title: NT_vs_OsHDAC1 replicate 3

description: Biological replicate 3 of 3

source_name: mRNA RNA from 14-d-old OsHDAC1 seedling roots with Cy3

tag: OsHDAC1 seedling roots


title: NT_vs_OsHDAC1 replicate 2

status: Public on Jun 29 2009

type: RNA

city: Pyeongchang

first: Pil Joong

last: Chung

state: Gangwondo

address: Pyeongchang daero 1447

department: Crop Biotechnology Institute

country: South Korea

institute: Seoul National University

description: Biological replicate 2 of 3

hyb_protocol: Hybridization buffer (Genispere) were added, and microarray were applied to MAUI hybidization chamber

scan_protocol: scanned with a Genepix 4000B (Axon Instruments, USA)

data_processing: Analyzed with statistical R language and sma package in Bioconductor project (http://www.bioconductor.org/)

molecule: total RNA

organism: Oryza sativa

source_name: mRNA RNA from 14-d-old OHDAC1 seedling roots labeled with Cy5

label_protocol: Performed as procedures provided by Genisphere 3DNA Array Detection Array 50 kit (v. 2, Genisphere, Hatfield, PA)

extract_protocol: TRI REAGENT (MRC, Inc., USA) as described in manufacturer's instructions

tag: Age

source_name: mRNA RNA from 14-d-old NT seedling roots labeled with Cy3

tag: NT seedling roots


title: C57BL6 1750mJ/cm2 UVA vs C57BL6 unirradiated control, rep3

city: Sydney

first: Michael

middle: Peter

last: Stapelberg

state: NSW

address: The University of Sydney

department: Medicine

country: Australia

institute: The University of Sydney

description: Analysis used RNA from unirradiated control C57BL/6 mouse.

hyb_protocol: Prior to hybridisation, 4.25 ml of 20 SSC and 0.75 ml of 10% SDS was added to each labelled probe to make a final volume of 25 ml. Each labelled probe was then denatured through incubation in the thermal cycler at 99 ºC for 2 min. Immediately after denaturation, the denatured probe was added directly to the center of a glass compugen 22k mouse oligonucleotide microarray slide (The Clive and Vera Ramaciotti Centre for Gene Function Analysis, Sydney Australia) and covered with a 24 x 50 mm glass cover slip (Chase Scientific Glass, Rockwood, TN, USA) taking care not to trap any air bubbles. Each microarray slide was then placed in a 50 ml falcon tube containing a folded sheet of kimwipe (Kimberly-Clark, Erie, PA, USA) saturated with 2x SCC to maintain a humid hybridisation environment. Each hybridisation chamber was then placed in an incubation oven at 65 ºC for 16 h. Following incubation, microarray slides were removed from their hybridisation chambers and washed in a solution containing 2x SSC and 0.1% SDS for 1 min, followed by 1x SSC for a further 1 min and finally in 0.2x SSC for 1 min. All washing steps were performed at room temperature with gentle agitation and at no point were the microarray slides allowed to dry. After washing, each microarray slide was placed in a 50 ml falcon tube and centrifuged at 800x g at room temperature for 5 min.

scan_protocol: Each microarray was scanned immediately after washing using an axon scanner (Axon Instruments, Molecular Devices, Sunnyvale, CA, USA) with GenePix Pro 5.0 microarray image acquisition and image analysis software (Axon Instruments, Molecular Devices, Sunnyvale, CA, USA). For each microarray scan the laser power was set to 100% and the pixel resolution at 5 mm.

data_processing: The first component of the microarray analysis was done using the R software package Linear Models for Microarray Data (LIMMA) (Wettenhall and Smyth, 2004) and involved no background correction, within-array print-tip loess normalisation, followed by scale normalisation for each unirradiated control and UV irradiated group.

organism: Mus musculus

source_name: skin from C57BL6 mouse irradiated with 1750mJ/cm2 UVA

label_protocol: For the microarray study a direct incorporation of Cyanine 3-dCTP and Cyanine 5-dCTP fluorescent dyes (Perkin Elmer Life Sciences, Inc. Boston, MA, USA) was used for cDNA synthesis. For each UV dose, a reference design was used to compare an unirradiated control against an irradiated sample. A fluorescent dye swap was done for each alternate hybridisation to reduce systematic dye bias of incorporated fluorescent dyes.

extract_protocol: 24 hours after UVA, UVB and ssUV irradiation a 1 cm2 uniform section of skin was excised from the dorsal surface of irradiated and control mice. Total RNA was then extracted from the whole skin using TRIzol reagent (Gibco Invitrogen Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions, purified, DNase treated and reverse transcribed into cDNA.

treatment_protocol: Female C57BL/6 and Balb/c mice aged 8-9wks at the start of irradiations were used for these experiments (Animal Resource Centre, Perth, WA, Australia), which were conducted with the approval of the University of Sydney animal ethics committee. Prior to each irradiation the dorsal trunk was shaved and the mice were then allowed to rest for 24h. Mice to be irradiated were then placed in an animal-restraining cage covered with a quartz glass lid. All irradiation times were less than 2 min and air-conditioning was used to ensure that the mouse body temperature did not increase during irradiation. Single irradiations for microarray and RT-PCR experiments and 3 on consecutive days for contact sensitivity experiments were given to each mouse and all irradiations were always performed at the same time of day. A 1000 W xenon arc solar simulator (Oriel, Stratford, CT) with two dichroic mirrors that allow wavelengths between 200 nm and 400 nm to pass through were used with a filter that blocks UVB to produce a UVA spectrum. For ssUV and UVB filters were used to attenuate the visible and infrared wavelengths and remove UVC (< 290 nm) so that it simulated sunlight (ssUV), or comprised predominantly UVB. The spectra have previously been described (Byrne et al., 2002a). The intensity (mW per cm2) of the UVA, UVB and ssUV output was measured regularly using a radiometer (Solar Light Company, PA) which had been calibrated against the source with an OL-754 spectroradiometer (Optronics Laboratories, Orlando, FL), and the timing of UV exposure was adjusted using an automated timing device to deliver consistent UV doses. The spectral output was regularly measured using the OL-754 spectroradiometer calibrated against standard lamps. The UVA doses were 1750 and 3500 mJ/cm2 respectively and for simplicity will be referred to as the lower and higher UVA doses. The UVB and ssUV doses were 285 mJ/cm2 and 3860 mJ/cm2 respectively (comprising 285 mJ/cm2 UVB with 3575 mJ/cm2 UVA) and for simplicity will be referred to as the UVB and ssUV doses. The UV doses used in this study are physiological and representative of typical human sunlight exposure. The UVB and higher UVA doses are the amounts in sunlight that would cause barely detectable sunburn. The ssUV dose is the same amount of UVB combined with UVA to approximate the solar spectrum and give a barely detectable sunburn.

tag: strain

tag: gender

value: female

tag: tissue

value: skin

tag: treatment

value: UVA irradiation

source_name: skin from C57BL6 mouse not irradiated with UV

value: unirradiated


title: NT_vs_OsHDAC1 replicate 1

description: Biological replicate 1 of 3

source_name: mRNA RNA from 14-d-old OsHDAC1 seedling roots labeled with Cy5


title: BY4742; +carnitine +H2O2; biological rep2

city: Stellenbosch

first: Jaco

last: Franken

state: Western Cape

address: Victoria Street

department: Institute for Winebiotechnology

country: South Africa

institute: University of Stellenbosch

description: gene expression data of yeast cultures grown to mid-log phase in the presence of L-carnitine and subsequently treated with 0.4 mM H2O2 for 30 min

hyb_protocol: Performed according to Affymetrix instructions

scan_protocol: Gene chips were scanned using GeneChip® Scanner 3000

data_processing: Acquisition and quantification of array images and data filtering were performed using Affymetrix GeneChip® Operating Software (GCOS) version 1.4.  All arrays were scaled to a target value of 500 using the average signal from all gene features using GCOS.

label: Biotin

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae cultures grown to mid-log in the presence of L-carnitine and exposed to hydrogen peroxide

growth_protocol: 50 ml fresh synthetic complete dextrose medium was inocculated to and OD600 of 0.1 and grown to mid-log phase (OD600 between 0.4 and 0.5) before harvesting

extract_protocol: Acid phenol chloroform extration of RNA was performed

treatment_protocol: Culture's were grown to mid log in synthetic yeast media with and without carnitine 1000 mg/L) supplementation.  A separate set was treated similarly and exposed to 0.4 mM H2O2 30 min to induce oxidative stress before harvesting and RNA isolation.

tag: genotype

value: MATa his3 leu2 lys2 ura3


title: T.2128.Tumor.Cy3

city: St. Louis

first: Robert

last: Lesurf

state: MO

address: 4444 Forest Park Ave

department: McDonnell Genome Institute

country: USA

institute: Washington University in St. Louis

description: RNA isolated from whole flash frozen mammary tissue/tumor.

hyb_protocol: Following fragmentation, 750ng of cRNA was hybridized to Agilent's Whole Mouse Genome expression array (G4122A) according to the protocols provided by the manufacturer.

scan_protocol: Array was scanned using Agilent's dual-laser microarray scanner (Model G2505B), and Cy5/Cy3-signals were quantified using Agilent's Feature Extraction software (Palo Alto, CA).

data_processing: Raw Cy5 and Cy3 intensities were background corrected using the RMA background correction algorithm. Data was transformed to log2 ratios and within array normalization was performed using spatial and intensity-dependent loess.

source_name: PTEN/NIC tumor from whole murine mammary gland

label_protocol: 500ng of total RNA was subjected to one round of linear T7 RNA amplification (Amino Allyl MessageAmp aRNA kit, Ambion) according to manufacturer's protocol.  Cy3-labeled aRNA was prepared from 10ug aRNA using Cy Post-labeling Reactive Dye Pack (Amersham Biosciences).

extract_protocol: RNeasy Midi Kit (Qiagen)

tag: Sample identifier

value: T.2128; Sex:Female; Strain:FVB/N

source_name: Stratagene universal mouse reference

label_protocol: 500ng of total RNA was subjected to one round of linear T7 RNA amplification (Amino Allyl MessageAmp aRNA kit, Ambion) according to manufacturer's protocol. Cy5-labeled aRNA was prepared from 10ug aRNA using Cy Post-labeling Reactive Dye Pack (Amersham Biosciences).

extract_protocol: No extraction


title: BY4742; +H2O2; biological rep2

description: gene expression data of yeast cultures grown to mid-log phase and treated with 0.4 mM H2O2 for 30 min

source_name: Saccharomyces cerevisiae cultures grown to mid-log and exposed to hydrogen peroxide

label_protocol: Performed according to Affymetrix instructions


title: BY4742; +H2O2; biological rep1


title: BY4742; biological rep1

description: gene expression data of yeast cultures grown to mid-log phase

source_name: Saccharomyces cerevisiae cultures grown to mid-log


title: T.9318.Tumor.Cy3

value: T.9318; Sex:Female; Strain:FVB/N


title: BY4742; biological rep2


title: NBRC1950-2

city: Tsukuba

first: Jun

last: Shima

state: Ibaraki

address: 2-1-12 Kannondai

country: Japan

institute: National Food Research Institute

hyb_protocol: At 45degree for 16-18h

scan_protocol: GeneChip scanner

data_processing: GeneChip operating system (GCOS)

molecule: polyA RNA

label_protocol: According to the Affymetrix user's mannual

extract_protocol: Each time samples of total RNA were extracted using the hot phenol method. Poly A RNA was enriched from total RNA with Oligotex dT30.


title: T.9524.Tumor.Cy3

value: T.9524; Sex:Female; Strain:FVB/N


title: X2180-1


title: X2180-2


title: T.9524.Tumor.Cy5


title: T.2128.Tumor.Cy5


title: Post-natal day 9 mouse cornea sample 2

status: Public on Jun 28 2009

city: Bethesda

first: Yan

last: Li

state: MD

address: 5625 Fishers Lane, Room 1S-02

institute: NIH\NEI

description: 568 miRNAs were analysed across 4 biological replicates of the developing (PN9) mouse corneaornea

hyb_protocol: The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 L 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: The data process includes background subtraction, Cy5 channel normalization. Background is determined using a regression-based background mapping method.  The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots.  Raw data matrix is then subtracted by the background matrix. Normalization is carried out using a cyclic LOWESS (Locally-weighted Regression) method to remove system related variations, such as sample amount variations and signal gain differences of scanners.

