiling of IMCC3 cells

source_name: IMCC3 cells

value: ovarian cancer cells


title: patient 05

description: paired control tissue

value: patient 05


title: IGROV1

description: Baseline profiling of IGROV1 cells

source_name: IGROV1 cells


title: 14268707 - Mock 6h RB1 vs 14028 6h RB1

value: columbia mutant (col0)

value: Salmonella WT 6h,salmonella typhimurium

source_name: Mock 6h RB1


title: Ejaculate resulting in pregnancy, F12

tag: pregnancies


title: Leaf Biological Replicate 2

description: Leaf Biological replicate 2 of 3,Guang-lu-ai 4(test) vsNipponbare(control)

source_name: Nipponbare-leaf [reference]

value: leaf

tag: subspecies

value: Japonica

tag: cultivar

value: Nipponbare

value: Indica

value: Guang-lu-ai 4


title: 14268703 - 14028 6h RB1 vs Mock 6h RB1

tag: cultivar/ecotype

tag: harvest date

tag: treatment

value: control 6h,mgcl2 10mm


title: 14269059 - prgh 24h RB2 vs Mock 24h RB2

hyb_protocol: Mock 24h RB2 Cy5 / prgh 24h RB2 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: Mock 24h RB2

extract_protocol: Mock 24h RB2:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:control 24h - pathogen - pathogen infection,mgcl2 10mm:time 24hour . addition of bacterial solution (in MgCl2 10 mM) at OD600 nm= 0,2 with salmonella WT 14028 or Salmonella mutant prgh or mock treatment (MgCl2 10 mM same volume) to liquid medium.

value: control 24h,mgcl2 10mm

source_name: prgh 24h RB2

extract_protocol: prgh 24h RB2:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:Salmonella mutant 24h - pathogen - pathogen infection,salmonella typhimurium:time 24hour . addition of bacterial solution (in MgCl2 10 mM) at OD600 nm= 0,2 with salmonella WT 14028 or Salmonella mutant prgh or mock treatment (MgCl2 10 mM same volume) to liquid medium.

value: Salmonella mutant 24h,salmonella typhimurium


title: patient 03

description: paired control tissue

source_name: thyroid tumor

tag: individual

value: patient 03

source_name: normal thyroid tissue

value: pool of paired control normal thyroid tissue


title: HEYA8

description: Baseline profiling of HEYA8 cells

source_name: HEYA8 cells

tag: cell line

tag: cell type


title: Ejaculate resulting in pregnancy, F9

tag: tissue

value: ejaculate

tag: ivf outcome

value: pregnancy

tag: motility (a+b) [%]


title: 14269058 - Mock 24h RB2 vs prgh 24h RB2

hyb_protocol: prgh 24h RB2 Cy5 / Mock 24h RB2 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: time


title: patient 01

description: paired control tissue

value: macrofollicular adenoma

value: patient 01


title: patient 02

description: paired control tissue

value: patient 02


title: patient 04

description: paired control tissue

value: patient 04


title: DOV13

description: Baseline profiling of DOV13 cells

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques.  Arrays are hybridized for 18 hours at 45C with vigorous mixing.   Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed.  Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

source_name: DOV13 cells

value: ovarian cancer cells


title: SC_T48_infected1

city: Rio de Janeiro

first: Anna Beatriz

middle: Robottom

last: Ferreira

state: Rio de Janeiro

address: Rua Adolfo Lutz 55 apt 201

country: Brazil

institute: Fundação Oswaldo Cruz

hyb_protocol: RNA was sent to Applied Biosystems which carreid out the labelling, hybridization and scanning according to the companies protocols.

data_processing: Spots with SNR less than or equal to 3 were filtered out and remaining data was normalized by the A-quantile method (Irizarry, 2003).

label: DIG

growth_protocol: Primary Human Schwann cells were purchased from SceinCell Research Laboratories and grown by passaging in Human Schwann Cell Medium from the same company and maintained at 37C until infection.

extract_protocol: RNA was extracted from cells 24 or 48 hours after infection with M. leprae using the Promega RNAgents Total RNA Isolation System, following the manufacturer's protocol.

treatment_protocol: Cells were infected with viable M. leprae harvested from the nude mouse footpad and checked for over 75% viability at a multiplicity of infection of 100 bacteria per cell  or media in case of non-infected cells. Cells were maintained at 33 degrees Celcius until RNA extraction.

