title: 13420263 - ColO-0min-2 vs wrky19-0min-2

hyb_protocol: wrky19-0min-2 Cy5 / ColO-0min-2 Cy3 : 30pmol. 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: Uberp10_0045(Rpr1_ts|WT.A)

status: Public on Jun 01 2008

type: RNA

city: Lexington

first: Gregg

middle: Brooks

last: Whitworth

state: VA

address: 204 West Washington St

department: Biology

country: USA

institute: Washington and Lee Unversity

description: a complete description of the sample collection protocol and source strains can be found in PMID: PENDING EPUB DATE

hyb_protocol: Competitive hybridization at 65oC for 12h

scan_protocol: images were acquired using an Axon Instruments GenePix 4000B scanner, reading at wavelengths of 635nm and 532nm (Axon Instruments). Image analysis was performed using Axon Instruments GenePix Pro version 4.0.

data_processing: Spot ratio data were log2 transformed and normalized within each array using global loess regression implemented in the Bioconductor marray package

molecule: total RNA

organism: Saccharomyces cerevisiae

label_protocol: aa-dUTP incorporation during cDNA synthesis

extract_protocol: Acid phenol

tag: 'Genotype

value: matched wt for rpr1-ts'


title: Uberp10_0042(Streptavidin_Aptamer|untagged.B)

tag: 'Factor

value: untagged control'


title: 13419852 - mkk2-30min-1 vs ColO-30min-1

status: Public on Jul 01 2008

city: Evry

first: Frederique

last: Bitton

address: 2 rue Gaston Cremieux

country: France

institute: INRA

description: early response targets of MKK2 upon cold stress treatment and its role in adaptation.

hyb_protocol: ColO-30min-1 Cy5 / mkk2-30min-1 Cy3 : 30pmol. 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,650V,laser power 100%, Cy5:635nm,pmt voltage 620V,laser power 100%

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

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 indirect, amplification=yes, DNA 5 ug. 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: aerial - 1/2 MS with 1.5g Sucrose/l 24°C light : long day conditions

treatment_protocol: Name:cold-30min - abiotic stress - temperature,temperature:quantity 4° time 30min .

tag: Arabidopsis thaliana (columbia)  - dev.stage (Boyes et al. Plant Cell 2001):boyes

tag: Arabidopsis thaliana (columbia)  mutant (mkk2) - dev.stage (Boyes et al. Plant Cell 2001):boyes


title: MeWo_X-rays_2Gy3h_1

city: Chiba-shi

first: Yoshitaka

last: Matsumoto

state: Chiba

address: 4-9-1, Anagawa, Inage-ku

department: Research Center for Charged Particle Therapy

country: Japan

institute: National Institute of Radiological Sciences

hyb_protocol: Hybridization was performed according to the CodeLink manual http://www4.amershambiosciences.com/APTRIX/upp00919.nsf/Content/WD%3ACodeLink+Gene+E%28270810969-B500%29?OpenDocument&hometitle=WebDocs

scan_protocol: Scanning was performed according to the CodeLink manual http://www4.amershambiosciences.com/APTRIX/upp00919.nsf/Content/WD%3AScanning+CodeLi%28248345081-B500%30?OpenDocument&hometitle=WebDocs

data_processing: global median normalization

label: biotin

organism: Homo sapiens

source_name: cell line

label_protocol: Labeling was performed according to the CodeLink manual http://www4.amershambiosciences.com/APTRIX/upp00919.nsf/Content/WD%3ACodeLink+Gene+E%28270813678-B500%29?OpenDocument&hometitle=WebDocs

tag: cell lines_human malignant melanoma_MeWo


title: Uberp10_0047(Pop1_ts1|WT.B)

source_name: WT>B

value: matched WT for pop1-ts1'


title: MeWo_X-rays_2Gy3h_3


title: MeWo_X-rays_2Gy1h_1


title: MeWo_X-rays_2Gy1h_2


title: MeWo_X-rays_2Gy3h_2


title: MeWo_X-rays_2Gy1h_3


title: MeWo_X-rays_0Gy_3


title: MeWo_C-ions_2Gy3h_3


title: MeWo_C-ions_2Gy3h_2


title: MeWo_C-ions_2Gy1h_1


title: HMV-II_X-rays_2Gy3h_3

tag: cell lines_human malignant melanoma_HMV-II


title: MeWo_C-ions_2Gy1h_2


title: MeWo_X-rays_0Gy_2


title: MeWo_C-ions_2Gy1h_3


title: HMV-II_X-rays_2Gy1h_2


title: HMV-II_X-rays_2Gy1h_3


title: MeWo_X-rays_0Gy_1


title: MeWo_C-ions_0Gy_3


title: HMV-II_X-rays_2Gy3h_2


title: HMV-II_X-rays_2Gy3h_1


title: HMV-II_X-rays_2Gy1h_1


title: HMV-II_X-rays_0Gy_2


title: MeWo_C-ions_0Gy_1


title: MeWo_C-ions_0Gy_2


title: MeWo_C-ions_2Gy3h_1


title: HMV-II_X-rays_0Gy_1


title: HMV-II_C-ions_2Gy3h_1


title: Colo679_X-rays_2Gy3h_3

tag: cell lines_human malignant melanoma_Colo679


title: HMV-II_C-ions_2Gy3h_3


title: HMV-II_C-ions_0Gy_3


title: HMV-II_C-ions_2Gy1h_2


title: HMV-II_X-rays_0Gy_3


title: HMV-II_C-ions_2Gy1h_3


title: HMV-II_C-ions_2Gy1h_1


title: Colo679_X-rays_2Gy3h_2


title: HMV-II_C-ions_2Gy3h_2


title: EAC tumor biopsy from 40363

type: genomic

city: Herston

first: Derek

middle: John

last: Nancarrow

state: Queensland

address: 300 Herston Road

department: Genetics & Population Health

country: Australia

institute: Queensland Institute of Medical Research

description: The EAC biopsies used in this study were collected as part of the Australian Cancer Study.

hyb_protocol: The dried precipitated pellet was then resuspended in WG-RA1 and hybridized to a beadchip along with WG-RA1 and formamide. The arrays were then incubated overnight at 48°C, after which they underwent single-base extension on a Teflow chamber rack system (Tecan, Männedorf, Switzerland) using WG-XC1, WG-XC2, and WG-TEM.

scan_protocol: After the single-base extension step, the beadchips were stained with WG-LTM and WG-ATM, dried for 1 h, then imaged using a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using Beadstudio 2.0 (Illumina). EAC samples log_R_ratio values were generated using the squamous sample 192R as a reference. All genomic positions were based upon hg17 from the UCSC Genome Browser.

label: C-Bio and A-DNP

molecule: genomic DNA

source_name: Esopageal Adenocarcinoma Tumor Biopsy

label_protocol: The Infinium II assay was done using Illumina Sentrix HumanHap300 genotyping BeadChip arrays (317K, TagSNP Phase I, v1.1) according to the manufacturer's specifications (Illumina, San Diego, CA). Briefly, 750 ng of genomic DNA were amplified at 37°C overnight, using solutions WG-AMM and WG-MP1. After overnight incubation, the amplified DNA was fragmented using WG-FRG and precipitated with isopropanol after the addition of WG-PA1.

extract_protocol: As per QIAGEN tissue lyser protocol using ALLPREP Kit

treatment_protocol: Fresh tissue was placed directly into RNAlater solution, stored at 4°C overnight, then -20°C. Long-term storage was then at -80°C after access RNAlater was removed.

tag: Biopsy taken by endoscopy prior to treatment. Subject details

tag: Gender

value: male

tag: Age

value: 69 years

tag: Tissue

value: EAC tumor

tag: Tumor stage

value: I


title: Colo679_X-rays_2Gy3h_1


title: HMV-II_C-ions_0Gy_1


title: Colo679_X-rays_2Gy1h_1


title: HMV-II_C-ions_0Gy_2


title: Colo679_X-rays_2Gy1h_3


title: Colo679_C-ions_2Gy1h_3


title: Colo679_X-rays_2Gy1h_2


title: Colo679_C-ions_2Gy3h_3


title: Colo679_C-ions_2Gy3h_1


title: Colo679_C-ions_2Gy1h_1


title: Colo679_C-ions_2Gy1h_2


title: Colo679_C-ions_0Gy_1


title: Colo679_C-ions_0Gy_3


title: Colo679_C-ions_0Gy_2


title: Colo679_C-ions_2Gy3h_2


title: C32TG_X-rays_2Gy1h_1

tag: cell lines_human malignant melanoma_C32TG


title: Colo679_X-rays_0Gy_1


title: C32TG_X-rays_2Gy3h_3


title: C32TG_X-rays_2Gy1h_2


title: 192R_normal squamous biopsy from 40328

description: The EAC biopsies used in this study were collected as part of the Australian Cancer Study. This squamous sample (192R) was used as a reference for all EACs in the series.

data_processing: Image data was analyzed using Beadstudio 2.0 (Illumina). This samples log_R_ratio values were generated against the Illumina reference panel.  This squamous sample (192R) was used as a reference for all EACs in the series. All genomic positions were based upon hg17 from the UCSC Genome Browser.

