title: 13969359 - WOX14-6D Repeat1 vs N8514-6D Repeat1

hyb_protocol: N8514-6D Repeat1 Cy5 / WOX14-6D Repeat1 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: 13969355 - Untreated-Root Repeat2 vs Worm-Root Repeat2

status: Public on Oct 01 2010

type: RNA

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Do earthworms affect plant growth through signal molecules?

hyb_protocol: Worm-Root Repeat2 Cy5 / Col-Root Repeat2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

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

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

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Worm-Root

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: roots - Media=soil  hygrometry=70%  Temperature=18°C Night / 20°C Day  Light=200 µmol photons.m2.s-1

treatment_protocol: Name:Earthworms - environmental treatment - earthworms,earthworms:time 42day . Pots were weighting 6 kg of dry soil. After soil humectation for 1 week at 75% of the readily available water capacity, earthworms (Aporrectodea caliginosa) were introduced at 0.5 g.kg-1 of dry soil in the presence treatment. One week later, 30 seeds were sown, distributed on 5 small circles of 2cm diameter. One week later, 5 of the 6 seedlings of each circles were removed, to keep 5 homogeneous seedlings per pot.

tag: ecotype

value: Columbia

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

source_name: Untreated-Root

treatment_protocol: no treatment


title: 13969357 - N8514-6D Repeat1 vs WOX14-6D Repeat1

description: The WOX13 OG contained the most conserved plant WOX proteins including the only WOX detected in the highly proliferating basal unicellular and photosynthetic organism Ostreococcus tauri. In Arabidopsis thaliana, AtWOX13 was dynamically expressed during primary and lateral root initiation and development, in gynoecium and during embryo development. An intriguing clade, represented by the functional AtWOX14 gene inside the WOX13 OG, was only found in the Brassicaceae. Compared to AtWOX13, the gene expression profile of AtWOX14 was restricted to the early stages of lateral root formation and specific to developing anthers. A mutational insertion upstream of the AtWOX14 homeodomain sequence led to abnormal root development, a delay in the floral transition and premature anther differentiation. Our scope is to establish a functional link to organ initiation and development in Arabidopsis by identifying genes that are deregulated in the wox14 mutant background.

hyb_protocol: WOX14-6D Repeat1 Cy5 / N8514-6D Repeat1 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.

growth_protocol: seedling - Media=1/2 MS 1% sucrose  Temperature=22  Light=long day

tag: genotype/variation

value: mutant (wox14 -/-)

tag: age


title: 13969354 - Worm-Root Repeat1 vs Untreated-Root Repeat1

hyb_protocol: Col-Root Repeat1 Cy5 / Worm-Root Repeat1 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: 13969353 - Untreated-Root Repeat1 vs Worm-Root Repeat1

hyb_protocol: Worm-Root Repeat1 Cy5 / Col-Root Repeat1 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: 13969356 - Worm-Root Repeat2 vs Untreated-Root Repeat2

hyb_protocol: Col-Root Repeat2 Cy5 / Worm-Root Repeat2 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: JBM442

status: Public on Sep 30 2010

city: Oslo

first: Johannes

middle: L

last: Bjørnstad

address: Kirkeveien 166

department: Dept. of Cardiothoracic Surgery

country: Norway

institute: Oslo University Hospital Ulleval

description: 4 weeks after aortic banding

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: Microarray pre-processing involved background adjustment using gcrma (Guanine Cytosine Robust Multi-Array Analysis) which normalizes data and adjusts for background intensities taking optical noise and non-specific binding into account and control of false discovery rate (FDR) according to Benjamini and Hochberg.

label: biotin

organism: Mus musculus

source_name: left ventricular myocardium

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 7-week-old male C57BL/6 mice were sbjected to aortic banding (AB) or sham (sAB). After 4 weeks a debanding operation (DB/sDB) was performed. Mice were sacrificed 4 weeks after banding/sham or 3 days after debanding.

extract_protocol: Total RNA was isolated with an RNeasy Mini Kit from Qiagen according to the manufacturer's instructions.

treatment_protocol: Following saccrifice,  the left ventricle was separated from the right ventricle and the atria and snap frozen in liquid nitrogen and stored in a superfreezer untill processing.

tag: strain

tag: stress

value: aortic banding (AB)


title: JBM438

description: 3 days after debanding (sham)

value: sham procedure and subsequent debanding (sDB3)


title: 13969349 - Untreated-Leaf Repeat1 vs Worm-Leaf Repeat1

hyb_protocol: Worm-Leaf Repeat1 Cy5 / Col-Leaf Repeat1 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: Worm-Leaf

source_name: Untreated-Leaf

growth_protocol: aerial - Media=soil  hygrometry=70%  Temperature=18°C Night / 20°C Day  Light=200 µmol photons.m2.s-1


title: JBM445

description: 4 weeks after aortic banding


title: 13969350 - Untreated-Leaf Repeat2 vs Worm-Leaf Repeat2

hyb_protocol: Worm-Leaf Repeat2 Cy5 / Col-Leaf Repeat2 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: JBM431

description: 3 days after debanding

value: banding and subsequent debanding (DB3)


title: 13969348 - Worm-Leaf Repeat1 vs Untreated-Leaf Repeat1

hyb_protocol: Col-Leaf Repeat1 Cy5 / Worm-Leaf Repeat1 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: JBM504

description: 4 weeks after aortic banding (sham)

value: sham procedure (sAB)


title: JBM401

description: 3 days after debanding (sham)


title: JBM499

description: 4 weeks after aortic banding (sham)


title: JBM382

description: 3 days after debanding (sham)


title: JBM493

description: 4 weeks after aortic banding (sham)


title: 13969352 - Worm-Leaf Repeat2 vs Untreated-Leaf Repeat2

hyb_protocol: Col-Leaf Repeat2 Cy5 / Worm-Leaf Repeat2 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: JBM432

description: 3 days after debanding


title: JBM328

description: 3 days after debanding


title: JBM439

description: 4 weeks after aortic banding


title: 3T3-L1_t4_rep1

city: Cambridge

first: Tarjei

middle: S

last: Mikkelsen

state: MA

address: 7 Cambridge Center

country: USA

institute: Broad Institute

description: no additional information

hyb_protocol: As recommended by Affymetrix

scan_protocol: As recommended by Affymetrix

data_processing: The data were extracted and RMA normalized using GenePattern (http://genepattern.broadinstitute.org)

source_name: 3T3-L1 adipocyte, day 7, replicate 1

label_protocol: As recommended by Affymetrix from 1 ug total RNA/sample

growth_protocol: 3T3-L1 pre-adipocytes were maintained in DMEM supplemented with 10% calf serum. Two days after confluence, the cells were induced with DMEM supplemented with 10% FBS, 1uM dexamethasone, 1.7uM insulin, and 0.5mM 3-isobutyl-1-methylxanthine (IBMX). 48h later, the medium was replaced with DMEM supplemented with 10% FBS and the cells were fed every two days.

extract_protocol: Total RNA were extracted using TRIzol (Invitrogen)

tag: cell type

value: 3T3-L1 adipocyte


title: 3T3-L1_t4_rep2

description: no additional information

source_name: 3T3-L1 adipocyte, day 7, replicate 2


title: 3T3-L1_t3_rep2

description: no additional information

source_name: 3T3-L1 adipocyte, day 2, replicate 2


title: 3T3-L1_t2_rep1

description: no additional information

source_name: 3T3-L1 pre-adipocyte, day 0, replicate 1

value: 3T3-L1 pre-adipocyte


title: 3T3-L1_t1_rep2

description: no additional information

source_name: 3T3-L1 pre-adipocyte, day -2, replicate 2


title: WW-ctrl for pDr, Rep2

city: Blacksburg

first: Andy

last: Pereira

state: VA

address: Washington Street MC0477

department: Virginia Bioinformatics Institute

institute: Virginia Tech

description:
pDr_WW-ctrl_Rep2
Well-watered control for pDr.

hyb_protocol: 4 µg RNA samples were hybridized to the Affymetrix (ATH1 25K) GeneChip. The hybridization protocol was done using the GeneChip Hybridization, Wash, and Stain kit. The cocktail includes 12.5 ug aRNA, control oligo B2, 20x hyb controls of bioB, bioC, bioD, and cre, 2X hyb mix, and DMSO. The hybridization mix was heated at 99C for 5 min, 45C for 5 min, and then hybridized for 16h at 45C.

scan_protocol: Arrays were stained using the Affymetrix FS450 fluidics station with FS450_0001 fluidics protocol. Afterwards, arrays were scanned with the Affymetrix Gene Chip Scanner 3000 with HR (high resolution).

data_processing:
For each of the drought experiments, mDr-Day1, mDr-Day10 and pDr, raw data were background corrected, normalized and summarized according to the custom CDF using RMA (Irizarry et al., 2003). RMA was implemented in the 'affy' Bioconductor package within the R statistical computing environment.

Each of the mDr-Day01, mDr-Day10 and pDr sample groups (along with their controls, for a total of 4 samples per group) were normalized separately.

The custom CDF was built by uniquely mapping 232,697 probe sequences to 21,389 Arabidopsis (TAIR8) gene-based probe sets in the following manner: (i) probes that have perfect sequence identity with a single target gene were selected, (ii) probes mapping to reverse complements of genes were annotated separately as antisense probes (not used in the above counts), and finally, (iii) probes were grouped into probe sets, each corresponding to a single gene, and probe sets having at least 3 unique sequences were retained (>99% probe sets have >=5 probes). Note that these stringent criteria used to construct the CDF make it possible to reliably measure expression values of members of multigene families (free from cross-hybridization between paralogs showing high sequence similarity).

source_name: Young leaf samples from plants subjected to well-watered conditions after 35 DAS

label_protocol: RNA preparation/labeling was done using the Affymetrix 3' IVT Express kit, with biotin as label. The cRNA (or aRNA) is purified via beads and fragmented before hybridization.

growth_protocol: Arabidopsis (Columbia) seeds were sown in moistened peat pellets, stratified at 4°C for 2 days, and then transferred to a growth room kept at 10 hours light (100 µmole m-2 s-1) and 22°C.

extract_protocol: For RNA isolation, two biological replicate samples of 5 pooled plants were collected at early (day1) and late stage (day10) for mDr, and first day of wilting for pDr, along with controls for mDr and pDr. RNA was isolated using RNeasy Kit (Qiagen, USA).  After that, genomic DNA was eliminated using DNase kit (Qiagen, USA).