value: Primary human Scwhann cells (Sceincel cat # 1700)

tag: infection

value: M. leprae Thai-53 (harvested from nude mouse footpad model)

tag: time points

value: 48 hours of infection


title: 14269051 - Mock 24h RB2 vs 14028 24h RB2

hyb_protocol: 14028 24h RB2 Cy5 / Mock 24h RB2 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: 14028 24h RB2:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:Salmonella WT 24h - pathogen - pathogen infection,salmonella typhimurium:time 24hour . addition of bacterial solution (in MgCl2 10 mM) at OD600 nm= 0,2 with salmonella WT 14028 or Salmonella mutant prgh or mock treatment (MgCl2 10 mM same volume) to liquid medium.

value: columbia mutant (col0)

value: Salmonella WT 24h,salmonella typhimurium


title: SC_T48_uninfected1

scan_protocol: RNA was sent to Applied Biosystems which carreid out the labelling, hybridization and scanning according to the companies protocols.

value: uninfected (addition of media with no Mybacteria)

value: 48 hours following addition of media


title: CHICisR

description: Baseline profiling of CHICisR cells

source_name: CHICisR cells

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation.  Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.

value: CHICisR


title: patient 45

description: paired control tissue

hyb_protocol: The microarrays were first incubated at 50°C in a 50mM Ethanolamine - 100mM Tris base – SDS 0.1% solution for 15 minutes, and in a SSC 4x – 0.1% SDS solution for 15 minutes. The microarrays were then pre-hybridized 1 hour at 42°C. For each test, 20 µg of Cy3 labelled fragmented and hybridization mix resuspended samples were mixed with 20 µg of Cy5 labelled fragmented and hybridization mix resuspended reference. These mixes were denatured 2 minutes at 100°C and incubated 10 minutes at 37°C before hybridization. The microarrays were hybridized overnight at 42°C.

value: tumor of uncertain malignancy

value: patient 45


title: 14269050 - 14028 12h RB2 vs Mock 12h RB2

hyb_protocol: Mock 12h RB2 Cy5 / 14028 12h RB2 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: Mock 12h RB2

value: control 12h,mgcl2 10mm

extract_protocol: 14028 12h RB2:5ug. (Qiagen_RNeasy.pdf)

value: Salmonella WT 12h,salmonella typhimurium


title: SC_T48_uninfected2

label_protocol: RNA was sent to Applied Biosystems which carreid out the labelling, hybridization and scanning according to the companies protocols.


title: SC_T48_infected2


title: 14269052 - 14028 24h RB2 vs Mock 24h RB2

hyb_protocol: Mock 24h RB2 Cy5 / 14028 24h RB2 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: control 24h,mgcl2 10mm


title: CAOV3

description: Baseline profiling of CAOV3 cells

source_name: CAOV3 cells


title: CHI

description: Baseline profiling of CHI cells

source_name: CHI cells

value: CHI


title: FUOV1

description: Baseline profiling of FUOV1 cells

source_name: FUOV1 cells


title: 14269049 - Mock 12h RB2 vs 14028 12h RB2

hyb_protocol: 14028 12h RB2 Cy5 / Mock 12h RB2 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: Mock 12h RB2:5ug. (Qiagen_RNeasy.pdf)


title: SC_T24_infected2

value: 24 hours of infection


title: patient 43

description: paired control tissue

extract_protocol: The total RNA were extracted using a trizol® Reagent extraction procedure. RNA quality was checked on a bionalyzer and considered when RIN> 8

value: patient 43

value: pool of paired control normal thyroid tissue


title: SC_T24_uninfected1

value: Primary human Scwhann cells (Sceincel cat # 1700)

value: 24 hours following addition of media


title: SC_T24_uninfected2


title: 14269048 - 14028 6h RB2 vs Mock 6h RB2

hyb_protocol: Mock 6h RB2 Cy5 / 14028 6h RB2 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: Mock 6h RB2

value: control 6h,mgcl2 10mm

extract_protocol: 14028 6h RB2:5ug. (Qiagen_RNeasy.pdf)

value: Salmonella WT 6h,salmonella typhimurium


title: C13

description: Baseline profiling of C13 cells

source_name: C13 cells

value: ovarian cancer cells


title: CAOV2

description: Baseline profiling of CAOV2 cells

source_name: CAOV2 cells


title: 14269047 - Mock 6h RB2 vs 14028 6h RB2

hyb_protocol: 14028 6h RB2 Cy5 / Mock 6h RB2 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: columbia mutant (col0)


title: patient 44

description: paired control tissue

value: patient 44


title: patient 42

description: paired control tissue

value: patient 42


title: Vru mutant_late exp_1 vs S. uberis 0140J_late exp_3

city: Sutton Bonington

first: Sharon

last: Egan

state: Leicestershire

address: Sutton Bonington Campus

department: School of Veterinary Medicine and Sciences

country: United Kingdom

institute: University of Nottingham

description: Array 1_6

hyb_protocol: Cy3- and Cy5-labelled probes were mixed together in the appropriate combinations, with the fragmented RNA and hybridization buffer applied to the microarray hybridization chamber (Agilent Technologies) and incubated at 65°C for 17 hours with 10 RPM rotation. Following hybridization, microarrays were washed using Gene Expression Wash Buffer (Agilent Technologies).

