title: rad50S 5h ChIP rep3

city: Bethesda

last: Lichten

state: MD

address: 37 Convent Dr

department: LBMB

institute: National Cancer Institute

description: S. cerevisiae (SK1)

hyb_protocol: 500 ng of each labeled sample were hybridized to an Agilent yeast whole genome oligonucleotide array (Agilent, G4486A) for 17 hours at 60˚C in the 1X hybridization buffer supplied by Agilent. Slides were washed for 5 min in 6X SSPE, 0.05% (w/v) N-lauroylsarcosine, once in 0.06X SSPE for 5 minutes, and were then rinsed in the stabilizing and drying solutions supplied by Agilent.

scan_protocol: Slides were canned using an Axon 4000B scanner set at 10 µm resolution with automatically adjusting laser PMT values to achieve a maximum fluorescence saturation of 0.005%. Fluorescence data was extracted using GenePix 6.0 (Axon) software. For each channel, features were filtered according to the following criteria.  First, all spots with a diameter less than 50 µm were removed. The background fluorescence in each channel was then calculated using the mean fluorescence value of 315 empty array elements. All array elements with fluorescence less than background + 2 standard deviations were removed, as were all array elements with a signal to background ratio (signal +background)/ background) less than 3.

data_processing: Background normalization of fluorescence signals in each channel was performed using a subset of probes for which the presence of meiotic single strand DNA is unlikely. The median fluorescence intensity of background probes was used to normalize the fluorescence intensity for each spots in each channel. (see Buhler et al, Table S2 for details about the choices of background probes used in this study)

organism: Saccharomyces cerevisiae

source_name: ChIP

label_protocol: Two successive primer extensions (Round A) were performed on DNA samples using T7 sequenase polymerase (USB) and primerA (5'-GTTTCCCAGTCACGATCNNNNNNNNN-3'), the first 17 nt of which are absent from S. cerevisiae genome. For ssDNA-enriched material, the first extension was performed without prior denaturation to select for the single strand templates; for ChIP samples both extensions were preceded by denaturation. The following program was used: 10 °C to 37 °C ramp over 8 min; 37 °C for 8 min; 94 °C for 2 min; 10°C for 5 min while adding sequenase; 10 °C to 37 °C over 8 min; 37°C for 8 min; 24 ˚C for 10 sec. All amplifications included a second round (Round B) using Taq polymerase (Promega) and primer B (5'-GTTTCCCAGTCACGATC-3') using the following program: 95 ˚C for 30 sec; 47 ˚C for 30 sec; 72 ˚C for 2 min; for 15, 18, 21, 24 or 27 cycles. The extent of amplification was assayed by displaying 5% of each reaction on a 1.5% agarose gel and staining with SYBR green (Molecular Probes). Samples with the least number of amplification cycles showing detectable product were selected, and primer dimmers were removed by two successive filtration/wash cycles using Microcon YM-100 spin filters (Millipore) and 500 µl of TE. Aminoallyl-dUTP was then incorporated by PCR (Round C) using the same program and primers as in Round B, but a 3/2 ratio of aadUTP/dTTP and 15 units of Taq polymerase per reaction. Amplified material was purified by two successive filtration/wash cycles using Microcon YM-100 spin filters (Millipore) 500 µl of 10 mM Na2CO3 pH 8.9. 2µg of amplified material from Round C was labeled with Cy-5 monoreactive dye (GE Healthcare) and 500 ng of similarly amplified control material (BND cellulose input or whole cell extract) was labeled with Cy-3 (GE Healthcare) in 50 mM Na2CO3 pH 8.9 for 1 hour in the dark. Unincorporated dye was removed by 3 successive washes with 400 µl MES 50 mM pH 7.2 (Sigma) using Microcon YM-50 spin filters (Millipore). Dye incorporation was estimated using by measuring dye adsorbance at 550 nm (Cy-3) and 650 nm (Cy-5) in final products.

extract_protocol: glass beads DNA preparation was used

treatment_protocol: Chromatin immunoprecipitation of HA-tagged Spo11 from a rad50S strain was performed as described in the following references with only minor modifications, using cells from a culture 5 hr after initiation of sporulation (Borde V, Lin W, Novikov E, Petrini JH, Lichten M, et al. (2004) Mol Cell 13: 389-401 and Gerton JL, DeRisi J, Shroff R, Lichten M, Brown PO, et al. (2000) Proc Natl Acad Sci U S A 97: 11383-11390.

tag: anti-Spo11-HA ChIP


title: rad50S 5h ChIP rep2

status: Public on Dec 31 2007

type: genomic

first: Michael

country: USA

description: S. cerevisiae (SK1)

molecule: genomic DNA


title: Wildtype Input 3h

description: S. cerevisiae (SK1)

source_name: Input

extract_protocol: Phenol/chloroform extraction

tag: genomic DNA from strain MJL1083


title: rad50S 5h Input rep2

description: S. cerevisiae (SK1)

tag: genomic DNA


title: rad50S 5h Input rep3

description: S. cerevisiae (SK1)


title: stage13_mef2(424)_Rep1

type: RNA

city: Cardiff

middle: Victor

last: Taylor

state: S. Glam

address: Main Building, Park Place

department: School of Biosciences

country: United Kingdom

institute: Cardiff University

description: Drosophila_embryo_stage13_mef2(424)_Rep1

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45ºC on Affymetrix GeneChip Drosophila Genome 1 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip scanner 3000 7G.

data_processing: Data were processed and normalised using MAS5.0 algorithm

label: biotin

molecule: total RNA

organism: Drosophila melanogaster

source_name: Whole embryo Stage 13 mef2(424) Allele

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix)

growth_protocol: Flies were raised in standard conditions.  Embryo collections were as follows.  Following 2 x 1 hour prelays, 30 minute embryo collections were aged at 25ºC for 6.5 hours prior to sorting.  Mutant embryos were individually selected by absence of the GFP fluorescent balancer chromosome (CyO P(Gal4-twi)P(UAS-2eGFP)).  Both mutant and control embryos were accurately staged at mid 12 using autofluorescence to visualise the germ band to ensure that all were within a 30-minute window.  Pools of 150 embryos were allowed to develop until mid stage 13, dechorionated, inspected to ensure normal development had continued.

extract_protocol: Total RNA was extracted using TriZol (Invitrogen) and cleaned up by RNeasy mini-kit (Qiagen) according to the manufacturer's instructions

treatment_protocol: The staged, dechorionated stage 13 embryos were immediately homogenised in TriZol prior to storage at –80ºC.

tag: Age

value: Stage 13, Tissue:Whole embryo


title: rad50S 5h ChIP rep1

description: S. cerevisiae (SK1)


title: rad50S 5h Input rep1

description: S. cerevisiae (SK1)


title: rad51dmc1 5h rep1

description: S. cerevisiae (SK1)

source_name: BND

extract_protocol: Phenol/chloroform extraction except for rad50S samples where a glass beads DNA preparation was used

treatment_protocol: Meiotic single strand DNA enrichment on BND cellulose. 10 µg of genomic DNA prepared by direct phenol/chloroform extraction  was digested with HindII and SspI (Roche) for 4 hours (2 units per µg of DNA), which results in a predicted median fragment size of 400 bp. 100 µl of BND cellulose slurry (corresponding to 50 µl of packed matrix) was equilibrated in TEN buffer (Tris 10 mM, EDTA 1 mM, 1M NaCl pH 8.0) by three successive centrifugations (1 min, 1000g) and resuspensions in 450 µl TEN buffer to remove particules. NaCl (5M) was added to restriction digests to 1M final, and digested material was combined with the packed BND cellulose. After 10 min incubation at room temperature with occasional mixing, matrix plus bound DNA was isolated by five successive centrifugations (1000g, 1 min) with intervening resuspension in 450 µl TEN. Single strand-enriched DNA was eluted in 5 similar washes of 450 µl of TEN + 1.7% (w/v) caffeine (Sigma). Caffeine-eluted fractions were combined, remaining BND cellulose was removed using a glass filter spin columns (Harvard Apparatus), and pooled fractions concentrated and desalted by 5 successive buffer exchanges with 500 µl TE, using a Microcon YM-30 spin-filter. Caffeine removal was monitored by measuring decrease of flow-through absorbance at 270nm against TEN buffer.