treatment_protocol: For drought treatment, pellets were weighed before sowing to determine the amount of water in pellets at the beginning of the experiment. Controlled moderate drought (mDr) was maintained by giving plants water to keep the soil moisture level at 30% of field capacity, which is 200% or 2 g H2O g-1 dry soil. Water was withheld at 30 days after sowing (DAS). For progressive drought (pDr) treatment, plants were grown in a growth room as described above, water was withheld at 35 DAS, and pellets were allowed to dry and monitored by weighing the pellets until the required pDr level was reached.

tag: tissue

value: young leaves

tag: treatment

value: well-watered control


title: BJ_Fibroblast_Untransfected

city: Boston

first: Hu

last: Li

address: 3 Blackfan Circle

institute: Wyss Institute

description: Gene expression data obtained from fibroblasts

hyb_protocol: cDNA was fragmented and 10ug hybridized to an Affymetrix U133 Plus 2.0 array for 16 hours. Arrays were washed and stained using the Affy 450 Fluidics Station according to the manufacturer's protocol

scan_protocol: Arrays were scanned using a GeneChip 3000 scanner according to the manufacturers recommendation

data_processing: RMA (Bioconductor Affy Package)

organism: Homo sapiens

source_name: fibroblast, untransfected

label_protocol: Preparation of biotinylated cDNA was performed according to the standard Nugen amplification sample preparation protocol, starting with 100ng of total RNA

growth_protocol: Fibroblasts were grown in alpha-MEM containing 10 % inactivated fetal serum (IFS), 50 U/ml penicillin, 50 mg/ml streptomycin, and 1 mM L-glutamine. Replacement,10 ng/ml bFGF, 1 mM L-glutamine, 100 uM nonessential amino acids, 100 uM 2-mercaptoethanol, 50 U/ml penicillin, and 50 mg/ml streptomycin).

extract_protocol: Trizol isolation followed by Rneasy (Qiagen) column purification were performed according to manufacturer's specifications

value: BJ fibroblast

tag: reprogramming protocol


title: MRC5_RiPS_1.9

description: Gene expression data obtained from MRC5 RNA iPS

source_name: RNA iPS

growth_protocol: Refer to online method of publication

value: iPS cells derived from MRC5 fibroblast

value: RNA derived iPS


title: BJ_Fibroblast_Modified-RNA

source_name: fibroblast, modified-RNA transfected

value: modified-RNA (i.e., synthetic mRNA with GFP)


title: 3T3-L1_t2_rep2

description: no additional information

source_name: 3T3-L1 pre-adipocyte, day 0, replicate 2


title: BJ_RiPS_1.3

description: Gene expression data obtained from BJ RNA iPS

value: iPS cells derived from BJ fibroblast


title: CF_RiPS_1.3

description: Gene expression data obtained from CF RNA iPS

value: iPS cells derived from CF fibroblast


title: MRC5_RiPS_1.11


title: MRC5_RiPS_1.8


title: dH1F_RiPS_1.2

description: Gene expression data obtained from dH1F RNA iPS

value: iPS cells derived from dH1F fibroblast


title: 3T3-L1_t3_rep1

description: no additional information

source_name: 3T3-L1 adipocyte, day 2, replicate 1


title: dH1F_RiPS_1.7


title: dH1F_RiPS_1.6


title: CF_RiPS_1.4


title: BJ_Fibroblast_Vehicle

source_name: fibroblast, vehicle-transfected

value: vehicle control


title: CF_RiPS_1.2


title: H1_OGNES_IH

description: Gene expression data obtained from human ES

source_name: human ES

growth_protocol: standard HESC growth conditions as described in Pick et al. (2009).

tag: cell line

value: H1 Human OGNES embryonic stem cells


title: BJ_RiPS_1.2


title: dH1F_RiPS_1.3


title: BJ_RiPS_1.1


title: 3T3-L1_t1_rep1

description: no additional information

source_name: 3T3-L1 pre-adipocyte, day -2, replicate 1


title: dH1CF16_iPS5_IH32

description: Gene expression data obtained from dH1F iPS

source_name: viral derived iPS

growth_protocol: For feeder-free culture of iPSCs, the plate was coated with 0.3mg/ml Matrigel (BD-Bioscience, San Jose, CA) and mTeSR (StemCell Technologies, Vancouver, Canada) was used according to the manufacturer’s instruction.

value: iPS cells derived from dH1CF fibroblast

value: viral derived iPS


title: MRC5_iPS2_2_IH

description: Gene expression data obtained from MRC5 iPS


title: 3T3-L1_t1

description: no additional information

hyb_protocol: As recommended by Illumina

scan_protocol: As recommended by Illumina

data_processing: The data were extracted, background subtracted and quantile normalized using GenomeStudio 2009 (Illumina)

source_name: 3T3-L1 pre-adipocyte, day -2

label_protocol: As recommended by Illumina

extract_protocol: Total RNA were extracted using TRIzol (Invitrogen) and subjected to miRNA-DASL


title: 3T3-L1_t4

description: no additional information

source_name: 3T3-L1 adipocyte, day 7


title: 3T3-L1_t2

description: no additional information

source_name: 3T3-L1 pre-adipocyte, day 0


title: dH1CF16_iPS5_IH10


title: dH1CF16_iPS5_IH20


title: BJ_iPS_IH

description: Gene expression data obtained from BJ iPS


title: dH1CF16_iPS5_IH30


title: dH1F_iPS3_IH3


title: MRC5_Fibroblast_2

value: MRC5 fibroblast


title: 3T3-L1_t3

description: no additional information

source_name: 3T3-L1 adipocyte, day 2


title: hASC_t9_rep2

description: no additional information

source_name: hASC pre-adipocyte, day 14

growth_protocol: hASCs were grown in MesenPRO RS medium (Invitrogen) plus 4ng/ml FGF-2 on plates coated with 10ug/cm2 collagen I (Invitrogen). Two days after confluence, the cells were placed in induction medium (DMEM/F12 supplemented with 10% FBS plus 1uM dexamethasone, 1.7uM insulin, 0.5mM IBMX, 5uM rosiglitazone, 40ng/ml BMP4, 17uM pantothenic acid, and 33uM biotin). 72h later, the medium was replaced with maintenance medium (DMEM/F12 with 10% FBS plus 1uM dexamethasone, 1.7uM insulin, 17uM pantothenic acid, and 33uM biotin) and media was replaced every two days thereafter.

tag: gender

value: female

value: adipose stromal cells


title: hASC_t9_rep1

description: no additional information


title: hASC_t6_rep2

description: no additional information

source_name: hASC pre-adipocyte, day 5


title: hASC_t8_rep1

description: no additional information

source_name: hASC pre-adipocyte, day 9


title: MRC5_Fibroblast_1


title: hASC_t7_rep1

description: no additional information

source_name: hASC pre-adipocyte, day 7


title: LSC17

city: Fukuoka

first: Yoshikane

last: Kikushige

address: 3-1-1 Maidashi, Higashiku

country: Japan

institute: Kyushu University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using Gene Spring GX11.01 software (Agilent Technologies).According to the guided workflow for Illumina single color experiment, normalization algorithm of 75-percentile shift was used, and the preprocessing baseline was adjusted to median of all samples.

source_name: bone marrow

label_protocol: Biotinylated complementary RNA was synthesized with two round amplification steps using MessageAmpⅡ aRNA Amplification Kit and Illumina TotalPrep RNA Amplification Kit (Applied Biosystems)

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: disease

value: acute myeloid leukemia

tag: cell phenotype

tag: fab classification of aml


title: hASC_t3_rep1

description: no additional information

source_name: hASC pre-adipocyte, day 1


title: hASC_t4_rep2

description: no additional information

source_name: hASC pre-adipocyte, day 2


title: normal HSC3

value: healthy control


title: LSC10


title: hASC_t8_rep2

description: no additional information


title: normal HSC1


title: hASC_t5_rep2

description: no additional information

source_name: hASC pre-adipocyte, day 3


title: hASC_t1_rep2

description: no additional information

source_name: hASC pre-adipocyte, day -2


title: hASC_t2_rep2

description: no additional information

source_name: hASC pre-adipocyte, day 0


title: hASC_t6_rep1

description: no additional information


title: normal HSC4


title: hASC_t4_rep1

description: no additional information


title: normal HSC5


title: LSC26


title: LSC29


title: hASC_t5_rep1

description: no additional information


title: LSC15


title: LSC16


title: LSC5


title: hASC_t1_noFGF_rep2

description: no additional information

source_name: hASC pre-adipocyte, day -2, no FGF


title: hASC_t9_rep2

description: no additional information

data_processing: The data were extracted, background subtracted and quantile normalzied using GenomeStudio 2009 (Illumina)


title: hASC_t9_rep1

description: no additional information


title: hASC_t1_rep1

description: no additional information


title: hASC_t1_noFGF_rep1

description: no additional information


title: hASC_t2_rep1

description: no additional information


title: LSC9


title: Glioma - 30634

city: salamanca

first: Juan

middle: Luis

last: Garcia

address: Campus Miguel de Unamuno

country: Spain

institute: Center Cancer Research

description: Fresh tissues of the brain tumor

hyb_protocol: The labeled RNA was then fragmented and hybridized to HU-133A oligonucleotide array (Affymetrix, Santa Clara, CA, USA), which contained 22 283 probe sets, according to Affymetrix protocols.

scan_protocol: The arrays were scanned using the Gene Array Scanner (Affymetrix).

data_processing: Expression value for each probe set was calculated using the MAS 5.0. software (Affymetrix). All samples had a scaling factor lower than threefold and a 3'/5' of GAPDH  probe set <2.5. Gene expression levels were transformed to base two logarithms. A median normalization approach was applied.

label: Biotin

source_name: Fresh tissue

label_protocol: Double-stranded cDNA and afterwards biotinylated cRNA were synthesized using a T7-polyT primer and the BioArray RNA labeling kit (Enzo, Farmingdale, NY, USA), respectively.

extract_protocol: Total RNA was extracted using Trizol reagent (Life Technologies, Gaithersburg, MD, USA) and purified with RNeasy Mini Kit (Quiagen, Valencia, CA, USA). The RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA).

value: male

tag: type

value: glioma grade IV


title: LSC11


title: LSC27


title: Glioma - 31079

description: Fresh tissues of the brain tumor


title: LSC28


title: hASC_t8_rep2

description: no additional information


title: Glioma - 33353

description: Fresh tissues of the brain tumor

value: glioma grade III


title: Glioma - 33479

description: Fresh tissues of the brain tumor


title: Glioma - 31096

description: Fresh tissues of the brain tumor


title: Glioma - 33294

description: Fresh tissues of the brain tumor


title: Glioma - 27452

description: Fresh tissues of the brain tumor


title: Glioma - 27780

description: Fresh tissues of the brain tumor


title: Glioma - 30520

description: Fresh tissues of the brain tumor


title: hASC_t7_rep2

description: no additional information


title: hASC_t7_rep1

description: no additional information


title: Glioma - 30350

description: Fresh tissues of the brain tumor


title: hASC_t6_rep2

description: no additional information


title: Glioma - 29278

description: Fresh tissues of the brain tumor


title: Human pancreatic islet-like cell clusters, biological rep1

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

description: The mRNA profilings of T3ES, T3EB and T3pi cells were analyzed using Affymetrix Human Genome U133 plus 2.0 GeneChip according to the Manufacturer¡¦s protocols (Santa Clara, CA, USA, http://www.affymetrix.com).