scan_protocol: Arrays were scanned on an Agilent C scanner at 5 um using the XDR function at 10%. The images were then feature extracted using Agilent feature extraction version 10.5.1.1 using the GE2_105_Jan09 extraction protocol

data_processing: Data were loess and scale normalized and analyzed for differential expression using limma. Data analysis was performed on the average of each of the triplicate values for each probe/gene on each array.  These were then averaged for the three replicates for each time point. The data were loess and scale normalized and analyzed for differential expression using limma . Linear models were fitted to the data to compare the vru mutant with the S. uberis 0140J strain at both early and late logarithmic growth phase. The resultant p-values were adjusted for the false discovery rate. Genes were considered to be differentially expressed if the difference between the two strains was greater than 4 fold by analysis of the duplicate probes for each gene and the comparison of the data sets preferentially showed an adjusted P-value of <0.001  [log fold change (LogFC) data is available as a Series Supplementary file]

organism: Streptococcus uberis

source_name: Vru mutant_late exp_1

label_protocol: Fluorescently labeled probes for microarray hybridization were generated from 500ng total RNA using the MessageAmp II-Bacteria RNA amplification kit (Ambion) according to the manufacturer's instruction. A total of 5µg of the resulting amplified antisense RNA (aRNA) was purified using the RNeasy minElute clean up kit (Qiagen) and hybridisation performed using the Gene expression hybridization kit (Agilent). Samples were labeled with either Cy3 or Cy5 NHS ester reactive dyes (GE healthcare) according to the manufacturer's instruction

growth_protocol: Aliquots (15-20ml) of bacterial culture grown in Todd Hewit Broth at 37C of either S. uberis 0140J or Vru mutant were harvested at OD550nm of 0.42 for early logarithmic or OD550nm of 0.75 for late logarithmic growth phases

extract_protocol: Total RNA was extracted by resuspension of  cells in 1ml of RLT buffer (Qiagen) containing 1% (v/v) β-mercaptoethanol (Sigma-Aldrich). Cells were mechanically disrupted in a Mini-beadbeater-8 (Biospec) using acid-washed glass beads (Sigma). Following disruption, glass beads and cell debris were removed by centrifugation (17,000 × g, 10 sec). Supernatants were removed and mixed with an equal volume of 70% ethanol. Total RNA was extracted using an RNeasy column (Qiagen) according to the manufacturer's instruction, with RNA finally eluted in 50µl of nuclease-free water. Contaminating DNA was removed from  samples by DNase treatment using the DNA-free™ DNase Treatment kit (Ambion) and resulting samples were further purified by ethanol precipitation.

treatment_protocol: Two volumes of RNAprotect Bacterial Reagent (Qiagen) were immediately added to each sample,  incubated for 5 min at room temp. Samples were centrifuged (5,000 × g, 10 min), the supernatant discarded and the cell pellets stored at -80°C until RNA extraction was performed

tag: strain

tag: genotype/variation

value: vru (sub0144) mutant

tag: growth phase

value: late exponential (OD550 =0.75)

tag: growth conditions

value: THB media stationary cultre 37C

source_name: S. uberis 0140J_late exp_3

value: wild type


title: patient 41

description: paired control tissue

value: tumor of uncertain malignancy

value: patient 41


title: BG1

description: Baseline profiling of BG1 cells

source_name: BG1 cells


title: S. uberis 0140J_late exp_2 vs Vru mutant_late exp_3

description: Array 1_5

source_name: S. uberis 0140J_late exp_2

source_name: Vru mutant_late exp_3


title: patient 40

description: paired control tissue

source_name: thyroid tumor

value: patient 40


title: SC_T24_infected1

value: M. leprae Thai-53 (harvested from nude mouse footpad model)

value: 24 hours of infection


title: 14269045 - Mock 4h RB2 vs prgh 4h RB2

hyb_protocol: prgh 4h RB2 Cy5 / Mock 4h RB2 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: prgh 4h RB2

extract_protocol: prgh 4h RB2:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:Salmonella mutant 4h - pathogen - pathogen infection,salmonella typhimurium:time 4hour . addition of bacterial solution (in MgCl2 10 mM) at OD600 nm= 0,2 with salmonella WT 14028 or Salmonella mutant prgh or mock treatment (MgCl2 10 mM same volume) to liquid medium.