source_name: Normal Squamous Biopsy from EAC Patient

tag: Biopsy taken by endoscopy prior to treatment. This sample was used as a reference against all others in the series. Subject details

value: 65 years

value: Normal Squamous Biopsy from EAC Patient

value: III


title: Colo679_X-rays_0Gy_3


title: C32TG_X-rays_2Gy3h_2


title: C32TG_X-rays_2Gy3h_1


title: C32TG_C-ions_2Gy3h_3


title: C32TG_X-rays_0Gy_3


title: C32TG_X-rays_2Gy1h_3


title: Colo679_X-rays_0Gy_2


title: C32TG_C-ions_2Gy3h_2


title: C32TG_X-rays_0Gy_1


title: C32TG_C-ions_2Gy3h_1


title: C32TG_C-ions_0Gy_1


title: C32TG_C-ions_2Gy1h_2


title: 92-1_X-rays_2Gy3h_2

tag: cell lines_human malignant melanoma_92-1


title: C32TG_C-ions_0Gy_2


title: C32TG_C-ions_2Gy1h_3


title: 92-1_X-rays_2Gy1h_3


title: C32TG_C-ions_0Gy_3


title: 92-1_X-rays_2Gy3h_3


title: 92-1_X-rays_2Gy3h_1


title: 92-1_X-rays_0Gy_3


title: 92-1_X-rays_0Gy_2


title: C32TG_X-rays_0Gy_2


title: 92-1_X-rays_0Gy_1


title: 92-1_X-rays_2Gy1h_1


title: 92-1_C-ions_2Gy3h_2


title: 92-1_X-rays_2Gy1h_2


title: 92-1_C-ions_2Gy1h_3


title: 92-1_C-ions_2Gy3h_1


title: 92-1_C-ions_2Gy1h_1


title: 92-1_C-ions_0Gy_1


title: 92-1_C-ions_2Gy3h_3


title: 92-1_C-ions_0Gy_3


title: HMV-I_C-ions_2Gy3h_3

tag: cell lines_human malignant melanoma_HMV-I


title: 92-1_C-ions_0Gy_2


title: HMV-I_C-ions_2Gy1h_3


title: HMV-I_C-ions_2Gy3h_2


title: HMV-I_X-rays_0Gy_3

scan_protocol: Scanning was performed according to the CodeLink manual http://www4.amershambiosciences.com/APTRIX/upp00919.nsf/Content/WD%3AScanning+CodeLi%28248345081-B500%32?OpenDocument&hometitle=WebDocs


title: 30 Post

city: TRONDHEIM

first: Anja

last: Bye

address: Olav Kyrres gt 9

country: Norway

institute: NTNU

description: 30 Post exercise

hyb_protocol: RNA from each sample was hybridized to Applied Biosystem (AB) Human Genome Survey microarray v.2.0. The order of labeling and hybridization was randomised to avoid technical batch effects. The microarray analyses were performed on the AB 1700 Array Expression System.

scan_protocol: According to manufacture's instructions

data_processing: The data files from the AB 1700 Chemiluminescent Microarray Analyzer Software were processed using J-Express Pro v.2.7 to filter and normalize the data from each hybridisation and compile gene expression profile matrix (gene by sample) data sets for further analysis. The pre-normalized intensity values were extracted per spot from the data files, and all flagged, weak and control spots were filtered out. An unsupervised analysis of all samples using the Correspondence Analysis tool in JExpress was performed in order to spot any microarray-outliers in the dataset. A filtering value of signal to noise ratio (S/N) of minimum 3.0 was chosen to reduces most of the noise The S/N filter creates missing values. Genes with low S/N for several samples had less confidence and was removed from the analysis. Since this dataset contained a relative small number of paired samples, we decided to be strict on the number of missing values allowed, in order to have enough values to calculate the missing values from, in the imputation step. Before compiled into an expression profile data matrix, all arrays were quantile normalized to be comparable. Quantile normalization is a widely used method for 1-channel data. Genes with at most 10% missing values were allowed in the final data set. The signal intensities in the dataset were further log transformed (base 2) and missing values were replaced by imputation using Adaptive LSimpute

label: Biotin

source_name: blood, 30 Post exercise

label_protocol: According to manufacture's instructions

extract_protocol: RNA was isolated from whole blood using the PAXgene Blood RNA Kit (Qiagen, Germantown, MD) and then globin RNA was removed with GLOBINclear (Ambion, Austin, TX) according to the manufacturer's instructions. RNA integrity, purity and quantity were assessed by Bioanalyzer (Agilent Technologies, Santa Clara, CA) and Nanodrop (NanoDrop Technologies, Baltimore, MD). The concentration of total RNA was measured by Nanodrop with ultraviolet spectrophotometry at 260/280 nm. RNA quality was assessed by electrophoresis on Bioanalyzer chips (Agilent Technologies Santa Clara, CA). High quality RNA was classified as a 260/280 ratio above 1.8. Only samples with a 260/280 ratio between 1.8-2.2 and no signs of degradation were used for analysis.

treatment_protocol: The participants performed endurance training, walking/running 'uphill' on a treadmill 3 times per week for 16 weeks. They warmed-up for 10 minutes at 70% of maximal heart frequency (Hfmax) before performing 4 intervals of 4 minutes at 90-95% of Hfmax, with 3 minutes of active recovery at 70% of Hfmax between each interval. In the end, they had a 5-minute cool-down period, creating a total of 40 minutes

tag: Sex

value: Female, Age:76, Diagnosis:Metbolic Syndrome, Intervention:Interval training, BMI:29,69 (Pre-intervention)


title: HMV-I_X-rays_2Gy1h_1


title: HMV-I_X-rays_2Gy3h_1


title: 30 Pre

description: 30 Pre exercise

source_name: blood, 30 Pre exercise


title: HMV-I_C-ions_0Gy_3


title: 22 Post

description: 22 Post exercise

source_name: blood, 22 Post exercise

value: Male, Age:44, Diagnosis:Metbolic Syndrome, Intervention:Interval training, BMI:24,34 (Pre-intervention)


title: HMV-I_C-ions_2Gy3h_1


title: C32TG_C-ions_2Gy1h_1


title: HMV-I_X-rays_0Gy_2

scan_protocol: Scanning was performed according to the CodeLink manual http://www4.amershambiosciences.com/APTRIX/upp00919.nsf/Content/WD%3AScanning+CodeLi%28248345081-B500%31?OpenDocument&hometitle=WebDocs


title: 27 Post

description: 27 Post exercise

source_name: blood, 27 Post exercise

value: Male, Age:40, Diagnosis:Metbolic Syndrome, Intervention:Interval training, BMI:34,19 (Pre-intervention)


title: HMV-I_C-ions_2Gy1h_2


title: HMV-I_X-rays_2Gy3h_3


title: HMV-I_C-ions_2Gy1h_1


title: HMV-I_X-rays_2Gy3h_2


title: HMV-I_X-rays_2Gy1h_2


title: HMV-I_X-rays_0Gy_1


title: HMV-I_C-ions_0Gy_2


title: 26 Pre

description: 26 Pre exercise

source_name: blood, 26 Pre exercise

value: Male, Age:56, Diagnosis:Metbolic Syndrome, Intervention:Interval training, BMI:29,78 (Pre-intervention)


title: 15 Pre

description: 15 Pre exercise

source_name: blood, 15 Pre exercise

value: Female, Age:51, Diagnosis:Metbolic Syndrome, Intervention:Interval training, BMI:19,83 (Pre-intervention)


title: HMV-I_C-ions_0Gy_1


title: HMV-I_X-rays_2Gy1h_3


title: 26 Post

description: 26 Post exercise

source_name: blood, 26 Post exercise


title: 22 Pre

description: 22 Pre exercise

source_name: blood, 22 Pre exercise


title: 27 Pre

description: 27 Pre exercise

source_name: blood, 27 Pre exercise


title: 15 Post

description: 15 Post exercise

source_name: blood, 15 Post exercise


title: ob/ob Saline treated-2

city: Baltimore

first: vikas

last: misra

state: MD

address: 615 N. Wolfe street, E6609

department: Environmental health sciences

institute: Johns Hopkins University School of public health

description: ob/ob Saline treated Lung gene expression

hyb_protocol: Following fragmentation, 1 200 ul of hybridization cocktail containing 10 ug of fragmented cRNA placed on chip - Hybridized for 18 hours in GeneChip Hybridization Oven 640 - Washed and stained using 2 strepavidin stains and one antibody stain on GeneChip Fluidics Station 400 for 1.5 hours (GeneChip Expression Analysis Technical Manul- Affymetrix)

scan_protocol: Arrays were scanned with a GCS300 Scanner (Affymetrix) for images and intensities.

data_processing: Data extraction was processed by Affy GeneChip® Operating Software v1.3 (Affymetrix). Global scaling was equal to 500. Normalization factor was equal to 1. Analysis of differentially expressed transcripts was accomplished using a pairwise comparative analysis (Affy Data Mining Tool v3.1; Affymetrix). 3 sets ob/ob leptin-treated 1 month x 3 sets ob/ob saline-treated 1 month comparison (1.5 fold cutoff (FC), Mann-Whitney test < 0.05, 6 out of 9 comparisons).

organism: Mus musculus

source_name: ob/ob Saline treated-2 lung

label_protocol: cDNA step using Invitrogen SuperScript Double-stranded cDNA Synthesis Kit cDNA cleanup by Affymetrix GeneChip Sample Cleanup Module, cRNA amplification by Ambion MEGAscript T7 Kit, Cleanup by Qiagen RNeasy Mini Kit. cDNA synthesis by Invitrogen SuperScript Double-stranded cDNA Synthesis Kit using a T7-Oligo(dT) promoter primer from Affymetrix, cRNA amplification using ENZO BioArray HighYield RNA Transcript Labeling Kit, Metal-induced hydrolysis by Affymetrix 5 X Fragmentation Buffer, External controls (spikes)- Control Oligo B2 (3 nM), Eukaryotic Hybridization control (Affymetrix Small Sample Labeling Protocol vII, Affymetrix).

growth_protocol: no growth protocol

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

treatment_protocol: Saline treatment

tag: B6.V-Lepob/J mouse strain (Jackson Lab) gender- female, age- 1 month, n = 1, # of tissue = 1 tissue

value: Lung


title: MB_DN5h2

city: Stanford

first: Eric

middle: D

last: Hoopfer

state: CA

address: 385 Serra Mall

institute: Stanford University

description:
EcRDN-expressing MB neurons around the first signs of axon pruning (5h APF)
EcRDN-expressing pupal MB neurons at 5h after puparium formation, biological rep1

hyb_protocol: Standard Affymetrix procedures.

scan_protocol: Standard Affymetrix procedures.

data_processing: Normalized of probe signal intensity levels across arrays was done using the Robust Multichip Average (RMA; Irizarry et al., 2003) implemented in Expression Console Software (Affymetrix).

organism: Drosophila melanogaster

source_name: Mushroom body neurons

label_protocol: Approximately 22ng of total RNA was linearly amplified (2 rounds) using the RiboAmp HS RNA amplification kit (Arcturus), and biotin-labeled using the GeneChip IVT labeling kit (Affymetrix).

growth_protocol: Larvae were raised on standard fly food.  Pupae at pupariation, or 0 hours after puparium formation (APF), were collected as white pupae.

extract_protocol: Isolation of RNA from mushroom body (MB) neurons was accomplished using laser capture micro-dissection.  Briefly, 15 micrometer frozen sections were cut from larvae or pupae, dehydrated through an ethanol series and fixed in 100% Xylene for 5 minutes.  MB neurons expressing mCD8::GFP driven by OK107-GAL4 were micro-dissected using the Arcturus LCM 1110 system.  Each capture consisted of about 100 cell bodies and 40 captures were pooled to obtain each replicate.  Total RNA was extracted using the PicoPure RNA isolation kit (Arcturus).