hyb_protocol: Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hr at 45oC on Affymetrix Human Genome U133 plus 2.0 GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips from the hybridization experiments were read by the Affymetrix GeneChip scanner 3000.

data_processing: The data were processed by GeneSpring GX software version 7.3.1 GC-RMA preprocessor to use on the CEL files

source_name: Human pancreatic islet-like cell clusters derived from human embryonic stem cell line hES-T3 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms purified cRNA (Expression Analysis Technical Manual, 2004, Affymetrix, http://www.affymetrix.com).

growth_protocol: Human embryonic stem cell line hES-T3 has been continuously cultured on mitomycin C (10 ug/ml) mitotically inactivated MEF feeder in hES medium under 5% CO2 at 37oC. The hES culture medium consisted of DMEM/F12 (1:1, GIBCO) supplemented with 20% KSR (Invitrogen), 1% non-essential amino acids, 1 mM L-glutamine, 0.1 mM £]-mercaptoethanol, and 4 ng/ml human basic fibroblast growth factor (bFGF; Life Technologies). The five-stage procedure for in vitro differentiation of hES-T3 cells into pancreatic islet-like cell clusters was described as follows: Stage I: Expansion of undifferentiated hES cells. The hES-T3 cells (passage 36) were maintained on MEF feeder in hES medium containing 4 ng/ml bFGF as described above. The hES-T3 cells grown on MEF feeder were designated as T3ES. Stage II: Formation of embryoid bodies. The undifferentiated hES-T3 colonies were mechanically dissected into pieces that were transferred and grown with very slow shaking (20 rpm) in the EB medium containing 80% knockout DMEM, 20% ES-qualified FBS (GIBCO), 1% non-essential amino acids, and 1 mM L-glutamine without MEF feeder layer in bacterial Petri dish plate (£\-plus, 10 cm) under 5% CO2 at 37oC for 7 days with change of medium every two days. These embryoid bodies are designated as T3EB. Stage III: Plating EBs in ITSF medium. The EBs were transferred to 0.1% gelatin coated-plate in DMEM/F12 medium supplemented with 1% ITS (1 g/L insulin, 0.55 g/L transferring, 0.67 mg/L selenium), 5 ug/ml fibronectin and 1 mM L-glutamine under 5% CO2 at 37oC for 7 days with change of medium every two days. Stage IV: Expansion of pancreatic progenitor cells. The cells were dissociated with 0.05% trypsin at 37oC for 5 minutes, and plated on 0.1% gelatin-coated dish in DMEM/F12 medium supplemented with 1% N2 supplement (500 ug/ml insulin, 10 mg/ml transferrin, 0.63 ug/ml progesterone, 1.611 mg/ml putrascin, and 0.52 ug/ml selenite, GIBCO), 2% B27 supplement (GIBCO), 1 mM L-glutamine and 10 ng/ml bFGF under 5% CO2 at 37oC for 7 days with change of medium daily. Stage V: Formation of pancreatic islet-like cell clusters. The DMEM (containing no glucose)/F12 medium was supplemented 1% N2 supplement, 2% B27 supplement, 1mM L-glutamin, and 10 mM nicotinamide (instead of bFGF) under 5% CO2 at 37oC for 7 days with change of medium every two days. These hES-T3 derived pancreatic islet-like cell clusters were designated as T3pi.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNAs extracted using TRIZOL reagent were quantified spectrophotometrically. The cDNA synthesis was carried out by using SUPERSCRIPTTM one-step RT-PCR kit (Invitrogen). For the reverse transcription step, the whole 5 ul of the resuspended RNAs were incubated for 60 min at 42oC, then 15 min at 72oC in 50 ul of reaction mixture containing 25 ul of 2x Reaction Mix (Invitrogen) and 1 ul of RT/PLANTINUM Taq Mix (Invitrogen). 28.5 ul of the cDNAs present in the 50 ul RT reaction mixture purified by Microarray Target Purification Kit (Roche Applied Science, Indianapolis, ID, USA, http://www.roche-applies-science.com) were used as templates to amplify cDNA by Microarray Target Amplification Kit. The amplified cDNAs were purified by Microarray Target Purification Kit, and complementary RNAs (cRNAs) were synthesized from 200 ng cDNA with Microarray RNA Target Synthesis Kit (Roche Applied Science).

treatment_protocol: Non

tag: sample type

value: pancreatic islet-like cell clusters derived from T3ES


title: Glioma - 26825

description: Fresh tissues of the brain tumor


title: LSC34


title: Glioma - 24448

description: Fresh tissues of the brain tumor


title: hASC_t8_rep1

description: no additional information


title: hASC_t6_rep1

description: no additional information


title: Glioma - 24535

description: Fresh tissues of the brain tumor


title: hASC_t5_rep2

description: no additional information


title: hASC_t5_rep1

description: no additional information


title: hASC_t4_rep2

description: no additional information


title: Glioma - 25081

description: Fresh tissues of the brain tumor


title: Glioma - 26058

description: Fresh tissues of the brain tumor


title: hASC_t3_rep2

description: no additional information


title: hASC_t4_rep1

description: no additional information


title: hASC_t3_rep1

description: no additional information


title: Glioma - 25383

description: Fresh tissues of the brain tumor


title: hASC_t2_rep2

description: no additional information


title: Human pancreatic islet-like cell clusters, biological rep2


title: Glioma - 24444


title: Glioma - 22907

value: glioma grade V


title: hASC_t2_rep1

description: no additional information


title: Glioma - 22849


title: Glioma - 23473


title: hASC_t1_rep2

description: no additional information


title: HepG2_siCONTROL_2

city: Davis

first: Seth

middle: Eric

last: Frietze

state: CA

address: 451 Health Sciences Dr. GBSF 4617A

department: Genome Center

institute: UC Davis

description:
control replicate 2
4763734020_L

data_processing: The data were normalised using quantile normalisation with Beadstudio

source_name: HepG2 cells

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: HepG2 cells were grown in DMEM supplemented with 10%FBS.

treatment_protocol: Cells were transfected with 20nM siRNA non-targeting control duplex using lipofectamine2000.

tag: sirna treatment

value: CONTROL


title: Glioma - 26269

description: Fresh tissues of the brain tumor


title: hASC_t1_noFGF

description: no additional information


title: Glioma - 24038


title: HepG2_siCONTROL_3

description:
control replicate 3
4763734020_K


title: HepG2_siCONTROL_1

description:
control replicate 1
4763734020_J


title: Glioma - 24020


title: Glioma - 23814


title: Control 2.2

status: Public on Sep 29 2010

city: Charlestown

first: Okay

last: Saydam

address: Building 149, 13th st. 6th Floor, Room:6101

department: Neurology

institute: MGH

description: LMW RNA

hyb_protocol: For hybridization, membranes were first prehybridized in MicroHyb Hybridization Buffer (Invitrogen) at 37ºC for 30 min followed by an overnight hybridization in the same solution containing RNA probes.

scan_protocol: Following hybridization, membranes were washed and exposed to a phosphor storage screen, scanned using a Phosphor Imager (Massachusetts General Hospital, core facility), and hybridization signals were quantified using ImageQuant software (Molecular Dynamics).

data_processing: RNA samples were considered independent measurements for the purposes of the two-tailed, two-sample t test. Probe signals that showed high variance in tumor tissue samples (more than 2-fold with p values >0.05) were excluded from further analysis. miRNA array data was first normalized using median-centric method within BRBArrayTools (http://linus.nci.nih.gov/BRB-ArrayTools.html) and was further subjected to quantile normalization in Partek Genomics Suite (http://www.partek.com/). Differentiated miRNA lists comparing expression in control to all meningioma samples for miRNA arrays were generated using the significance analysis of microarrays (SAM) method (43) with cutoffs for FDR <30% and p value <0.05. The normalized array data for the derived differentiated miRNAs list was then transformed to z-scores for data of each miRNA across samples using WPS utility program (46), which was subjected to heatmap clustering analysis and visualization using TM4 program from TIGR (http://www.tm4.org/). The normalized array data for the derived differentiated miRNAs list was then transformed to z-scores for data of each miRNA across samples using WPS utility program (46), which was subjected to heatmap clustering analysis and visualization using TM4 program from TIGR (http://www.tm4.org/).

source_name: control

label_protocol: The LMW RNA was end-labeled with 30 µCi у33-P dATP (3000 Ci/mmole) by T4 polynucleotide kinase (New England Biolabs, Ipswich, MA) and purified using the Qiagen Nucleotide Removal Kit (Valencia, CA).

extract_protocol: Total RNA was isolated from tissues with Trizol (Invitrogen). RNA labeling and hybridization on a microarray was performed as previously described (21,27).  Briefly, 10 mg total RNA from each sample were filtered through Microcon YM-100 concentrators to obtain a low molecular weight (LMW) fraction of RNA enriched in molecules under 60 bp.

value: nerve


title: Control 1.1

description: LMW RNA


title: Glioma - 20975

description: Fresh tissues of brain tumor.


title: hASC_t1_rep1

description: no additional information


title: Glioma - 22382

description: Fresh tissues of brain tumor.


title: Glioma - 22817


title: Glioma - 22560


title: Glioma - 22713


title: Glioma - 19209

description: Fresh tissues of brain tumor.


title: Patient 8 GF200 008.1

description: LMW RNA

source_name: Human Schwannoma Tumors

tag: nf2 association

value: NF2 negative

value: Schwannoma Tumor


title: Patient 10 GF200 010.1

description: LMW RNA


title: Patient 8 GF200 008.2

description: LMW RNA


title: Patient 5 GF200 005.2

description: LMW RNA


title: Patient 6 GF200 006.1

description: LMW RNA


title: Patient 7 GF200 007.1

description: LMW RNA


title: Patient 9 GF200 009.2

description: LMW RNA


title: Patient 6 GF200 006.2

description: LMW RNA


title: Patient 5 GF200 005.1

description: LMW RNA


title: Patient 10 GF200 010.2

description: LMW RNA


title: Patient 7 GF200 007.2

description: LMW RNA


title: Patient 4 GF200 004.2

description: LMW RNA


title: Patient 9 GF200 009.1

description: LMW RNA


title: Control 2.1

description: LMW RNA


title: normal HSC2


title: Patient 3 GF200 003.2

description: LMW RNA


title: Patient 3 GF200 003.1

description: LMW RNA


title: Patient 2 GF200 002.2

description: LMW RNA


title: Patient 1 GF200 001.2

description: LMW RNA


title: Patient 2 GF200 002.1

description: LMW RNA


title: Patient 1 GF200 001.1

description: LMW RNA


title: Control 1.2

description: LMW RNA


title: Glioma - 20526

description: Fresh tissues of brain tumor.