value: Salmonella mutant 4h,salmonella typhimurium

source_name: Mock 4h RB2

extract_protocol: Mock 4h RB2:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:control 4h - pathogen - pathogen infection,mgcl2 10mm:time 4hour . addition of bacterial solution (in MgCl2 10 mM) at OD600 nm= 0,2 with salmonella WT 14028 or Salmonella mutant prgh or mock treatment (MgCl2 10 mM same volume) to liquid medium.

value: control 4h,mgcl2 10mm


title: 14268923 - prgh 2h RB2 vs Mock 2h RB2

hyb_protocol: Mock 2h RB2 Cy5 / prgh 2h RB2 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: Mock 2h RB2

extract_protocol: Mock 2h RB2:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:control 2h - pathogen - pathogen infection,mgcl2 10mm:time 2hour . addition of bacterial solution (in MgCl2 10 mM) at OD600 nm= 0,2 with salmonella WT 14028 or Salmonella mutant prgh or mock treatment (MgCl2 10 mM same volume) to liquid medium.

value: control 2h,mgcl2 10mm

source_name: prgh 2h RB2

extract_protocol: prgh 2h RB2:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:Salmonella mutant 2h - pathogen - pathogen infection,salmonella typhimurium:time 2hour . addition of bacterial solution (in MgCl2 10 mM) at OD600 nm= 0,2 with salmonella WT 14028 or Salmonella mutant prgh or mock treatment (MgCl2 10 mM same volume) to liquid medium.

value: Salmonella mutant 2h,salmonella typhimurium


title: Vru mutant_late exp _2 vs S. uberis 0140J_late exp_1

description: Array 1_4

source_name: Vru mutant_late exp_2

source_name: S. uberis 0140J_late exp_1


title: S. uberis 0140J_early exp_3 vs Vru mutant_early exp_1

description: Array 1_3

source_name: S. uberis 0140J_early exp_3

value: early exponential (OD550 =0.42)

source_name: Vru mutant_early exp_1


title: A2780S

description: Baseline profiling of A2780S cells

source_name: A2780S cells

value: ovarian cancer cells


title: 14268921 - 14028 4h RB2 vs Mock 4h RB2

hyb_protocol: Mock 4h RB2 Cy5 / 14028 4h RB2 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: columbia mutant (col0)

extract_protocol: 14028 4h RB2:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:Salmonella WT 4h - pathogen - pathogen infection,salmonella typhimurium:time 4hour . addition of bacterial solution (in MgCl2 10 mM) at OD600 nm= 0,2 with salmonella WT 14028 or Salmonella mutant prgh or mock treatment (MgCl2 10 mM same volume) to liquid medium.

value: Salmonella WT 4h,salmonella typhimurium


title: 14269046 - prgh 4h RB2 vs Mock 4h RB2

hyb_protocol: Mock 4h RB2 Cy5 / prgh 4h RB2 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: 14268922 - Mock 2h RB2 vs prgh 2h RB2

hyb_protocol: prgh 2h RB2 Cy5 / Mock 2h RB2 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: Plasmodium falciparum, Ficoll control, C

city: Tuebingen

first: Evelyn

last: Boettger

address: Wilhelmstrasse 27

institute: Institute of Tropical Medicine

description: FCR3-CSA separated over a Ficoll gradient (Ficoll control).

hyb_protocol: Standard Affymetrix Hybridization Protocol.

scan_protocol: Standard Affymetrix Scanning Protocol.

data_processing: Signals were normalized using GC-RMA.

organism: Plasmodium falciparum

source_name: Plasmodium falciparum FCR3, Ficoll control

label_protocol: Standard Affymetrix labeling protocol.

growth_protocol: FCR3CSA was maintained in continuous culture as described by Trager and Jensen.

extract_protocol: RNA was isolated with Trizol according to manufacturer's instructions.

treatment_protocol: Prior to each experiment, FCR3CSA parasites were selected for chondroitin sulfate A (CSA) adhesion by panning. Both strains were constantly synchronized with 5% sorbitol and mature trophozoite-infected erythrocytes (iRBCs) were purified by magnetic cell sorting LD columns (MACS; Miltenyi Biotec). After 24 hours culture of FCR3CSA-infected erythrocytes at 37ºC in 5% CO2, the parasites were separated by Ficoll gradient centrifugation.