tag: BND cellulose enriched DNA from rad51dmc1 cells 5h after transfer to sporulation media


title: rad51dmc1 5h rep2

description: S. cerevisiae (SK1)

tag: BND cellulose enriched DNA from dmc1 cells 5h after transfer to sporulation media


title: rad51 5h

description: S. cerevisiae (SK1)

tag: BND cellulose enriched DNA from rad51 cells 5h after transfer to sporulation media


title: spo11YFdmc1 5h rep2

description: S. cerevisiae (SK1)

tag: BND cellulose enriched DNA from spo11YFdmc1 cells 5h after transfer to sporulation media


title: dmc1 5h BND rep3

description: S. cerevisiae (SK1)


title: Wildtype BND 3h

description: S. cerevisiae (SK1)

tag: BND cellulose enriched DNA from WT cells 3h after transfer to sporulation media


title: rad51dmc1spo11YF 5h rep2

description: S. cerevisiae (SK1)

tag: BND cellulose enriched DNA from rad51dmc1spo11YF cells 5h after transfer to sporulation media


title: spo11YFrad51

description: S. cerevisiae (SK1)

tag: BND cellulose fractionation


title: Y/W_Female_Drosophila melanogaster_Acetone_topical_Replicate1

city: Guelph

first: Andreas

last: Heyland

state: ON

address: 50 Stone Rd East

department: Integrative Biology

country: Canada

institute: University of Guelph

description: A study to look at the antagonistic effects of JH and 20E on the expression of antimicrobial peptides (AMPs) in Drosophila.

hyb_protocol: Standard Affymetrix Protocol

scan_protocol: Standard Affymetrix Protocol

data_processing: Expression data were analyzed for significant over- or underrepresentation of gene ontology (GO) terms with the web application FatiGO (Al-Shahrour et al., 2004), using a two-fold change criterion. To test whether JH treatment significantly suppresses expression of AMPs we used t-tests implemented in JMP IN 5.1. (SAS Institute; Sall et al., 2004).

label_protocol: Standard Affymetrix Protocol

growth_protocol: Flies were grown on regular yeast diet, switched to no-yeast food within one hour of eclosion, and yeast-starved for 5 days posteclosion to lower their endogenous JH titer and to synchronize their physiology (cf. Tu and Tatar, 2003; Gershman et al., 2007).

extract_protocol: Trizole/Chloroform extraction

treatment_protocol: We anesthetized flies on ice and topically treated them with 0.1 microliter of 187 mM JH III in acetone or with 0.1 microliter 100% acetone (control) using a 1 ul Hamilton syringe with a repeating dispenser. 12 hours after hormone administration, samples were snap-frozen in liquid nitrogen and stored at -80°C. RNA was isolated from samples (2 JH samples, 2 control samples, each with 30 females) by lysis, as described in Gershman et al. (2007). cDNA products were hybridized at the Brown University Genomics Core Facility to Affymetrix GeneChip Drosophila_1 Genome Arrays (2 replicate chips per treatment). The dataset consisted of 14,009 probe sets, with 6,142 probe sets annotated. Expression data were analyzed for significant over- or underrepresentation of gene ontology (GO) terms with the web application FatiGO (Al-Shahrour et al., 2004), using a two-fold change criterion

tag: Strain

value: y,w

tag: Sex

value: females

tag: Stage

value: Adult

tag: Other


title: rad51dmc1spo11YF 5h rep1

description: S. cerevisiae (SK1)


title: maize_endo_4day_rep1

city: Peoria

first: Robert

last: Butchko

state: IL

address: 1815 N. University St.

institute: U.S. Dept. of Agriculture

hyb_protocol: Hybridization conducted by Nimblegen.

scan_protocol: Scan conducted by Nimblegen.

data_processing: Robust multiarray analysis following Bolstad, B., Irizarry, R., Astrand, M. and Speed, T. (2003) Bioinformatics, 19, 185–193.

organism: Fusarium verticillioides

source_name: Fusarium verticillioides cultured on maize endosperm four days

label_protocol: Biotin labeling conducted by Nimblegen.

extract_protocol: Ground material (0.5-1 gram) was suspended in 10 ml water-equilibrated phenol (pH 4.0) to which 10 ml Tris-HCl (pH 8.0) was added.  Phases were separated by centrifugation (10 min @ 12 000 x g, 4C) and the aqueous phase was subsequently extracted with 10 ml phenol:chloroform (1:1) and 10 ml chloroform:isoamyl alcohol (24:1).  RNA was precipitated overnight at -20C after the addition of ethanol to a final volume of 70%.  Precipitated RNA was pelleted by centrifugation (30 min @ 12 000 x g, 4C), air-dried briefly, and purified with the RNeasy RNA purification kit (Qiagen).

tag: F. verticillioides strain 7600


title: dmc1 5h Input rep3

description: S. cerevisiae (SK1)

tag: sheared genomic DNA by sonication to  an average size of 1kb


title: dmc1 5h rep2

description: S. cerevisiae (SK1)


title: Treated CD colon repl9

status: Public on Jan 01 2008

city: Cincinnati

first: Lee

last: Denson

state: OH

address: 3333 Burnet Avenue

institute: CCHMC

description: gene expression data from human colon

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the human HG-U133 Plus 2.0 GeneChip array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000.

data_processing: The data were analyzed with GeneSpring version 7.3 using RMA normalization with a custom CDF file(Hs133P_Hs_REFSEQ_8), then normalized to the batch-specific '107' internal control (see Series record for the '107' CEL files)

organism: Homo sapiens

source_name: human colon

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA  amplified with TargetAmp 1-round Aminoallyl-aRNA Amplication Kit 101 (Epicentre, WI) (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNeasy Plus Mini kit (QIAGEN, Hilden, Germany)

tag: treated CD replicate sample

tag: batch 3


title: dmc1 5h rep1

description: S. cerevisiae (SK1)

treatment_protocol: Meiotic single strand DNA enrichment on BND cellulose. 10 µg of genomic DNA prepared by direct phenol/chloroform extraction was digested with HindII and SspI (Roche) for 4 hours (2 units per µg of DNA), which results in a predicted median fragment size of 400 bp. 100 µl of BND cellulose slurry (corresponding to 50 µl of packed matrix) was equilibrated in TEN buffer (Tris 10 mM, EDTA 1 mM, 1M NaCl pH 8.0) by three successive centrifugations (1 min, 1000g) and resuspensions in 450 µl TEN buffer to remove particules. NaCl (5M) was added to restriction digests to 1M final, and digested material was combined with the packed BND cellulose. After 10 min incubation at room temperature with occasional mixing, matrix plus bound DNA was isolated by five successive centrifugations (1000g, 1 min) with intervening resuspension in 450 µl TEN. Single strand-enriched DNA was eluted in 5 similar washes of 450 µl of TEN + 1.7% (w/v) caffeine (Sigma). Caffeine-eluted fractions were combined, remaining BND cellulose was removed using a glass filter spin columns (Harvard Apparatus), and pooled fractions concentrated and desalted by 5 successive buffer exchanges with 500 µl TE, using a Microcon YM-30 spin-filter. Caffeine removal was monitored by measuring decrease of flow-through absorbance at 270nm against TEN buffer.