source_name: wild type C57/BL mouse cornea

label_protocol: the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase.  An oligonucleotide tag was then ligated to the poly(A) tail and labeled with Cy5 for later fluorescent detection.

growth_protocol: wild type C57/BL mice at the age of postnatal day 9 (PN9) and 6 weeks after birth were purchased from Charles River.

extract_protocol: Total RNA was extracted using Trizol according to the manufacturer's protocol (Invitrogen). 5 µg total RNA per sample was size fractionated using a YM-100 Microcon centrifugal filter (Millipore) to isolate small RNAs (<300 nt)

treatment_protocol: Corneas were dissected from C57BL/6 mice sacrificed at PN9 and 6 weeks (adult) after birth. Total RNAs were isolated from ten 6-week and sixteen PN9 whole corneas. Cornea dissection and RNA extraction for both the 6-week and PN9 corneas were repeated four times to collect altogether eight RNA samples (four adult cornea RNAs and four PN9 cornea RNAs).

value: cornea

tag: age

value: post-natal day 9


title: Post-natal day 9 mouse cornea sample 4

value: C57BL/6 s


title: C57BL6 3500mJ/cm2 UVA vs C57BL6 unirradiated control, rep1

source_name: skin from C57BL6 mouse irradiated with 3500mJ/cm2 UVA


title: Post-natal day 9 mouse cornea sample 1


title: T.9522.Tumor.Cy5

value: T.9522; Sex:Female; Strain:FVB/N


title: Post-natal day 9 mouse cornea sample 3


title: 6-week old mouse cornea sample 4

description: 568 miRNAs were analysed across 4 biological replicates of the mature (6-week-old) mouse cornea


title: 6-week old mouse cornea sample 3


title: T.8963.Tumor.Cy5

value: T.8963; Sex:Female; Strain:FVB/N


title: T.8963.Tumor.Cy3


title: T.9522.Tumor.Cy3


title: 6-week old mouse cornea sample 2


title: NBRC1950-1


title: BY4742; +carnitine; biological rep1

description: gene expression data of yeast cultures grown to mid-log phase in the presence of L-carnitine

source_name: Saccharomyces cerevisiae cultures grown to mid-log in the presence of L-carnitine


title: BY4742; +carnitine; biological rep2


title: Human HCT116-3(6) cells, untreated

status: Public on Jun 30 2009

type: genomic

city: La Jolla

first: Vera

last: Huang

state: CA

address: 3855 Health Science Drive, Room 4317

institute: UCSD-Moores Cancer Center

description: Human HCT116-3(6) cells, untreated

hyb_protocol: Probe labeling and hybridization were performed by NimbleGen (Reykjavik, Iceland).

scan_protocol: Slides were scanned by NimbleScan (NimbleGen).

data_processing: Data were processed by NimbleGen, Inc., log base 2 (immunoprecipitated DNA/input DNA) ratios were calculated after normalization.

molecule: genomic DNA

organism: Homo sapiens

source_name: HCT116-3(6) cells, untreated; p53 Antibody

extract_protocol: standard chromatin immunoprecipitatin procedure was carried out using a mixture of anti-p53 antibodies (Ab1 and Ab12).

tag: p53 Antibody

source_name: HCT116-3(6) cells, untreated; total input DNA

extract_protocol: input chromatin without undergoing immunoprecipitation was decrosslinked by heating at 65°C overnight. Following treatment with Proteinase K, DNA fragments were extracted with phenol/chloroform 2X. DNA was treated with RNAse A and purified using Qiaquick PCR purification columns (Qiagen).

tag: control total input


title: hog1_H60_0200_exp2

status: Public on Jun 27 2009

city: Seoul

first: Yong-Sun

last: Bahn

address: 134 Shinchon-dong Seodaemun-gu

department: Biotechnology

institute: Yonsei University

description:
Ctr vs △hog1 H60
exp2

hyb_protocol: Microarray Hybridization and Washing.  A C. neoformans serotype D 70-mer microarray slide containing 7,936 probes (Duke University) was pre-hybridized at 42°C in 60 ml of pre-hybridization buffer (42.4 ml sterile distilled water, 2 ml 30% BSA (Sigma), 600 µl 10% SDS, 15 ml 20x SSC (Saline-Sodium Citrate, 3 M NaCl, 0.3 M Na-citrate, pH 7.0)), washed with distilled water and isopropanol, and dried by brief centrifugation (110 xg, 2 min).  The Cy3- and Cy5-labeled cDNA samples were combined, concentrated through a Microcon30 filter, and vacuum-dried.  The dried cDNA samples were resuspended with 24 µl of 1x hybridization buffer (250 µl 50% formamide, 125 µl 20x SSC, 5 µl 10% SDS, 120 µl dH2O, total 500 µl), added with 1 µl polyA tail DNA (Sigma), further incubated at 100°C for 3 min and allowed to cool for 5 min at room temperature.  The microarray slides were aligned into the hybridization chamber (DieTech), removed of any dust, and covered by Lifterslips (Erie Scientific).  The Cy3/Cy5-labeled cDNA samples were applied in between Lifterslips and slides.  To prevent slides from drying, 10 µl of 3x SSC buffer was applied onto the slides, which were subsequently incubated for 16 hr at 42°C.  After incubation, the microarray slides were washed with three different washing buffers (wash buffer 1 (10 ml 20x SSC, 600 µl 10% SDS, 189.4 ml dH2O, preheated at 42°C), wash buffer 2 (3.5 ml 20x SSC, 346.5 ml dH2O), wash buffer 3 (0.88 ml 20x SSC, 349.12 ml dH2O)) for 2, 5, and 5 min, respectively, on an orbital shaker.  Three independent DNA microarrays with 3 independent biological replicates were performed, including one-dye swap experiment.

scan_protocol: After hybridization and washing, the microarray slides were scanned with a GenePix 4000B scanner (Axon Instrument) and the signals were analyzed with GenePix Pro (Ver. 4.0) and gal file (http://genome.wustl.edu/activity/ma/cneoformans).

data_processing: Since total RNAs isolated from serotype A C. neoformans strains were hybridized on the microarray slides printed with the serotype D 70-mer oligonucleotide sequences, the serotype A gene sequences were mapped to those of the serotype D using BLASTN.  C. neoformans H99 gene sequences that were updated at 24 November 2008 were downloaded from Broad institute (http://www.broad.mit.edu/annotation/genome/cryptococcus_neoformans).  The serotype D C. neoformans JEC21 gene sequences that were updated 27 April 2005 were downloaded from JCVI (ftp://ftp.tigr.org/pub/data/Eukaryotic_Projects/c_neoformans/).  The functional category of each C. neoformans H99 gene was assigned using the NCBI KOG database (http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi).  Using the serotype A gene sequence, each S. cerevisiae gene name or ID listed in the supplementary tables of the manuscript was identified by blastp search (e-value cut-off: e-6). For hierarchical and statistical analysis, data transported from GenePix software were analyzed with GeneSpring (Agilent) by employing LOWESS normalization, reliable gene filtering, clustering (standard correlation and average linkage) and zero-transformation, and ANOVA analysis (P<0.01), and Microsoft Excel software (Microsoft).

organism: Cryptococcus neoformans

source_name: hog1, hydrogen peroxide, 60min

label_protocol: For cDNA synthesis, the total RNA concentration was adjusted to 1 µg/µl with DEPC-treated water, and 15 µl of the total RNA (15 µg) was added to 1 µl of 5 µg/µl oligo dT (5’-TTTTTTTTTTTTTTTTTTTTV-3’)/pdN6 (Amersham, 1:1 mixture of 10 µg/µl, respectively), incubated at 70°C for 10 min, and placed on ice for 10 min.  Then 15 µl of cDNA synthesis mixture (3 µl 0.1 M DTT, 0.5 µl RNasin (Promega), 0.6 µl aa-dUTP (5-(3-aminoallyl)-2’-deoxyuridine 5’-triphosphate)/dNTPs (a mixture of 6 µl dTTP (100 mM), 4 µl aa-dUTP (100 mM), 10 µl dATP (100 mM), 10 µl dCTP (100 mM), 10 µl dGTP (100 mM)), 1.5 µl AffinityScript reverse transcriptase (Stratagene), 3 µl AffinityScript buffer, 7 µl water) was added and incubated at 42°C for 2 hrs.  Then 10 µl of 1 N NaOH and 10 µl of 0.5 M EDTA (pH 8.0) were added and incubated at 65°C for 15 min.  After incubation, 25 µl of 1 M HEPES buffer (pH 8.0) and 450 µl of DEPE-treated water were added, and the whole mixture was concentrated through a Microcon30 filter (Millipore) and vacuum-dried for 1 hr.  For Cy3 and Cy5 (Amersham) labeling of the prepared cDNA, Cy3 and Cy5 were dissolved in 10 µl DMSO and 1.25 µl of each dye was aliquoted into separate tubes.  The cDNAs prepared as described above were added to 9 µl of 0.05 M Na-bicarbonate (pH 8.0) and incubated at room temperature for 15 min.  The cDNAs prepared from pooled reference RNAs were mixed with Cy3 as a control and the cDNAs prepared from each test RNA (each experimental condition) were mixed with Cy5.  For a dye-swap experiment, control and test RNAs were labeled oppositely.  Each mixture was further incubated at room temperature for 1 hr in the dark and purified by QIAquick PCR purification kit (QIAGEN).

growth_protocol: The WT H99, hog1Δ (YSB64), ssk1Δ (YSB261), and skn7Δ (YSB349) mutant strains were grown in 50 ml YPD medium at 30°C for 16 hr.  Then 5 ml of the overnight culture was inoculated into a 100 ml of fresh YPD medium and further incubated for 4-5 hr at 30°C until it approximately reaches to the 1.0 of optical density (OD) at 600 nm (OD600nm = 1.0).

extract_protocol: For total RNA isolation, the lyophilized cell pellets were added to 3 ml volume of sterile 3 mm glass bead (SIGMUND LINDER), homogenized by shaking, added to 4 ml of TRizol reagent (Tri reagent, Molecular Research Center), and allowed to incubate at room temperature for 5 min.  Then 800 µl of chloroform was added, incubated for 3 min at room temperature, transferred to 15 ml round-bottom tubes (SPL), and centrifuged by 10,000 rpm at 4°C for 15 min (Sorvall SS-34 rotor).  Two milliliters of the supernatant was transferred to a new round-bottom tube, 2 ml isopropanol was added, inverted several times, and allowed to incubate for 10 min at room temperature.  Then the mixture was re-centrifuged at 10,000 rpm at 4°C for 10 min, and the pellet was washed with 4 ml of 75% ethanol diluted with diethylpyrocarbonate (DEPC)-treated water and centrifuged at 8,000 rpm at 4°C for 5 min.  The pellet was dried and resuspended with 500 µl DEPC-treated water.  Concentration and purity of total RNA samples were calculated by measuring OD260nm and gel-electrophoresis, respectively.  For control total RNA, all total RNAs prepared from WT, hog1Δ, ssk1Δ, and skn7Δ mutant cells grown in conditions described above were pooled (pooled reference RNAs).

treatment_protocol: For zero-time samples, 50 ml out of the 100 ml culture was sampled and rapidly frozen in liquid nitrogen.  To the remaining 50 ml culture, 50 ml of YPD containing 2 M NaCl, 40 µg/ml fludioxonil (PESTANAL, Sigma, 50 mg/ml stock solution in dimethylsulfoxide), or 5 mM H2O2 was added (final concentration of 1 M NaCl, 20 µg/ml fludioxonil, or 2.5 mM H2O2, respectively).  During incubation in each stress-inducing medium, 50 ml of the culture was sampled at 30 and 60 min, pelleted in a tabletop centrifuge, frozen in liquid nitrogen, and lyophilized overnight. The lyophilized cells were subsequently used for total RNA isolation.  As biological replicates for DNA microarrays, three independent cultures for each strain and growth condition were prepared for total RNA isolation.