tag: Genotype

value: 5 hours after puparium formation


title: MB_DN5h3

description:
EcRDN-expressing MB neurons around the first signs of axon pruning (5h APF)
EcRDN-expressing pupal MB neurons at 5h after puparium formation, biological rep2


title: MB_DN5h1

description:
EcRDN-expressing pupal MB neurons at the onset of axon pruning (0h APF)
EcRDN-expressing pupal MB neurons at 0h after puparium formation, biological rep7

value: 0 hours after puparium formation


title: MB_DN0h3

description:
EcRDN-expressing pupal MB neurons at the onset of axon pruning (0h APF)
EcRDN-expressing pupal MB neurons at 0h after puparium formation, biological rep3


title: MB_DN0h4

description:
EcRDN-expressing pupal MB neurons at the onset of axon pruning (0h APF)
EcRDN-expressing pupal MB neurons at 0h after puparium formation, biological rep4


title: ob/ob Saline treated-1

label: ENZO BioArray HighYield RNA Transcript Labeling Kit

source_name: ob/ob Saline treated-1 lung


title: 92-1_C-ions_2Gy1h_2

source_name: cell line


title: MB_YW0h7

description:
yw pupal MB neurons at the onset of axon pruning (0h APF)
Pupal MB neurons at 0h relative to puparium formation, biological rep7

growth_protocol: Larvae were raised on standard fly food.  Early third instar larvae between approximately 18 hours before puparium formation were staged by addition of 0.05% bromophenol blue to the food and collected as wandering larvae with dark blue guts.  Newly formed white pre-pupae were selected, which we define as 0h relative to puparium formation, and aged for 5 hours.


title: MB_DN0h6

description:
EcRDN-expressing pupal MB neurons at the onset of axon pruning (0h APF)
EcRDN-expressing pupal MB neurons at 0h after puparium formation, biological rep6


title: MB_DN0h1

description:
EcRDN-expressing pupal MB neurons at the onset of axon pruning (0h APF)
EcRDN-expressing pupal MB neurons at 0h after puparium formation, biological rep1


title: MB_DN0h2

description:
EcRDN-expressing pupal MB neurons at the onset of axon pruning (0h APF)
EcRDN-expressing pupal MB neurons at 0h after puparium formation, biological rep2


title: MB_DN5h4

description:
EcRDN-expressing MB neurons around the first signs of axon pruning (5h APF)
EcRDN-expressing pupal MB neurons at 5h after puparium formation, biological rep3


title: MB_YW5h3

description:
yw pupal MB neurons around the first signs of axon pruning (5h APF)
Pupal MB neurons at 5h relative to puparium formation, biological rep3


title: MB_DN0h5

description:
EcRDN-expressing pupal MB neurons at the onset of axon pruning (0h APF)
EcRDN-expressing pupal MB neurons at 0h after puparium formation, biological rep5


title: MB_YW5h2

description:
yw pupal MB neurons around the first signs of axon pruning (5h APF)
Pupal MB neurons at 5h relative to puparium formation, biological rep2


title: MB_YW0h5

description:
yw pupal MB neurons at the onset of axon pruning (0h APF)
Pupal MB neurons at 0h relative to puparium formation, biological rep5


title: ob/ob Leptin treated-1

description: ob/ob Leptin treated Lung gene expression

source_name: ob/ob Leptin treated-1 lung

treatment_protocol: Leptin treatment


title: MB_YW0h4

description:
yw pupal MB neurons at the onset of axon pruning (0h APF)
Pupal MB neurons at 0h relative to puparium formation, biological rep4


title: MB_YW0h6

description:
yw pupal MB neurons at the onset of axon pruning (0h APF)
Pupal MB neurons at 0h relative to puparium formation, biological rep6


title: ob/ob Leptin treated-3

source_name: ob/ob Leptin treated-3 lung


title: MB_YW0h3

description:
yw pupal MB neurons at the onset of axon pruning (0h APF)
Pupal MB neurons at 0h relative to puparium formation, biological rep3


title: MB_YW5h1

description:
yw pupal MB neurons around the first signs of axon pruning (5h APF)
Pupal MB neurons at 5h relative to puparium formation, biological rep1


title: ob/ob Leptin treated-2

source_name: ob/ob Leptin treated-2 lung


title: MB_YW0h2

description:
yw pupal MB neurons at the onset of axon pruning (0h APF)
Pupal MB neurons at 0h relative to puparium formation, biological rep2


title: MB_YW0h1

description:
yw pupal MB neurons at the onset of axon pruning (0h APF)
Pupal MB neurons at 0h relative to puparium formation, biological rep1


title: MB_YWL7

description:
yw third instar larval MB neurons prior to ecdysone pulse
third instar larval MB neurons -18h relative to puparium formation, biological rep7

value: third instar larvae 18 hours before puparium formation


title: MB_YWL2

description:
yw third instar larval MB neurons prior to ecdysone pulse
third instar larval MB neurons -18h relative to puparium formation, biological rep2


title: MB_YWL6

description:
yw third instar larval MB neurons prior to ecdysone pulse
third instar larval MB neurons -18h relative to puparium formation, biological rep6


title: ob/ob Saline treated-3

description: ob/ob Saline treated Lung gene expression

source_name: ob/ob Saline treated-3 lung


title: MB_YWL5

description:
yw third instar larval MB neurons prior to ecdysone pulse
third instar larval MB neurons -18h relative to puparium formation, biological rep5


title: MB_YWL3

description:
yw third instar larval MB neurons prior to ecdysone pulse
third instar larval MB neurons -18h relative to puparium formation, biological rep3


title: Mfav_partial_bleach_genet1

status: Public on May 31 2008

city: San Francisco

first: Michael

last: DeSalvo

department: Department of Anesthesia

institute: UC San Francisco

description: A time course experiment was conducted with 4 genets of M. faveolata sampled from 2 separate reefs 21 km apart. Each colony was broken into 8 fragments using a hammer and chisel.  For each colony, 4 fragments were placed in a control aquarium, and 4 fragments were placed in an experimental aquarium fitted with 2 heaters, such that a pair of aquaria represented each colony (total of 4 control and 4 heated aquaria, all 75-liter).  After an acclimation period of 4 days at the natural temperature of the seawater system (mean temperature = 30.29±0.07oC), a fragment from each control and experimental aquaria was frozen in liquid nitrogen (time zero).  After time zero sampling, the heaters in each of the experimental aquaria were turned on.  The mean temperature of the control aquaria during the entire experiment was 29.74±0.03oC, and the mean temperature of the heated aquaria was 32.72±0.32oC.  Control and experimental fragments were sampled again one day after turning on the heaters, at the first signs of slight bleaching (2-4 days after heating began, depending on genotype), and lastly, when all experimental fragments were partially bleached (9 days after heating began).

hyb_protocol: Prior to hybridization, microarrays were post-processed by: 1) UV crosslinking at 60 mJ; 2) a “shampoo” treatment (3x SSC, 0.2% SDS at 65oC); 3) blocking with 5.5g succinic anhydride dissolved in 335mL 1-methyl-2-pyrrilidinone and 15mL sodium borate; and 4) drying via centrifugation. Dye-coupled cDNAs were cleaned (Zymo), and appropriate Cy3 and Cy5 labeled cDNAs were mixed together in a hybridization buffer containing 0.25% SDS, 25mM HEPES, and 3x SSC.  The hybridization mixtures were boiled for 2min at 99oC then allowed to cool at room temperature for 5min.  The cooled hybridization mixtures were pipetted under an mSeries Lifterslip (Erie Scientific), and hybridization took place in Corning hybridization chambers overnight at 63oC.  Microarrays were washed twice in 0.6x SSC and 0.01% SDS followed by a rinse in 0.06x SSC and dried via centrifugation.  Slides were immediately scanned using an Axon 4000B scanner.

scan_protocol: Scanned using Axon 4100B scanner with GenePix 6.0 software.

data_processing:
Data analysis followed a reference design in which all heat-stressed RNA samples (4 per time point) were compared to a pooled reference RNA sample composed of RNA from all control (untreated) coral fragments over all time points.  Since all experimental RNA samples were compared to the reference sample, direct comparisons of gene expression across all time points can be performed.
Background-subtracted mean intensity values were rlowess-normalized and log base2-transformed using J/MAANOVA.  A MAANOVA fixed-effects model was fit to the intensity data with array and sample terms.  Differentially expressed genes were identified using the same statistical methods described above.  To visualize the temporal expression of differentially expressed genes, K-means clustering was performed using TIGR TMEV 4.0 software.

organism: Orbicella faveolata

label_protocol:
Labeled using Amersham CyDye Post-labeling kit.
http://cat.ucsf.edu/pdfs/hybCourseProtocols_v2.7.pdf
Specifically, 10ug of total RNA were primed with 5ug/uL of Oligo-dT primer for 10min at 70oC.   Reverse transcription (RT) lasted for 2hr at 42oC using a master mix containing a 3:2 ratio of aminoallyl-dUTP to TTP.  Following RT, single-stranded RNA was hydrolyzed by incubating the RT reactions in 10uL 0.5M EDTA and 10uL 1M NaOH for 15min at 65oC.  After hydrolysis, RT reactions were cleaned using Zymo Clean and Concentrator columns.  Cy3 and Cy5 dyes (GE Healthcare) were dissolved in 17uL DMSO, and the coupling reactions lasted for 2hr at room temperature in the dark.

extract_protocol:
Qiazol used to extract total RNA.
RNeasy Mini kit used to clean RNA.
Details: Total RNA from all frozen coral fragments was isolated using Qiazol lysis reagent (QIAGEN).  Live tissue was chiseled off each coral fragment and homogenized using a pre-chilled mortar and pestle embedded in dry ice.  Frozen coral powder was transferred directly to Qiazol.  Two chloroform extractions were performed, followed by isopropanol precipitation and 2 washes in 80% ethanol.  RNA pellets were re-dissolved in nuclease-free water and cleaned further over RNeasy Mini columns (QIAGEN).  RNA quality and quantity were assessed with a NanoDrop ND-1000 spectrophotometer and an Agilent 2100 Bioanalyzer. Microarray protocols followed those established by the Center for Advanced Technology at the University of California, San Francisco (http://cat.ucsf.edu/).

tag: RNA pool from many non-stressed control fragments.