title: maize_germ_4day_rep1

source_name: F verticillioides cultured on maize germ tissue four days


title: maize_germ_4day_rep2

source_name: Fusarium verticillioides cultured on maize germ four days


title: cecum mucosa FOS 32

city: Wageningen

first: Wendy

last: Rodenburg

address: Bornsesteeg 45

department: Food Bioactives Group

country: Netherlands

institute: RIKILT-Institute of food safety

description: Rat Cecum Mucosa

hyb_protocol: Equal volumes of Cy5 target sample and Cy3 reference sample were combined, mixed with 2x hybridisation buffer (Agilent Technoloiges) and 10x control targets (Agilent Technologies) and hybridized to a Whole Rat Genome oligo array (G4131A, Agilent Technologies), for 17 hours at 60°C in an Agilent hybridization oven with rotation (Agilent Technologies). After hybridization the arrays were washed with an SSPE wash procedure (Agilent Technologies) according to manufacturers protocol.

scan_protocol: Arrays were scanned using the Scanarray Express HT (Perkin Elmer, Wellesley, MA) at a laserpower of 90% and a photomultiplier tube voltage of 55% for Cy5 and 60% for Cy3.

data_processing: The signals were extracted using ArrayVision (version 7.0, Imaging Research, Ontario, Canada). The signal intensity of each spot was measured as median density. Data was exported into GeneMaths XT (Applied Maths, Sint-Martens-Latem, Belgium) for analysis. Spots with an average Cy5 signal intensity, over all arrays, lower than 2-fold average Cy5 local background were discarded. Subsequently, the remaining Cy5 signal intensities were normalized against the Cy3 reference using RIKILT normalization protocol (Pellis L, et al. (2003) Physiol Genomics 16: 99-106).

organism: Rattus norvegicus

source_name: Reference RNA. This consists of a pool of equal molar total RNA samples of all groups analyzed.

label_protocol: 20 µg of total RNA was mixed with 4 µg T21 primer, heated at 65C for 3 min (RNA denaturation) followed by 25C for 10 min (primer annealing). cDNA was synthesized by adding 5x first strand buffer (Invitrogen), 10 mM DTT, 0.5mM dATP, 0.5 mM dGTP, 0.5 mM dTTP, 0.04 mM dCTP, 0.04 mM Cy3-dCTP, 1.2U RnaseOUT and 6U SuperScript II Reverse Transcriptase to a total volume of 62.5 µl. The reaction was incubated at 42 degrees C for 2 h. The reaction was precipitated using 1/10 volume of 3 M sodium-acetate (pH 5.2) and 2.5 volumes of 96% ethanol and RNA was broken down by 2.5 µl 1 M NaOH and incubation at 37 degrees C for 10 minutes. The reaction was neutralized with 2.5 µl 1 M Tris-HCl, pH 6.8 and 2µl 1M HCl. The Cy5 and Cy3 reactions were purified with the Qiaquick PCR purification kit (Westburg) and precipitated overnight at -20 degrees C using NaAc/ EtOH. The cDNAs were resolved in 100 µl RNase free H2O.

extract_protocol: Total RNA was isolated from the cecum homogenates using TRIzol reagent (Invitrogen, San Diego, CA) according to the manufacturer’s instructions. Total RNA was purified using Rneasy columns (Qiagen, Chatsworth, CA).

treatment_protocol: Cecum scrapings were homogenized in liquid N2 using a mortar and pestle cooled with liquid N2.(Fisher Emergo, Landsmeer, The Netherlands).

tag: Wistar, Gender

value: Male, Age:10 weeks, Tissue:Cecum Mucosa.

source_name: cecum mucosa control

label_protocol: 20 µg of total RNA was mixed with 4 µg T21 primer, heated at 65C for 3 min (RNA denaturation) followed by 25C for 10 min (primer annealing). cDNA was synthesized by adding 5x first strand buffer (Invitrogen), 10 mM DTT, 0.5mM dATP, 0.5 mM dGTP, 0.5 mM dTTP, 0.04 mM dCTP, 0.04 mM Cy5-dCTP, 1.2U RnaseOUT and 6U SuperScript II Reverse Transcriptase to a total volume of 62.5 µl. The reaction was incubated at 42 degrees C for 2 h. The reaction was precipitated using 1/10 volume of 3 M sodium-acetate (pH 5.2) and 2.5 volumes of 96% ethanol and RNA was broken down by 2.5 µl 1 M NaOH and incubation at 37 degrees C for 10 minutes. The reaction was neutralized with 2.5 µl 1 M Tris-HCl, pH 6.8 and 2µl 1M HCl. The Cy5 and Cy3 reactions were purified with the Qiaquick PCR purification kit (Westburg) and precipitated overnight at -20 degrees C using NaAc/ EtOH. The cDNAs were resolved in 100 µl RNase free H2O.

value: Male, Age:10 weeks, Tissue:cecum Mucosa.


title: Endometrium_day 18_low P4_rep4

city: Lindau

first: Stefan

middle: Michael

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

country: Switzerland

institute: University of Zurich

description: endometrium tissue from heifers at five stages of the estrous cycle

hyb_protocol: Pre-hybridization was done for five arrays together in one 15 cm glass hybridization bottle, respectively: 2 x 10 min 10 ml 0.1 x PBS / 1 % SDS at 85 °C; 3 x 10 min 10 ml 1 x PBS / 10 % SDS at 65 °C; 1 x 10 ml 1 x PBS / 10 % SDS at room temperature. Hybridization was done in plastic vials (Poly-Q vials, 18 ml; Beckmann Coulter, Munich, Germany) in 2,5 ml 1 x PBS / 10 % SDS for 47 h at 65 °C. Subsequently, the hybridization solution was decanted and the vials filled immediately with 1 x PBS / 10 % SDS. For washing five arrays were put together in 15 cm glass hybridization bottles, respectively, and processed as follows: 3 x 5 min 10 ml 1 x PBS / 10 % SDS at 65 °C; 3 x 10 min 10 ml 1 x PBS / 10 % SDS at 65 °C; 3 x 10 min 10 ml 0.1 x PBS / 1 % SDS at 65 °C; 3 x 5 min 10 ml 1 x PBS / 1 % SDS / 2 mM EDTA at 30 °C. Membranes were dried by baking at 80 °C for 20 min.

scan_protocol: The arrays were exposed to an imaging plate BAS-SR (Fuji Photo Film Co) for 16 to 30 hrs. Imaging plates were scanned with a phosphor imager (Typhoon Imager, GE Healthcare Life Sciences).

data_processing: Array evaluation was done using AIDA Image Analyzer (Version 3.52, Raytest, Straubenhardt, Germany), backround was subtracted with the 'Lowest Grid Dot' function. Raw data (integral minus background) were normalized with vsn (vsn; BioConductor).

organism: Bos taurus

source_name: endometrium, day 18, low P4

label_protocol: 33P-labelled cDNA probes were generated from ds cDNA corresponding to 7.5-15 µg total RNA. cDNA was heat-denatured for 10 min at 96 °C and then chilled on ice. High Prime reaction mixture (Roche), dNTP mixture (dCTP final concentration 10 pmol/µl, dATP, dGTP and dTTP final concentration each 100 pmol/µl)and 90 µCi [a-33P] dCTP were added to a final colume of 20 µl. Reactions were incubated for 1 h at 37 °C and subsequently purified with ProbeQuant G-50 Micro Columns (GE Healthcare, Buckinghamshire, UK) to remove unincorporated nucleotides and to estimate labeling efficiency.