title: NORM#9_19-23

city: Oxford

first: charles

last: lawrie

address: John Radcliffe Hospital

department: NDCLS

country: United Kingdom

institute: University of Oxford

hyb_protocol: Hybridization protocol	Samples were hybridised using the Array 900microRNA direct kit from Genisphere (Hatfield, PA) as described by the manufacturer on a A-hyb machine (Miltenyi Biotec).

scan_protocol: Slides were scanned on a Perkin-Elmer ArrayExpress scanner

data_processing: Image analysis was carried out with BlueFuse software (BlueGnome, Cambridge, UK). Raw image data were global LOESS-normalized within arrays and normalized between arrays using the LIMMA package. The normalized log ratios (average of four replicates per probe) were used for subsequent analysis in Genespring 7.2 (Agilent Technologies, CA, US).

source_name: purified CD138+ plasma cells from control

label_protocol: enriched microRNA (500ng) samples were labeled with either Cy3 or Cy5 dyes using an Array 900microRNA direct kit from Genisphere (Hatfield, PA)

extract_protocol: MicroRNA was isolated from samples using Trizol (Invitrogen, Paisley, UK) and RNeasy columns as described by the manufacturer (Qiagen, Crawley, UK)

value: 55 yrs

tag: Sex

source_name: tonsil

value: pooled tonsils (n=12)


title: MGUS#2_19-38

source_name: purified CD138+ plasma cells from MGUS patient

tag: age

value: 67 yrs


title: NORM#8_19-31

value: 54 yrs


title: MM#18_19-30

source_name: purified CD138+ plasma cells from myeloma patient

value: 62 yrs


title: MM#44_19-43


title: NORM#7_17-18

hyb_protocol: Hybridization protocol	Samples were hybridised using the Array 900microRNA direct kit from Genisphere (Hatfield, PA) as described by the manufacturer on a A-hyb machine (Miltenyi Biotec)

label_protocol: Enriched microRNA (500ng) samples were labeled with either Cy3 or Cy5 dyes using an Array 900microRNA direct kit from Genisphere (Hatfield, PA)

extract_protocol: MicroRNA was isolated from samples using Trizol (Invitrogen, Paisley, UK) and RNeasy columns as described by the manufacturer (Qiagen, Crawley, UK).

value: 39 yrs


title: MM(RPMI8226)_19-08

source_name: cell line


title: NORM#1_17-11

value: 56 yrs


title: MM#47_19-46

value: 51 yrs

value: female


title: MM#46_18-43

value: 60 yrs

value: male


title: MM#(JJN3)_19-13

value: NK


title: NORM#6_17-17


title: MM#(NCI-H929)_19-40


title: MM(Thiel)_19-11

value: THIEL


title: NORM#3_17-14.

value: 69 yrs


title: NORM#4_17-15

value: 73 yrs


title: NORM#5_17-16


title: NORM#2_17-12

value: 72 yrs


title: Patient 4 GF200 004.1

description: LMW RNA

value: NF2 negative

value: Schwannoma Tumor


title: MM#35_17-10

value: 61 yrs

value: pooled tonsils (n=12)


title: Ptch+/-p53-/- tumors, LDE225 treated for 26 days, 80 mg/kg/day bid (aCGH)

type: genomic

first: John

middle: E

last: Monahan

address: 250 Massachusetts Ave

department: Oncology Translational Research

institute: Novartis

description: Medulloblastoma tumors derived from Ptch+/-p53-/- transgenic mouse allografted in nude mice

hyb_protocol: The microarrays were scanned using the Agilent Microarray Scanner System.

data_processing: The data were anaylzed with Agilent Feature Extraction and CGH Analytics software using Agilent default analyis settings.  Chromosomal aberrations were determined using Agilent's ADM-2 (Aberration Detection Method 2) algorithm with a threshhold setting of 12 and 1 MB analysis window.

molecule: genomic DNA

label_protocol: Following labeling the entire amount of each labeled product was then hybridized with an equal amount of mouse reference sample. The DNAs were hybridized for 24 hr at 65C on Agilent Whole Mouse Genome Oligo CGH 244K Microarray.  Arrays were washed and processed in the Agilent hybridization chamber.

growth_protocol: Nude mice were allografted with medulloblastoma tumors derived from Ptch+/-p53-/- transgenic mouse

extract_protocol: Differentially labeled Cy3 and Cy5 DNA was prepared according to the standard Agilent protcol from 500 ng total DNA (Oligonucleotide Array-Based CGH for Genomic DNA Analysis v.5.0).

treatment_protocol: Genomic DNA was extracted from tumors using the DNeasyBlood and Tissue kit (Qiagen)

tag: genotype

tag: tumor

value: Medulloblastoma

tag: tumor status

value: Resistant

tag: dose

value: 80 mg/kg/day bid

tag: dosing schedule

value: bid (twice a day)

tag: treatment protocol

value: The resistant tumors were observed after 13 of continuous dosing of NVP-LDE225.  The mice were treated until the tumors were harvested at day 26 of treatment.

tag: treatment time

value: 26 days

tag: sample id

source_name: reference, mouse liver DNA

value: liver

value: wildtype

tag: dna status

value: normal DNA


title: Ptch+/-p53-/- tumors, LDE225 treated for 26 days, 40 mg/kg/day bid (aCGH)

scan_protocol: The microarrays were scanned using the Agilent Microarray Scanner System.

tag: treatment

value: 40 mg/kg/day bid

tag: tissue


title: MM#45_18-42

value: 43 yrs

value: male


title: MM#36_19-32

value: 65 yrs


title: MM#43_18-39

value: 73 yrs

value: female


title: MM#41_18-41

value: 63 yrs


title: Ptch+/-p53-/- tumors, vehicle treated for 26 days, 3 (aCGH)

value: Sensitive

value: Vehicle


title: Ptch+/-p53-/- tumors, vehicle treated for 26 days, 160 mg/kg/day bid (aCGH)

value: Medulloblastoma

value: Resistant

value: 160 mg/kg/day bid


title: Ptch+/-p53-/- tumors, vehicle treated for 26 days, 2 (aCGH)


title: Ptch+/-p53-/- tumors, vehicle treated for 26 days, 1 (aCGH)


title: MM#34_17-08

value: 60 yrs

value: pooled tonsils (n=12)


title: MM#33_18-37

value: 88 yrs


title: MM#31_19-34

value: 72 yrs


title: MM#16_17-09

value: 62 yrs


title: MM#32_19-26

value: 51 yrs


title: MM#29_18-40

value: 78 yrs


title: MM#27_19-37

value: 58 yrs

value: male


title: MM#30_19-16

value: 67 yrs


title: MGUS#6_18-48

value: 73 yrs


title: MM#17_17-13

value: 61 yrs


title: MM#26_19-36

value: 56 yrs


title: MM#23_19-39

value: 55 yrs

value: female


title: MM#24_19-44


title: MM#13_15-04

value: 69 yrs


title: MM#25_20-03

value: 86 yrs


title: MM#10_18-27

value: 60 yrs


title: MM#21_19-29

value: 85 yrs

value: pooled tonsils (n=12)


title: MGUS#3_18-26


title: MM#14_17-04

value: 47 yrs


title: MM#15_17-07

value: 89 yrs


title: MGUS#4_18-38


title: MM#12_19-28


title: MM#28_20-08

value: 76 yrs


title: MM#9_20-06

value: 81 yrs


title: MM#8_20-04

value: 63 yrs


title: MGUS#1_19-10

value: male


title: MM#11_18-45

value: 66 yrs


title: BV2_Curcumin_rep3

city: Regensburg

first: Thomas

last: Langmann

address: Franz-Josef-Strauss-Allee 11

department: University of Regensburg

country: Germany

institute: Institute of Human Genetics

description: Gene expression of Curcimun-treated BV2 cells

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Expression Arrays (4x44k) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_105_metrix_Jan09)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100-1000ng of high quality RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: BV2 microglial cells were cultured as described recently (Dirscherl et al. J Neuroinflammation. 2010 Jan 14;7:3.)

extract_protocol: Total RNA was extracted using the Qiagen Rneasy kit according to the protocol of the manufacturer

treatment_protocol: BV2 microglial cells were left untreated or were treated for 6h with 100 ng/ml LPS, 20 µM Curcumin, or 100ng/ml LPS + 20 µM Curcumin

tag: cell line

value: Curcimun


title: BV2_LPS_rep3

description: Gene expression of LPS-treated BV2 cells

value: LPS


title: BV2_LPS+Curcumin_rep1

description: Gene expression of LPS+Curcumin-treated BV2 cells

value: LPS+Curcumin


title: BV2_rep1

description: Gene expression of untreated BV2 cells

value: untreated


title: BV2_LPS_rep1


title: BV2_Curcumin_rep2


title: BV2_Curcumin_rep1


title: BV2_LPS+Curcumin_rep3


title: BV2_LPS_rep2


title: NUID-0000-0092-8701

first: Michael

last: Morrissey

department: Oncology

institute: Novartis Institutes for Biomedical Research

description: LDE225AZ 40 mg/kg#1-3

hyb_protocol: Following fragmentation cRNA was hybridized at 45ºC for approximately 18 hours, arrays were stained on GeneChip Fluidics Workstation 450 and scanned on GeneArray Scanner 3000 according to manufacturer’s technical manual (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000 according to manufacturer’s technical manual (Affymetrix).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

source_name: NVP-LDE225 treated Ptch+/-p53-/-  medulloblastoma tumors

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.5 to 5 µg of total RNA

extract_protocol: Total RNA from approximately 100 mg of flash frozen tumor tissue was purified using the Aurum total RNA fatty and fibrous tissue kit (Biorad, Hercules CA) according to the manufacturer's instructions.

treatment_protocol: Mouse Ptch+/−p53−/− medulloblastoma cells (1.0 x 106), dissociated directly from tumors, were inoculated subcutaneously into the right flank of Harlan nu/nu mice. Treatment was initiated approximately 10 days after implantation. Animals were randomized into treatment groups with similar mean tumor volumes.