label_protocol:
Labeled using Amersham CyDye Post-labeling kit.
http://cat.ucsf.edu/pdfs/hybCourseProtocols_v2.7.pdf
Details same as for channel 1

extract_protocol:
Qiazol used to extract total RNA.
RNeasy Mini kit used to clean RNA.
Details same as for channel 1

tag: Genet1 sampled at a partially bleached appearance.


title: Mfav_partial_bleach_genet2

tag: Genet2 sampled at a partially bleached appearance.


title: Low capacity runner-soleus-trained-1

description: We used rats artificial selected for high and low aerobic capacity, starting from the N: NIH stock obtained from the National Institutes of Health (USA). Briefly, the rats in each generation were tested for exercise capacity by treadmill running at 11 weeks of age. The individuals with the highest and lowest running capacity were selected and each group served as the mating population for the next generation. Female rats from generation 16 were used in this study. The study includes four groups; LCR trained (LCR-T) (n=4), LCR sedentary (LCR-S) (n=4), HCR trained (HCR-T) (n=4) and HCR sedentary (HCR-S) (n=4). Experimental protocols were approved by the respective Institutional Animal Research Ethics Councils

hyb_protocol: According to manufacture's instructions. Labeled cRNA was prepared and hybridized to the RAE 230 2.0 chip from Affymetrix GeneChip (Affymetrix, Santa Clara, CA) comprised of 31,042 probe sets. On the Affymetrix GeneChip arrays, each gene is represented by a set of 11-20 probe pairs consisting of a perfect match (PM) and a mismatch (MM) probe. The statistical analysis is based on summary expression measures for each probe set.

data_processing:
Computing summary measures (RMA)
The summary measure for each probeset is computed based on a linear statistical model for background-corrected, normalized and log-transformed PM values for each probe pair by use of the robust multiarray average (RMA) method. The PM values are normalized using the quantile normalization method, normalizing the arrays such that the empirical distribution of the expression measures is equal across arrays.
Statistical analysis for finding differentially expressed genes
For each gene (probeset), a linear regression model, including parameters representing the effect of aerobe capacity is specified. Based on the estimated effects, tests for significant differential expression are performed using moderated T-tests.
To account for multiple testing, we calculated adjusted p-values controlling the False Discovery Rate (FDR), with the use of the Benjamini-Hochberg step-up procedure. Consequently, selecting differentially expressed genes based on a threshold of 0.05 on the adjusted FDR p-values means that the expected proportion of genes falsely classified as differential expressed should be below 0.05.
All statistical analyses on the gene expression data are performed using the R language (R Development Core Team, 2004) and packages affy, affyPLM and limma from the Bioconductor project.

organism: Rattus norvegicus

source_name: Low capacity runner, Soleus muscle, trained-1

extract_protocol:
Tissue samples (20 mg) were homogenized in 100 µL TRIzol (Life Technologies, Gaithersburg, MD) using a Mixer Mill MM301 (Company, City, State/Country) at 20-25 Hz. RNA clean-up was performed using RNA Mini kit (Qiagen, Germantown, MD). Total RNA was isolated and RNA clean up was performed according to the manufacturer's instructions.
RNA integrity, purity and quantity were assessed by Bioanalyzer (Agilent Technologies, Santa Clara, CA) and Nanodrop (NanoDrop Technologies, Baltimore, MD). The concentration of total RNA was measured by Nanodrop with ultraviolet spectrophotometry at 260/280 nm. RNA quality was assessed by electrophoresis on Bioanalyzer chips (Agilent Technologies).
High quality RNA was classified as a 260/280 ratio above 1.8. Only samples with a 260/280 ratio between 1.8-2.2 and no signs of degradation were used for analysis.

treatment_protocol:
4 rats from each strain was exposed to an aerobic interval training program. Briefly, after 10 minutes of warm-up, rats ran uphill (25°) on a treadmill for 1.5 hours, alternating between 8 minutes at an exercise intensity corresponding to 85-90% of VO2max, and 2 minutes active recovery at 50 - 60%. Exercise was performed 5 days per week over 8 week; controls were age-matched rats that remained sedentary. We measured VO2max every week in exercising rats to adjust speed in order to maintain the intended intensity throughout the experimental period. The VO2max-testprotocol consisted of 20 minutes warm-up at 50-60% of VO2max, whereupon treadmill velocity was increased by 0.03 m/s every 2 minute until VO2 plateau despite of increased workload. The animals in the sedentary groups were treated similar to the exercise groups, except being exposed to exercise training and VO2max-tests.
At approximately 7 months of age, and 48 hours after the last exercise session all the animals were sacrificed. One of the soleus muscles was formalin fixated for immunohistochemistry and morphological studies, whereas the other was snap frozen in liquid nitrogen and stored at -80oC for later genetic screening and protein analysis.


title: Mfav_slight_bleach_genet4

tag: Genet4 sampled at a slightly bleached appearance.


title: Low capacity runner-soleus-trained-3

scan_protocol: According to manufacture's instructions.

source_name: Low capacity runner, Soleus muscle, trained-3


title: Low capacity runner-soleus-trained-4

source_name: Low capacity runner, Soleus muscle, trained-4

label_protocol: According to manufacture's instructions.


title: High capacity runner-soleus-sedentary-3

source_name: High capacity runner, Soleus muscle, sedentary-3


title: Mfav_slight_bleach_genet3

tag: Genet3 sampled at a slightly bleached appearance.


title: Mfav_partial_bleach_genet3

tag: Genet3 sampled at a partially bleached appearance.


title: Low capacity runner-soleus-sedentary-3

source_name: Low capacity runner, Soleus muscle, sedentary-3


title: High capacity runner-soleus-trained-3

source_name: High capacity runner, Soleus muscle, trained-3


title: Mfav_partial_bleach_genet4

tag: Genet4 sampled at a partially bleached appearance.


title: MB_YWL1

description:
yw third instar larval MB neurons prior to ecdysone pulse
third instar larval MB neurons -18h relative to puparium formation, biological rep1

tag: Age


title: High capacity runner-soleus-trained-2

source_name: High capacity runner, Soleus muscle, trained-2


title: High capacity runner-soleus-sedentary-4

source_name: High capacity runner, Soleus muscle, sedentary-4


title: High capacity runner-soleus-sedentary-2

source_name: High capacity runner, Soleus muscle, sedentary-2


title: High capacity runner-soleus-trained-1

source_name: High capacity runner, Soleus muscle, trained-1


title: Mfav_slight_bleach_genet2

tag: Genet2 sampled at a slightly bleached appearance.


title: Mfav_1day_genet4

tag: Genet4 sampled after 1 day of thermal stress.


title: Mfav_1day_genet3

tag: Genet3 sampled after 1 day of thermal stress.


title: Low capacity runner-soleus-trained-2

source_name: Low capacity runner, Soleus muscle, trained-2


title: Low capacity runner-soleus-sedentary-4

source_name: Low capacity runner, Soleus muscle, sedentary-4

extract_protocol:
Tissue samples (20 mg) were homogenized in 100 ÂµL TRIzol (Life Technologies, Gaithersburg, MD) using a Mixer Mill MM301 (Company, City, State/Country) at 20-25 Hz. RNA clean-up was performed using RNA Mini kit (Qiagen, Germantown, MD). Total RNA was isolated and RNA clean up was performed according to the manufacturer's instructions.
RNA integrity, purity and quantity were assessed by Bioanalyzer (Agilent Technologies, Santa Clara, CA) and Nanodrop (NanoDrop Technologies, Baltimore, MD). The concentration of total RNA was measured by Nanodrop with ultraviolet spectrophotometry at 260/280 nm. RNA quality was assessed by electrophoresis on Bioanalyzer chips (Agilent Technologies).
High quality RNA was classified as a 260/280 ratio above 1.8. Only samples with a 260/280 ratio between 1.8-2.2 and no signs of degradation were used for analysis.

tag: Soleus muscle


title: MB_YWL4

description:
yw third instar larval MB neurons prior to ecdysone pulse
third instar larval MB neurons -18h relative to puparium formation, biological rep4

source_name: Mushroom body neurons


title: Low capacity runner-soleus-sedentary-2

source_name: Low capacity runner, Soleus muscle, sedentary-2


title: High capacity runner-soleus-trained-4

source_name: High capacity runner, Soleus muscle, trained-4


title: Mfav_1day_genet2

tag: Genet2 sampled after 1 day of thermal stress.


title: Low capacity runner-soleus-sedentary-1

source_name: Low capacity runner, Soleus muscle, sedentary-1


title: High capacity runner-soleus-sedentary-1

source_name: High capacity runner, Soleus muscle, sedentary-1


title: Mfav_1day_genet1

tag: RNA pool from many non-stressed control fragments

tag: Genet1 sampled after 1 day of thermal stress.


title: Mfav_time_zero_genet2

tag: Time zero control fragment -- sampled prior to thermal stress.


title: Mfav_time_zero_genet4


title: Mfav_time_zero_genet1


title: Mfav_time_zero_genet3


title: Mfav_bleaching_rep5_dyeswap

description: A single time point, single genotype thermal stress experiment was performed.  A large colony of Montastraea faveolata was divided into ten coral “plugs” using a 2.5cm diameter punch tool.  The fragments were divided evenly between 2 identical 75-liter aquaria, ca. 25cm deep, and kept at ambient temperature (29.23±0.48oC) for 3 days.  After the acclimation period, 2 200-Watt aquarium heaters were turned on in the experimental aquarium, which subsequently heated to 32.23±0.48oC. The experiment lasted 10 days and 17 hours, after which all fragments were frozen in liquid nitrogen for molecular analysis.

hyb_protocol: Prior to hybridization, microarrays were post-processed by: 1) UV crosslinking at 60 mJ; 2) a “shampoo” treatment (3x SSC, 0.2% SDS at 65oC); 3) blocking with 5.5g succinic anhydride dissolved in 335mL 1-methyl-2-pyrrilidinone and 15mL sodium borate; and 4) drying via centrifugation. Dye-coupled cDNAs were cleaned (Zymo), and appropriate Cy3 and Cy5 labeled cDNAs were mixed together in a hybridization buffer containing 0.25% SDS, 25mM HEPES, and 3x SSC.  The hybridization mixtures were boiled for 2min at 99oC then allowed to cool at room temperature for 5min.  The cooled hybridization mixtures were pipetted under an mSeries Lifterslip (Erie Scientific), and hybridization took place in Corning hybridization chambers overnight at 63oC.  Microarrays were washed twice in 0.6x SSC and 0.01% SDS followed by a rinse in 0.06x SSC and dried via centrifugation.  Slides were immediately scanned using an Axon 4000B scanner.  Microarray data analysis followed a dye-swap design where each of the 5 control fragments was randomly paired to one of the 5 heat-stressed fragments.  Each hybridization was performed twice with dye swapping between technical replicates, which allows for the measurement of dye labeling bias. http://cat.ucsf.edu/pdfs/hybCourseProtocols_v2.7.pdf

data_processing: Data analysis was performed using J/MAANOVA in the R statistical environment. Background-subtracted mean intensity values were log2 transformed and normalized using the spatial-intensity joint lowess algorithm.  A fixed-effect MAANOVA model was fit to the intensity data with array, sample, and dye terms.  Differentially expressed genes were identified by testing the sample term according to the Empirical-Bayes Fs statistic.  P-values for each gene were generated by shuffling the residuals over 500 permutations. FDR adjustments were applied to the p-values using a step-down FDR control method.