tag: csa adhesion

value: yes

tag: developmental stage

value: 24h after late trophozoite stage

value: passed over Ficoll gradient


title: Plasmodium falciparum, Ficoll control, B


title: A2780CP

description: Baseline profiling of A2780CP cells

source_name: A2780CP cells


title: A2008

description: Baseline profiling of A2008 cells

source_name: A2008 cells


title: Vru mutant_early exp_3 vs S. uberis 0140J_early exp_2

description: Array 1_2

source_name: Vru mutant_early exp_3

value: vru (sub0144) mutant

value: THB media stationary cultre 37C

source_name: S. uberis 0140J_early exp_2

value: wild type


title: Salmonella_enterica_serovar_Typhimurium_UK1_5mM hydrogen peroxide_wild-type_rep1

city: Seoul

first: Yong Keun

last: Park

address: Anam-dong 5Ga, Seoungbuk-Gu

department: School of Life Sciences and Biotechnology

country: South Korea

institute: Korea University

description: This sample is of wild-type Salmonella enterica serovar Typhimurium UK1. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Labeled cDNAs were hybridized to a NimbleGen 4-plex array which was designed based on S. Typhimurium strain LT2 (Roche NimbleGen) for 12 h at 42 °C using MAUI system (Biomicro systems).

scan_protocol: Arrays were washed and scanned using an Axon GenePix 4000B scanner (Molecular Devices).

data_processing: Gene expression levels were calculated with NimbleScan software version 2.4 (Roche NimbleGen) using the median polish normalization method and relative signal intensities were generated using the robust multi-array average algorithm. Data analysis was performed using GeneSpring GX 7.3.1 (Agilent Technologies).

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. UK-1

source_name: Salmonella enterica serovar Typhimurium UK1 wild-type

label_protocol: Each total RNA sample was labeled with Cyanine 3 (Cy3)-conjugated dCTP by a reverse transcription reaction, and then was resuspended in 10 µl of hybridization solution (GenoCheck, Korea).

growth_protocol: Salmonellal enterica serovar Typhimurium UK1 and ∆RsiM mutant were grown upto O.D.600nm 0.6 in LB broth. then, 5.0 mM hydroperoxide was treated and bacteria were grown and stressed for 30 minutes.

extract_protocol: Total RNA was extracted from Hot phenol method and concentration was measured by analysis with a Nano drop.

treatment_protocol: 5.0mM hydrogen peroxide were treated in LB media after grown until O.D.600nm 0.6 and incubated for 30 min.

tag: genotype

value: Wild-type

tag: phenotype

value: normal

tag: accession


title: Plasmodium falciparum, co-cultured with NK cells, C

description: Co-culture of FCR3-CSA with NK92.

source_name: Plasmodium falciparum FCR3, co-cultured with NK92 cells

growth_protocol: FCR3CSA was maintained in continuous culture as described by Trager and Jensen. NK92 Cells were kept in culture at a concentration of 0.2-0.6x106 cells/ml in alpha-MEM (75%; Sigma-Aldrich) supplemented with FBS (12,5%; Sigma-Aldrich), horse serum (12,5%; Sigma-Aldrich), L-glutamine (2 mM; Sigma-Aldrich), penicillin – streptomycin (10ml/L; Invitrogen) and recombinant human interleukin-2 (rIL-2; 10 ng/ml; Invitrogen). Saturated cultures were split 1:2 every second day.

treatment_protocol: Prior to each experiment, FCR3CSA parasites were selected for CSA adhesion by panning. Both strains were constantly synchronized with 5% sorbitol and mature trophozoite-infected erythrocytes (iRBCs) were purified by magnetic cell sorting LD columns (MACS; Miltenyi Biotec). After 24 hours co-culture of NK92 and FCR3CSA-infected erythrocytes (1:3) at 37ºC in 5% CO2, cells and parasites were separated by Ficoll gradient centrifugation.

tag: treatment

value: co-culture with NK92

tag: treatment time


title: S. uberis 0140J_early exp_1 vs Vru mutant_early exp_2

description: Array 1_1

source_name: S. uberis 0140J_early exp_1

source_name: Vru mutant_early exp_2


title: Salmonella_enterica_serovar_Typhimurium_UK1_5mM hydrogen peroxide_wild-type_rep2

description: This sample is of wild-type Salmonella enterica serovar Typhimurium UK1. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: 14268920 - Mock 4h RB2 vs 14028 4h RB2

hyb_protocol: 14028 4h RB2 Cy5 / Mock 4h RB2 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: cultivar/ecotype

tag: harvest date

source_name: Mock 4h RB2


title: 14268919 - 14028 2h RB2 vs Mock 2h RB2

hyb_protocol: Mock 2h RB2 Cy5 / 14028 2h RB2 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: Mock 2h RB2

extract_protocol: 14028 2h RB2:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:Salmonella WT 2h - pathogen - pathogen infection,salmonella typhimurium:time 2hour . addition of bacterial solution (in MgCl2 10 mM) at OD600 nm= 0,2 with salmonella WT 14028 or Salmonella mutant prgh or mock treatment (MgCl2 10 mM same volume) to liquid medium.