value: Medulloblastoma

value: Resistant


title: NUID-0000-0092-8705

description: LDE225AZ 40 mg/kg#1-7


title: BV2_rep2

description: Gene expression of untreated BV2 cells


title: NUID-0000-0092-8709

description: LDE225AZ 160 mg/kg#2-3


title: BV2_rep3

description: Gene expression of untreated BV2 cells


title: NUID-0000-0092-8707

description: LDE225AZ 160 mg/kg#2-1


title: BV2_LPS+Curcumin_rep2


title: NUID-0000-0092-8711

description: LDE225AZ 160 mg/kg#2-5


title: NUID-0000-0092-8703

description: LDE225AZ 40 mg/kg#1-5


title: NUID-0000-0092-8712

description: LDE225AZ 160 mg/kg#2-6

source_name: NVP-LDE225 resistant Ptch+/-p53-/-  medulloblastoma tumors


title: NUID-0000-0092-8708

description: LDE225AZ 160 mg/kg#2-2


title: NUID-0000-0092-8710

description: LDE225AZ 160 mg/kg#2-4


title: NUID-0000-0092-8706

description: LDE225AZ 40 mg/kg#1-8


title: NUID-0000-0092-8713

description: LDE225AZ 160 mg/kg#2-7


title: NUID-0000-0092-8714

description: LDE225AZ 160 mg/kg#2-8


title: NUID-0000-0092-8704

description: LDE225AZ 40 mg/kg#1-6


title: NUID-0000-0092-8702

description: LDE225AZ 40 mg/kg#1-4


title: NUID-0000-0092-8699

description: LDE225AZ 40 mg/kg#1-1


title: NUID-0000-0092-8700

description: LDE225AZ 40 mg/kg#1-2


title: NUID-0000-0092-8696

source_name: Vehicle treated Ptch+/-p53-/-  medulloblastoma tumors

value: Vehicle

value: Sensitive


title: spliceostatin A vs methanol

city: Toyama

first: Daisuke

last: Kaida

state: Toyama

address: 2630 Sugitani

department: Frontier Research Core for Life Sciences

institute: University of Toyama

description: Affected regions by spliceosotain A treatment. Biological Rep 1-3

hyb_protocol: The end-labelled cDNA targets were applied to GeneChip human tiling 2.0R E arrays. Hybridization was performed using F450-001 fluidics wash and stain script on the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned using the Affymetrix GCS 3000 7G GeneChip Operating Software (GCOS).

data_processing: For tiling array analysis, we produced .BAR files from the .CEL files using the Affymetrix Tiling Analysis Software (TAS) version 1.1 to visualize on the Integrated Genome Browser (IGB).

source_name: RNA from spliceostatin A treated cells

label_protocol: Labelled cDNA targets were prepared using the GeneChip WT amplified Double-Stranded cDNA Synthesis Kit and the GeneChip WT Double-Stranded DNA Terminal Labelling Kit according to the manufacturer’s directions.

growth_protocol: HeLa cells were grown in DMEM + 10% FBS in humdified incubator with 5% CO2.

extract_protocol: Total RNA was extractedusing TRIzol according to manufacturer's recommendation.

treatment_protocol: Cells were transfected with antisense morpholino and culture for 8 hours or treated with methanol or spliceostatin A for 8 hours.

value: HeLa

source_name: RNA from methanol treated cells


title: NUID-0000-0087-6689

description: LDE225AZ 40 mg/kg 8hr #1

source_name: NVP-LDE225 resistant Ptch+/-HIC+/-  medulloblastoma tumors

growth_protocol: Nude mice were allografted with medulloblastoma tumors derived from Ptch+/-HIC+/- transgenic mouse

treatment_protocol: Mouse Ptch+/−HIC+/- medulloblastoma cells (1.0 x 106), dissociated directly from tumors, were inoculated subcutaneously into the right flank of Harlan nu/nu mice. Treatment was initiated approximately 10 days after implantation. Animals were randomized into treatment groups with similar mean tumor volumes.

value: Ptch+/-HIC+/-


title: NUID-0000-0087-6675

description: Vehicle #2

source_name: Vehicle treated Ptch+/-HIC+/-  medulloblastoma tumors


title: NUID-0000-0092-8698


title: NUID-0000-0088-4068

description: Vehicle 4hr #1


title: U2 vs control

description: Affected regions by U2 snRNP inhibition. Biological Rep 1-3

source_name: RNA from U2 morpholino treated cells

source_name: RNA from control morpholino treated cells


title: NUID-0000-0087-6685

description: Vehicle 4hr #2


title: NUID-0000-0087-6687

description: LDE225AZ 40 mg/kg 4hr #2


title: NUID-0000-0087-6691

description: LDE225AZ 40 mg/kg 8hr #3


title: NUID-0000-0092-8697


title: U1 vs control

description: Affected regions by U1 snRNP inhibition. Biological Rep 1-3

source_name: RNA from U1 morpholino treated cells


title: NUID-0000-0087-6673

description: LDE225AZ 40 mg/kg 48hr #4

source_name: NVP-LDE225 treated Ptch+/-HIC+/-  medulloblastoma tumors


title: NUID-0000-0087-6674

description: Vehicle #1


title: NUID-0000-0087-6676

description: Vehicle #3


title: NUID-0000-0087-6688

description: LDE225AZ 40 mg/kg 4hr #3


title: NUID-0000-0087-6672

description: LDE225AZ 40 mg/kg 48hr #3


title: NUID-0000-0087-6690

description: LDE225AZ 40 mg/kg 8hr #2


title: NUID-0000-0087-6692

description: LDE225AZ 40 mg/kg 24hr #1


title: NUID-0000-0087-6669

description: LDE225AZ 40 mg/kg 24hr #2


title: NUID-0000-0087-6671

description: LDE225AZ 40 mg/kg 48hr #1


title: NUID-0000-0087-6686

description: LDE225AZ 40 mg/kg 4hr #1


title: NUID-0000-0087-6670

description: LDE225AZ 40 mg/kg 24hr #3


title: NUID-0000-0087-6679

description: LDE225AZ 40 mg/kg resistant #3


title: vcc522 8 h rabbit experiment 5

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Infection, pathogenesis
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36498.gif

hyb_protocol: not provided

scan_protocol: Microarrays were scanned with a GenePix 400A instrument (Axon Instruments), using the GENEPIX 5.0 software.

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

organism: Vibrio cholerae

source_name: 2ug mid log reference

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: 2ug mid log reference

source_name: 2ug vc RNA from 8 h rabbit loop

extract_protocol: The bacteria were then resuspended in Trizol reagent and frozen on dry ice. The wild-type bacteria from three independent experiments in three different rabbits were analyzed. RNA was isolated from the Trizol agent, treated with DNaseI (Ambion, Austin, Texas, United States), and cleaned by using the RNeasy kit (Qiagen, Valencia, California, United States). To avoid microarray expression artifacts imparted by the presence of host RNA, RNA was prepared from a healthy rabbit and added to the V. cholerae reference RNA, isolated as described above from bacteria grown to mid exponential phase in LB broth. The amount of host RNA added to the V. cholerae reference RNA was determined as follows. RT-PCR analysis using Taq Man probe specific for V. cholerae 16S rRNA was used to estimate the amount of V. cholerae RNA in the total RNA fraction. This estimate was used to determine the amount of rabbit RNA that was added to the mid log phase reference V. cholerae RNA. Labeling of cDNA and microarray hybridizations were performed as described [Yiliz et al. 2001, Mol. Micro. 53: 497-515].

tag: experiment

value: 2ug vc RNA from 8 h rabbit loop


title: NUID-0000-0087-6677

description: LDE225AZ 40 mg/kg resistant #1


title: vcc904 rabbit exp 21

description:
Simple annotation: Infection, wild-type
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43252.gif

source_name: wt mid log reference RNA/ rabbit RNA (1:1.5) 2 ugRNA

value: wt mid log reference rna/ rabbit rna (1:1.5) 2 ugRNA

source_name: wt in fluid (2 ug RNA)

value: wt in fluid (2 ug RNA)


title: NUID-0000-0087-6678

description: LDE225AZ 40 mg/kg resistant #2


title: NUID-0000-0087-6682

description: LDE225AZ 160 mg/kg resistant #3


title: vcc1116 rabit exp 17

description:
Simple annotation: Enteric environment, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41429.gif

source_name: wt mid log reference RNA/ rabbit RNA (1:2)

value: wt mid log reference rna/ rabbit rna (1:2)

source_name: wt RNA (from vibrio in ileal loop fluid) 8h rabbit


title: NUID-0000-0087-6681

description: LDE225AZ 160 mg/kg resistant #2


title: NUID-0000-0087-6680

description: LDE225AZ 160 mg/kg resistant #1


title: vcc523 rabit exp 16

description:
Simple annotation: Enteric environment, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41435.gif

source_name: wt mid log reference RNA/ rabbit RNA (1:2.5)

value: wt mid log reference rna/ rabbit rna (1:2.5)

source_name: wt RNA (from vibrio attached to epothelium) 12h rabbit

extract_protocol: The mucus gel/cell associated fraction was suspended in Trizol and frozen on dry ice. Total RNA, which includes RNA from the infecting bacteria and from the host (see below), was isolated from the thawed Trizol suspension, treated with DNaseI (Applied Biosystems, Austin, TX) and cleaned by using the RNeasy kit (Qiagen, Valencia, CA). To avoid microarray expression artifacts imparted by the presence of host RNA, RNA was prepared from a healthy rabbit and added to the V. cholerae reference RNA, isolated as described above from bacteria grown to mid exponential phase in LB broth. The amount of host RNA added to the V. cholerae reference RNA was determined as follows. RT-PCR analysis using Taq Man probe specific for V. cholerae 16S rRNA was used to estimate the amount of V. cholerae RNA in the total RNA fraction. This estimate was used to determine the amount of rabbit RNA that was added to the mid log phase reference V. cholerae RNA. Labeling of cDNA and microarray hybridizations were performed as described [ Nielsen AT, et al. (2006) PLoS Pathog 2(10):e109]


title: 9 vcb1270-rabbit exp 5

description:
Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24795.gif

source_name: mid log reference LB 37 C 1.5 ug RNA

value: mid log reference LB 37 C 1.5 ug RNA

source_name: 8h ileal loop 1.5 ug RNA

value: 8h ileal loop 1.5 ug RNA


title: vcc688 rabit exp 17

description:
Simple annotation: Enteric environment, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41430.gif

value: wt RNA (from vibrio in ileal loop fluid) 8h rabbit


title: LDE RES 160 mg/kg/day bid, Mouse 3 (mRNA)

source_name: NVP-LDE225 resistant Ptch+/-p53-/-  medulloblastoma tumors

value: 160 mg/kg/day bid

value: bid (twice a day)

value: The resistant tumors were observed after 13 of continuous dosing of NVP-LDE225.  The mice were treated until the tumors were harvested at day 26 of treatment.