source_name: control fragment 3

label_protocol:
Labeled using Amersham CyDye Post-labeling kit.
http://cat.ucsf.edu/pdfs/hybCourseProtocols_v2.7.pdf
Specifically, 1ug of total RNA was amplified using the MessageAmp II aRNA kit (Ambion), and 3ug of aRNA per sample were primed with 5ug/uL random nonamer for 10min at 70oC.   Reverse transcription (RT) lasted for 2hr at 42oC using a master mix containing a 3:2 ratio of aminoallyl-dUTP to TTP.  Following RT, single-stranded RNA was hydrolyzed by incubating the RT reactions in 10uL 0.5M EDTA and 10uL 1M NaOH for 15min at 65oC.  After hydrolysis, RT reactions were cleaned using Zymo Clean and Concentrator columns.  Cy3 and Cy5 dyes (GE Healthcare) were dissolved in 17uL DMSO, and the coupling reactions lasted for 2hr at room temperature in the dark.

tag: fragment kept at control temperature for 11 days

source_name: bleached fragment 1

tag: fragment thermal stressed for 11 days


title: Mfav_bleaching_rep1_dyeswap

source_name: control fragment 1

source_name: bleached fragment 3


title: Mfav_bleaching_rep3_dyeswap

source_name: control fragment 2

source_name: bleached fragment 4


title: Mfav_bleaching_rep2_dyeswap

source_name: control fragment 5

source_name: bleached fragment 5


title: Mfav_bleaching_rep4_dyeswap

source_name: control fragment 4

source_name: bleached fragment 2


title: 13602840 - 8_aba2+ABA_R2 vs 6_aba2-2_R2

status: Public on May 29 2008

city: Evry Cedex

first: Agnes

last: Yu

address: 2 rue Gaston Cremieux CP 5708

department: URGV

description: Identification of genes regulated by maternal and embryonic ABA

hyb_protocol: 6_aba2-2_R2 Cy5 / 8_aba2+ABA_R2 Cy3 : 30pmol. 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 6.0, Cy3:pmt voltage 532nm,500V,laser power 30%, Cy5:635nm,pmt voltage 500V,laser power 30%

growth_protocol: seed - medium : soil hygrometry : 70 temperature : 21/18 light : 16h

treatment_protocol: no treatment

tag: Arabidopsis thaliana (columbia)  mutant (aba2-2) - dev.stage (Boyes et al. Plant Cell 2001):boyes

treatment_protocol: Name:ABA_treatment_RA07-02 - compound based treatment - compound addition,aba:quantity 0.1mM .

tag: Arabidopsis thaliana (columbia)  mutant (aba2-2+ABA) - dev.stage (Boyes et al. Plant Cell 2001):boyes


title: Wild-type 4

status: Public on May 30 2008

type: mixed

first: Jun

middle: S

last: Song

address: 513 Parnassus Avenue, Box 0794

department: Institute for Human Genetics

institute: UCSF

description: Wild-type 4

hyb_protocol: The purified mono-nucleosomal DNA and the purified naked control DNA were labeled with Cy5-dUTP (PerkinElmer) and Cy3-dUTP (PerkinElmer), respectively, and purified using BioPrime Array CGH Genomic Labeling Module (Invitrogen 45-0048) and Purification Module (Invitrogen 45-0049), respectively. 1ug Cy5-labeled single nucleosome and 1ug Cy3-labeled naked control DNA were hybridized on Agilent's 4x44k tiling array at 65C for 40h and slides were washed following the standard Agilent Mammalian ChIP-on-ChIP protocol (Agilent version 9.0).

scan_protocol: The slides were scanned using a GenePix 4000B scanner and processed with a GenePix 6.0 software.

data_processing: The Cy5/Cy3 ratios were denoised using wavelets

organism: Schizosaccharomyces pombe

source_name: Genomic Input DNA

label_protocol: Random primer labeling

extract_protocol: To prepare naked DNA as control, the spheroplasts from wild type yeast cell were incubated in Lysis buffer at 36C for 12 min, then was stopped by adding EDTA to final concentration of 20mM and SDS to final concentration of 1%. The total lyses was incubated with 0.1mg/ml Proteinase K at 50C for 2h. DNA was extracted with phenol/chloroform, digested with RNase, phenol/chloroform re-extracted, precipitated with ethanol, and resuspened in Lysis buffer. The naked DNA was treated with 10-500 units/ml of MNase at 36C for 7 min. The reaction was stopped by adding EDTA to final concentration of 20mM.   To purify DNA, electrophoresis was carried out in 2.5% agarose gel, and the band corresponding to mononucleosomes was gel-extracted using  QIAEX II Gel Extraction Kit (Qiagen).

tag: Genomic Input DNA

molecule: other

source_name: MNase digested and gel-extracted DNA, Wild-type 4

extract_protocol: To prepare nucleosomal DNA, the spheroplasts suspension (8x10^8 cells/ml) were prewarmed at 36C for 5 min and then treated with micrococcal nuclease (MNase) (500 units/ml, Roche) at 36C for 15 sec-7 min. The reaction was stopped by adding EDTA to final concentration of 20mM and SDS to final concentration of 1%. The suspension was centrifuged at 14000 rpm for 20 min. The supernatant containing the nuclease-digested nuclei was incubated with 0.1mg/ml Proteinase K at 50C for 2h. DNA was extracted with phenol/chloroform, digested with RNase, re-extracted with phenol/chloroform, precipitated with ethanol, and resuspended in TE (10mM Tris-HCl, 1mM EDTA, pH8.0). To purify DNA, electrophoresis was carried out in 2.5% agarose gel, and the band corresponding to mononucleosomes was gel-extracted using  QIAEX II Gel Extraction Kit (Qiagen).

tag: MNase treated mononucleosomal DNA


title: 13602834 - 6_aba2-2_R2 vs 7_aba2xCol_R2

hyb_protocol: 7_aba2xCol_R2 Cy5 / 6_aba2-2_R2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: Arabidopsis thaliana (columbia)  mutant (aba2-2xCol) - dev.stage (Boyes et al. Plant Cell 2001):boyes


title: Wild-type partial MNase digestion 2

description: Wild-type partial MNase digestion 2

source_name: MNase digested and gel-extracted DNA, Wild-type partial MNase digestion 2


title: Wild-type 2

description: Wild-type 2

source_name: MNase digested and gel-extracted DNA, Wild-type 2


title: 13602844 - 6_aba2-2_R2 vs 8_aba2+ABA_R2

hyb_protocol: 8_aba2+ABA_R2 Cy5 / 6_aba2-2_R2 Cy3 : 30pmol. 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: Ams2 null 2

description: Ams2 null 2

source_name: MNase digested and gel-extracted DNA, Ams2 null 2


title: Mal2ts mutant

description: Mal2ts mutant

source_name: MNase digested and gel-extracted DNA, Mal2ts mutant


title: Wild-type partial MNase digestion

description: Wild-type partial MNase digestion

source_name: MNase digested and gel-extracted DNA, Wild-type partial MNase digestion


title: 13584894 - 2_aba2-2_R1 vs 1_WT(Col0)_R1

hyb_protocol: 1_WT(Col0)_R1 Cy5 / 2_aba2-2_R1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: Arabidopsis thaliana (columbia)  - dev.stage (Boyes et al. Plant Cell 2001):boyes


title: Wild-type partial MNase digestion 3

description: Wild-type partial MNase digestion 3

source_name: MNase digested and gel-extracted DNA, Wild-type partial MNase digestion 3


title: 13584893 - 3_aba2xCol_R1 vs 2_aba2-2_R1

hyb_protocol: 2_aba2-2_R1 Cy5 / 3_aba2xCol_R1 Cy3 : 30pmol. 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: Wild-type 3

description: Wild-type 3

source_name: MNase digested and gel-extracted DNA, Wild-type 3


title: Cnp1ts mutant

description: Cnp1ts mutant

source_name: MNase digested and gel-extracted DNA, Cnp1ts mutant


title: Mis18ts mutant

description: Mis18ts mutant

source_name: MNase digested and gel-extracted DNA, Mis18ts mutant


title: Ams2 null

description: Ams2 null

source_name: MNase digested and gel-extracted DNA, Ams2 null


title: Mis12ts mutant

description: Mis12ts mutant

source_name: MNase digested and gel-extracted DNA, Mis12ts mutant


title: 13561088 - 2_aba2-2_R1 vs 4_aba2+ABA_R1

hyb_protocol: 4_aba2+ABA_R1 Cy5 / 2_aba2-2_R1 Cy3 : 30pmol. 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: 13561091 - 1_WT(Col0)_R1 vs 2_aba2-2_R1

hyb_protocol: 2_aba2-2_R1 Cy5 / 1_WT(Col0)_R1 Cy3 : 30pmol. 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: 13561092 - 2_aba2-2_R1 vs 3_aba2xCol_R1

hyb_protocol: 3_aba2xCol_R1 Cy5 / 2_aba2-2_R1 Cy3 : 30pmol. 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: Cnp1p over expression

description: Cnp1p over expression

source_name: MNase digested and gel-extracted DNA, Cnp1p over expression


title: 13561089 - 4_aba2+ABA_R1 vs 2_aba2-2_R1

hyb_protocol: 2_aba2-2_R1 Cy5 / 4_aba2+ABA_R1 Cy3 : 30pmol. 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: 13602833 - 7_aba2xCol_R2 vs 6_aba2-2_R2

hyb_protocol: 6_aba2-2_R2 Cy5 / 7_aba2xCol_R2 Cy3 : 30pmol. 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: Mfav_slight_bleach_genet1

tag: RNA pool from many non-stressed control fragments.