extract_protocol: Tissue samples of the middle or caudal part of the ipsilateral uterine horn were carefully cut from the lamina propria of the intercaruncular endometrium with a scalpel and conserved in RNAlater (Ambion, Huntingdon, Cambridgeshire, UK). Total RNA was isolated using Trizol reagent (Invitrogen) according to the manufactorer's recommendations. The quantity and quality of total RNA were determined by spectrometry and agarose gel electrophoresis respectively.

tag: SEX

value: female

tag: AGE

value: 21 months

tag: LOKALISATION

value: ipsilateral, middle


title: Endometrium_day 18_low P4_rep2

value: 20 months


title: Endometrium_day 18_low P4_rep1

value: 22 months

value: ipsilateral, back


title: cecum mucosa FOS 26

description: Rat Cecum Mucosa


title: cecum mucosa control 31

description: Rat Cecum Mucosa


title: spo11YFdmc1 5h rep1

description: S. cerevisiae (SK1)


title: Endometrium_day 18_high P4_rep2

source_name: endometrium, day 18, high P4


title: Endometrium_day 18_high P4_rep3


title: cecum mucosa FOS 02

description: Rat Cecum Mucosa


title: cecum mucosa FOS 08

description: Rat Cecum Mucosa


title: Endometrium_day 18_low P4_rep3


title: cecum mucosa control 07

description: Rat Cecum Mucosa


title: cecum mucosa FOS 54

description: Rat Cecum Mucosa


title: cecum mucosa FOS 46

description: Rat Cecum Mucosa


title: maize_endo_4day_rep2

label: Biotin

extract_protocol: Ground material (0.5-1 gram) was suspended in 10 ml water-equilibrated phenol (pH 4.0) to which 10 ml Tris-HCl (pH 8.0) was added.  Phases were separated by centrifugation (10 min @ 12 000 x g, 4C) and the aqueous phase was subsequently extracted with 10 ml phenol:chloroform (1:1) and 10 ml chloroform:isoamyl alcohol (24:1).  RNA was precipitated overnight at -20C after the addition of ethanol to a final volume of 70%.  Precipitated RNA was pelleted by centrifugation (30 min @ 12 000 x g, 4C), air-dried briefly, and purified with the RNeasy RNA purification kit (Qiagen).


title: cecum mucosa control 53

description: Rat Cecum Mucosa


title: cecum mucosa control 37

description: Rat Cecum Mucosa


title: Endometrium_day 18_high P4_rep1


title: cecum mucosa control 41

description: Rat Cecum Mucosa


title: cecum mucosa FOS 20

description: Rat Cecum Mucosa


title: Endometrium_day 12_rep2

source_name: endometrium, day 12

value: 31 months


title: Endometrium_day 12_rep4

value: 18 months


title: Endometrium_day 18_high P4_rep4


title: cecum mucosa control19

description: Rat Cecum Mucosa


title: Endometrium_day 12_rep1


title: cecum mucosa control 45

description: Rat Cecum Mucosa


title: cecum mucosa FOS 14

description: Rat Cecum Mucosa


title: Endometrium_day 3.5_rep4

source_name: endometrium, day 3.5


title: Endometrium_day 3.5_rep1

value: 17 months


title: Endometrium_day 3.5_rep2


title: cecum mucosa control 49

description: Rat Cecum Mucosa


title: cecum mucosa control 01

description: Rat Cecum Mucosa


title: Endometrium_day 0_rep2

source_name: endometrium, day 0

value: 29 months


title: Endometrium_day 0_rep4


title: Endometrium_day 0_rep3


title: cecum mucosa FOS 38

description: Rat Cecum Mucosa


title: cecum mucosa FOS 50

description: Rat Cecum Mucosa


title: cecum mucosa control 57

description: Rat Cecum Mucosa


title: Endometrium_day 3.5_rep3

value: 19 months


title: cecum mucosa FOS 58

description: Rat Cecum Mucosa


title: cecum mucosa FOS 42

description: Rat Cecum Mucosa


title: Endometrium_day 0_rep1

value: 23 months


title: HepG2_DHA&Cd48h rep3

city: Sapporo

first: Akinobu

last: Ito

address: North-13, West-8, Kitaku

department: Graduate School of Engineering

country: Japan

institute: Hokkaido University

description: Gene expression data from Cd treated Hep G2 cells that were loaded with vitamine C beforehand

hyb_protocol: Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). Labeled cRNA was fragmented by incubation at 94 °C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate. Ten ug of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 °C. After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).

scan_protocol: probe arrays were scanned with the Genechip System confocal scanner (Affymetrix, Santa Clara, CA).

data_processing: The data were analyzed with MAS5 using Avadis 4.3 prophetic (Strand Genomics, Redwood City, CA).

source_name: Hep G2 treated with dehydroascorbic acid and Cadmium chloride 2.5-hydrate

label_protocol: Target preparation was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). cDNA was synthesized from the 5 ug of total RNA by using One-Cycle cDNA Synthesis kit (Invitrogen, Carlsbad, CA) with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. cRNA was synthesized from the cDNA and biotin-labeled by in vitro transcription using IVT Labeling kit (Affymetrix, Santa Clara, CA).

growth_protocol: Cells were cultured in Eagle's minimal essential medium (MEM) (Nissui, Tokyo, Japan) supplemented with 1% non-essential amino acid (Invitrogen, Carlsbad, CA), 10% fetal bovine serum and 60 mg/ml kanamycin at 37 °C and 5% CO2.

extract_protocol: The cells were were washed with phosphate buffered saline (PBS) and lysed directly on culture dishes. Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).

treatment_protocol: Cells at 70% confluency in 60 mm culture dishes were incubated in PBS containing 1 mM dehydroascorbic acid for 60min at 37 °C. After washing with PBS, cells were incubated in the culture medium containing 2 uM cadmium chloride 2.5-hydrate for 48h at 37 °C.

tag: Cell bank no

tag: Cell name

value: Hep G2

value: male

tag: Age of sampling

value: 15 years

tag: Tissue derived

value: liver

tag: Case history

value: hepatocyte carcinoma

tag: Life span

value: infinite

tag: Classification

value: Transformed


title: HepG2_DHA&Ni48h rep3

description: Gene expression data from Ni treated Hep G2 cells that were loaded with vitamine C beforehand

source_name: Hep G2 treated with dehydroascorbic acid and Nickel (II) chloride hexahydrate

treatment_protocol: Cells at 70% confluency in 60 mm culture dishes were incubated in PBS containing 1 mM dehydroascorbic acid for 60min at 37 °C. After washing with PBS, cells were incubated in the culture medium containing 150 uM Nickel (II) chloride hexahydrate for 48h at 37 °C.

tag: Sex


title: HepG2_DHA&Cd48h rep2


title: HepG2_DHA&Ni48h rep1


title: HepG2_DHA&Ni48h rep2


title: HepG2_DHA&As48h rep3

description: Gene expression data from As treated Hep G2 cells that were loaded with vitamine C beforehand

source_name: Hep G2 treated with dehydroascorbic acid and Arsenic (III) oxide

treatment_protocol: Cells at 70% confluency in 60 mm culture dishes were incubated in PBS containing 1 mM dehydroascorbic acid for 60min at 37 °C. After washing with PBS, cells were incubated in the culture medium containing 6 uM Arsenic (III) oxide for 48h at 37 °C.