tag: variety

value: grubii

tag: serotype

value: A

tag: exposed stress

value: Hydrogen peroxide

tag: time

value: 60 minutes

source_name: pooled total RNA from all strains, all time points, all stresses


title: hog1_N30_0209_exp3

description:
Ctr vs △hog1 N30
exp3

source_name: hog1, NaCl, 30min

value: NaCl

value: 30 minutes


title: hog1_N60_0210_exp3

description:
Ctr vs △hog1 N60
exp3

source_name: hog1, NaCl, 60min


title: hog1_F30_DS_0050_exp4_dye_swap

description:
Ctr vs △hog1 F30
exp4_dye_swap

source_name: hog1, fludioxonil, 30min

value: Fludioxonil


title: hog1_F60_0212_exp3

description:
Ctr vs △hog1 F60
exp3

source_name: hog1, fludioxonil, 60min


title: hog1_00_0208_exp3

description:
Ctr vs △hog1 00
exp3

source_name: hog1, 00min

value: Normal

value: 0 minutes


title: T.9318.Tumor.Cy5


title: hog1_F60_DS_0051_exp4_dye_swap

description:
Ctr vs △hog1 F60
exp4_dye_swap


title: hog1_H30_0213_exp3

description:
Ctr vs △hog1 H30
exp3

source_name: hog1, hydrogen peroxide, 30min


title: hog1_H30_DS_0052_exp4_dye_swap

description:
Ctr vs △hog1 H30
exp4_dye_swap


title: hog1_H60_DS_0053_exp4_dye_swap

description:
Ctr vs △hog1 H60
exp4_dye_swap


title: hog1_F30_0211_exp3

description:
Ctr vs △hog1 F30
exp3


title: BY4742; +carnitine +H2O2; biological rep1

source_name: Saccharomyces cerevisiae cultures grown to mid-log in the presence of L-carnitine and exposed to hydrogen peroxide

value: MATa his3 leu2 lys2 ura3


title: hog1_H60_0214_exp3

description:
Ctr vs △hog1 H60
exp3


title: hog1_N60_DS_0049_exp4_dye_swap

description:
Ctr vs △hog1 N60
exp4_dye_swap


title: 6-week old mouse cornea sample 1


title: hog1_F60_0198_exp2

description:
Ctr vs △hog1 F60
exp2


title: hog1_H30_0199_exp2

description:
Ctr vs △hog1 H30
exp2


title: hog1_F30_0197_exp2

description:
Ctr vs △hog1 F30
exp2


title: hog1_N60_0196_exp2

description:
Ctr vs △hog1 N60
exp2


title: hog1_00_0194_exp2

description:
Ctr vs △hog1 00
exp2


title: hog1_N30_0195_exp2

description:
Ctr vs △hog1 N30
exp2


title: hog1_H60_0186_exp1

description:
Ctr vs △hog1 H60
exp1


title: hog1_H30_0185_exp1

description:
Ctr vs △hog1 H30
exp1


title: ssk1_H60_0009_exp3

description:
Ctr vs △ssk1 H60
exp3

source_name: ssk1, hydrogen peroxide, 60min


title: hog1_F60_0184_exp1

description:
Ctr vs △hog1 F60
exp1


title: hog1_N60_0182_exp1

description:
Ctr vs △hog1 N60
exp1


title: hog1_F30_0183_exp1

description:
Ctr vs △hog1 F30
exp1


title: ssk1_H30_0008_exp3

description:
Ctr vs △ssk1 H30
exp3

source_name: ssk1, hydrogen peroxide, 30min


title: hog1_N30_0181_exp1

description:
Ctr vs △hog1 N30
exp1


title: hog1_00_0180_exp1

description:
Ctr vs △hog1 00
exp1


title: ssk1_F30_0006_exp3

description:
Ctr vs △ssk1 F30
exp3

source_name: ssk1, fludioxonil, 30min


title: ssk1_H60_DS_0016_exp2_dye_swap

description:
Ctr vs △ssk1 H60
exp2_dye_swap


title: ssk1_F60_0007_exp3

description:
Ctr vs △ssk1 F60
exp3

source_name: ssk1, fludioxonil, 60min


title: ssk1_00_0003_exp3

description:
Ctr vs △ssk1 00
exp3

source_name: ssk1, 00min


title: ssk1_N60_0005_exp3

description:
Ctr vs △ssk1 N60
exp3

source_name: ssk1, NaCl, 60min


title: ssk1_N30_0004_exp3

description:
Ctr vs △ssk1 N30
exp3

source_name: ssk1, NaCl, 30min


title: hog1_N30_DS_0048_exp4_dye_swap

description:
Ctr vs △hog1 N30
exp4_dye_swap


title: ssk1_H30_DS_0015_exp2_dye_swap

description:
Ctr vs △ssk1 H30
exp2_dye_swap


title: ssk1_F60_DS_0014_exp2_dye_swap

description:
Ctr vs △ssk1 F60
exp2_dye_swap


title: H3K64me3 ChIP ES cells, Replicate 2

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description: No description

hyb_protocol: Hybridization was performed by NimbleGen Inc. according to standard procedures.

scan_protocol: Scanning was performed by NimbleGen Inc. according to standard procedures.

data_processing: log2 (ChIP/Input) ratios, not normalized

source_name: Total input from embryonic stem cells

label_protocol: Labeling was performed by NimbleGen Inc. according to standard procedures.

extract_protocol: Genomic DNA prepared from sonicated input chromatin and amplified by ligation-mediated PCR

tag: cell type

value: embryonic stem cells

value: mixed 129-c57bl/6 background

value: male

tag: antibody

source_name: H3K64me3 ChIP from mouse embryonic stem cells

extract_protocol: Genomic DNA associated with H3K64me3 modified histones prepared by ChIP using the antibody characterized in Daujat et al, 2009, amplified by ligation-mediated PCR


title: ssk1_F30_DS_0013_exp2_dye_swap

description:
Ctr vs △ssk1 F30
exp2_dye_swap

source_name: pooled total RNA from all strains, all time points, all stresses


title: ssk1_N60_DS_0012_exp2_dye_swap

description:
Ctr vs △ssk1 N60
exp2_dye_swap


title: ssk1_N30_DS_0011_exp2_dye_swap

description:
Ctr vs △ssk1 N30
exp2_dye_swap


title: ssk1_H30_DS_0238_exp1_dye_swap

description:
Ctr vs △ssk1 H30
exp1_dye_swap


title: ssk1_00_DS_0010_exp2_dye_swap

description:
Ctr vs △ssk1 00
exp2_dye_swap


title: ssk1_H60_DS_0239_exp1_dye_swap

description:
Ctr vs △ssk1 H60
exp1_dye_swap


title: H3K64me3 ChIP ES cells, Replicate 4

description: No description


title: H3K9me3 ChIP ES cells, Replicate 2

description: No description

source_name: H3K9me3 ChIP from mouse embryonic stem cells

extract_protocol: Genomic DNA associated with H3K9me3 modified histones prepared by ChIP with an H3K9me3 specific antibody (Upstate), amplified by ligation-mediated PCR


title: ssk1_F60_DS_0237_exp1_dye_swap

description:
Ctr vs △ssk1 F60
exp1_dye_swap


title: skn7_H60_DS_0046_exp4_dye_swap

description:
Ctr vs △skn7 H60
exp4_dye_swap

source_name: skn7, hydrogen peroxide, 60min


title: skn7_F30_DS_0043_exp4_dye_swap

description:
Ctr vs △skn7 F30
exp4_dye_swap

source_name: skn7, fludioxonil, 30min


title: skn7_H30_DS_0045_exp4_dye_swap

description:
Ctr vs △skn7 H30
exp4_dye_swap

source_name: skn7, hydrogen peroxide, 30min


title: skn7_N60_DS_0042_exp4_dye_swap

description:
Ctr vs △skn7 N60
exp4_dye_swap

source_name: skn7, NaCl, 60min


title: skn7_00_DS_0040_exp4_dye_swap

description:
Ctr vs △skn7 00
exp4_dye_swap

source_name: skn7, 00min


title: ssk1_00_DS_0233_exp1_dye_swap

description:
Ctr vs △ssk1 00
exp1_dye_swap


title: ssk1_N60_DS_0235_exp1_dye_swap

description:
Ctr vs △ssk1 N60
exp1_dye_swap


title: ssk1_F30_DS_0236_exp1_dye_swap

description:
Ctr vs △ssk1 F30
exp1_dye_swap


title: skn7_N30_DS_0041_exp4_dye_swap

description:
Ctr vs △skn7 N30
exp4_dye_swap

source_name: skn7, NaCl, 30min


title: skn7_F60_DS_0044_exp4_dye_swap

description:
Ctr vs △skn7 F60
exp4_dye_swap

source_name: skn7, fludioxonil, 60min


title: H3K9me3 ChIP ES cells, Replicate 1

description: No description


title: H3K64me3 ChIP ES cells, Replicate 3

description: No description


title: H3K64me3 ChIP ES cells, Replicate 1

description: No description


title: skn7_F60_0037_exp3

description:
Ctr vs △skn7 F60
exp3


title: skn7_H30_0038_exp3

description:
Ctr vs △skn7 H30
exp3


title: skn7_F30_0036_exp3

description:
Ctr vs △skn7 F30
exp3


title: skn7_00_0033_exp3

description:
Ctr vs △skn7 00
exp3


title: skn7_H60_0039_exp3

description:
Ctr vs △skn7 H60
exp3


title: skn7_N30_0034_exp3

description:
Ctr vs △skn7 N30
exp3


title: skn7_N60_0035_exp3

description:
Ctr vs △skn7 N60
exp3


title: skn7_F30_0029_exp2

description:
Ctr vs △skn7 F30
exp2


title: skn7_F60_DS_0230_exp1_dye_swap

description:
Ctr vs △skn7 F60
exp1_dye_swap


title: skn7_H60_DS_0232_exp1_dye_swap

description:
Ctr vs △skn7 H60
exp1_dye_swap


title: skn7_H30_DS_0231_exp1_dye_swap

description:
Ctr vs △skn7 H30
exp1_dye_swap


title: skn7_N30_0027_exp2

description:
Ctr vs △skn7 N30
exp2


title: skn7_N60_0028_exp2

description:
Ctr vs △skn7 N60
exp2


title: skn7_N60_DS_0228_exp1_dye_swap

description:
Ctr vs △skn7 N60
exp1_dye_swap


title: skn7_F60_0030_exp2

description:
Ctr vs △skn7 F60
exp2


title: skn7_00_0026_exp2

description:
Ctr vs △skn7 00
exp2


title: skn7_F30_DS_0229_exp1_dye_swap

description:
Ctr vs △skn7 F30
exp1_dye_swap


title: skn7_N30_DS_0227_exp1_dye_swap

description:
Ctr vs △skn7 N30
exp1_dye_swap


title: E2_rep3

city: Columbia

first: Julia

middle: A

last: Taylor

address: 114 Lefevre Hall

department: Biological Sciences

institute: University of Missouri

description: Cultured fetal prostate mesenchyme cells.

hyb_protocol: cRNA was purified and fragmented using the GeneChip Sample Cleanup Module, and then hybridized to the Affymetrix mouse genome 430A array. Quality control, hybridization, washing and scanning were performed according to the GeneChip Expression Analysis Technical Manual.

scan_protocol: Scanning was performed with an Agilent microarray scanner.

data_processing: Scanned data were analyzed with Affymetrix GeneChip Operating Software.

label: biotin

source_name: UGS mesenchyme cells, estradiol-treated

label_protocol: Total RNA preparations were used to synthesize double-stranded cDNA using the Affymetrix One-Cycle cDNA Synthesis kit, and then amplified and biotinylated using the GeneChip IVT Labeling kit.

growth_protocol: Fetal UGS tissue was disrupted by collagenase treatment. Epithelial cells were discarded, and the collected mesenchymal cells were cultured at 37oC under 5% CO2 in RPMI-1640 without phenol red, supplemented with 2 mM L-glutamine, 100 units penicillin G sodium/ml, 100 mg streptomycin sulfate/ml, and 0.25 mg fungizone/ml, with 10% (v/v) fetal bovine serum (FBS).  Cells were grown to 95 % confluence, and then passaged by digestion with 0.05 % trypsin in 0.53 mM EDTA.

extract_protocol: Total RNA was isolated from the Trizol lysate and purified with the RNeasy Mini kit  according to the manufacturers’ instructions.  RNA quality was checked on an Agilent Bioanalyzer.