value: Salmonella WT 2h,salmonella typhimurium


title: 14268918 - Mock 2h RB2 vs 14028 2h RB2

hyb_protocol: 14028 2h RB2 Cy5 / Mock 2h RB2 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: Plasmodium falciparum, parasite control, C

description: Control culture.

source_name: Plasmodium falciparum FCR3, parasite control

treatment_protocol: Prior to each experiment, FCR3CSA parasites were selected for chondroitin sulfate A (CSA) adhesion by panning. Both strains were constantly synchronized with 5% sorbitol and mature trophozoite-infected erythrocytes (iRBCs) were purified by magnetic cell sorting LD columns (MACS; Miltenyi Biotec). After 24 hours culture of FCR3CSA-infected erythrocytes at 37ºC in 5% CO2, RNA was extracted.


title: Plasmodium falciparum, co-cultured with NK cells, B

description: Co-culture of FCR3-CSA with NK92.


title: 14268917 - prgh 4h RB1 vs Mock 4h RB1

hyb_protocol: Mock 4h RB1 Cy5 / prgh 4h RB1 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: Mock 4h RB1

extract_protocol: Mock 4h RB1:5ug. (Qiagen_RNeasy.pdf)

value: control 4h,mgcl2 10mm

source_name: prgh 4h RB1

extract_protocol: prgh 4h RB1:5ug. (Qiagen_RNeasy.pdf)

value: Salmonella mutant 4h,salmonella typhimurium


title: Plasmodium falciparum, co-cultured with NK cells, A

description: Co-culture of FCR3-CSA with NK92.


title: Ms4a8a-transfected RAW264.7 1

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: Gene expression from Ms4a8a-transfected RAW264.7

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 4, from SAS. Gene expression profiling was performed using arrays of Mouse430_2 -type from Affymetrix. A Custom CDF Version 14 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization.

organism: Mus musculus

source_name: Ms4a8a-transfected RAW264.7 1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Raw 264.7 cells were cultivated with DMEM medium supplemented with 10%FCS, 100IU penicillin, 100 µg/ml penicillin, 100 µg/ml streptomycin, 1% pyruvic acid, 1% non essential amino acids. Authentication of cell lines was assured by regular morphology checks and growth curve analyses. Cells were regularly tested for mycoplasma infection by PCR.

extract_protocol: RNA was isolated from these cultures using Qiagen RNeasy Kit

treatment_protocol: Ms4a8a-transfected and empty vector-transfected RAW264.7 cells were incubated for 6 h with 5 µg/ml LPS in DMEM medium supplemented with 10% FCS, 100 IU penicillin, 100 µg/ml streptomycin, 1% pyruvic acid, 1% non essential amino acids.

tag: cloneid

tag: cell line

tag: transfection

value: Ms4a8a-transfected RAW264.7


title: Plasmodium falciparum, Ficoll control, A


title: Plasmodium falciparum, parasite control, B

description: Control culture.


title: 14268915 - prgh 2h RB1 vs Mock 2h RB1

hyb_protocol: Mock 2h RB1 Cy5 / prgh 2h RB1 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: Mock 2h RB1

extract_protocol: Mock 2h RB1:5ug. (Qiagen_RNeasy.pdf)

value: control 2h,mgcl2 10mm

tag: time

source_name: prgh 2h RB1

extract_protocol: prgh 2h RB1:5ug. (Qiagen_RNeasy.pdf)

value: Salmonella mutant 2h,salmonella typhimurium


title: Plasmodium falciparum, parasite control, A

description: Control culture.

tag: strain


title: vector-transfected RAW264.7 mock 1

description: Gene expression from empty vector transfected Raw264.7 macrophages

source_name: vector-transfected RAW264.7 mock

value: vector


title: Ms4a8a-transfected RAW264.7 rep 2

description: Gene expression from Ms4a8a transfected Raw264.7 macrophages

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 4, from SAS. Gene expression profiling was performed using arrays of Mouse430_2 -type from Affymetrix. A Custom CDF Version 13 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization.

source_name: Ms4a8a-transfected RAW264.7

extract_protocol: RNA was isolated from these cultures using Trizol®-Reagent (Gibco brl). and Qiagen RNeasy Kit


title: vector-transfected RAW264.7 mock 2


title: Ms4a8a-transfected RAW264.7 rep 3


title: 14268916 - Mock 4h RB1 vs prgh 4h RB1

hyb_protocol: prgh 4h RB1 Cy5 / Mock 4h RB1 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: columbia mutant (col0)


title: 14268912 - Mock 4h RB1 vs 14028 4h RB1

hyb_protocol: 14028 4h RB1 Cy5 / Mock 4h RB1 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: 14028 4h RB1:5ug. (Qiagen_RNeasy.pdf)

value: Salmonella WT 4h,salmonella typhimurium


title: Short term BB_OVX-pool1

city: Little rock

first: Kartik

last: Shankar

state: AR

address: 1120 Marshall Street, Slot 512-20B

department: Pharmacology and Toxicology

institute: University of Arkansas for Medical Sciences/Arkansas Childrens Nutrition Center

description:
ST_BB_OVX_P10
osteogenic gene expression

hyb_protocol: Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Porcine arrays (N = 3/treatment) for 16 h at 45ºC in the hybridization oven set at 60 rpm.