title: chicken intestine 25

city: Blacksburg

first: Huifeng

last: Li

state: VA

address: 3570 Litton Reaves Hall

department: Animal and Poultry Sciences

institute: Virginia Tech

hyb_protocol: - GeneChip is prehybridized with 200ul 1x Hybridization buffer at 45C 10min at 60rpm        - 200ul denatured Hybridization cocktail is applied to GeneChip        - GeneChip is hybridized 16 hr at 45C and 60rpm in GeneChip Hybridization Oven 640.

scan_protocol: Arrays were scanned with an Affymetrix GeneChip Scanner 3000 at 570nm.

data_processing: GC-RMA

organism: Gallus gallus

source_name: Day14 chick intestine

label_protocol:
Enzo BioArray High Yield RNA Transcipt Labeling Kit
     10ul  purified cDNA
       12ul  DEPC H2O
       4ul   10x Hy reaction Buffer                            (1x final conc.)
       4ul   10x Biotin Labeled Ribonucleotides        (1x final Conc.)
       4ul   10x DTT                                              (1x final conc.)
       4ul   10x RNase Inhibitor mix                          (1x final Conc.)
       2ul   20x T7 RNA polymerase                        (1x final Conc.)
       - Incubate at 37C 5 hours mixing every 0.5 hour.

extract_protocol: Total RNA was isolated for both microarray and real-time absolute quantification reverse transcriptase polymerase chain reaction (AQRT-PCR) studies.  Tissue samples were ground in a mortar and pestle under liquid nitrogen.  Total RNA from intestinal segments of six male birds at each time point were isolated using the RNeasy Mini Kit (Qiagen).

tag: gender

tag: tissue

value: whole intestine


title: chicken intestine 27


title: HepG2_DHA&As48h rep2


title: HepG2_DHA&Cd48h rep1


title: chicken intestine 28


title: chicken intestine 24

source_name: Day7 chick intestine


title: chicken intestine 26


title: HepG2_DHA&As48h rep1


title: HepG2_Ni48h rep2

description: Gene expression data from Ni treated (48h) Hep G2 cells

source_name: Hep G2 treated with Nickel (II) chloride hexahydrate

treatment_protocol: Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 150 uM Nickel (II) chloride hexahydrate for 48h at 37 °C.


title: chicken intestine 23


title: HepG2_Ni48h rep3


title: chicken intestine 19

source_name: Day3 chick intestine


title: HepG2_Ni48h rep1


title: chicken intestine 21


title: HepG2_Cd48h rep3

description: Gene expression data from Cd treated (48h) Hep G2 cells

source_name: Hep G2 treated with Cadmium chloride 2.5-hydrate

treatment_protocol: Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 2 uM cadmium chloride 2.5-hydrate for 48h at 37 °C.


title: chicken intestine 14

source_name: Day1 chick intestine


title: HepG2_Cd48h rep1


title: chicken intestine 17


title: chicken intestine 22


title: chicken intestine 15


title: HepG2_Cd48h rep2


title: HepG2_As48h rep3

description: Gene expression data from As treated (48h) Hep G2 cells

source_name: Hep G2 treated with Arsenic (III) oxide for 48h

treatment_protocol: Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 6 uM Arsenic (III) oxide for 48h at 37 °C.


title: HepG2_As48h rep1


title: chicken intestine 18


title: chicken intestine 16


title: chicken intestine 20


title: HepG2_As48h rep2


title: chicken intestine 13


title: HepG2_DMNQ48h rep2

description: Gene expression data from DMNQ treated Hep G2 cells

source_name: Hep G2 treated with DMNQ for 48h

treatment_protocol: Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 10 uM 2,3-Dimethoxy-1,4-naphthoquinone for 48h at 37 °C.


title: HepG2_DMNQ48h rep3


title: HepG2_TCE rep2

description: Gene expression data from TCE treated Hep G2 cells

source_name: Hep G2 treated with TCE for 48h

treatment_protocol: Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 2 mM tetrachloroethylene for 48h at 37 °C.


title: HepG2_TCE rep1


title: HepG2_DMNQ48h rep1


title: chicken intestine 8

source_name: embryonic day 20 chick intestine


title: chicken intestine 12

source_name: Day of hatch, chick intestine


title: chicken intestine 11


title: HepG2_TCE rep3


title: chicken intestine 10


title: HepG2_TPA rep3

description: Gene expression data from TPA treated Hep G2 cells

source_name: Hep G2 treated with TPA for 48h

treatment_protocol: Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 0.1 uM 12-o-tetradecanoylphorbol-13-acetate (TPA) for 48h at 37 °C.


title: HepG2_TPA rep2


title: chicken intestine 6


title: HepG2_TPA rep1


title: chicken intestine 4

source_name: embryonic day 18 chick intestine


title: chicken intestine 9


title: chicken intestine 5


title: chicken intestine 2


title: chicken intestine 1

label_protocol:
Enzo BioArray High Yield RNA Transcipt Labeling Kit
     10ul  purified cDNA
       12ul  DEPC H2O
       4ul   10x Hy reaction Buffer                            (1x final conc.)
       4ul   10x Biotin Labeled Ribonucleotides        (1x final Conc.)
       4ul   10x DTT                                                 (1x final conc.)
       4ul   10x RNase Inhibitor mix                          (1x final Conc.)
       2ul   20x T7 RNA polymerase                        (1x final Conc.)
       - Incubate at 37C 5 hours mixing every 0.5 hour.


title: chicken intestine 3


title: Testis_OA_ID-St30

city: Isehara

first: Tajima

last: Atsushi

state: Kanagawa

address: 143 Shimokasuya

institute: Tokai University School of Medicine

description: All patients were underwent testicular sperm extraction (TESE) for assisted reproduction.

hyb_protocol: 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit Plus protocol. Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol. Array slides were washed using SSC wash protocol.

scan_protocol: Slides were scanned using Agilent Microarray Scanner (G2565AA) at 10um resolution.

data_processing: Agilent Feature Extraction software (v.7.5) was used to assess spot quality and obtain signal intensity statistics in default setting. Agilent GeneSpring GX (v.7.3) was used for lowess normalization of Cy5/Cy3 ratio.

label_protocol: 150 ng of total RNA were amplified and labeled with the  Agilent Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer’s instructions.

extract_protocol: Total RNA from testicular biopsy was extracted using TRIzol reagent (Invitrogen).

tag: Biopsied testis from Japanese OA patient

source_name: Human Testis Total RNA

tag: Pooled RNA from 39 Caucasians


title: Testis_OA_ID17


title: chicken intestine 7


title: Testis_OA_ID14


title: Testis_OA_ID-St12


title: Testis_OA_ID10


title: Testis_OA_ID08


title: Testis_OA_ID-St09


title: Testis_NOA_ID-St39

tag: Biopsied testis from Japanese NOA patient


title: Testis_NOA_ID-St38


title: Testis_NOA_ID-St33


title: Testis_OA_ID11


title: Testis_NOA_ID-St40


title: Testis_OA_ID05


title: Testis_OA_ID01


title: Testis_NOA_ID-St36


title: Testis_NOA_ID-St34


title: Testis_NOA_ID-St29


title: Testis_NOA_ID-St31


title: Testis_NOA_ID-St32


title: Testis_NOA_ID-St26


title: Testis_NOA_ID-St24


title: Testis_NOA_ID-St21


title: Testis_NOA_ID-St25


title: Testis_NOA_ID-St23


title: Testis_OA_ID12


title: Testis_NOA_ID-St20


title: Testis_NOA_ID-St27


title: N satisfaction NH4 aerial (L18_NH4PAT2)