treatment_protocol: First passage cells were seeded at 0.315 x 10e6 cells/well in 35 mm dishes, in the same RPMI medium with endogenous hormones removed by substituting 5 % (v/v) charcoal-stripped FBS and 5 % (v/v) charcoal-stripped horse serum (Sigma, St. Louis, MO) for the 10% whole FBS, and further supplementing with ITS supplement, for final concentrations of 10 μg insulin/ml, 10 μg transferrin/ml, and 10 ng selenium/ml.   Cells were maintained in a constant background of 690 pM DHT (200 pg/ml) during treatment with estradiol.   Cells were maintained in estrogen-free medium for three days, with one medium change, before the start of estrogen treatment, and then treated with 100 nM estradiol for four days with daily medium changes.  At the end of the treatment period the cells were washed once with PBS, and immediately lysed on ice in Trizol.

tag: developmental stage

value: gestation day 17

value: prostate

value: urogenital sinus mesenchyme

value: estradiol


title: skn7_00_DS_0226_exp1_dye_swap

description:
Ctr vs △skn7 00
exp1_dye_swap

value: grubii


title: E2_rep1


title: 2032_short survivor

city: Genova

first: PAOLA

last: SCARUFFI

state: GE

address: LARGO R. BENZI, 10

country: Italy

institute: "San Martino" Hospital

description: Images were processed by Feature Extraction software v. 9.5.3.1 (Agilent Technologies).

hyb_protocol: We followed the miRNA Microarray System protocol v. 1.5 (Agilent Technologies).

scan_protocol: Slides were scanned by Agilent G2565BA scanner according to the miRNA Microarray System protocol v. 1.5 (Agilent Technologies).

data_processing: Tab-delimited text file were analyzed in R v. 2.7.2 software environment (www.r-project.org) using the limma package v. 2.14.16 (16) of Bioconductor (www.bioconductor.org). Only spots with signal minus background flagged as positive and significant were used in the following analysis as ‘detected’ spot. Probes with less than 50% of detected spots across all arrays were removed from the analysis. Similarly, arrays with a number of detected spots smaller than 50% of all spots on the array were removed. Background corrected intensities of replicated spots on each array were averaged. Data were then log2-transformed and normalized for between-array comparison using  quantile normalization (Bolstad, B. M., Irizarry R. A., Astrand, M., and Speed, T. P. (2003), A comparison of normalization methods for high density oligonucleotide array data based on bias and variance. Bioinformatics 19, 185-193).

source_name: Stage 4 neuroblastoma

label_protocol: We performed miRNA expression profiling starting from 100 µg of total RNA and following the miRNA Microarray System protocol v. 1.5 (Agilent Technologies). In dephosphorylation and ligation steps, 17 Units of Calf Intestine Alkaline Phosphatase (Takara Bio Inc., Shiga, Japan) and 20 Units of T4 RNA ligase (Takara Bio Inc.) have been used, respectively.

extract_protocol: Total RNA was extracted from frozen tumors by PerfectPureTM RNA Tissue Kit (5Prime, Hamburg, Germany), including RNase-free DNase I treatment (Ambion, TX, USA). Total and small RNAs were quantified and quality control was assessed by RNA 6000 Nano® and Small RNA® assays, respectively, on the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: diagnosis

value: Stage 4 neuroblastoma

tag: age at diagnosis

value: > 1 year

tag: survivor

value: dead with disease within 36 months from diagnosis

value: at least 80% of neuroblasts


title: 1439_short survivor

tag: tissue


title: WT_H30_DS_059_exp4_dye_swap

description:
Ctr vs WT H30
exp4_dye_swap

source_name: WT, hydrogen peroxide, 30min

tag: strain

value: A

value: Hydrogen peroxide

value: 30 minutes


title: ctrl_rep3

source_name: UGS mesenchyme cells, control

tag: gender

tag: treatment

value: control


title: WT_F30_DS_057_exp4_dye_swap

description:
Ctr vs WT F30
exp4_dye_swap

source_name: WT, fludioxonil, 30min

value: Fludioxonil


title: 1506_short survivor


title: ctrl_rep2


title: 2348_long-survivor

value: alive with an overall survival time > 36 months


title: 2200_long-survivor


title: 2704_short-survivor


title: WT_00_DS_054_exp4_dye_swap

description:
Ctr vs WT 00
exp4_dye_swap

source_name: WT, 00min

value: Normal

value: 0 minutes


title: E2_rep2

value: male

value: gestation day 17


title: WT_N60_DS_056_exp4_dye_swap

description:
Ctr vs WT N60
exp4_dye_swap

source_name: WT, NaCl, 60min

value: NaCl

value: 60 minutes


title: 1900_short-survivor


title: WT_N30_DS_055_exp4_dye_swap

description:
Ctr vs WT N30
exp4_dye_swap

source_name: WT, NaCl, 30min

value: grubii


title: WT_H60_0222_exp3

description:
Ctr vs WT H60
exp3

source_name: WT, hydrogen peroxide, 60min

source_name: pooled total RNA from all strains, all time points, all stresses


title: ctrl_rep1

value: prostate

value: urogenital sinus mesenchyme


title: WT_H60_DS_060_exp4_dye_swap

description:
Ctr vs WT H60
exp4_dye_swap


title: 1893_long-survivor

value: Stage 4 neuroblastoma

value: > 1 year


title: WT_H30_0221_exp3

description:
Ctr vs WT H30
exp3

value: A


title: WT_F60_0220_exp3

description:
Ctr vs WT F60
exp3

source_name: WT, fludioxonil, 60min


title: WT_F60_DS_058_exp4_dye_swap

description:
Ctr vs WT F60
exp4_dye_swap


title: WT_F30_0219_exp3

description:
Ctr vs WT F30
exp3


title: WT_N60_0218_exp3

description:
Ctr vs WT N60
exp3


title: 1401_long-survivor

value: at least 80% of neuroblasts


title: WT_N30_0217_exp3

description:
Ctr vs WT N30
exp3

value: 30 minutes


title: 1243_short-survivor

value: dead with disease within 36 months from diagnosis


title: 2040_short-survivor


title: WT_00_0216_exp3

description:
Ctr vs WT 00
exp3


title: WT_H30_DS_206_exp2_dye_swap

description:
Ctr vs WT H30
exp2_dye_swap

value: Hydrogen peroxide


title: WT_H60_DS_207_exp2_dye_swap

description:
Ctr vs WT H60
exp2_dye_swap


title: 1995_short-survivor


title: 2035_short-survivor


title: 1869_short-survivor


title: WT_N30_DS_202_exp2_dye_swap

description:
Ctr vs WT N30
exp2_dye_swap


title: WT_00_DS_201_exp2_dye_swap

description:
Ctr vs WT 00
exp2_dye_swap


title: 2140_long-survivor

value: alive with an overall survival time > 36 months


title: 2362_long-survivor


title: WT_N60_DS_203_exp2_dye_swap

description:
Ctr vs WT N60
exp2_dye_swap


title: 1965_short-survivor


title: 806_short-survivor


title: 1558_long-survivor


title: 1889_long-survivor


title: 1641_long-survivor


title: 1445_long-survivor


title: 2497_short-survivor


title: WT_H60_0193_exp1

description:
Ctr vs WT H60
exp1


title: REF subpopulation of MDA-MB-231 cell line, biological rep4

city: Paris

first: Nadejda

last: Vintonenko

address: 1 Avenue Claude Vellefaux

country: France

institute: Inserm

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials according to manufacturer's instructions (i.e., Heat cocktails at 99°C for 5 minutes, then 45°C for 5 minutes, centrifuge at max speed for 1 minute. Transfer 80ul of hyb solution to each array, then tape holes and parafilm. Hybridize 17 hours at 45°C at 60rpm. Fluidics washing is FS450_0007).

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using Affymetrix Expression Console software. Gene level expression data were summarized and then normalized using the RMA-Sketch default algorithm.

source_name: REF

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: INV and  REF subpopulations of MDA-MB-231 cell line were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 1% sodium pyruvate and 1% penicillin sodium and 1% streptomycin antibiotics (10% FCS-DMEM) at 37°C in a humidified atmosphere containing 5% carbon dioxide.

extract_protocol: Total RNA from 8 cell cultures (i.e., four biological replicates corresponding to four different passages of INV and REF cells) were isolated using RNeasy mini kit (Qiagen) by direct lysis on the 10cm culture dish with 600 μl RLT Buffer following manufacturer’s instructions. cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix) starting from 300 ng total RNA.

tag: cell line

tag: cell line origin

value: breast cancer

tag: cell line subpopulation

value: reference


title: REF subpopulation of MDA-MB-231 cell line, biological rep3


title: 2100_short-survivor


title: 1905_long-survivor


title: INV subpopulation of MDA-MB-231 cell line, biological rep4

source_name: INV

value: invasive


title: 1864_long-survivor


title: 789_long-survivor


title: WT_H30_0192_exp1

description:
Ctr vs WT H30
exp1

tag: variety


title: WT_F30_0190_exp1

description:
Ctr vs WT F30
exp1

tag: serotype

value: Fludioxonil


title: 1699_short survivor


title: WT_N30_188_exp1

description:
Ctr vs WT N30
exp1

tag: exposed stress

value: NaCl


title: WT_F60_0191_exp1

description:
Ctr vs WT F60
exp1

tag: time

value: 60 minutes


title: 1684_long survivor


title: 1560_short-survivor


title: 1276_short-survivor


title: WT_N60_0189_exp1

description:
Ctr vs WT N60
exp1

value: grubii


title: INV subpopulation of MDA-MB-231 cell line, biological rep3


title: INV subpopulation of MDA-MB-231 cell line, biological rep2


title: REF subpopulation of MDA-MB-231 cell line, biological rep1


title: REF subpopulation of MDA-MB-231 cell line, biological rep2


title: INV subpopulation of MDA-MB-231 cell line, biological rep1


title: dosTKO_log_1_hour_NO_rep2

status: Public on Jun 26 2009

city: Aurora

first: Ryan

middle: William

last: Honaker

state: CO

department: Microbiology

institute: University of Colorado Denver

hyb_protocol: Arrays were prehybridized in water, SSC, BSA, and SDS. Labeling reaction was concentrated to 5ul in a microcon 10 filter tube, added to tRNA, SSC, formamide, and SDS, and heated to 98 C for two minutes. Samples were hybridzed overnight at 50 C.

scan_protocol: Scanned on Molecular Device's Genepix 4000B.

data_processing: Spot intensities were obtained using GenePix Pro 6.0. Data analysis was performed as previously described in PMID: 12953092 (Voskuil M, et al., J Exp Med. 2003 Sep 1;198(5):705-13).

organism: Mycobacterium tuberculosis H37Rv

source_name: ΔdosT, log 1 hour NO treatment

label_protocol: 1.5 ug of RNA was primed with N6 primers, heated for two minutes at 98 C, then incubated 10 minutes at 25 C followed by 90 minutes at 42 C. 5mM A,G,C and 0.2mM T dNTP mix was used.

extract_protocol: Cell pellets were flash frozen on dry ice, resuspended in Trizol, and bead-beaten 3 x 40 seconds. Resulting cell lysate was added to chloroform and nucleic acids were then precipitated in isopropanol, rehydrated in 75% ethanol, then DNAse treated. Fur further purification, Qiagen RNeasy kit was used according to the manufacturer's instructions.

tag: mutation

value: ΔdosT

tag: condition

value: log phase culture, 1 hour NO treatment

source_name: wild type, log 1 hour NO treatment

value: wild type


title: WT_00_0187_exp1

description:
Ctr vs WT 00
exp1

value: Normal

value: 0 minutes


title: dosSTKO_24_hour_Gaspak_rep3

source_name: ΔdosS/T, 24 hours gaspak treatment

value: ΔdosS/T

value: 24 hours in anaerobic chamber with anaerobic envelope

source_name: wild type, 24 hours gaspak treatment


title: dosSTKO_24_hour_Gaspak_rep2


title: dosSKO_log_1_hour_NO_rep1

source_name: ΔdosS, log 1 hour NO treatment

value: ΔdosS


title: Memory B cells_rep6

city: New York

first: Katia

last: Basso

state: NY

address: 1150 St. Nicholas Avenue

department: Institute for Cancer Genetics

institute: Columbia University

description: Biological replicate 6 of 6.

hyb_protocol: Hybridization mix was prepared using the Human miRNA Microarray kit (Agilent Technologies) following the manufacturer's instructions. Hybridization was performed at 55C for 20h. Washing was performed using the Gene Expression Wash Buffer kit (Agilent Technologies) following the manufacturer's instructions.

scan_protocol: Scanning was performed by the Agilent Microarray Scanner and the Agilent's Scan Control Software v. A.7.0.1 (Agilent Technologies) using the XDR feature and the recommended parameter settings.