title: LDE RES 160 mg/kg/day bid, Mouse 2 (mRNA)

value: Medulloblastoma

value: Resistant


title: vcc521 8 h rabbit experiment 5

description:
Simple annotation: Infection, pathogenesis
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36497.gif


title: vcc1439 rabbit exp 21

description:
Simple annotation: Infection, wild-type
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43251.gif


title: vcc694 rabbit exp 21

description:
Simple annotation: Infection, wild-type
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43253.gif


title: vcc1029 rabbit exp 24

description:
Simple annotation: Infection, pathogenesis
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44946.gif

source_name: wt mid log in LB 2 ug RNA

value: wt mid log in LB 2 ug RNA

value: wt RNA (from vibrio attached to epothelium) 12h rabbit


title: LDE RES 160 mg/kg/day bid, Mouse 1 (mRNA)

description: Medulloblastoma tumors derived from Ptch+/-p53-/- transgenic mouse allografted in nude mice


title: vcc1130 rabit exp 17

description:
Simple annotation: Enteric environment, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41432.gif


title: MM#7_19-35

source_name: purified CD138+ plasma cells from myeloma patient

value: 71 yrs

value: male

source_name: tonsil

tag: sample type

value: pooled tonsils (n=12)


title: vcc852 rabbit exp 24

description:
Simple annotation: Infection, pathogenesis
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44950.gif


title: vcc724 rabbit exp 24

description:
Simple annotation: Infection, pathogenesis
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44951.gif


title: LDE RES 20 mg/kg/day bid, Mouse 2 (mRNA)

value: 20 mg/kg/day bid


title: LDE RES 20 mg/kg/day bid, Mouse 1 (mRNA)


title: vcc1125 rabit exp 16

description:
Simple annotation: Enteric environment, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41437.gif

source_name: wt RNA (from vibrio attached to epithelium) 12h rabbit


title: LDE-48h 20 mg/kg/day qd, Mouse 2 (mRNA)

source_name: NVP-LDE225 treated Ptch+/-p53-/-  medulloblastoma tumors

value: Sensitive

value: 20 mg/kg/day qd

value: qd (once a day)


title: LDE-48h 20 mg/kg/day qd, Mouse 1 (mRNA)


title: LDE-16h 20 mg/kg/day qd, Mouse 3 (mRNA)


title: LDE-16h 20 mg/kg/day qd, Mouse 2 (mRNA)


title: vcc693 rabit exp 16

description:
Simple annotation: Enteric environment, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41439.gif

value: wt mid log reference rna/ rabbit rna (1:2.5)

value: wt RNA (from vibrio attached to epithelium) 12h rabbit


title: DEED+activin+RA (ExpIII)

city: Hong Kong

first: Hui

last: Zhao

address: The Chinese University of Hong Kong

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

description: Animal caps were injected with DEED-As, and then treated with activin and retinoic acid in experiment III.

hyb_protocol: Total 2.2 microgram fargmented, biotin labeled amplified cDNA was used for hybridization, and the hybridization last for 18 hours.

scan_protocol: Scanning was performed by using GeneChip Scanner 3000 driven by GCOS1.4.

data_processing: Single Array Analysis were performed by using GCOS1.4. Briefly, the “Target Signal” for “all probe set” was set to 500. Select “User Defined” and place a “1” as the "Normalization Value” in the “Normalization” tab. Detection p-value less than 0.04 is assigned a Present call, and above 0.06 is assigned an Absent call. Marginal calls are given to probe sets which have p-values between 0.04 and 0.06. 

organism: Xenopus laevis

source_name: DEED+activin+RA (ExpIII)

label_protocol: Biotinylated probe was prepared from 100 ng total RNA using the OVATION RNA amplification system (Nugen Technologies, Inc).

growth_protocol: The DEED-As injected animal caps were cultured in 1X Danilchik’s solution with 1X10-4 M retinoic acid and 10ng/ml Activin till the sibling embryos reached stage 12.5.

extract_protocol: The dissected explants were homogenized in Stat 60 (TEL TEST), RNA was precipitated by isopropanol, treated with DNase I, and purified using the RNeasy kit (Qiagen).

treatment_protocol: The embryos at two cell stage were injected with DEED-As nucleotide against Xenopus lhx1.The animal caps were dissected from the injected embryos at stage 9, and then treated with 1X10-4 M retinoic acid and 10ng/ml Activin.

value: animal cap cells dissected from embryos injected with DEED antisense (DEED-As) nucleotide against Xenopus lhx1

tag: treatment group

value: treated with activin and retinoic acid


title: vcc1127 rabit exp 16

description:
Simple annotation: Enteric environment, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41436.gif


title: vcc720 rabbit experiment 23

description:
Simple annotation: Infection, pathogenesis
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44701.gif

source_name: wt mid log in LB RNA (2 ug)

value: wt mid log in LB RNA (2 ug)

source_name: wt RNA (from vibrio attached to epithelium) 8h rabbit


title: DEED+activin+RA (ExpI)

description: Animal caps were injected with DEED-As, and then treated with activin and retinoic acid in experiment I.

source_name: DEED+activin+RA (ExpI)


title: LDE-4h 20 mg/kg/day qd, Mouse 3 (mRNA)


title: vcc717 rabbit experiment 23

description:
Simple annotation: Infection, pathogenesis
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44697.gif

value: wt RNA (from vibrio attached to epithelium) 8h rabbit


title: vcc1128 rabit exp 17

description:
Simple annotation: Enteric environment, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41424.gif

value: wt mid log reference rna/ rabbit rna (1:2)


title: vcc716 rabbit exp 24

description:
Simple annotation: Infection, pathogenesis
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44953.gif

source_name: wt mid log reference in LB 37 C (2 ug RNA)


title: DEED+activin+RA (ExpII)

description: Animal caps were injected with DEED-As, and then treated with activin and retinoic acid in experiment II.

source_name: DEED+activin+RA (ExpII)


title: LDE-16h 20 mg/kg/day qd, Mouse 1 (mRNA)

value: Medulloblastoma


title: vcc1114 rabit exp 17

description:
Simple annotation: Enteric environment, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41421.gif

source_name: wt mid log reference RNA/ rabbit RNA (1:2)


title: vcc719 rabbit experiment 23

description:
Simple annotation: Infection, pathogenesis
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44699.gif


title: LDE-4h 20 mg/kg/day qd, Mouse 2 (mRNA)


title: Activin+RA cap (ExpIII)

description: Animal caps were treated with retinoic acid and Activin in experiment III.

source_name: Activin+RA cap (ExpIII)

growth_protocol: The animal caps were cultured in 1X Danilchik’s solution with 1X10-4 M retinoic acid and 10ng/ml Activin till the sibling embryos reached stage 12.5.

treatment_protocol: The animal caps were dissected from stage 9 embryos of Xenopus laevis, and then treated with 1X10-4 M retinoic acid and 10ng/ml Activin.

value: animal cap cells


title: vcc1129 rabit exp 17

description:
Simple annotation: Enteric environment, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41426.gif


title: DEED animal cap (ExpII)

description: Animal caps were injected with DEED-As in experiment II.

source_name: DEED animal cap (ExpII)

growth_protocol: The DEED-As injected animal caps were cultured in 1X Danilchik’s solution till the sibling embryos reached stage 12.5.

treatment_protocol: The embryos at two cell stage were injected with DEED-As nucleotide against Xenopus lhx1.The animal caps were dissected from the injected embryos at stage 9.


title: Activin+RA cap (ExpII)

description: Animal caps were treated with retinoic acid and Activin in experiment II.

source_name: Activin+RA cap (ExpII)


title: Veh-16h, Mouse 2 (mRNA)

description: Medulloblastoma tumors derived from Ptch+/-p53-/- transgenic mouse allografted in nude mice

source_name: Vehicle treated Ptch+/-p53-/-  medulloblastoma tumors

value: Vehicle


title: vcc1133 rabit exp 17

description:
Simple annotation: Enteric environment, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41422.gif


title: Veh-48h, Mouse 1 (mRNA)


title: DEED animal cap (ExpIII)

description: Animal caps were injected with DEED-As in experiment III.

source_name: DEED animal cap (ExpIII)


title: vcc1449 rabbit experiment 23

description:
Simple annotation: Infection, pathogenesis
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44698.gif


title: Veh-16h, Mouse 1 (mRNA)


title: Veh-48h, Mouse 3 (mRNA)


title: Veh-16h, Mouse 3 (mRNA)


title: Activin+RA cap (ExpI)

description: Animal caps were treated with retinoic acid and Activin in experiment I.

source_name: Activin+RA cap (ExpI)


title: DEED animal cap (ExpI)

description: Animal caps were injected with DEED-As in experiment I.

source_name: DEED animal cap (ExpI)


title: control animal cap (ExpII)

description: Control animal cap in experiment II.

source_name: control animal cap (ExpII)

growth_protocol: The animal caps were cultured in 1X Danilchik’s solution till the sibling embryos reached stage 12.5.

treatment_protocol: The animal caps were dissected from stage 9 embryos of Xenopus laevis


title: control animal cap (ExpI)

description: Control animal cap in experiment I.

hyb_protocol: totoal 2.2 microgram Fargmented, biotin labeled amplified cDNA was used for hybridization, and the hybridization last for 18 hours.

source_name: control animal cap (ExpI)


title: LDE-4h 20 mg/kg/day qd, Mouse 1 (mRNA)

source_name: NVP-LDE225 treated Ptch+/-p53-/-  medulloblastoma tumors


title: TE fraction 57

status: Public on Sep 28 2010

first: David

middle: Scott

last: Johnson

department: Genetics

institute: Stanford University

hyb_protocol: as per Illumina's instructions except reduced time to 6 hours

scan_protocol: iScan scanner

data_processing: Genotypes are inherently inaccurate in single cell microarray data due to biases introduced during multiple displacement amplification. Therefore  genotypes were not produced, and instead raw intensity data was used to build probabilistic models under the framework of the Parental Support   algorithm.

label: C-Bio and A-DNP

source_name: TE fraction

label_protocol: as per Illumina's instructions except reduced amplification time to 6 hours

extract_protocol: We thawed all fractions at 22°C, and then added Arcturus PicoPure Lysis Buffer (Molecular Devices, Sunnyvale, CA) to each of the biopsies. The tubes were incubated at 56°C for one hour, and then heat inactivated at 95°C for 10 minutes. DNA from the lysed biospsies was amplified using a commercial kit (GE Healthcare, Waukesha, WI) for multiple displacement amplification (MDA). MDA reactions were incubated at 30°C for 2.5 hours and then heat-inactivated at 65°C for five minutes.