tag: Genet1 sampled at a slightly bleached appearance.


title: 13561083 - 5_WT(Col0)_R2 vs 6_aba2-2_R2

hyb_protocol: 6_aba2-2_R2 Cy5 / 5_WT(Col0)_R2 Cy3 : 30pmol. 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: AML patient 27 Relapse

status: Public on May 01 2008

city: London

first: Manoj

last: Raghavan

address: Charterhouse Square

department: Centre for Medical Oncology, Institute of Cancer

country: United Kingdom

institute: Barts and the London, Queen Mary's School of Medicine and Dentistry

description: SNP genotype data from AML patient at relapse

hyb_protocol: Affymetrix 10K mapping assay protocol

scan_protocol: Affymetrix GeneChip scanner 3000

data_processing: GCOS, GTYPE. Genotype calling algorithm MPAM

source_name: AML blood/marrow cells relapse

label_protocol: Affymetrix 10K mapping assay protocol

extract_protocol: Phenol chloroform

treatment_protocol: AML cells collected from blood or bone marrow. Ficoll separation, and cryopreserved in liquid nitrogen.

tag: FAB_type = M5

tag: cytogenetics = No sample


title: AML patient 26 Relapse

tag: FAB_type = M5A


title: AML patient 24 Relapse

tag: FAB_type = M1


title: AML patient 23 Relapse

tag: FAB_type = M4


title: AML patient 21 Relapse

tag: cytogenetics = 46,XY


title: AML patient 25 Relapse


title: AML patient 17 Relapse


title: AML patient 12 Relapse

tag: FAB_type = M2


title: AML patient 15 Relapse


title: AML patient 20 Relapse

tag: cytogenetics = 46,XY[20]


title: AML patient 7 Relapse

tag: cytogenetics = 46,XY[47]


title: AML patient 19 Relapse


title: AML patient 22 Relapse


title: AML patient 11 Relapse


title: AML patient 6 Relapse


title: AML patient 5 Relapse


title: AML patient 16 Relapse


title: AML patient 8 Relapse


title: 13585129 - 6_aba2-2_R2 vs 5_WT(Col0)_R2

hyb_protocol: 5_WT(Col0)_R2 Cy5 / 6_aba2-2_R2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: Arabidopsis thaliana (columbia)  mutant (aba2-2) - dev.stage (Boyes et al. Plant Cell 2001):boyes


title: AML patient 13 Relapse


title: Wild-type 1

description: Wild-type 1

source_name: MNase digested and gel-extracted DNA, Wild-type 1


title: Nuf2ts mutant

description: Nuf2ts mutant

source_name: MNase digested and gel-extracted DNA, Nuf2ts mutant


title: AML patient 4 Relapse


title: AML patient 18 Relapse


title: AML patient 3 Relapse

tag: cytogenetics = 47,XX,+11/46,XX


title: AML patient 2 Relapse


title: AML patient 1 Relapse


title: AML patient 27 Diagnosis

description: SNP genotype data from AML patient at diagnosis

source_name: AML blood/marrow cells diagnosis

tag: cytogenetics = 47,XY,+8/46,XY


title: AML patient 25 Diagnosis


title: AML patient 26 Diagnosis


title: AML patient 16 Diagnosis

tag: cytogenetics = 46,XX [25]


title: AML patient 21 Diagnosis


title: AML patient 19 Diagnosis


title: AML patient 8 Diagnosis


title: AML patient 13 Diagnosis


title: AML patient 11 Diagnosis


title: AML patient 7 Diagnosis


title: AML patient 5 Diagnosis


title: AML patient 15 Diagnosis


title: AML patient 3 Diagnosis

tag: cytogenetics = 46,XX


title: AML patient 6 Diagnosis


title: AML patient 23 Diagnosis


title: DMS79 cell line (DMS79.s6)

city: Abbott Park

first: Mark

last: Anderson

state: IL

address: 100 Abbott Park Road

institute: Abbott Laboratories

hyb_protocol: Affy protocol, midi_euk_2v3

data_processing: GCOS

source_name: DMS79 cell line

label_protocol: Enzo kit

extract_protocol: Trizol

value: 1.9 ± 0.05 (3 replicates)


title: DMS79 cell line (DMS79.s5)


title: AML patient 12 Diagnosis


title: AML patient 22 Diagnosis


title: AML Patient 1 Diagnosis


title: AML patient 2 Diagnosis


title: AML patient 17 Diagnosis

tag: cytogenetics = 47,XX,+8[10]


title: NCI-H69 cell line (NCI-H69.0)

source_name: NCI-H69 cell line

value: 0.71 ± 0.26 (3 replicates)


title: SHP77 cell line (SHP77.1)

source_name: SHP77 cell line

value: 3.9 ± 2.6 (6 replicates)


title: NCI-H1048 cell line (NCI-H1048.2)

source_name: NCI-H1048 cell line

value: 2.86 ± 0.43 (6 replicates)


title: AML patient 20 Diagnosis


title: NCI-H1048 cell line (NCI-H1048.1)


title: DMS79 cell line (DMS79.s4)


title: NCI-H446 cell line (NCI-H446.3)

source_name: NCI-H446 cell line

value: 4.1 ± 0.9 (3 replicates)


title: NCI-H740 cell line (NCI-H740c)

source_name: NCI-H740 cell line

value: >10 (3 replicates)


title: AML patient 10 Relapse


title: AML patient 14 Relapse


title: NCI-H1688 cell line (NCI-H1688a)

source_name: NCI-H1688 cell line


title: NCI-H1688 cell line (NCI-H1688b)


title: SHP77 cell line (SHP77.2)


title: DMS114 cell line (DMS114.1)

source_name: DMS114 cell line

value: 33.9 ± 0.2 (3 replicates)


title: Vegetative Wild Type vs. bkd sample 2

city: Davis

first: Mitchell

last: Singer

address: 1 Shields Ave

department: Microbiology

institute: The University of California, Davis

description: standard protocol as referenced in Diodati et. al., 2006. J Bacteriol. 188:1733-1744.

data_processing: GenePix, Excel, normailzed ratios to Cy3

organism: Myxococcus xanthus

source_name: Vegetative DK5643

label_protocol: standard protocol

extract_protocol: standard protocol

tag: strain DK5643 (delta bkd), 1x10^8 cells/ml, 28 degrees C

source_name: Vegetative Wild-Type

tag: strain DK1622, 1x10^8 cells/ml, 28 degrees C


title: AML patient 9 Relapse

tag: cytogenetics = 46,XX[25]


title: Vegetative Wild Type vs. bkd sample 3

hyb_protocol: standard protocol as referenced in Diodati et. al., 2006. J Bacteriol. 188:1733-1744.


title: Vegetative Wild Type vs. bkd sample 4

scan_protocol: standard protocol as referenced in Diodati et. al., 2006. J Bacteriol. 188:1733-1744.


title: DMS114 cell line (DMS114.2)


title: NCI-H446 cell line (NCI-H446.0)


title: Vegetative Wild Type vs. bkd sample 6


title: AML patient 14 Diagnosis


title: AML patient 9 Diagnosis


title: AML patient 24 Diagnosis

tag: cytogenetics = 46,XX[20]


title: Vegetative Wild Type vs. bkd sample 5


title: NCI-H740 cell line (NCI-H740a)


title: AML patient 18 Diagnosis


title: SV.D09.v2.109393

city: Suwon

first: ChangMuk

last: Lee

address: 224, Suinro, Gwonseon-Gu

department: Microbial Genetics Division

country: South Korea

institute: National Institute of Agricultural Biotechnology

description:
Starvation for 9 days in reduced DUBOS medium (10%, pH7.0).
Replicates 4 of 6, Grown in rolling bottle, Normal aeration

hyb_protocol: Hybridization, blocking and washing was performed following the procedure provided at TIGR, PFGRC; http://pfgrc.jcvi.org/index.php/microarray/protocols.html

scan_protocol: QuantArray (ver. 3.0, Perkin Elmer) was used for 16-bit TIFF image quantification and intial visualization.

data_processing: scal-MAD and ratio-intensity quantile normalization using R (ver. 2.1.1) package (http://www.bioconductor.org) & S-plus ArrayAnalyzer (ver.2.0). Regardless of dyes used in dye-swap cases, signals from reference sample were always denoted as Green during normaliztion. Signals from scratched or bad spots (ie. Intensity - Background <0) were tagged and removed before normalization.

organism: Mycobacterium tuberculosis H37Rv

source_name: M. tuberculosis H37Rv grown without multiple stress in normal Dubos medium (pH7.0) with glycerol until OD600=0.2.

label_protocol: Labeled cDNA was prepared as follows: 10 μg of total RNA and 2 μg of random oligonucleotide hexamers (Invitrogen, CA) were incubated 15 min at 65 °C, cooled on ice, combined with Stratascript RTase buffer, 0.5 mM dATP, 0.5 mM dGTP, 0.5 mM dCTP, 0.02 mM dUTP, 1.5 nmol aminoallyl-dUTP (Amersham, NJ), and 2 μl Stratascript RTase II (Invitrogen, CA) in a total volume of 30 μl. This mixture was incubated 10 min at room temperature, and 42 °C overnight. Synthesized cDNA was purified by QIAquick PCR purification kit (Qiagen, CA) according to the manufacturer’s recommendation. The aminoallyl-dUTP-conjugated cDNA probes was spin-dried (SpeedVac, Savant), resuspended in 50 mM sodium carbonate buffer (pH 9.3) and cyanine monofunctional dyes (Amersham) for 1 h at room temperature followed by quenching with 4 M hydoxylamine. Cyanine-labeled probes were purified again by QIAquick PCR purification kit (Qiagen).

growth_protocol: Wild-type M. tuberculosis H37RV was grown in the complete normal Dubos medium supplemented with 1.5% glycerol at pH7.0. The cells were incubated in vented cap bottles aerobically at 37C until OD600 reached to 0.2. To synchronize growth before inoculation, cells were diluted in the same medium and grown again until OD600 value of 0.2 before harvest (i.e. seed culture for microarray control sets).

extract_protocol: Cells were harvested and quickly frozen in a dry ice-ethanol both. Total RNA was isolated using glass beads (Bio101, Lysing Matrix B), a TRIzol (InVitrogen) extraction and purified by Rneasy (Qiagen) kit according to the manufacturers' recommendations.

treatment_protocol: Once the seed culture reached the above OD600 (OD600=0.2), part of the cell culture was harvested, and frozen in liquid nitrogen before storing at -80C. The total RNA isolated from each harvest cells served as control in the microarray hybridization.