data_processing: Raw image data were processed by the Feature Extraction software 9.5.1 (Agilent Technologies).

source_name: Memory B cells isolated from tonsil

label_protocol: 100 ng of RNA were labeled using the Human miRNA Microarray kit (Agilent Technologies) following the manufacturer's instructions.

growth_protocol: Upon magnetic cell sorting, cells were lysated in Trizol Reagent (Invitrogen) and frozen.

extract_protocol: Total RNA was extracted using Trizol Reagent (Invitrogen) following the manufacturer's instructions.

value: tonsil

tag: cell type


title: dosSKO_log_1_hour_NO_rep3


title: dosSKO_log_1_hour_NO_rep2


title: dosTKO_log_1_hour_NO_rep1


title: Memory B cells_rep4

description: Biological replicate 4 of 6.


title: dosTKO_log_1_hour_NO_rep3


title: dosSKO_log_1_hour_NO_rep4


title: dosSKO_24_hour_Gaspak_rep3

source_name: ΔdosS, 24 hours gaspak treatment


title: Memory B cells_rep3

description: Biological replicate 3 of 6.


title: dosSTKO_24_hour_Gaspak_rep1


title: ssk1_N30_DS_0234_exp1_dye_swap

description:
Ctr vs △ssk1 N30
exp1_dye_swap

source_name: ssk1, NaCl, 30min

value: A

value: 30 minutes


title: Memory B cells_rep5

description: Biological replicate 5 of 6.


title: dosSKO_24_hour_Gaspak_rep1


title: dosTKO_24_hour_Gaspak_rep3

source_name: ΔdosT, 24 hours gaspak treatment


title: dosTKO_24_hour_Gaspak_rep2


title: dosSKO_24_hour_Gaspak_rep2


title: Memory B cells_rep2

description: Biological replicate 2 of 6.


title: Naïve B cells_rep6

description: Biological replicate 6 of 6.

source_name: Naïve B cells isolated from tonsil

value: IgD-positive CD27/CD10/ CD38-negative B-cells


title: dosSTKO_4_hour_Gaspak_rep3

source_name: ΔdosS/T, 4 hours gaspak treatment

value: 4 hours in anaerobic chamber with anaerobic envelope

source_name: wild type, 4 hours gaspak treatment


title: dosTKO_24_hour_Gaspak_rep1


title: Memory B cells_rep1

description: Biological replicate 1 of 6.


title: Naïve B cells_rep5

description: Biological replicate 5 of 6.


title: dosSKO_4_hour_Gaspak_rep1

source_name: ΔdosS, 4 hours gaspak treatment


title: dosSTKO_4_hour_Gaspak_rep2


title: Naïve B cells_rep2

description: Biological replicate 2 of 6.


title: Naïve B cells_rep3

description: Biological replicate 3 of 6.


title: dosTKO_4_hour_Gaspak_rep2

source_name: ΔdosT, 4 hours gaspak treatment


title: dosTKO_4_hour_Gaspak_rep3


title: Naïve B cells_rep1

description: Biological replicate 1 of 6.


title: Centroblasts_rep5

description: Biological replicate 5 of 6.

source_name: Centroblasts isolated from tonsil

value: CD77-positive B-cells


title: Centroblasts_rep6

description: Biological replicate 6 of 6.


title: dosTKO_4_hour_Gaspak_rep1


title: dosSTKO+pdosT_RAD_day6_rep3

source_name: ΔdosS/T+pDosT, anaerobic dormancy model day 6

value: ΔdosS/T+pDosT

value: model is anaerobic at day 6

source_name: wild type, anaerobic dormancy model day 6


title: Centroblasts_rep4

description: Biological replicate 4 of 6.


title: dosSKO_4_hour_Gaspak_rep2


title: Centroblasts_rep3

description: Biological replicate 3 of 6.


title: Naïve B cells_rep4

description: Biological replicate 4 of 6.


title: dosSTKO+pdosT_RAD_day6_rep2


title: dosSTKO_4_hour_Gaspak_rep1


title: Centroblasts_rep2

description: Biological replicate 2 of 6.


title: dosSTKO+pdosT_RAD_day6_rep1


title: dosSTKO_RAD_day6_rep2

source_name: ΔdosS/T, anaerobic dormancy model day 6


title: dosSTKO_RAD_day6_rep3


title: dosTKO_RAD_day6_rep3

source_name: ΔdosT, anaerobic dormancy model day 6


title: dosTKO_RAD_day6_rep2


title: Centroblasts_rep1

description: Biological replicate 1 of 6.


title: IL12_vs_input_rep2

city: indianapolis

first: Narayanan

middle: B

last: Perumal

state: IN

address: 719 Indiana Avenue Suite, WK311

department: School of Informatics

institute: Indiana University-Purdue University Indianapolis

hyb_protocol: Labeled DNA was hybridized to the Affymetrix GeneChip Mouse Promoter 1.0R Array at 45°C overnight.

scan_protocol: standard affymetrix

data_processing: The resulting CEL files were analyzed using Affymetrix TAS software that computed estimates of fold-enrichment over hybridization with input DNA in linear scale. This metric is referred to as peak binding intensity in the Analysis_results.xls Excel file and in the referred article. Graphing of peak binding values were generated using the Affymetrix Integrated Genome Browser.

source_name: ChIP DNA from IL12 stimulated CD4+ T cells

label_protocol: Amplified DNA was fragmented and labeled using the DNA Terminal Labeling Kit from Affymetrix.

growth_protocol: CD4+ T cells from C57BL/6 mice were activated for three days with anti-CD3 and anti-CD28.

extract_protocol: Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Cell lysates were sonicated to an average DNA fragment length of 300-500 bp. Genomic DNA from aliquots was purified for use as input. Chromatin was precleared with protein A agarose beads (Invitrogen) and STAT4-bound DNA sequences were isolated using specific antibodies (Santa Cruz sc-486). After incubation at 4°C overnight, protein A agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Quantitative PCR (Q-PCR) reactions were carried out in triplicate on specific genomic regions using SYBR Green Supermix (Bio-Rad). The resulting signals were normalized for primer efficiency by carrying out Q-PCR for each primer pair using input DNA.  ChIP (multiple reactions) and input DNAs were amplified using LM-PCR. The resulting amplified DNA was purified, quantified, and tested by QPCR at the same specific genomic regions as the original ChIP DNA to assess quality of the amplification reactions.

treatment_protocol: Activated CD4+ T cells were washed and incubated in the presence or absence of 5 ng/ml IL-12 for four hours before being processed for ChIP analysis.

tag: antibody

value: STAT4 rabbit polyclonal IgG

source_name: Input DNA from IL12 stimulated CD4+ T cells


title: IL12_vs_input_rep1


title: dosSTKO_RAD_day6_rep1


title: dosSKO_RAD_day6_rep2

source_name: ΔdosS, anaerobic dormancy model day 6


title: dosSKO_RAD_day6_rep3


title: dosTKO_RAD_day6_rep1

value: ΔdosT


title: dosSKO_RAD_day6_rep1


title: Halobacterium salinarum NRC-1 growth curve. Array 11015

status: Public on Jun 25 2009

city: Seattle

first: Tie

last: Koide

state: WA

address: 1441 N 34th street

institute: Institute for Systems Biology

description: Halobacterium NRC-1 at OD=2.580 versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M,Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35

scan_protocol: ScanArray 5000, using Packard BioChip ScanArray software. See http://www.systemsbiology.org/Scientists_and_Research/Technology/ISB_Facilities/Microarrayfor microarray scanning details

data_processing: AnalyzerDG software for spotfinding.  see http://www.systemsbiology.org/Scientists_and_Research/Technology/Data_Management/Microarray_Pipeline for more details

label: Alexa 532

organism: Halobacterium salinarum NRC-1

source_name: Halobacterium NRC-1 Reference sample

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35

growth_protocol: Standard mid-log phase (OD600:0.5-0.6) Halobacterium NRC-1 reference sample.

extract_protocol: Total DNA-free RNA prepared using the mirVana miRNA isolation kit (Ambion) and analyzed by PCR to rule out DNA contamination, with Agilent Bioanalyzer to verify integrity, and in NanoDrop for quantification.

tag: Halobacterium NRC-1 grown in standard growth media

label: Alexa 647

source_name: Halobacterium NRC-1 growth curve

growth_protocol: Halobacterium NRC-1 grown in rich media (CM), 200mL culture in 1L flask, shaking at 125RPM, and constant light.

tag: Halobacterium NRC-1 at OD=2.580, t=07740min, replica 2


title: Halobacterium salinarum NRC-1 growth curve. Array 11017

description: Halobacterium NRC-1 at OD=3.510 versus standard reference.

tag: Halobacterium NRC-1 at OD=3.510, t=08460min, replica 2


title: Halobacterium salinarum NRC-1 growth curve. Array 11025

description: Halobacterium NRC-1 at OD=5.640 versus standard reference.

tag: Halobacterium NRC-1 at OD=5.640, t=11700min, replica 2


title: Halobacterium salinarum NRC-1 growth curve. Array 11009

description: Halobacterium NRC-1 at OD=0.803 versus standard reference.

tag: Halobacterium NRC-1 at OD=0.803, t=05400min, replica 2


title: Halobacterium salinarum NRC-1 growth curve. Array 11005

description: Halobacterium NRC-1 at OD=0.762 versus standard reference.

tag: Halobacterium NRC-1 at OD=0.762, t=04476min, replica 2


title: Halobacterium salinarum NRC-1 growth curve. Array 11007

description: Halobacterium NRC-1 at OD=0.710 versus standard reference.

tag: Halobacterium NRC-1 at OD=0.710, t=05778min, replica 2


title: Halobacterium salinarum NRC-1 growth curve. Array 10999

description: Halobacterium NRC-1 at OD=0.259 versus standard reference.

tag: Halobacterium NRC-1 at OD=0.259, t=03720min, replica 2


title: Halobacterium salinarum NRC-1 growth curve. Array 11021

description: Halobacterium NRC-1 at OD=4.860 versus standard reference.

tag: Halobacterium NRC-1 at OD=4.860, t=10260min, replica 2


title: Halobacterium salinarum NRC-1 growth curve. Array 11013

description: Halobacterium NRC-1 at OD=1.329 versus standard reference.

tag: Halobacterium NRC-1 at OD=1.329, t=07020 min, replica 2


title: Halobacterium salinarum NRC-1 growth curve. Array 11023

description: Halobacterium NRC-1 at OD=5.130 versus standard reference.

tag: Halobacterium NRC-1 at OD=5.130, t=10980min, replica 2


title: Halobacterium salinarum NRC-1 growth curve. Array 11001

description: Halobacterium NRC-1 at OD=0.364 versus standard reference.

tag: Halobacterium NRC-1 at OD=0.364, t=03960min, replica 2


title: Halobacterium salinarum NRC-1 growth curve. Array 11016


title: Halobacterium salinarum NRC-1 growth curve. Array 11020


title: Halobacterium salinarum NRC-1 growth curve. Array 11003

description: Halobacterium NRC-1 at OD=0.590 versus standard reference.