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

description: Experiment has been designed to characterize the molecular expression patterns associated to a contrasted modification of the nitrogen status of the whole plant. The systemic effects of nitrogen status modifications are investigated and compared on non nodulated plant supplied with NO3, NH4 or nodulated plants (Sinorhizobium meliloti 2011) supplied with air. The root systems were separated in two compartments of unequal sizes (split root system). Two treatments were applied on the larger compartment in order to modulate the nitrogen status of the plant: for the S treatment, roots are supplied with nutrient solution containing 10 mM NH4NO3,, whereas for the C treatment, roots are supplied with nitrogen free medium. In the case of N2 fixing plants, N limitation was obtained by replacing air by a mixture of Ar and O2 80 per cent and 20 per cent. The effects of these treatments were investigated on roots of the minor compartment supplied continuously with either NO3 1 mM, NH4 1 mM or air (N2) and on the shoots. We were also interested in the molecular expression patterns associated to the roots deprived of N.

hyb_protocol: labelled extract quantity: 15ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

organism: Medicago truncatula

label_protocol: labelling Biotin direct, amplification=yes, RNAa 20 ug.

growth_protocol: aerial - Plants were grown hydroponically. Nutrient solution contained 1 mM KNO3, 1 mM KH2PO4 , 1 mM MgSO4 , 250 uM CaCl2 , 0.1 mM Na-Fe-EDTA, 50 uM KCl, 50 uM H3BO3, 5uM MnSO4, 1 uM ZnSO4, 1 uM CuSO4, 0.1 uM Na6Mo7O24, pH adjusted to 6 with KOH. Plants were cultivated in growth chamber with the following environmental parameters: light/dark cycle 8/16h, light intensity 250 umol.s-1.m-2 PAR, temperature 22degreeC/20degreeC, 70% hygrometry. The nutrient solution was renewed twice a week during the first part of the culture, and daily the last week before the experiment.

treatment_protocol: Name:N_satisfaction_NH4_aerial - growth conditions - nitrogen,nitrogen:time 4day . The root system of six plants is split into two parts. The major root part is supplied with a nutrient solution containing NH4NO3 10mM whereas the minor part is supplied with NH4plus 1mM. The nutrient solutions are renewed daily. After four days of this treatement of N-satisfaction, the shoots are individually collected, weighted, immediately frozen and stored at minus 80 degre Celsius.

tag: Medicago (truncatula)  - age:5week


title: Testis_NOA_ID-St16


title: Testis_NOA_ID-St19


title: Testis_NOA_ID-St14


title: Testis_NOA_ID-St17


title: N satisfaction NH4 aerial (L17_NH4PAT1)


title: N limitation NO3 1 (L7_NO3ONE1)

growth_protocol: root - Plants were grown hydroponically. Nutrient solution contained 1 mM KNO3, 1 mM KH2PO4 , 1 mM MgSO4 , 250 uM CaCl2 , 0.1 mM Na-Fe-EDTA, 50 uM KCl, 50 uM H3BO3, 5uM MnSO4, 1 uM ZnSO4, 1 uM CuSO4, 0.1 uM Na6Mo7O24, pH adjusted to 6 with KOH. Plants were cultivated in growth chamber with the following environmental parameters: light/dark cycle 8/16h, light intensity 250 umol.s-1.m-2 PAR, temperature 22degreeC/20degreeC, 70% hygrometry. The nutrient solution was renewed twice a week during the first part of the culture, and daily the last week before the experiment.

treatment_protocol: Name:N_limitation_NO3_1 - growth conditions - nitrogen,nitrogen:time 4day . the major part of the root system is privated of N and the minor part is fed with NO3- 1mM. The root system of six plants is split into two parts. The major root part is supplied with nitrogen-free nutrient solution whereas the minor part is supplied with NO3- 1mM. The nutrient solutions are renewed daily. After four days of this treatement of N-limitation, the root parts remained on NO3- 1mM are individually collected, weighted, immediately frozen and stored at minus 80 degre Celsius.Name: - growth conditions - nitrogen,nitrogen:time 4day . The root system of six plants is split into two parts. The major root part is supplied with nitrogen-free nutrient solution whereas the minor part is supplied with NO3- 1mM. The nutrient solutions are renewed daily. After four days of this treatement of N-limitation, the root parts remained on nitrogen-free nutrient solution are individually collected, weighted, immediately frozen and stored at minus 80 degre Celsius.


title: N limitation NH4 aerial (L16_NH4PAE2)

treatment_protocol: Name:N_limitation_NH4_aerial - growth conditions - nitrogen,nitrogen:time 4day . The root system of six plants is split into two parts. The major root part is supplied with nitrogen-free nutrient solution whereas the minor part is supplied with NH4plus 1mM. The nutrient solutions are renewed daily. After four days of this treatement of N-limitation, the shoots are individually collected, weighted, immediately frozen and stored at minus 80degre Celsius.


title: Testis_NOA_ID-St22


title: N satisfaction N2 aerial (L12_N2PAT2)

growth_protocol: aerial - Plants were grown hydroponically. Plants were cultivated in growth chamber with the following environmental parameters: light/dark cycle 8/16h, light intensity 250 umol.s-1.m-2 PAR, temperature 22degreeC/20degreeC, 70% hygrometry. The nutrient solution was renewed twice a week during the first part of the culture, and daily the last week before the experiment. Plants were grown during two weeks in a nutrient solution contained 1 mM KNO3, 1 mM KH2PO4 , 1 mM MgSO4 , 250 uM CaCl2 , 0.1 mM Na-Fe-EDTA, 50 uM KCl, 50 uM H3BO3, 5uM MnSO4, 1 uM ZnSO4, 1 uM CuSO4, 0.1 uM Na6Mo7O24, pH adjusted to 6 with KOH. After these two weeks, plants were transferred in the same nutrient solution devoid of nitrogen, adjusted to pH7 and they are inoculated with Sinorhizobium meliloti strain 2011. Strong aeration of nutrient solution is achieved by blowing air with an aquarium pump in pumice stone diffuser. Two weeks after inoculation, nodulated plants were transferred on aerated nitrogen free nutrient solution, adjusted to pH6.

treatment_protocol: Name:N_satisfaction_N2_aerial - growth conditions - nitrogen,nitrogen:time 4day . The nodulated root system of six plants is split into two parts. The major root part is supplied with a nutrient solution containing NH4NO3 10mM whereas the minor part remain on air. The nutrient solutions are renewed daily. After four days of this treatement of N-satisfaction, the shoots are individually collected, weighted, immediately frozen and stored at minus 80 degre Celsius.N supply : the major part of the root system received a large quantity of N and the minor part remain on air


title: N limitation NH4 aerial (L15_NH4PAE1)


title: Testis_NOA_ID-St13


title: Testis_NOA_ID-St11


title: Testis_NOA_ID-St10


title: Testis_NOA_ID-St18


title: Testis_NOA_ID-St15


title: N limitation NO3 1 (L8_NO3ONE2)


title: N satisfaction N2 aerial (L11_N2PAT1)


title: N limitation N2 aerial (L10_N2PAE2)

treatment_protocol: Name:N_limitation_N2_aerial - growth conditions - nitrogen,nitrogen:time 4day . The nodulated root system of six plants is split into two parts. The major root part is supplied with nitrogen-free nutrient solution (N2 is replaced by argon) whereas the minor part remain on air. The nutrient solutions are renewed daily. After four days of this treatement of N-limitation, the shoots are individually collected, weighted, immediately frozen and stored at minus 80 degre Celsius.