tag: Reference cells diluted into normal but diluted DUBOS medium (10% DUBOS, pH7.0) at day 0.

source_name: M. tuberculosis H37Rv grown for 9 days in reduced Dubos medium (10%, pH7.0) without glycerol starting from OD600=0.2.

growth_protocol: The seed culture for microarray control sets was collected by centrifugation, and resuspended with 150 mL one tenth water dilution of the multiple stress medium to recover the original OD600 (OD600=0.2) in a 1 liter glass bottle with a 24/40 standard joint neck. To achieve starvation stress only, one tenth water dilution of the multiple stress medium was used with the supplemental surfactant (0.018% (v/v) Tyloxapol) at pH7.0. The head air space in each bottle was replaced every other day for 5 minutes with gas mixture (5% O2, 10% CO2 and 85 % N2) passing through a 0.2 um filter attached to a 18-G needle. Sealed culture bottles were rolled in a roller incubator at 37C.

treatment_protocol: Cells were harvested after 3, 9, and 18 days incubation under the given multiple stresses. After centrifugation, cells were snap-frozen in liquid nitrogen.

tag: Starved for 9 days


title: Vegetative Wild Type vs. bkd sample 1

tag: strain DK5643 (delta bkd), 5x10^8 cells/ml, 28 degrees C,

tag: strain DK1622, 5x10^8 cells/ml, 28 degrees C,


title: SV.D18.v2.109692

description:
Starvation for 18 days in reduced DUBOS medium (10%, pH7.0).
Replicates 6 of 6, Grown in rolling bottle, Normal aeration

source_name: M. tuberculosis H37Rv grown for 18 days in reduced Dubos medium (10%, pH7.0) without glycerol starting from OD600=0.2.

tag: Starved for 18 days


title: AML patient 10 Diagnosis

tag: FAB_type = M1


title: SV.D09.v2.109392

description:
Starvation for 9 days in reduced DUBOS medium (10%, pH7.0).
Replicates 3 of 6, Grown in rolling bottle, Normal aeration


title: F10.D18.v2.109387

description:
Multiple stress for 18 days in reduced DUBOS medium (10%, pH5.0).
Replicates 5 of 6, Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).

tag: Reference cells diluted into modified multiple stress medium (10% DUBOS, pH5.0) at day 0.

source_name: M. tuberculosis H37Rv grown for 18 days under multiple stress in reduced Dubos medium (10%, pH5.0) without glycerol starting from OD600=0.2.

growth_protocol: The seed culture for microarray control sets was collected by centrifugation, and resuspended with 150 mL one tenth water dilution of the acidic multiple stress medium to recover the original OD600 (OD600=0.2) in a 1 liter glass bottle with a 24/40 standard joint neck. To achieve more stringent starvation, one tenth water dilution of the acidic multiple stress medium was used with the supplemental surfactant (0.018% (v/v) Tyloxapol) at pH5.0. The head air space in each bottle was replaced every other day for 5 minutes with gas mixture (5% O2, 10% CO2 and 85 % N2) passing through a 0.2 um filter attached to a 18-G needle. The bottles were sealed with a rubber septum flip top cap, and molten paraffin wax on the outside of the cap to ensure air-tight. Sealed culture bottles were rolled in a roller incubator at 37C.

tag: Multiple stressed for 18 days


title: SV.D18.v2.109394

description:
Starvation for 18 days in reduced DUBOS medium (10%, pH7.0).
Replicates 5 of 6, Grown in rolling bottle, Normal aeration


title: F10.D09.v2.109385

description:
Multiple stress for 9 days in reduced DUBOS medium (10%, pH5.0).
Replicates 3 of 6, Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).

source_name: M. tuberculosis H37Rv grown for 9 days under multiple stress in reduced Dubos medium (10%, pH5.0) without glycerol starting from OD600=0.2.

tag: Multiple stressed for 9 days


title: SV.D03.v2.109391

description:
Starvation for 3 days in reduced DUBOS medium (10%, pH7.0).
Replicates 2 of 6, Grown in rolling bottle, Normal aeration

source_name: M. tuberculosis H37Rv grown for 3 days in reduced Dubos medium (10%, pH7.0) without glycerol starting from OD600=0.2.

tag: Starved for 3 days


title: F4.D06.v2.110338

description:
Multiple stress for 6 days
Replicates; Biological (3/4) - Technical (3/3), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).

tag: Reference cells diluted in multiple stress medium at day 0.

source_name: M. tuberculosis H37Rv grown under multiple stress for 6 days in Dubos medium (pH5.0) without glycerol starting from OD600=0.2.

growth_protocol: The seed culture for microarray control sets was collected by centrifugation, and resuspended with 150 mL standard multiple stress medium to recover the original OD600 (OD600=0.2) in a 1 liter glass bottle with a 24/40 standard joint neck. The standard multiple stress medium was prepared by mixing 1X Dubos Broth base and 10% (v/v) albumin supplement at pH5.0, finally comprising 0.75% Dextrose, 0.5% BSA, and 0.85% NaCl in acidic condition. No glycerol was added in the multiple stress medium except 0.02% (v/v) Tween 80. The head air space in each bottle was replaced every other day for 5 minutes with gas mixture (5% O2, 10% CO2 and 85 % N2) passing through a 0.2 um filter attached to a 18-G needle. The bottles were sealed with a rubber septum flip top cap, and molten paraffin wax on the outside of the cap to ensure air-tight. Sealed culture bottles were rolled in a roller incubator at 37C.

treatment_protocol: Cells were harvested after 0, 1, 2, 3, 6, and 12 days incubation under the given multiple stresses. After centrifugation, cells were snap-frozen in liquid nitrogen.

tag: Multiple stressed for 6 days


title: F10.D09.v2.109386

description:
Multiple stress for 9 days in reduced DUBOS medium (10%, pH5.0).
Replicates 4 of 6, Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: F7.D03.v2.109817

description:
Multiple stress for 3 days
Replicates; Biological (5/5) - Technical (2/4), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).

source_name: M. tuberculosis H37Rv grown under multiple stress for 3 days in Dubos medium (pH5.0) without glycerol starting from OD600=0.2.

tag: Multiple stressed for 3 days


title: F10.D03.v2.109220

description:
Multiple stress for 3 days in reduced DUBOS medium (10%, pH5.0).
Replicates 1 of 6, Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).

source_name: M. tuberculosis H37Rv grown for 3 days under multiple stress in reduced Dubos medium (10%, pH5.0) without glycerol starting from OD600=0.2.


title: F6.D06.v2.106062

description:
Multiple stress for 6 days
Replicates; Biological (4/4) - Technical (2/2), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: F6.D06.v2.105905

description:
Multiple stress for 6 days
Replicates; Biological (4/4) - Technical (1/2), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: F6.D03.v2.105901

description:
Multiple stress for 3 days
Replicates; Biological (4/5) - Technical (2/2), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: F4.D06.v2.110335

description:
Multiple stress for 6 days
Replicates; Biological (3/4) - Technical (2/3), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: F7.D03.v2.109810

description:
Multiple stress for 3 days
Replicates; Biological (5/5) - Technical (1/4), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: F7.D03.v2.109818

description:
Multiple stress for 3 days
Replicates; Biological (5/5) - Technical (3/4), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: F10.D03.v2.109299

description:
Multiple stress for 3 days in reduced DUBOS medium (10%, pH5.0).
Replicates 2 of 6, Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: F7.D02.v2.109570

description:
Multiple stress for 2 days
Replicates; Biological (3/3) - Technical (3/4), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).

source_name: M. tuberculosis H37Rv grown under multiple stress for 2 days in Dubos medium (pH5.0) without glycerol starting from OD600=0.2.

tag: Multiple stressed for 2 days


title: F4.D06.v2.110334

description:
Multiple stress for 6 days
Replicates; Biological (3/4) - Technical (1/3), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: SV.D03.v2.109390

description:
Starvation for 3 days in reduced DUBOS medium (10%, pH7.0).
Replicates 1 of 6, Grown in rolling bottle, Normal aeration


title: F6.D03.v2.105899

description:
Multiple stress for 3 days
Replicates; Biological (4/5) - Technical (1/2), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: F5.D03.v2.110745

description:
Multiple stress for 3 days
Replicates; Biological (3/5) - Technical (1/4), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: F7.D02.v2.109571

description:
Multiple stress for 2 days
Replicates; Biological (3/3) - Technical (4/4), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: F5.D03.v2.111487

description:
Multiple stress for 3 days
Replicates; Biological (3/5) - Technical (4/4), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: Main root, 6 days after salt treatment

city: Hachioji

first: Yuichi

last: Tada

state: Tokyo

address: 1404-1 Katakura

institute: Tokyo University of Technology

description: Lateral root from Bruguiera gymnorhiza treated with 500 mM NaCl for hours.

hyb_protocol: Following fragmentation, 12 microg of cRNA were hybridized to the CustomArray 12K (CombiMatrix Corporation, WA, USA). The microarray contained 11,997 oligoprobes (35-40 mers oligonuleotide)  from B. gymnorhiza.

scan_protocol: GeneChips were scanned using the ScanArray 4000XL (Perkin Elmer, MA, USA)

data_processing: Spot signal intensities were qualified with MicroArray Imager software (CombiMatrix, WA, USA) and analyzed using ArrayAssist software (STRATAGENE, CA, USA). Local background substitution, Lowess normalization and pair wise t-test were applied to identify differentially expressed genes.

organism: Bruguiera gymnorhiza

source_name: Main root from Bruguiera gymnorhiza under salt stress

label_protocol: aRNA was labelled with Cy5 using the Kreatech ULS labelling system (Kreatech Biotechnology, Amsterdam, Netherlands).