tag: Halobacterium NRC-1 at OD=0.590, t=04320min, replica 2


title: Halobacterium salinarum NRC-1 growth curve. Array 11018

tag: Halobacterium NRC-1 at OD=4.860, t=09540min, replica 2


title: Halobacterium salinarum NRC-1 growth curve. Array 11024


title: Halobacterium salinarum NRC-1 growth curve. Array 11019


title: Halobacterium salinarum NRC-1 growth curve. Array 11014


title: Halobacterium salinarum NRC-1 growth curve. Array 11022


title: Halobacterium salinarum NRC-1 growth curve. Array 11006


title: Halobacterium salinarum NRC-1 growth curve. Array 11012


title: Halobacterium salinarum NRC-1 growth curve. Array 11002


title: Halobacterium salinarum NRC-1 growth curve. Array 11004


title: Halobacterium salinarum NRC-1 growth curve. Array 11008


title: Halobacterium salinarum NRC-1 growth curve. Array 10998


title: Halobacterium salinarum NRC-1 growth curve. Array 10764

tag: Halobacterium NRC-1 at OD=4.860, t=10260min, replica 1


title: Halobacterium salinarum NRC-1 growth curve. Array 10754

tag: Halobacterium NRC-1 at OD=0.803, t=05400min, replica 1


title: Halobacterium salinarum NRC-1 growth curve. Array 10758

tag: Halobacterium NRC-1 at OD=2.580, t=07740min, replica 1


title: Halobacterium salinarum NRC-1 growth curve. Array 10762

tag: Halobacterium NRC-1 grown in standard growth media

tag: Halobacterium NRC-1 at OD=4.860, t=09540min, replica 1


title: Halobacterium salinarum NRC-1 growth curve. Array 11000


title: Halobacterium salinarum NRC-1 growth curve. Array 10768

tag: Halobacterium NRC-1 at OD=5.640, t=11700min, replica 1


title: Halobacterium salinarum NRC-1 growth curve. Array 10750

tag: Halobacterium NRC-1 at OD=0.762, t=04476min, replica 1


title: Halobacterium salinarum NRC-1 growth curve. Array 10759

tag: Halobacterium NRC-1 at OD=3.510, t=08460min, replica 1


title: Halobacterium salinarum NRC-1 growth curve. Array 10765

tag: Halobacterium NRC-1 at OD=5.130, t=10980min, replica 1


title: Halobacterium salinarum NRC-1 growth curve. Array 10767


title: Halobacterium salinarum NRC-1 growth curve. Array 10744

tag: Halobacterium NRC-1 at OD=0.259, t=03720min, replica 1


title: Halobacterium salinarum NRC-1 growth curve. Array 10757


title: Halobacterium salinarum NRC-1 growth curve. Array 10761


title: Halobacterium salinarum NRC-1 growth curve. Array 10746

tag: Halobacterium NRC-1 at OD=0.364, t=03960min, replica 1


title: Halobacterium salinarum NRC-1 growth curve. Array 10749


title: Halobacterium salinarum NRC-1 growth curve. Array 10709


title: Halobacterium salinarum NRC-1 growth curve. Array 10747

tag: Halobacterium NRC-1 at OD=0.590, t=04320min, replica 1


title: Halobacterium salinarum NRC-1 growth curve. Array 10752

tag: Halobacterium NRC-1 at OD=0.710, t=05778min, replica 1


title: Halobacterium salinarum NRC-1 growth curve. Array 10755

tag: Halobacterium NRC-1 at OD=1.329, t=07020 min, replica 1


title: Halobacterium salinarum NRC-1 growth curve. Array 10742


title: Halobacterium salinarum NRC-1 growth curve. Array 10756


title: Halobacterium salinarum NRC-1 growth curve. Array 10751


title: Halobacterium salinarum NRC-1 growth curve. Array 10743


title: Halobacterium salinarum NRC-1 growth curve. Array 10753


title: Halobacterium salinarum NRC-1 growth curve. Array 10745


title: Halobacterium salinarum NRC-1 growth curve. Array 10748


title: IP fraction of ChIP-Chip sample from Cmyc-tagged TFBd, Halobacterium GTF growth curve experiment. Array 11453

description: IP sample of Cmyc tagged TFBd expressed in Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBd grown to OD600= 1.343 in standard growth media with 20microgram/ml mevinolin versus a whole cell extract from the same sample

label: Alexa 546

source_name: Halobacterium NRC1, Whole Cell Extract (WCE) from Cmyc-tagged TFBd

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBd grown in standard growth media with 20microgram/ml mevinolin

extract_protocol: Cells were cross-linked with 1.2% formaldehyde and subsequently lysed via sonication. DNA was sheared via sonication. A small fraction of total DNA was kept for a whole cell extract (wce) background while the rest of the DNA was immunoprecipitated with antibody against the epitope tag in question. Each DNA sample was treated with protease and RNAase and amplified by PCR utilizing ligated universal linkers as templates for amplification. The resulting DNA was cleaned and quantified.

tag: Whole Cell Extract (WCE) of Cmyc-tagged transcription factor TFBd grown in standard growth media with mevinolin to OD600=1.343

source_name: Halobacterium NRC1, IP fraction of ChIP-Chip sample from Cmyc-tagged TFBd at OD600=1.343

tag: IP sample of ChIP-Chip experiment of plasmid-based expression of Cmyc-tagged transcription factor TFBd grown in standard growth media with mevinolin to OD600=1.343


title: IP fraction of ChIP-Chip sample from Cmyc-tagged TFBd, Halobacterium GTF growth curve experiment. Array 11450

description: IP sample of Cmyc tagged TFBd expressed in Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBd grown to OD600= 0.786 in standard growth media with 20microgram/ml mevinolin versus a whole cell extract from the same sample

source_name: Halobacterium NRC1, IP fraction of ChIP-Chip sample from Cmyc-tagged TFBd at OD600=0.786

tag: IP sample of ChIP-Chip experiment of plasmid-based expression of Cmyc-tagged transcription factor TFBd grown in standard growth media with mevinolin to OD600=0.786

tag: Whole Cell Extract (WCE) of Cmyc-tagged transcription factor TFBd grown in standard growth media with mevinolin to OD600=0.786


title: IP fraction of ChIP-Chip sample from Cmyc-tagged TFBd, Halobacterium GTF growth curve experiment. Array 11452


title: IP fraction of ChIP-Chip sample from Cmyc-tagged TFBd, Halobacterium GTF growth curve experiment. Array 11449

description: IP sample of Cmyc tagged TFBd expressed in Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBd grown to OD600= 0.287 in standard growth media with 20microgram/ml mevinolin versus a whole cell extract from the same sample

tag: Whole Cell Extract (WCE) of Cmyc-tagged transcription factor TFBd grown in standard growth media with mevinolin to OD600=0.287

source_name: Halobacterium NRC1, IP fraction of ChIP-Chip sample from Cmyc-tagged TFBd at OD600=0.287

tag: IP sample of ChIP-Chip experiment of plasmid-based expression of Cmyc-tagged transcription factor TFBd grown in standard growth media with mevinolin to OD600=0.287


title: IP fraction of ChIP-Chip sample from Cmyc-tagged TFBd, Halobacterium GTF growth curve experiment. Array 11445

description: IP sample of Cmyc tagged TFBd expressed in Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBd grown to OD600= 0.807 in standard growth media with 20microgram/ml mevinolin versus a whole cell extract from the same sample

tag: Whole Cell Extract (WCE) of Cmyc-tagged transcription factor TFBd grown in standard growth media with mevinolin to OD600=0.807

source_name: Halobacterium NRC1, IP fraction of ChIP-Chip sample from Cmyc-tagged TFBd at OD600=0.807

tag: IP sample of ChIP-Chip experiment of plasmid-based expression of Cmyc-tagged transcription factor TFBd grown in standard growth media with mevinolin to OD600=0.807


title: IP fraction of ChIP-Chip sample from Cmyc-tagged TFBd, Halobacterium GTF growth curve experiment. Array 11448


title: IP fraction of ChIP-Chip sample from Cmyc-tagged TFBd, Halobacterium GTF growth curve experiment. Array 11442

description: IP sample of Cmyc tagged TFBd expressed in Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBd grown to OD600= 0.29 in standard growth media with 20microgram/ml mevinolin versus a whole cell extract from the same sample

source_name: Halobacterium NRC1, IP fraction of ChIP-Chip sample from Cmyc-tagged TFBd at OD600=0.29

tag: IP sample of ChIP-Chip experiment of plasmid-based expression of Cmyc-tagged transcription factor TFBd grown in standard growth media with mevinolin to OD600=0.29

tag: Whole Cell Extract (WCE) of Cmyc-tagged transcription factor TFBd grown in standard growth media with mevinolin to OD600=0.29


title: IP fraction of ChIP-Chip sample from Cmyc-tagged TFBd, Halobacterium GTF growth curve experiment. Array 11451


title: IP fraction of ChIP-Chip sample from Cmyc-tagged TFBd, Halobacterium GTF growth curve experiment. Array 11446

description: IP sample of Cmyc tagged TFBd expressed in Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBd grown to OD600= 1.455 in standard growth media with 20microgram/ml mevinolin versus a whole cell extract from the same sample

source_name: Halobacterium NRC1, IP fraction of ChIP-Chip sample from Cmyc-tagged TFBd at OD600=1.455

tag: IP sample of ChIP-Chip experiment of plasmid-based expression of Cmyc-tagged transcription factor TFBd grown in standard growth media with mevinolin to OD600=1.455

tag: Whole Cell Extract (WCE) of Cmyc-tagged transcription factor TFBd grown in standard growth media with mevinolin to OD600=1.455


title: IP fraction of ChIP-Chip sample from Cmyc-tagged TFBd, Halobacterium GTF growth curve experiment. Array 11444


title: IP fraction of ChIP-Chip sample from Cmyc-tagged TFBd, Halobacterium GTF growth curve experiment. Array 11447


title: Halobacterium salinarum NRC-1 growth curve. Array 10760

description: Halobacterium NRC-1 at OD=3.510 versus standard reference.

tag: Halobacterium NRC-1 grown in standard growth media

tag: Halobacterium NRC-1 at OD=3.510, t=08460min, replica 1


title: IP fraction of ChIP-Chip sample from Cmyc-tagged TFBd, Halobacterium GTF growth curve experiment. Array 11443


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210070

description: Halobacterium NRC-1 at OD=4.540 versus standard reference.

hyb_protocol: see http://www.chem.agilent.com/Scripts/PDS.asp?lPage=34519 for details

data_processing: Agilent FeatureExtraction for spotfinding/quantitation. See http://www.systemsbiology.org/Scientists_and_Research/Technology/Data_Management/Microarray_Pipeline for more details

growth_protocol: Halobacterium NRC-1 grown in rich media (CM), 200mL culture in 1L flask, shaking at 125RPM) and constant light.

extract_protocol: Total DNA-free RNA prepared using the mirVana miRNA isolation kit(Ambion) and analyzed by PCR to rule out DNA contamination, with Agilent Bioanalyzer to verify integrity, and in NanoDrop for quantification.

tag: Halobacterium NRC-1 at OD=4.540, t=10260min, replica 2

growth_protocol: Standard mid-log phase (OD600-0.5-0.6) Halobacterium NRC-1 reference sample.


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210073

description: Halobacterium NRC-1 at OD=5.730 versus standard reference.

tag: Halobacterium NRC-1 at OD=5.730, t=11700min, replica 2


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210059

description: Halobacterium NRC-1 at OD=2.681 versus standard reference.

tag: Halobacterium NRC-1 at OD=2.681, t=07740min, replica 2


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210064


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210068


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210060

description: Halobacterium NRC-1 at OD=3.840 versus standard reference.

tag: Halobacterium NRC-1 at OD=3.840, t=08460min, replica 2


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210055

description: Halobacterium NRC-1 at OD=0.722 versus standard reference.

tag: Halobacterium NRC-1 at OD=0.722, t=05778min, replica 2


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210047

description: Halobacterium NRC-1 at OD=0.578 versus standard reference.

tag: Halobacterium NRC-1 at OD=0.578, t=04320min, replica 2


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210051

description: Halobacterium NRC-1 at OD=0.715 versus standard reference.

tag: Halobacterium NRC-1 at OD=0.715, t=04476min, replica 2


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210063

description: Halobacterium NRC-1 at OD=4.9350 versus standard reference.

tag: Halobacterium NRC-1 at OD=4.9350, t=10980min, replica 2


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210054

description: Halobacterium NRC-1 at OD=1.318 versus standard reference.

tag: Halobacterium NRC-1 at OD=1.318, t=07020min, replica 2


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210065


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210043

description: Halobacterium NRC-1 at OD=0.409 versus standard reference.

tag: Halobacterium NRC-1 at OD=0.409, t=03960min, replica 2


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210050


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210057


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210037

description: Halobacterium NRC-1 at OD=5.130 versus standard reference.

tag: Halobacterium NRC-1 at OD=5.130, t=10980min , replica 1


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210053


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210044

description: Halobacterium NRC-1 at OD=0.234 versus standard reference.

tag: Halobacterium NRC-1 at OD=0.234, t=03720min, replica 2


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210048


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210052

description: Halobacterium NRC-1 at OD=0.780 versus standard reference.

tag: Halobacterium NRC-1 at OD=0.780, t=05400min, replica 2


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210046


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210036

description: Halobacterium NRC-1 at OD=5.640 versus standard reference.

tag: Halobacterium NRC-1 at OD=5.640, t=11700min, replica 1


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210049


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210041


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210069

description: Halobacterium NRC-1 at OD=4.690 versus standard reference.