value: trophectoderm


title: TE fraction 91


title: TE fraction 93


title: ICM fraction 56

source_name: ICM fraction

value: inner cell mass


title: TE fraction 55


title: ICM fraction 54


title: Veh-4h, Mouse 3 (mRNA)


title: TE fraction 53


title: ICM fraction 52


title: control animal cap (ExpIII)

description: Control animal cap in experiment III.

source_name: control animal cap (ExpIII)


title: ICM fraction 92


title: TE fraction 51


title: ICM fraction 50


title: ICM fraction 48


title: TE fraction 47


title: Veh-4h, Mouse 1 (mRNA)


title: ICM fraction 45


title: TE fraction 46


title: TE fraction 44


title: TE fraction 43


title: ICM fraction 42


title: TE fraction 41


title: TE fraction 40


title: TE fraction 38


title: TE fraction 49


title: TE fraction 35


title: ICM fraction 36


title: TE fraction 32


title: Veh-4h, Mouse 2 (mRNA)


title: TE fraction 37


title: TE fraction 31


title: ICM fraction 39


title: ICM fraction 30


title: TE fraction 34


title: ICM fraction 28


title: ICM fraction 26


title: TE fraction 27


title: TE fraction 25


title: TE fraction 29


title: ICM fraction 22


title: ICM fraction 33


title: TE fraction 21


title: TE fraction 23


title: TE fraction 20


title: ICM fraction 19


title: TE fraction 17


title: ICM fraction 16


title: TE fraction 15


title: ICM fraction 24


title: TE fraction 18


title: Bcl6 -/- BCR-ABL1-driven ALL 1

city: Los Angeles

first: Markus

last: Müschen

address: 4650 Sunset Blvd

department: Childrens Hospital Los Angeles

institute: University of Southern California

description: Processed data file: KO 372033A01_SLOT47_segMNT.txt

hyb_protocol: Performed according to NimbleGen protocols (performed by MOgeneLC)

scan_protocol: Scanning was performed in accordance with the NimbleGen protocol

data_processing: Analyzed with Nexus Biodiscovery program using the FASST-segmentation algorithm

source_name: genomic DNA from splenocytes [control]

extract_protocol: Genomic DNA were extracted using PureLink from Invitrogen

tag: strain

tag: age

value: 4 weeks

value: spleen

tag: cell type

value: splenocyte

tag: disease state

value: normal, untransformed

source_name: BCL6 -/- BCR-ABL1-driven ALL [test]

value: 5 months

tag: cell culture

value: BCR-ABL1 transformed pre-B cells

value: BCR-ABL1-driven ALL

tag: genotype/variation

value: BCL6 knockout


title: ICM fraction 13


title: ICM fraction 10


title: Bcl6 -/- BCR-ABL1-driven ALL 2

description: Processed data file: KO 372033A02_SLOT47_segMNT.txt

label_protocol: Performed according to NimbleGen protocols (performed by MOgeneLC)


title: TE fraction 12


title: Bcl6 +/+ BCR-ABL1-driven ALL 2

description: Processed data file: WT 372032A02_SLOT46_segMNT.txt

source_name: BCL6 +/+ BCR-ABL1-driven ALL [test]

value: BCL6 wildtype


title: TE fraction 9


title: TE fraction 14


title: TE fraction 8


title: Bcl6 -/- BCR-ABL1-driven ALL 3

description: Processed data file: KO 372033A03_SLOT47_segMNT.txt


title: 1991_p_1

city: Chiba

first: Shuhei

last: Noda

state: Chiba

address: Anagawa 4-9-1

department: Frontier research center

institute: National institute of radiological sciences

description: prior to treatment, chemoradiotherapy

data_processing: global median normalization

source_name: biopsy, prior to treatment, chemoradiotherapy

extract_protocol: ISOGEN(NIPPON GENE)+RNeasy(QIAGEN)

tag: female, cervical cancer


title: 2031_p_2

description: prior to treatment, chemoradiotherapy


title: 785_p_2

description: prior to treatment, chemoradiotherapy


title: 1991_p_2

description: prior to treatment, chemoradiotherapy


title: 2031_p_1

description: prior to treatment, chemoradiotherapy


title: Bcl6 +/+ BCR-ABL1-driven ALL 3

description: Processed data file: WT 372032A03_SLOT46_segMNT.txt


title: 2650_p_2

description: prior to treatment, chemoradiotherapy


title: ICM fraction 7


title: 785_p_1

description: prior to treatment, chemoradiotherapy


title: TE fraction 6


title: 2652_p_2

description: prior to treatment, chemoradiotherapy


title: 2652_p_1

description: prior to treatment, chemoradiotherapy


title: 2650_p_1

description: prior to treatment, chemoradiotherapy


title: TE fraction 5


title: ICM fraction 4


title: ICM fraction 3


title: TE fraction 2


title: Bcl6 +/+ BCR-ABL1-driven ALL 1

description: Processed data file: WT 372032A01_SLOT46_segMNT.txt


title: 2321_p_2

description: prior to treatment, chemoradiotherapy


title: ICM fraction 1


title: TE fraction 127


title: TE fraction 128


title: TE fraction 130


title: ICM fraction 129


title: ICM fraction 126


title: TE fraction 125


title: ICM fraction 124


title: ICM fraction 122


title: TE fraction 121


title: TE fraction 11


title: 2319_p_1

source_name: biopsy, prior to treatment, carbon-ion radiotherapy


title: TE fraction 117


title: TE fraction 119


title: ICM fraction 118


title: TE fraction 116


title: 2035_p_2

description: prior to treatment, radiotherapy alone

source_name: biopsy, prior to treatment, radiotherapy alone


title: 2316_p_2

description: prior to treatment, carbon-ion radiotherapy


title: 2317_p_1

description: prior to treatment, radiotherapy alone


title: 1849_p_1

description: prior to treatment, chemoradiotherapy


title: 2321_p_1

description: prior to treatment, chemoradiotherapy


title: 2035_p_1

description: prior to treatment, radiotherapy alone


title: 1847_p_1

description: prior to treatment, chemoradiotherapy


title: ICM fraction 115


title: 2317_p_2

description: prior to treatment, radiotherapy alone


title: 1843_p_2

description: prior to treatment, radiotherapy alone


title: 2033_p_1

description: prior to treatment, radiotherapy alone


title: 1843_p_1

description: prior to treatment, radiotherapy alone


title: TE fraction 114


title: ICM fraction 120


title: 1847_p_2

description: prior to treatment, chemoradiotherapy


title: TE fraction 123


title: 1987_p_2

description: prior to treatment, radiotherapy

source_name: biopsy, prior to treatment, radiotherapy


title: 2319_p_2


title: 2316_p_1


title: 1849_p_2

description: prior to treatment, chemoradiotherapy


title: ICM fraction 113


title: 2033_p_2

description: prior to treatment, radiotherapy alone


title: 1679_p_1


title: 1987_p_1

description: prior to treatment, radiotherapy


title: TE fraction 112


title: ICM fraction 111


title: TE fraction 110


title: 1679_p_2


title: 1689_p_1

description: prior to treatment, chemoradiotherapy


title: ICM fraction 109


title: 1689_p_2

description: prior to treatment, chemoradiotherapy


title: TE fraction 107


title: TE fraction 108


title: ICM fraction 106


title: TE fraction 105


title: ICM fraction 103


title: TE fraction 104


title: 1602_p_1

description: prior to treatment, chemoradiotherapy


title: 1602_p_2

description: prior to treatment, chemoradiotherapy


title: TE fraction 101


title: TE fraction 99


title: 1600_p_1


title: 1598_p_2

description: prior to treatment, radiotherapy alone


title: 1601_p_2


title: TE fraction 98


title: TE fraction 102


title: ICM fraction 97


title: 1601_p_1


title: 1596_p_2

description: prior to treatment, chemoradiotherapy


title: TE fraction 96


title: 1600_p_2


title: 1594_p_2

description: prior to treatment, radiotherapy alone


title: 1598_p_1

description: prior to treatment, radiotherapy alone


title: ICM fraction 100


title: TE fraction 95


title: 1593_p_2

description: prior to treatment, chemoradiotherapy


title: 1593_p_1

description: prior to treatment, chemoradiotherapy


title: 1352_p_2


title: 1594_p_1

description: prior to treatment, radiotherapy alone


title: 1596_p_1

description: prior to treatment, chemoradiotherapy


title: 1589_p_1

description: prior to treatment, chemoradiotherapy


title: 1589_p_2

description: prior to treatment, chemoradiotherapy


title: 1352_p_1


title: 1349_p_1

description: prior to treatment, chemoradiotherapy


title: 782_p_2


title: 1349_p_2

description: prior to treatment, chemoradiotherapy


title: ICM fraction 90


title: TE fraction 89


title: TE fraction 88


title: ICM fraction 87


title: ICM fraction 94


title: TE fraction 86


title: TE fraction 85


title: ICM fraction 84


title: Alveolar echinococcosis mice at 3 month time point replicate 3 32K array

city: Urumqi

first: guo

middle: dong

last: lv

state: Xinjiang

address: liyushan

department: clinical cases reserch center

country: China

institute: Xinjiang medical hospital

description: Biology replicate 3 of 3. Compare gene expression profiles of alveolar echinococcosis mice anterior liver at 3 month with healthy BALB/c mice anterior liver.

hyb_protocol: standard CapitalBio Methods

scan_protocol: Luxscan 10K (CapitalBio)

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. capitalbio software was used.

source_name: The anterior liver tissue of alveolar echinococcosis mice group

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP, Amersham Pharmacia Biotech, Piscataway, NJ) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction. the amplified RNA (aRNA) was purified with NucleoSpin Extract II (MN). We took a cDNA labeling approach with Klenow enzyme after reverse transcription.

growth_protocol: Pathogen-free female BALB/c mice (8-10-week old) purchased from animal center of Xijiang Medical University were housed in cages with a 12-h light/dark cycle and provided with rodent chow and water.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: To produce alveolar echinococcosis mice, 0.1 mL pooled lesions (~1000 protoscoleces) of Echinococcus multilocularis was injected into the anterior liver lobe of pathogen-free female BALB/c mice. And the control mice was received an intra-hepatic injection of 0.1 mL of saline in the anterior liver lobe using the same surgical procedure. Mice were killed at 1 and 3 months, respectively.

value: BALB/c

value: anterior liver

value: injected with 0.1 mL pooled lesions (~1002 protoscoleces) of Echinococcus multilocularis

source_name: the pool RNA of healthy BALB/c mice anterior liver


title: Alveolar echinococcosis mice at 3 month time point replicate 1 32K array

description: Biology replicate 1 of 3. Compare gene expression profiles of alveolar echinococcosis mice anterior liver at 3 month with healthy BALB/c mice anterior liver.