extract_protocol:
Plants were pulled from pots, the roots were washed briefly in water, wiped with paper, separated from the rest of the plant.
RNA extraction was parformed as previously described (Miyama and Hanagata 2007). Total RNA was then cleaned up using an RNeasy Plant RNA purification Kit (QIAGEN, Tokyo, Japan). aRNA was amplified from 1 µg of total RNA using Ambion MessageAmpII kit (Ambion, TX, USA)

tag: Main root,

tag: Age

value: 4 months,

tag: Period of salt treatment

value: 6 days,

tag: NaCl concentration applied


title: F5.D03.v2.111486

description:
Multiple stress for 3 days
Replicates; Biological (3/5) - Technical (3/4), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: Main root, 12 days after salt treatment

value: 12 days,


title: F7.D03.v2.109822

description:
Multiple stress for 3 days
Replicates; Biological (5/5) - Technical (4/4), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: F7.D02.v2.109569

description:
Multiple stress for 2 days
Replicates; Biological (3/3) - Technical (2/4), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: F5.D03.v2.111481

description:
Multiple stress for 3 days
Replicates; Biological (3/5) - Technical (2/4), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: Main root, 24 hours after salt treatment

value: 24 hours,


title: F5.D02.v2.111491

description:
Multiple stress for 2 days
Replicates; Biological (1/3) - Technical (4/4), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: Main root, 12 hours after salt treatment b

tag: Main root

value: 4 months

value: 12 hours


title: F6.D02.v2.105893

description:
Multiple stress for 2 days
Replicates; Biological (2/3) - Technical (1/2), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: Main root, 3 days after salt treatment

value: 3 days


title: F7.D02.v2.109568

description:
Multiple stress for 2 days
Replicates; Biological (3/3) - Technical (1/4), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: F5.D02.v2.110346

description:
Multiple stress for 2 days
Replicates; Biological (1/3) - Technical (2/4), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: Main root, 12 hours after salt treatment c


title: Main root, 6 hours after salt treatment b

value: 6 hours


title: Main root, 12 hours after salt treatment


title: F5.D02.v2.111490

description:
Multiple stress for 2 days
Replicates; Biological (1/3) - Technical (3/4), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: F7.D01.v2.109567

description:
Multiple stress for 1 day
Replicates; Biological (3/3) - Technical (4/4), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).

source_name: M. tuberculosis H37Rv grown under multiple stress for 1 day in Dubos medium (pH5.0) without glycerol starting from OD600=0.2.

tag: Multiple stressed for 1 day


title: Main root, 6 hours after salt treatment c


title: Main root, 6 hours after salt treatment a


title: F2.D12.v1.12947612

description:
Multiple stress for 12 days
Replicates; Biological (2/2) - Technical (4/4), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).

source_name: M. tuberculosis H37Rv grown under multiple stress for 12 days in Dubos medium (pH5.0) without glycerol starting from OD600=0.2.

tag: Multiple stressed for 12 days


title: F7.D01.v2.109565

description:
Multiple stress for 1 day
Replicates; Biological (3/3) - Technical (2/4), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: F10.D18.v2.109389

description:
Multiple stress for 18 days in reduced DUBOS medium (10%, pH5.0).
Replicates 6 of 6, Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: Main root, 3 hours after salt treatment b

value: 3 hours


title: F6.D02.v2.105898

description:
Multiple stress for 2 days
Replicates; Biological (2/3) - Technical (2/2), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: F5.D02.v2.110345

description:
Multiple stress for 2 days
Replicates; Biological (1/3) - Technical (1/4), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: Brucella_melitensis_BlxR_mutant_broth_rep5

city: Madison

first: Gary

last: Splitter

state: WI

address: 1656 Linden Dr

department: Pathobiological Sciences

institute: University of Wisconsin - Madison

description: cDNA levels normalized to gDNA levels

hyb_protocol: Cy3-labeled cDNA was mixed with 0.75 g cy5-labeled gDNA, and hybridization buffer (Pronto Plus Kit, Promega) was added to a final volume of 35 l.  The entire sample was loaded onto the printed array and covered with a HybriSlip coverslip (Molecular Probes).  Arrays were placed in specialized hybridization chambers (Telechem Inc., Sunnyvale, CA), and incubated at 42°C overnight.  Slides were washed using the Pronto Plus Hybridization System (Promega) and dried by centrifugation at 1000 rpm for 5 min.

scan_protocol: Slides were scanned using the GenePix4000B scanner (Axon Instruments) with independent excitation of the fluorophores Cy3 and Cy5.  Background intensities for each spot were calculated using GenPixPro 3.0 software (Axon Instruments) via the segmentation method.  The signal intensity for each spot was calculated as the difference between the average signal intensity and the average local background intensity.

data_processing: Data was normalized to gDNA levels by calculating the ratios of cDNA to gDNA for each spot.  Data was then log2 transformed, and the signal ratio for each spot was divided by the mean signal ratio of the entire array to validate comparisons between different arrays.  Data normalization and statistical analysis were performed using TIGR MeV

organism: Brucella melitensis

source_name: Brucella melitensis delta blxR, log phase, in broth

label_protocol: cDNA was synthesized from 7 ug of total RNA in the presence of CyDye-3-dCTP (Amersham Biosciences).  The labeled cDNA was purified using the ChipShot cDNA System (Promega).  For each sample, RNA was extracted from two independently grown cultures and cDNA was generated three times for each RNA sample.

growth_protocol: Bacteria were grown in TSB until mid/late-log phase.  Before RNA isolation, phenol-ethanol (1:19) was added, cells were pelleted by centrifugation and stored at -80°C.  Total RNA was extracted from cell pellets using the MasterPure RNA Purification Kit (Epicentre), and DNA was removed using TURBO DNA-free (Ambion).

treatment_protocol: Brucella melitensis, strain 16M delta blxR, log phase growth in broth


title: F2.D12.v1.12947611

description:
Multiple stress for 12 days
Replicates; Biological (2/2) - Technical (3/4), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: F2.D12.v1.12947601

description:
Multiple stress for 12 days
Replicates; Biological (2/2) - Technical (1/4), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: Main root, 3 hours after salt treatment c

description: Lateral root from Bruguiera gymnorhiza treated with 500 mM NaCl for hours.


title: Brucella_melitensis_BlxR_mutant_broth_rep3

description: cDNA levels normalized to gDNA levels

extract_protocol: Bacteria were grown in TSB until mid/late-log phase.  Before RNA isolation, phenol-ethanol (1:19) was added, cells were pelleted by centrifugation and stored at -80°C.  Total RNA was extracted from cell pellets using the MasterPure RNA Purification Kit (Epicentre), and DNA was removed using TURBO DNA-free (Ambion).

tag: Brucella melitensis delta blxR, log phase, in broth


title: Brucella_melitensis_BlxR_mutant_broth_rep6

description: cDNA levels normalized to gDNA levels


title: F7.D01.v2.109566

description:
Multiple stress for 1 day
Replicates; Biological (3/3) - Technical (3/4), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: F1.D12.v1.12958476

description:
Multiple stress for 12 days
Replicates; Biological (1/2) - Technical (7/7), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: Main root, 3 hours after salt treatment a


title: Main root, 1 hour after salt treatment c

value: 1 hour


title: Brucella_melitensis_BlxR_mutant_broth_rep2

description: cDNA levels normalized to gDNA levels

tag: Brucella melitensis blxR mutant, log phase, in broth


title: Brucella_melitensis_BlxR_mutant_broth_rep4

description: cDNA levels normalized to gDNA levels


title: F1.D12.v1.12958454

description:
Multiple stress for 12 days
Replicates; Biological (1/2) - Technical (6/7), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: F7.D01.v2.109564

description:
Multiple stress for 1 day
Replicates; Biological (3/3) - Technical (1/4), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: Brucella_melitensis_BlxR_mutant_broth_rep1

description: cDNA levels normalized to gDNA levels

source_name: Brucella melitensis, log phase, in broth

treatment_protocol: Bacteria were grown in TSB until mid/late-log phase.  Before RNA isolation, phenol-ethanol (1:19) was added, cells were pelleted by centrifugation and stored at -80°C.  Total RNA was extracted from cell pellets using the MasterPure RNA Purification Kit (Epicentre), and DNA was removed using TURBO DNA-free (Ambion).

tag: Brucella melitensis, strain 16M, log phase growth in broth


title: Main root, 1 hour after salt treatment b


title: F2.D12.v1.12947603

description:
Multiple stress for 12 days
Replicates; Biological (2/2) - Technical (2/4), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: Main root, 1 hour after salt treatment a


title: F5.D01.v2.111489

description:
Multiple stress for 1 day
Replicates; Biological (1/3) - Technical (4/4), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: F5.D01.v2.110344

description:
Multiple stress for 1 day
Replicates; Biological (1/3) - Technical (2/4), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: F6.D01.v2.105842

description:
Multiple stress for 1 day
Replicates; Biological (2/3) - Technical (2/2), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: F1.D12.v1.12946949

description:
Multiple stress for 12 days
Replicates; Biological (1/2) - Technical (4/7), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: B_melitensis_16M_broth_rep6

description: cDNA levels normalized to gDNA levels

growth_protocol: TSB


title: F5.D01.v2.111488

description:
Multiple stress for 1 day
Replicates; Biological (1/3) - Technical (3/4), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: B_melitensis_16M_broth_rep7

description: cDNA levels normalized to gDNA levels


title: F1.D12.v1.12946946

description:
Multiple stress for 12 days
Replicates; Biological (1/2) - Technical (2/7), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: Main root, 0 hour after salt treatment b

value: 0 hour


title: B_melitensis_16M_broth_rep8

description: cDNA levels normalized to gDNA levels


title: F1.D12.v1.12946947

description:
Multiple stress for 12 days
Replicates; Biological (1/2) - Technical (3/7), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: Lateral root, 12 days after salt treatment b

source_name: Lateral root from Bruguiera gymnorhiza under salt stress

tag: Lateral root

value: 12 days


title: B_melitensis_16M_broth_rep4

description: cDNA levels normalized to gDNA levels


title: B_melitensis_16M_broth_rep5

description: cDNA levels normalized to gDNA levels


title: Lateral root, 6 days after salt treatment

value: 6 days


title: Lateral root, 3 days after salt treatment


title: F6.D01.v2.105841

description:
Multiple stress for 1 day
Replicates; Biological (2/3) - Technical (1/2), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: Lateral root, 12 days after salt treatment a


title: F2.D06.v1.12947609

description:
Multiple stress for 6 days
Replicates; Biological (2/4) - Technical (4/4), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: F1.D12.v1.12946950

description:
Multiple stress for 12 days
Replicates; Biological (1/2) - Technical (5/7), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: F5.D01.v2.110343

description:
Multiple stress for 1 day
Replicates; Biological (1/3) - Technical (1/4), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: Main root, 0 hour after salt treatment

description: Lateral root from Bruguiera gymnorhiza treated with 500 mM NaCl for hours.


title: B_melitensis_16M_broth_rep3

description: cDNA levels normalized to gDNA levels


title: F2.D06.v1.12947608

description:
Multiple stress for 6 days
Replicates; Biological (2/4) - Technical (3/4), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: Lateral root, 24 hours after salt treatment

value: 24 hours