tag: Halobacterium NRC-1 at OD=4.690, t=09540min, replica 2


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210056

tag: Halobacterium NRC-1 grown in standard growth media


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210067


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210058


title: Metarhizium CGH rep3

city: College Park

first: Sibao

last: Wang

address: Baltimore Avenue

department: Entomology

institute: University of Maryland

description:
Metarhizium anisopliae 2575 is a generalist entomopathogenic fungus
Metarhizium anisopliae var acredium 324 is a specialist entomopathogenic fungus

hyb_protocol: Each strain’s DNA was co-hybridized with strain ARSEF 2575 DNA in dye swapping replicate experiments and the relative hybridization efficiency (fluorescence ratio) of their DNA for strain ARSEF 2575 genes was compared. We used standard microarray hybridization conditions for this work (Wang and St. Leger, 2005) providing a stringency at which 90% matching over 60 bases should suffice to form a stable hybrid (Xu et al., 2001).

scan_protocol: The Axon Scanner 4200 (Molecular Devices) was used to capture images of the microarrays after hybridization according manual.

data_processing: The intensity of the spots on the cDNA slides was calculated using the Spotfinder v 2.2.4 program from the Microarray software suit TM4 from JCVI (http://www.tm4.org/spotfinder.html) applying local background subtraction for each spot. The spotted microarray data pre-processing platform--Ginkgo was used for CGH analysis (http://pfgrc.jcvi.org/index.php/bioinformatics/ginkgo.html). Intensity-dependant variation was normalized using the Histogram Mode Centering (HMC) algorithm with mean and standard deviation as parameters. Dye consistency check was performed after normalization to eliminate systematic errors. This flip-dye analysis used a standard deviation fold criteria of 3 to filter spots with inconsistent values. Consolidation of the triplicate intensity values of channels A and B (1756 unigenes, channel A referring to the reference strain 2575) was also performed using the in-slide replicate algorithm of this platform

organism: Metarhizium anisopliae

source_name: Metarhizium 2575 genomic DNA

label_protocol:
For DNA labeling experiments, 2 ug of total genomic DNA was fragmented by restriction endonuclease digestion with RsaI and MseI (New England Biolabs). The digested genomic DNAs were labeled by random priming with the BioPrime DNA labeling system (Invitrogen) according to the manufacturer instructions.
The digested genomic DNAs were labeled by random priming with the BioPrime DNA labeling system (Invitrogen) according to the manufacturer instructions.

growth_protocol: Fungal mycelia from 48 h SDB cultures was collected by filtration and washed with sterile distilled water three times.

extract_protocol: The high-molecular-mass total genomic DNA of each strain was prepared as described in Wang et al (2004). The construction of the cDNA microarrays used in this study has been previously described (Wang et al., 2005).

tag: strain

source_name: Metarhizium 324 genomic DNA

value: var acredium 324


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210028

description: Halobacterium NRC-1 at OD=0.762 versus standard reference.

tag: Halobacterium NRC-1 at OD=0.762, t=04476min, replica 1


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210032

description: Halobacterium NRC-1 at OD=0.710 versus standard reference.

tag: Halobacterium NRC-1 at OD=0.710, t=05778min, replica 1


title: Metarhizium CGH rep2


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210014

description: Halobacterium NRC-1 at OD=4.860 versus standard reference.

tag: Halobacterium NRC-1 at OD=4.860, t=10260min, replica 1


title: Metarhizium CGH rep1

description:
Meatarhizium anisopliae 2575 is a generlist entomopathogenic fungus
Metarhizium anisopliae var acredium 324 is specialist entomopathogenic fungus


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210016


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210010

description: Halobacterium NRC-1 at OD=2.580 versus standard reference.

tag: Halobacterium NRC-1 at OD=2.580, t=07740min , replica 1


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210034


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210025

tag: Halobacterium NRC-1 at OD=4.860, t=09540min, replica 1


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210017

description: Halobacterium NRC-1 at OD=0.590 versus standard reference.

tag: Halobacterium NRC-1 at OD=0.590, t=04320min, replica 1


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210012


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210003

description: Halobacterium NRC-1 at OD=0.364 versus standard reference.

tag: Halobacterium NRC-1 at OD=0.364, t=03960min, replica 1


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210002

description: Halobacterium NRC-1 at OD=0.259 versus standard reference.

tag: Halobacterium NRC-1 at OD=0.259, t=03720min, replica 1


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210031


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210009

description: Halobacterium NRC-1 at OD=3.510 versus standard reference.

tag: Halobacterium NRC-1 at OD=3.510, t=08460min, replica 1


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210007


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210029


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210005


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBd, Halobacterium GTF. Array 63616

description: IP sample of Cmyc tagged TFBd expressed in Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBd in standard growth media with 20microgram/ml mevinolin versus a whole cell extract from the same sample

source_name: Halobacterium NRC1, Whole Cell Extract (WCE) from Cmyc tagged TFBd

tag: fraction

value: Whole Cell Extract (WCE)

tag: growth protocol

value: standard growth media with mevinolin.

source_name: Halobacterium NRC1, IP fraction of ChIP-Chip sample from Cmyc tagged TFBd

value: IP sample of ChIP-Chip experiment of plasmid based expression

tag: protocol

value: expression of Cmyc-tagged transcription factor TFBd

tag: antibody

value: anti-C-Myc Epitope Tag antibody


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210013

tag: Halobacterium NRC-1 at OD=5.130, t=10980min , replica 1


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210011


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210001

description: Halobacterium NRC-1 at OD=1.329 versus standard reference.

tag: Halobacterium NRC-1 at OD=1.329, t=07020 min, replica 1


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210008

tag: Halobacterium NRC-1 grown in standard growth media


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBd, Halobacterium GTF. Array 81868


title: HCT116 Dicer-/- #2, mock vs. HCT116 Dicer-/- #2 miR-17-3p, 25nM, 10hr

first: Irena

last: Ivanovska

address: 401 Terry Ave N

institute: Merck

description: microRNAs in the miR-106b family are overexpressed in multiple tumor types and are correlated with the expression of genes that regulate the cell cycle. Consistent with these observations, miR-106b family gain of function promotes cell cycle progression, whereas loss of function reverses this phenotype. Microarray profiling uncovers multiple targets of the family, including the cyclin-dependent kinase inhibitor p21/CDKN1A. We show that p21 is a direct target of miR-106b and that its silencing plays a key role in miR-106b-induced cell cycle phenotypes. We also show that miR-106b overrides a doxorubicin-induced DNA damage checkpoint. Thus, miR-106b family members contribute to tumor cell proliferation in part by regulating cell cycle progression and by modulating checkpoint functions.

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

source_name: HCT116 Dicer -/-

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

treatment_protocol: mock

tag: cell line

value: HCT116 Dicer-/- #2


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210022

description: Halobacterium NRC-1 at OD=0.803 versus standard reference.

tag: Halobacterium NRC-1 at OD=0.803, t=05400min, replica 1


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210020


title: Total RNA sample from Cmyc tagged TFBd, Halobacterium NRC-1. Array 77972

description: RNA sample of Cmyc tagged TFBd expressed in Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBd in standard growth media with 20microgram/ml mevinolin versus a Reference RNA sample.

source_name: Halobacterium NRC1, Reference RNA

growth_protocol: Standard mid-log phase (OD600-0.5-0.6) Halobacterium NRC-1 reference sample

extract_protocol: Total DNA-free RNA prepared using RNA isolation kit (Stratagene) and analyzed by PCR to rule out DNA contamination, with Agilent Bioanalyzer to verify integrity.

value: control

value: standard growth media

source_name: Halobacterium NRC1, total RNA sample from Cmyc tagged TFBd

value: plasmid based expression of Cmyc tagged transcription factor TFBd


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBf, Halobacterium GTF. Array 81533

description: IP sample of Cmyc tagged TFBf expressed in Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBf in standard growth media with 20microgram/ml mevinolin versus a whole cell extract from the same sample

source_name: Halobacterium NRC1, Whole Cell Extract (WCE) from Cmyc tagged TFBf

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBf grown in standard growth media with 20microgram/ml mevinolin

source_name: Halobacterium NRC1, IP fraction of ChIP-Chip sample from Cmyc tagged TFBf

value: expression of Cmyc-tagged transcription factor TFBf


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210019

source_name: Halobacterium NRC-1 Reference sample

source_name: Halobacterium NRC-1 growth curve

tag: Halobacterium NRC-1 at OD=0.762, t=04476min, replica 1


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBa, Halobacterium GTF. Array 81534

description: IP sample of Cmyc tagged TFBa expressed in Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBa in standard growth media with 20microgram/ml mevinolin versus a whole cell extract from the same sample

source_name: Halobacterium NRC1, Whole Cell Extract (WCE) from Cmyc tagged TFBa

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBa grown in standard growth media with 20microgram/ml mevinolin

source_name: Halobacterium NRC1, IP fraction of ChIP-Chip sample from Cmyc tagged TFBa

value: expression of Cmyc-tagged transcription factor TFBa


title: Total RNA sample from Cmyc tagged TFBd, Halobacterium NRC-1. Array 95767


title: MOCK, 96 hai - rep3

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

description:
R3MOCK96H
Replication 3, Mock-inoculated rice, tissue collected at 96HAI

hyb_protocol: Affy- Eukaryotic Target Hybridization

scan_protocol: Affy- Array Scanning

data_processing: The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html. The normalization scripts are available from the PLEXdb team by request.

source_name: shoot, MOCK, 96 hai

label_protocol: Affy-Eukaryotic Target Preparation

extract_protocol: Hot Phenol/Guanidine Thiocyanate and RNeasy Clean up

tag: germplasm name

value: cv. nipponbare

tag: organism part

tag: development stage

value: PO:0007106 LP.03 three leaves visible

tag: age

value: 2 weeks after sowing

tag: growth media

value: LC-1 Soil Mix


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210023


title: MOCK, 96 hai - rep2

description:
R2MOCK96H
Replication 2, Mock-inoculated rice, tissue collected at 96HAI


title: MOCK, 96 hai - rep1

description:
R1MOCK96H
Replication 1, Mock-inoculated rice, tissue collected at 96HAI


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBd, Halobacterium GTF. Array 81660


title: MOCK, 24 hai - rep4

description:
R4MOCK24H
Replication 4, Mock-inoculated rice, tissue collected at 24HAI

source_name: shoot, MOCK, 24 hai


title: MOCK, 24 hai - rep1

description:
R1MOCK24H
Replication 1, Mock-inoculated rice, tissue collected at 24HAI


title: MOCK, 8 hai - rep1

description:
R1MOCK8H
Replication 1, Mock-inoculated rice, tissue collected at 8HAI

source_name: shoot, MOCK, 8 hai


title: MOCK, 24 hai - rep3

description:
R3MOCK24H
Replication 3, Mock-inoculated rice, tissue collected at 24HAI


title: MOCK, 4 hai - rep4

description:
R4MOCK4H
Replication 4, Mock-inoculated rice, tissue collected at 4HAI

source_name: shoot, MOCK, 4 hai


title: MOCK, 8 hai - rep3

description:
R3MOCK8H
Replication 3, Mock-inoculated rice, tissue collected at 8HAI


title: MOCK, 4 hai - rep3

description:
R3MOCK4H
Replication 3, Mock-inoculated rice, tissue collected at 4HAI


title: MOCK, 24 hai - rep2

description:
R2MOCK24H
Replication 2, Mock-inoculated rice, tissue collected at 24HAI


title: MOCK, 96 hai - rep4

description:
R4MOCK96H
Replication 4, Mock-inoculated rice, tissue collected at 96HAI


title: MOCK, 4 hai - rep2

description:
R2MOCK4H
Replication 2, Mock-inoculated rice, tissue collected at 4HAI


title: Halobacterium salinarum NRC-1 growth curve. Array 251596210033

description: Halobacterium NRC-1 at OD=5.640 versus standard reference.