value: injected with 0.1 mL pooled lesions (~1000 protoscoleces) of Echinococcus multilocularis


title: Alveolar echinococcosis mice at 3 month time point replicate 2 32K array

description: Biology replicate 2 of 3. Compare gene expression profiles of alveolar echinococcosis mice anterior liver at 3 month with healthy BALB/c mice anterior liver.

value: injected with 0.1 mL pooled lesions (~1001 protoscoleces) of Echinococcus multilocularis


title: Control mice at 3 month time point replicate 1 32K array

description: Biology replicate 1 of 3. Compare gene expression profiles of control mice anterior liver at 3 month with healthy BALB/c mice anterior liver.

source_name: The anterior liver tissue of control mice group

value: injected with 0.1 mL of saline


title: Alveolar echinococcosis mice at 1 month time point replicate 2 32K array

description: Biology replicate 2 of 3. Compare gene expression profiles of alveolar echinococcosis mice anterior liver at 1 month with healthy BALB/c mice anterior liver.


title: Alveolar echinococcosis mice at 1 month time point replicate 3 32K array

description: Biology replicate 3 of 3. Compare gene expression profiles of alveolar echinococcosis mice anterior liver at 1 month with healthy BALB/c mice anterior liver.


title: Control mice at 3 month time point replicate 2 32K array

description: Biology replicate 2 of 3. Compare gene expression profiles of control mice anterior liver at 3 month with healthy BALB/c mice anterior liver.


title: 781_p_1


title: TE fraction 83

value: trophectoderm


title: 515_p_2

description: prior to treatment, radiotherapy alone


title: Alveolar echinococcosis mice at 1 month time point replicate 1 32K array

description: Biology replicate 1 of 3. Compare gene expression profiles of alveolar echinococcosis mice anterior liver at 1 month with healthy BALB/c mice anterior liver.


title: 782_p_1


title: 515_p_1

description: prior to treatment, radiotherapy alone


title: TE fraction 82


title: Control mice at 3 month time point replicate 3 32K array

description: Biology replicate 3 of 3. Compare gene expression profiles of control mice anterior liver at 3 month with healthy BALB/c mice anterior liver.


title: ICM fraction 81

value: inner cell mass


title: 512_p_1

description: prior to treatment, radiotherapy alone


title: 513_p_2

description: prior to treatment, radiotherapy alone


title: 513_p_1

description: prior to treatment, radiotherapy alone


title: Control mice at 1 month time point replicate 2 32K array

description: Biology replicate 2 of 3. Compare gene expression profiles of control mice anterior liver at 1 month with healthy BALB/c mice anterior liver.


title: TE fraction 80


title: 512_p_2

description: prior to treatment, radiotherapy alone


title: TE fraction 79


title: Alveolar echinococcosis mice at 6 month time point replicate 3 36K array

description: Biology replicate 3 of 3. Compare gene expression profiles of alveolar echinococcosis mice anterior liver at 6 month with healthy BALB/c mice anterior liver.

treatment_protocol: To produce alveolar echinococcosis mice, 0.1 mL pooled lesions (~1000 protoscoleces) of Echinococcus multilocularis was injected into the anterior liver lobe of pathogen-free female BALB/c mice. And the control mice was received an intra-hepatic injection of 0.1 mL of saline in the anterior liver lobe using the same surgical procedure. Mice were killed at 2 and 6 months, respectively.


title: Alveolar echinococcosis mice at 6 month time point replicate 2 36K array

description: Biology replicate 2 of 3. Compare gene expression profiles of alveolar echinococcosis mice anterior liver at 6 month with healthy BALB/c mice anterior liver.


title: TE fraction 76


title: ICM fraction 75


title: Control mice at 1 month time point replicate 3 32K array

description: Biology replicate 3 of 3. Compare gene expression profiles of control mice anterior liver at 1 month with healthy BALB/c mice anterior liver.


title: 781_p_2


title: Control mice at 6 month time point replicate 2 36K array

description: Biology replicate 2 of 3. Compare gene expression profiles of control mice anterior liver at 6 month with healthy BALB/c mice anterior liver.


title: TE fraction 77


title: Control mice at 1 month time point replicate 1 32K array

description: Biology replicate 1 of 3. Compare gene expression profiles of control mice anterior liver at 1 month with healthy BALB/c mice anterior liver.


title: TE fraction 74


title: Alveolar echinococcosis mice at 2 month time point replicate 3 36K array

description: Biology replicate 3 of 3. Compare gene expression profiles of alveolar echinococcosis mice anterior liver at 2 month with healthy BALB/c mice anterior liver.


title: ICM fraction 73


title: Control mice at 6 month time point replicate 1 36K array

description: Biology replicate 1 of 3. Compare gene expression profiles of control mice anterior liver at 6 month with healthy BALB/c mice anterior liver.


title: Alveolar echinococcosis mice at 2 month time point replicate 1 36K array

description: Biology replicate 1 of 3. Compare gene expression profiles of alveolar echinococcosis mice anterior liver at 2 month with healthy BALB/c mice anterior liver.


title: Control mice at 6 month time point replicate 3 36K array

description: Biology replicate 3 of 3. Compare gene expression profiles of control mice anterior liver at 6 month with healthy BALB/c mice anterior liver.


title: Alveolar echinococcosis mice at 2 month time point replicate 2 36K array

description: Biology replicate 2 of 3. Compare gene expression profiles of alveolar echinococcosis mice anterior liver at 2 month with healthy BALB/c mice anterior liver.


title: TE fraction 72


title: ICM fraction 78


title: Alveolar echinococcosis mice at 6 month time point replicate 1 36K array

description: Biology replicate 1 of 3. Compare gene expression profiles of alveolar echinococcosis mice anterior liver at 6 month with healthy BALB/c mice anterior liver.


title: TE fraction 71


title: Control mice at 2 month time point replicate 3 36K array

description: Biology replicate 3 of 3. Compare gene expression profiles of control mice anterior liver at 2 month with healthy BALB/c mice anterior liver.


title: ICM fraction 70


title: Control mice at 2 month time point replicate 1 36K array

description: Biology replicate 1 of 3. Compare gene expression profiles of control mice anterior liver at 2 month with healthy BALB/c mice anterior liver.


title: Control mice at 2 month time point replicate 2 36K array

description: Biology replicate 2 of 3. Compare gene expression profiles of control mice anterior liver at 2 month with healthy BALB/c mice anterior liver.


title: 2515_p_2

description: prior to treatment, carbon-ion radiotherapy


title: 2515_p_1


title: 2038_p_2


title: TE fraction 68


title: ICM fraction 67


title: TE fraction 69


title: TE fraction 66


title: TE fraction 65


title: 2038_p_1


title: 2036_p_2


title: ICM fraction 64


title: TE fraction 63


title: TE fraction 62


title: 2312_p_1


title: 2029_p_2


title: 2036_p_1


title: Idd3 CD11b+ cells PGN stimulated, biological rep2

first: Vijay

last: Kuchroo

address: 77 Avenue Louis Pasteur, HIM 785

institute: Harvard Medical School

description:
Idd3 PGN-2
Idd3 PGN_1576B.CEL

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA normalization method, software- Expression File Creator

source_name: Idd3 CD11b+ PGN stimulated

label_protocol: Nugen Encore Biotin Module

growth_protocol: Cells were incubated at 37 degrees

extract_protocol: Qiagen Rneasy

treatment_protocol: Cells were incubated with either media alone (unstimulated condition) or with 5 ug/ml peptidoglycan

value: CD11b+ cells

tag: agent

value: PGN

tag: biological rep


title: Idd3 CD11b+ cells PGN stimulated, biological rep1

description:
Idd3 PGN-1
Idd3 PGN_5.28.09_1576F.CEL


title: Idd3 CD11b+ cells unstimulated, biological rep1

description:
Idd3 0-1
Idd3  0_5.28.09_1576E_RR1.CEL

source_name: Idd3 CD11b+ unstimulated

value: control


title: Idd3 CD11b+ cells unstimulated, biological rep2

description:
Idd3 0-2
Idd3 0_1576A.CEL


title: 2032_p_2


title: ptsN mutant replicate 2

city: Seoul

first: Yeong-Jae

last: Seok

address: San 56-1, Shillim-dong, Gwanak-gu

department: Biological Sciences

country: South Korea

institute: Seoul National University

description: gene expression profile of ptsN mutant in M9 minimal medium, replicate 2.

hyb_protocol: Equal amounts of the labeled cDNA were combined and used to hybridize the microarray slides at 42°C for 16 h. After hybridization, the arrays were washed, dried.

scan_protocol: GeneChips were scanned using GenePix 4000B (Axon Instruments, Foster City, CA).

data_processing: Data from two independent experiments were normalized and then analyzed using the GenePix Pro 3.0 software (Axon Instruments).

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

source_name: Escherichia coli wild type strain

label_protocol: Aminoallyl cDNA was synthesized using an aminoallyl cDNA-labeling kit according to the protocols of the manufacturer (Ambion, Austin, TX).The aminoallyl cDNA from the ptsN mutant and that from the wild type were labeled with Cy3 and Cy5 (Ambion), respectively.

growth_protocol: The E. coli K12 strain MG1655 and its isogenic ptsN mutant were grown in M9 minimal medium containing 0.5% glucose as carbon source. Cells from duplicate experiments were harvested in exponential growth phase when cultures reached an A600 of 0.4.

extract_protocol: RNA was extracted from each sample using a QIAGEN RNA extraction kit according to the manufacturer’s instruction

value: wild type

source_name: Escherichia coli ptsN mutant strain

value: delta ptsN


title: NOD CD11b+ cells PGN stimulated, biological rep2

description:
NOD PGN-2
NOD PGN_1576D_RR1.CEL

source_name: NOD CD11b+ PGN stimulated

value: NOD


title: 2312_p_2


title: 1586_p_1


title: ICM fraction 61

source_name: ICM fraction


title: NOD CD11b+ cells unstimulated, biological rep2

description:
NOD 0-2
NOD 0_1576C_RR1.CEL

source_name: NOD CD11b+ unstimulated


title: TE fraction 60

source_name: TE fraction


title: NOD CD11b+ cells unstimulated, biological rep1

description:
NOD 0-1
NOD  0_5.28.09_1576G.CEL


title: NOD CD11b+ cells PGN stimulated, biological rep1

description:
NOD PGN-1
NOD PGN_5.28.09_1576H.CEL


title: 1244_p_2


title: 1244_p_1


title: 1586_p_2


title: ICM fraction 58