scan_protocol: The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.

data_processing:
Cel files were generated using GCOS and utilized for analysis using GeneSpring Gx v 11.0
RMA normalization was utilized to generated values using GeneSpring v 11.0

organism: Rattus norvegicus

source_name: postnatal day 81-rat bone

label_protocol: First- and second- strand cDNA synthesis (from 8 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA  reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions

growth_protocol: Bone quality was compared among casein control diet sham operated, casein diet ovariectomized, long term BB diet ovariectomized and short term BB diet ovariectomized female rats

extract_protocol: Total bone RNA was isolated from the experimental rats using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion

treatment_protocol: Femur were collected from rats at sacrifice and flash frozen in liquid nitrogen

tag: gender

value: female

tag: diet

value: short term BB diet

tag: operation

value: ovariectomy

tag: age

value: postnatal day 81

tag: tissue

value: femur bone


title: vector-transfected RAW264.7 1

source_name: empty vector transfected Raw264.7 macrophages 1


title: A673_siEWSR1-FLI1l_replicat2

city: Paris

first: Franck

last: Tirode

address: 26 Rue d'Ulm

department: Inserm U830

institute: Institut Curie

description: Gene expression data from A673 Ewing cell line treated by EWSR1-FLI1 siRNA for 72 hours

hyb_protocol: As according to the manufacturer's instructions.

scan_protocol: GCOS 1.4

data_processing: All data were normalized using the gcrma package version 2.18.1 in R 2.10.1 environment  (R Development Core Team, 2005) with quantile normalisation using Brainarray EntrezGene CDF v14.1.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol using 2µg total RNA

growth_protocol: DMEM + 10% FCS + antibiotics

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

treatment_protocol: siRNA transfections were performed with 50nM of stealth siRNA using Lipofectamine RNAiMAX (Invitrogen)

value: Ewing cell line A673

tag: sirna

value: siRNA EWSR1-FLI1


title: Short term BB_OVX-pool3

description:
ST_BB_OVX_P12
osteogenic gene expression


title: 14268911 - 14028 2h RB1 vs Mock 2h RB1

hyb_protocol: Mock 2h RB1 Cy5 / 14028 2h RB1 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: 14028 2h RB1:5ug. (Qiagen_RNeasy.pdf)


title: 14268910 - Mock 2h RB1 vs 14028 2h RB1

hyb_protocol: 14028 2h RB1 Cy5 / Mock 2h RB1 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: A673_siEWSR1-FLI1l_replicat1


title: 14268914 - Mock 2h RB1 vs prgh 2h RB1

hyb_protocol: prgh 2h RB1 Cy5 / Mock 2h RB1 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: Long term BB_OVX-pool2

description:
LT_BB_OVX_P8
osteogenic gene expression

value: long term BB diet


title: OVX control-pool3

description:
OVXcontrol_P6
osteogenic gene expression

value: control (casein)


title: Long term BB_OVX-pool3

description:
LT_BB_OVX_P9
osteogenic gene expression


title: Long term BB_OVX-pool1

description:
LT_BB_OVX_P7
osteogenic gene expression


title: A673_siPRKCB_replicat3

description: Gene expression data from A673 Ewing cell line treated by PRKCB siRNA for 72 hours

value: siRNA PRKCB


title: Short term BB_OVX-pool2

description:
ST_BB_OVX_P11
osteogenic gene expression


title: A673_siPRKCB_replicat2


title: A673_siPRKCB_replicat1


title: OVX control-pool2

description:
OVXcontrol_P5
osteogenic gene expression


title: Female-Sham-pool3

description:
ratFsham_P3
osteogenic gene expression

value: control


title: OVX control-pool1

description:
OVXcontrol_P4
osteogenic gene expression


title: A673_siControl_replicat2

description: Gene expression data from A673 Ewing cell line treated by control siRNA for 72 hours

value: siRNA Control


title: 14268913 - 14028 4h RB1 vs Mock 4h RB1

description: What is the transcriptomic reprogramming after Salmonella infection, What is the importance of the T3SS in the plant infection, Are there differences in gene expression between the 2 bacterial strains? What are the functions of these genes,

hyb_protocol: Mock 4h RB1 Cy5 / 14028 4h RB1 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: control 4h,mgcl2 10mm


title: Female-Sham-pool2

description:
ratFsham_P2
osteogenic gene expression


title: sid-1_infection_3

status: Public on Jun 30 2012

city: Haifa

first: Itai

last: Yanai

address: Technion City

department: Biology

country: Israel

institute: Technion - Israel Institute of Technology

description: Strain=sid-1;Environment=infection;Replicate=3

hyb_protocol: Agilent one-color hybridization protocol.  To minimize post-amplification biases, we randomized the position and order of hybridizations.