title: N satisfaction NO3 aerial (L4_NO3PAT2)

treatment_protocol: Name:N_satisfaction_NO3_aerial - growth conditions - nitrogen,nitrogen:time 4day . After four days of this treatement of N-satisfaction, the shoots are individually collected, weighted, immediately frozen and stored at minus 80 degre Celsius.


title: Testis_NOA_ID-St08


title: Testis_NOA_ID-St02


title: Testis_NOA_ID-St04


title: Testis_NOA_ID-St06


title: N limitation NO3 aerial (L2_NO3PAE2)

treatment_protocol: Name:N_limitation_NO3_aerial - growth conditions - nitrogen,nitrogen:time 4day . The root system of six plants is split into two parts. The major root part is supplied with nitrogen-free nutrient solution whereas the minor part is supplied with NO3- 1mM. The nutrient solutions are renewed daily. After four days of this treatement of N-limitation, the shoots are individually collected, weighted, immediately frozen and stored at minus 80 degre Celsius.


title: Testis_NOA_ID-St05


title: Myelin OLs (80q)

city: Stanford

first: John

last: Cahoy

state: CA

address: 299 Campus Drive

department: Department of Neurobiology

institute: Stanford University

hyb_protocol: The labeling assay yielded labeled single-stranded DNA that was fragmented and hybridized to Affymetrix Mouse Exon 1.0 ST Arrays (exon-arrays) according to manufacturer’s protocols at the Stanford Protein and Nucleic Acid Facility

scan_protocol: Hybridized Affymetrix Mouse Exon 1.0 ST Arrays (exon-arrays) were scanned following the manufacturer’s protocols at the Stanford Protein and Nucleic Acid Facility

data_processing: Raw image files were processed using Affymetrix GCOS 1.3 software to generate CEL data files.  Exon-array expression indexes were calculated using the GeneBASE program (Kapur et al., 2007).  Briefly, the program employs a sequence-specific background model to correct background intensities of exon-array probes (Kapur et al., 2007), followed by an iterative probe selection procedure (Xing et al., 2006) that selects a subset of highly correlated probes of a gene for expression index computation.

organism: Mus musculus

source_name: Postnatal age day 17 MOG Myelin Oligodendrocytes

label_protocol: Biotinylated sense-strand DNA for hybridization to Affymetrix exon-arrays was prepared with the Affymetrix GeneChip whole transcript sense target labeling assay, using either the standard 1 μg total RNA method or the reduced starting material 100 ng method according to the manufacturer’s protocols (Affymetrix, 900854).  Briefly, for samples with 1 μg of total RNA, ribosomal RNA reduction was performed using the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen, K1550-01); ribosomal RNA reduction was not performed for the 100 ng reduced starting material samples.

growth_protocol: Preparation Of Mouse Astroglia: Preparation of astroglia cultures was as follows.  Cortices were isolated by crude dissection of six P1 mice from a S100β-EGFP transgenic litter, meninges were removed, and the tissue was chopped using a curved-blade surgical scalpel.  This tissue was enzymatically dissociated to make a suspension of single cells.  Briefly, the tissue was incubated at 33 °C for 75 minutes in 20 ml of a papain solution prepared in dissociation buffer containing EDTA and L-cysteine.;  After papain treatment the tissue was washed with 3 x 4 ml of DPBS containing BSA (1.5 mg/ml), ovomucoid (1.5 mg/ml), and DNase (125U/ml) (ovomucoid inhibitor).  The tissue was then mechanically dissociated by gentle sequential trituration using a 5 ml pipette with 5 x 4 ml fresh ovomucoid inhibitor to yield a suspension of single cells.  Dissociated cells were harvested by centrifugation at 220 x g for 10 minutes.  Cells were resuspended in 12 ml of concentrated ovomucoid inhibitor (5 mg/ml BSA and 5 mg/ml ovomucoid) and harvested by centrifugation.  Dissociated cells were resuspended in 15 ml of astroglia media and plated in 75 cm2 tissue culture flasks (BD Falcon, 353136) that were pre-coated with PDL (10 μg/ml in water, Sigma, P6407) at a density of 25-30 million cells per flask.  Astroglia media contained Dulbecco's modified eagle medium (DMEM, Invitrogen, 11960-044), 10% fetal bovine serum (FBS, Invitrogen, 10437-028), 2 mM glutamine (Invitrogen, 25030-081), 1 mM Na pyruvate (Invitrogen, 11360-070), 5 μg/ml N-Acetyl-L-cysteine (NAC, Sigma, A8199), 5 μg/ml insulin (Sigma, I6634), 100 U/ml penicillin-streptomycin (Invitrogen, 15140-122), and 10 μM hydrocortisone (Sigma, H0888).  When plated under these conditions most cells including neurons and mature astrocytes die, but a small percentage of immature cells are able to survive and proliferate.;  After 3 days the astroglia layer was confluent and the flask was rinsed once with DPBS and then shaken 3 times with DPBS containing phenol red to remove contaminating OL progenitor cells (OPCs), and fresh astroglia media was added.  OPCs grow on top of the single cell monolayer of astroglia, so they can be removed by vigorous shaking of the sealed tissue culture flask.  After 2 days, 10 μM cytosine arabinoside (AraC, Sigma, C1768) was added to kill dividing cells such as fibroblasts and microglia; the underlying monolayer of astrocytes is not affected by the antimitotic because astroglia divide slowly in dense cultures due to contact inhibition.  After 48 hours the astroglia were trypsinized off and plated onto PDL-coated 15 cm tissue culture dishes at 2 million cells per dish in astroglia media.;  For preparation of astroglia grown in serum free media, confluent cultures of astroglia prepared as described above were washed three times with DPBS and 20 ml serum-free media was added.  Serum-free medium, modified from Bottenstein and Sato (1979), contained neurobasal (Invitrogen, 21103-049), bovine serum albumin (100 μg/ml, BSA, Sigma, A4161), selenium (40 ng/ml, Sigma, S5261), putrescine (16 μg/ml, Sigma, P5780), transferrin (100 μg/ml, Sigma, T1147), progesterone (60 ng/ml, Sigma, P8783), triiodo-thyronine (40 ng/ml, Sigma, T6397), penicillin-streptomycin (100U/ml), insulin (5 μg/ml) NAC (5 μg/ml), pyruvate (1 mM), and glutamine (2 mM).

extract_protocol: Total RNA was isolated from acutely purified cells with the RNeasy micro kit (Qiagen, Valencia, CA) using Qiashredder columns for cell lysis and Qiagen on-column DNase treatment to remove any contaminating genomic DNA.  The integrity of RNA was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara , CA), and RNA concentration was determined using a NanoDrop ND-1000 spectrophotometer (NanoDrop, Rockland, DE).