tag: Halobacterium NRC-1 at OD=5.640, t=11700min, replica 1


title: MOCK, 8 hai - rep4

description:
R4MOCK8H
Replication 4, Mock-inoculated rice, tissue collected at 8HAI


title: MOCK, 8 hai - rep2

description:
R2MOCK8H
Replication 2, Mock-inoculated rice, tissue collected at 8HAI


title: MOCK, 2 hai - rep3

description:
R3MOCK2H
Replication 3, Mock-inoculated rice, tissue collected at 2HAI

source_name: shoot, MOCK, 2 hai


title: MOCK, 2 hai - rep4

description:
R4MOCK2H
Replication 4, Mock-inoculated rice, tissue collected at 2HAI


title: MOCK, 2 hai - rep1

description:
R1MOCK2H
Replication 1, Mock-inoculated rice, tissue collected at 2HAI


title: MOCK, 2 hai - rep2

description:
R2MOCK2H
Replication 2, Mock-inoculated rice, tissue collected at 2HAI


title: MOCK, 4 hai - rep1

description:
R1MOCK4H
Replication 1, Mock-inoculated rice, tissue collected at 4HAI


title: XOO, 96 hai - rep3

description:
R3XOO96H
Replication 3, Xoo-inoculated rice, tissue collected at 96HAI

source_name: shoot, XOO, 96 hai


title: XOO, 96 hai - rep4

description:
R4XOO96H
Replication 4, Xoo-inoculated rice, tissue collected at 96HAI


title: XOO, 96 hai - rep2

description:
R2XOO96H
Replication 2, Xoo-inoculated rice, tissue collected at 96HAI


title: XOO, 24 hai - rep3

description:
R3XOO24H
Replication 3, Xoo-inoculated rice, tissue collected at 24HAI

source_name: shoot, XOO, 24 hai


title: XOO, 24 hai - rep2

description:
R2XOO24H
Replication 2, Xoo-inoculated rice, tissue collected at 24HAI


title: XOO, 8 hai - rep2

description:
R2XOO8H
Replication 2, Xoo-inoculated rice, tissue collected at 8HAI

source_name: shoot, XOO, 8 hai


title: XOO, 2 hai - rep4

description:
R4XOO2H
Replication 4, Xoo-inoculated rice, tissue collected at 2HAI

source_name: shoot, XOO, 2 hai


title: XOO, 96 hai - rep1

description:
R1XOO96H
Replication 1, Xoo-inoculated rice, tissue collected at 96HAI


title: XOO, 4 hai - rep2

description:
R2XOO4H
Replication 2, Xoo-inoculated rice, tissue collected at 4HAI

source_name: shoot, XOO, 4 hai


title: XOO, 2 hai - rep3

description:
R3XOO2H
Replication 3, Xoo-inoculated rice, tissue collected at 2HAI


title: XOO, 2 hai - rep1

description:
R1XOO2H
Replication 1, Xoo-inoculated rice, tissue collected at 2HAI


title: XOO, 4 hai - rep4

description:
R4XOO4H
Replication 4, Xoo-inoculated rice, tissue collected at 4HAI


title: XOO, 4 hai - rep3

description:
R3XOO4H
Replication 3, Xoo-inoculated rice, tissue collected at 4HAI


title: XOO, 24 hai - rep4

description:
R4XOO24H
Replication 4, Xoo-inoculated rice, tissue collected at 24HAI


title: XOO, 8 hai - rep4

description:
R4XOO8H
Replication 4, Xoo-inoculated rice, tissue collected at 8HAI


title: XOC, 96 hai - rep4

description:
R4XOC96H
Replication 4, Xoc-inoculated rice, tissue collected at 96HAI

source_name: shoot, XOC, 96 hai


title: XOO, 4 hai - rep1

description:
R1XOO4H
Replication 1, Xoo-inoculated rice, tissue collected at 4HAI


title: retina_nhlh2_rep3

city: Belfast

first: David

middle: Arthur

last: Simpson

state: N. Ireland

address: The Wellcome – Wolfson Institute for Experimental Medicine, 97 Lisburn Road

department: Wellcome-Wolfson Institite for Experimental Medicine

country: United Kingdom

institute: Queen's University Belfast

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C on GeneChip MOE 430A. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: retina nhlh2 knockout

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2ug total RNA (Expression Analysis Technical Manual, 2005-2009, Affymetrix).

growth_protocol: Neonatal mice were euthanized at P4, eyes were enucleated and retinas dissected out

extract_protocol: Total RNA was extracted from the retinas using the Qiagen RNeasy Micro Kit according to the manufacturer's instructions

treatment_protocol: Retinas were transferred to RNase free microtubes and snap frozen on dry ice

tag: tissue

value: Retina

value: Postnatal day 4

tag: genotype

value: mixed C57/129


title: XOO, 24 hai - rep1

description:
R1XOO24H
Replication 1, Xoo-inoculated rice, tissue collected at 24HAI


title: retina_nhlh2_rep2


title: XOO, 8 hai - rep3

description:
R3XOO8H
Replication 3, Xoo-inoculated rice, tissue collected at 8HAI


title: XOO, 2 hai - rep2

description:
R2XOO2H
Replication 2, Xoo-inoculated rice, tissue collected at 2HAI


title: XOC, 96 hai - rep2

description:
R2XOC96H
Replication 2, Xoc-inoculated rice, tissue collected at 96HAI


title: XOO, 8 hai - rep1

description:
R1XOO8H
Replication 1, Xoo-inoculated rice, tissue collected at 8HAI


title: XOC, 96 hai - rep3

description:
R3XOC96H
Replication 3, Xoc-inoculated rice, tissue collected at 96HAI


title: retina_wt_rep2

source_name: retina wildtype


title: XOC, 96 hai - rep1

description:
R1XOC96H
Replication 1, Xoc-inoculated rice, tissue collected at 96HAI


title: retina_wt_rep3


title: XOC, 24 hai - rep4

description:
R4XOC24H
Replication 4, Xoc-inoculated rice, tissue collected at 24HAI

source_name: shoot, XOC, 24 hai


title: retina_wt_rep1


title: fer-1 (hc24ts) mutant young adult biological rep 5

city: Philadelphia

first: Predrag

last: Krajacic

state: PA

address: 3700 Hamilton Walk A700 Richards

institute: University of Pennsylvania

description: Gene expression data from young adult fer-1(hc24ts) mutant worms grown on 25ºC

hyb_protocol: Labeled cDNA was added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to GPL200 GeneChips (Affymetrix Inc., Santa Clara CA). The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: Affymetrix GCS3000 laser scanner was used to collect fluorescence signal after excitation at 570 nm.

data_processing: Affymetrix Command Console and Expression Console were used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Probes for each targeted gene were averaged and inter-array normalization performed using the GCRMA algorithm.

organism: Caenorhabditis elegans

source_name: adult worm

label_protocol: 100ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated the T7 promoter sequence.  Second-strand cDNA synthesis was followed by in vitro transcription with T7 RNA polymerase for linear amplification of each transcript, and the resulting cRNA was converted to cDNA, fragmented, assessed by Bioanalyzer, and biotinylated by terminal transferase end labeling.

growth_protocol: Hypochlorite synchronized L1 stage wild type, fer-1(hc1), or fer-1(hc24) animals were grown to the young adult stage on standard NGM plates at 25°.

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

treatment_protocol: Worms were washed from the plates with M9 solution and 1000 adult worms were collected into 1.5ml tubes using gating criteria on the COPAS Biosort that excluded L4 and younger animals.  Immediately following sorting, worms were pelleted at 2,000 RPM and the supernatant was aspirated, leaving ~100µl on top of the worm pellet.  400µl of Trizol was added and the solution was vortexed for two minutes.  Worms were stored at -80° until RNA isolation.

value: whole worm

tag: strain

value: fer-1 (hc24ts) mutant


title: retina_nhlh2_rep1


title: XOC, 24 hai - rep2

description:
R2XOC24H
Replication 2, Xoc-inoculated rice, tissue collected at 24HAI


title: XOC, 24 hai - rep1

description:
R1XOC24H
Replication 1, Xoc-inoculated rice, tissue collected at 24HAI


title: fer-1 (hc24ts) mutant young adult biological rep 2


title: XOC, 8 hai - rep4

description:
R4XOC8H
Replication 4, Xoc-inoculated rice, tissue collected at 8HAI

source_name: shoot, XOC, 8 hai


title: XOC, 8 hai - rep3

description:
R3XOC8H
Replication 3, Xoc-inoculated rice, tissue collected at 8HAI


title: fer-1 (hc24ts) mutant young adult biological rep 3


title: XOC, 8 hai - rep2

description:
R2XOC8H
Replication 2, Xoc-inoculated rice, tissue collected at 8HAI


title: fer-1 (hc1ts) mutant young adult biological rep 2

description: Gene expression data from young adult fer-1(hc1ts) mutant worms grown on 25ºC

value: fer-1 (hc1ts) mutant


title: fer-1 (hc24ts) mutant young adult biological rep 1


title: fer-1 (hc1ts) mutant young adult biological rep 5


title: XOC, 4 hai - rep4

description:
R4XOC4H
Replication 4, Xoc-inoculated rice, tissue collected at 4HAI

source_name: shoot, XOC, 4 hai


title: fer-1 (hc1ts) mutant young adult biological rep 6


title: XOC, 8 hai - rep1

description:
R1XOC8H
Replication 1, Xoc-inoculated rice, tissue collected at 8HAI


title: XOC, 4 hai - rep2

description:
R2XOC4H
Replication 1, Xoc-inoculated rice, tissue collected at 4HAI


title: XOC, 24 hai - rep3

description:
R3XOC24H
Replication 3, Xoc-inoculated rice, tissue collected at 24HAI


title: Wild-type young adult biological rep 6

description: Gene expression data from young adult wild type worms grown on 25ºC

value: wild type


title: fer-1 (hc1ts) mutant young adult biological rep 1


title: XOC, 4 hai - rep1

description:
R1XOC4H
Replication 1, Xoc-inoculated rice, tissue collected at 4HAI


title: XOC, 2 hai - rep4

description:
R4XOC2H
Replication 4, Xoc-inoculated rice, tissue collected at 2HAI

source_name: shoot, XOC, 2 hai


title: XOC, 2 hai - rep3

description:
R3XOC2H
Replication 3, Xoc-inoculated rice, tissue collected at 2HAI


title: XOC, 4 hai - rep3

description:
R3XOC4H
Replication 3, Xoc-inoculated rice, tissue collected at 4HAI


title: Juvenile_As exposed_172ppb_rep3

status: Public on Jun 24 2009

city: Pendleton

first: Lisa

middle: J

last: Bain

state: SC

address: P. O. Box 709

institute: Clemson University

description: As juvenile 172_3

hyb_protocol: The array membranes were prehybridized for 4-6 hour in Express hybridization solution (Clontech, Palo Alto, CA) containing 100mg/ml denatured salmon sperm.  The denatured probe was added to each tube and incubated overnight with the array at 68oC. After the incubation, the arrays were washed four times with 2X SSC/0.5%SDS at 64oC and four times with 0.5X SSC/0.5%SDS at 64oC.

scan_protocol: After washing, the membranes were wrapped in plastic, placed on a phosphorimaging screen, and developed using a Bio-Rad Molecular Imager FX (Hercules, CA).  The intensity of each spot was quantified using the Invitrogen ResGen Pathways 4-Universal Microarray Analysis Software (Carlsbad, CA).

data_processing: The raw pixel intensity was divided by the summed pixel intensity for each array.

organism: Fundulus heteroclitus

source_name: 7-10 pooled fish, arsenic

label_protocol: Probes were generated by reverse transcription using 2ug of RNA, 0.1mM oligo dT primer, 1.2mM dNTPs lacking dATP, [33P]dATP (3000Ci/mmol, Perkin Elmer, Boston, MA) and 200U MMLV-RT at 37oC for 2 hours. Each probe was purified using Amersham’s Probe Quant-50 columns (Piscataway, NJ) and denatured by heating to 100oC before adding to the hybridization.

extract_protocol: Total RNA was extracted with TriReagent and treated with DNase I.

value: whole juveniles

value: 6 weeks

tag: treatment

value: parental exposure to 172ppb sodium arsenite


title: Juvenile_control_172ppb_rep5

description: Control juvenile 172_5

source_name: 7-10 pooled fish, control


title: Male_As exposed_172ppb_rep1

description: As male 172_1

source_name: liver, male, 172ppb arsenic

tag: gender

value: male

value: liver

value: 172ppb sodium arsenite


title: Male_As exposed_172ppb_rep4

description: As male 172_4


title: Male_control_172ppb_rep5

description: Control male 172_5

source_name: liver, male, control


title: Juvenile_As exposed_172ppb_rep1

description: As juvenile 172_1


title: Juvenile_As exposed_172ppb_rep2

description: As juvenile 172_2


title: Male_As exposed_172ppb_rep3

description: As male 172_3


title: Juvenile_control_172ppb_rep3

description: Control juvenile 172_3