scan_protocol: Scanned at 10% laser power to avoid signal saturation

data_processing: Agilent Feature Extraction software (GE1-v5_95_Feb07) used to calculate fluorescence values which were then log2-transformed and rank-normalized across 120 hybridizations

molecule: polyA RNA

organism: Caenorhabditis elegans

label_protocol: 10 µg aRNA labeled with Cy3 using the Ambion MessageAmpII kit and 1.65µg labeled aRNA used to hybridize with each array

growth_protocol: We used standard methods to culture and handle C. elegans (Brenner, 1974), except we used the sporulation-defective Bacillus subtilis strain RL1275 (spoIIAC::erm in a PY79 background, kind gift from Richard Losick) as worm food, because B. subtilis is substantially less pathogenic to C. elegans than the standard C. elegans food E. coli OP50 at 25°C (Garsin et al., 2003).

extract_protocol: We collected embryos and purified RNA as described (Baugh et al., 2003), except we increased the number of embryos per sample to 50.  In brief, we picked young adults into water, chopped them in half, treated them with alkaline bleach to destroy any RNA and protein not protected by the eggshell, stopped the bleach reaction with bovine serum albumin, collected and washed early embryos in DEPC-treated water using a glass mouth pipette, flash-froze the embryos in liquid nitrogen in low-adhesion 600 μl microcentrifuge tubes, and transferred the tubes to a -80° freezer for storage.  For the microarray experiment, the total time from picking of the first worm to bleaching was not allowed to exceed 15 min.  For all subsequent experiments, the time was not allowed to exceed 8 min.  We added Trizol (phenol/guanidine isothiocyanate, Invitrogen), with added linear polyacrylamide and yeast tRNA as carriers, to the frozen embryos for RNA extraction and isopropanol precipitation.  We used the RNA pellet directly for RT (reverse transcription), starting from a T7-oligo-dT RT primer.  To obtain sufficient RNA for microarray analysis, RNA was amplified by two rounds of in vitro transcription (IVT) using the MessageAmpII kit (Ambion) with the following modifications designed to increase the average lengths of the aRNA populations (Baugh et al. 2001): First-round cDNA construction from total RNA was carried out at 1/5 of the recommended quantities and total volume, while IVT was carried out at 1/2 of the recommended volume.  100ng aRNA from the first round was used as input for the second round of amplification following the manufacturers protocol for amino-allyl modified nucleotides.

treatment_protocol: Before each of the experiments, we cultured the worms for at least three generations at 20°C without allowing the worms to deplete their food.  Other than the 25°C treatments, done in a 25±0.5° incubator, all incubations and procedures involving live worms were done in a temperature controlled room at 20±0.3°C.  To minimize temperature variation during handling, we used large (10 cm diameter) plates, wore insulated gloves while handling plates, and used an external light source for the dissecting microscope.  For the microarray experiment, we used a platinum wire loop to transfer several hundred embryos to fresh plates for each generation.  For the multigenerational follow-up experiments (not included in this accession because they were analyzed by RT-QPCR only), we used a platinum wire pick to transfer 60 L4 larvae to fresh plates for each generation.  The purpose of transferring L4s instead of embryos in the multigenerational experiment was to eliminate males from the cultures, thereby eliminating variation in the frequency of sex-specific imprinting (most C. elegans individuals are hermaphrodites, with a low rate of spontaneous males that increases with temperature).  For the same set of experiments, we used HOBO miniature temperature loggers (Onset) to continuously monitor culture temperatures.  For post-25° steps of all experiments, we interleaved the constant 20° (control) plates with post-25° treatment plates in common stacks whenever possible, so that treatment and control plates experience the same microenvironment on average.  In practice, the treatment plates were slightly staggered in time relative to the corresponding control plates of the same generation, because of time constraints and because development time from zygote to adult is ~17 hours faster at 25° than at 20°.  For the each condition and generation in the microarray experiment, we collected 3 replicates (50 embryos each replicate) of the standard C. elegans laboratory strain N2 and three replicates (50 embryos each replicate) of the strain HC445 (sid-1(qt9) in an N2 background).

tag: developmental stage

value: 4-cell stage

tag: environment

value: infection

tag: replicate


title: A673_siControl_replicat1