treatment_protocol: The purification procedures are based on previously described dissociation (Huettner and Baughman, 1986; Segal et al., 1998) and immunopanning purification protocols for other cell types (Barres et al., 1988; Barres et al., 1992; Meyer-Franke et al., 1995).  All aspects of the panning and FACS purification procedures are summarized below.;  Preparation Of Mouse Forebrain Cell Suspensions: Six to eight mice from a wild-type litter (C57BL/6, Charles River, Wilmington, MA) or S100β-EGFP transgenic litter (C57BL/6 x DBA (F1), Kosmos line, Zuo et al., 2004) were used.  The forebrain was isolated by removal of the olfactory lobes, cerebellum, and midbrain/hindbrain structures by crude dissection, and the tissue was diced with a curved-blade surgical scalpel (Feather, Osaka, Japan, GRF-2976 #10).  To isolate cerebral cortical gray matter astrocytes, the brain was sliced in 2-3 mm coronal sections and the cerebral cortex was carefully dissected away from the ventral white matter tracks.  This tissue was enzymatically dissociated to make a suspension of single cells, essentially as described by Huettner and Baughman (Huettner and Baughman, 1986; Segal et al., 1998).  Briefly, the tissue was incubated at 33 °C for 80 minutes (90 minutes for animals P16 and older) in 20 ml of a papain solution (20 U/ml, Worthington, Lakewood, NJ, LS03126) prepared in dissociation buffer with EDTA (0.5 mM), and L-cysteine-HCl (necessary to activate the papain, 1 mM, Sigma, St. Louis, MO, C7880).  The dissociation buffer contained Earle’s balanced salts (EBSS, Sigma, E7510), D(+)-glucose (22.5 mM), NaHCO3 (26 mM), and DNase (125U/ml, Worthington, LS002007) and requires careful equilibration with 5% CO2 and 95% O2 gas before use and during papain treatment.  When dissociation buffer is exposed to room air during trituration, minimizing surface area and avoiding bubbles is essential to maintain the proper pH and cell health.;  After papain treatment to loosen contacts in the extracellular matrix, the tissue was washed with 3 x 4 ml dissociation buffer containing BSA (1.0 mg/ml, Sigma, A-8806) and ovomucoid (also known as Trypsin Inhibitor, 1.0 mg/ml, Roche Diagnostics Corporation, Indianapolis, IN, 109878) (inhibitor solution) and then mechanically dissociated by gentle sequential trituration using a 5 ml pipette with 5 x 4 ml fresh inhibitor solution to yield a suspension of single cells.  Dissociated cells were layered on top of 12 ml of concentrated inhibitor solution (5 mg/ml BSA and 5 mg/ml ovomucoid) and harvested by centrifugation (140 x g for 5 minutes, 220 x g for 10 minutes when purifying OL lineage cells).  This method routinely yielded ~15-20 million cells per mouse pup forebrain, with excellent cell health as determined by morphology and viability (>90% by trypan blue exclusion).

tag: C57BL/6 x DBA (F1)

tag: total RNA RiboMinus 1 microgram


title: N satisfaction NO3 aerial (L3_NO3PAT1)


title: Astros P7 (81a)

source_name: Postnatal age day 7 Positive Astrocytes


title: N satisfaction N2 (N2S2)

growth_protocol: root - Plants were grown hydroponically. Plants were cultivated in growth chamber with the following environmental parameters: light/dark cycle 8/16h, light intensity 250 umol.s-1.m-2 PAR, temperature 22degreeC/20degreeC, 70% hygrometry. The nutrient solution was renewed twice a week during the first part of the culture, and daily the last week before the experiment. Plants were grown during two weeks in a nutrient solution contained 1 mM KNO3, 1 mM KH2PO4 , 1 mM MgSO4 , 250 uM CaCl2 , 0.1 mM Na-Fe-EDTA, 50 uM KCl, 50 uM H3BO3, 5uM MnSO4, 1 uM ZnSO4, 1 uM CuSO4, 0.1 uM Na6Mo7O24, pH adjusted to 6 with KOH. After these two weeks, plants were transferred in the same nutrient solution devoid of nitrogen, adjusted to pH7 and they are inoculated with Sinorhizobium meliloti strain 2011. Strong aeration of nutrient solution is achieved by blowing air with an aquarium pump in pumice stone diffuser. Two weeks after inoculation, nodulated plants were transferred on aerated nitrogen free nutrient solution, adjusted to pH6.

treatment_protocol: Name:N_satisfaction_N2 - growth conditions - nitrogen,nitrogen:time 4day . Nitrogen satisfaction : the major part of the nodulated root system is supplied with a solution containing NH4NO3 10mM and the minor part remain on air.The nodulated root system of six plants is split into two parts. The major root part is supplied with a nutrient solution containing NH4NO3 10mM whereas the minor part remain on air. The nutrient solutions are renewed daily. After four days of this treatement of N-satisfaction, the root parts remained on air are individually collected, weighted, immediately frozen and stored at minus 80 degre Celsius.

tag: Medicago (truncatula)  - age:5.5week


title: OLs (80p)

source_name: Postnatal age day 17 GC Oligodendrocytes


title: Neurons P7 (81b)

source_name: Postnatal age day 7 Negative Neurons


title: Testis_NOA_ID-St01


title: OPCs (80o)

source_name: Postnatal age day 17 PDGFRa OPCs


title: Cultured Astroglia (79e)

source_name: Culture day 12 Culture Cultured Astroglia Astroglia


title: Astros P17 (72a)

source_name: Postnatal age day 17 Positive Astrocytes

tag: total RNA 100 nano-gram


title: N satisfaction N2 (N2S1)


title: Testis_NOA_ID29


title: Testis_NOA_ID27


title: N limitation N2 aerial (N2C1)


title: N limitation N2 aerial (N2C2)


title: Cultured Astroglia (69e)


title: N satisfaction NO3 1 (NO3S1)

treatment_protocol: Name:N_satisfaction_NO3_1 - growth conditions - nitrogen,nitrogen:time 4day . Nitrogen satisfaction : the major part of the root system is supplied with a solution containing NH4NO3 10mM and the minor part is fed with NO3- 1mM.The root system of six plants is split into two parts. The major root part is supplied with a nutrient solution containing NH4NO3 10mM whereas the minor part is supplied with NO3- 1mM. The nutrient solutions are renewed daily. After four days of this treatement of N-satisfaction, the root parts remained on NO3- 1mM are individually collected, weighted, immediately frozen and stored at minus 80 degre Celsius.


title: N limitation N2 aerial (L9_N2PAE1)


title: Testis_NOA_ID30


title: Neurons P16n (61d)

source_name: Postnatal age day 16 Neg (Bsl1) Neurons


title: N satisfaction NH4 1 (NH4S2)

treatment_protocol: Name:N_satisfaction_NH4_1 - growth conditions - nitrogen,nitrogen:time 4day . Nitrogen satisfaction : the major part of the root system is supplied with a solution containing NH4NO3 10mM and the minor part is fed with NH4plus 1mM.The root system of six plants is split into two parts. The major root part is supplied with a nutrient solution containing NH4NO3 10mM whereas the minor part is supplied with NH4plus 1mM. The nutrient solutions are renewed daily. After four days of this treatement of N-satisfaction, the root parts remained on NH4plus 1mM are individually collected, weighted, immediately frozen and stored at minus 80 degre Celsius.


title: Testis_NOA_ID28


title: Astros P7 (56a)


title: Testis_NOA_ID26


title: Testis_NOA_ID07


title: Testis_NOA_ID-St28


title: N satisfaction NH4 1 (NH4S1)


title: Testis_NOA_ID13


title: Testis_NOA_ID04


title: Testis_NOA_ID15


title: Testis_NOA_ID16


title: N limitation NO3 1 (NO3C1)


title: N limitation NH4 1 (NH4C1)

treatment_protocol: Name:N_limitation_NH4_1 - growth conditions - nitrogen,nitrogen:time 4day . Nitrogen limitation : the major part of the root system is privated of N and the minor part is fed with NH4plus 1mM.The root system of six plants is split into two parts. The major root part is supplied with nitrogen-free nutrient solution whereas the minor part is supplied with NH4plus 1mM. The nutrient solutions are renewed daily. After four days of this treatement of N-limitation, the root parts remained on NH4plus 1mM are individually collected, weighted, immediately frozen and stored at minus 80 degre Celsius.


title: N limitation NH4 1 (NH4C2)


title: Testis_NOA_ID03


title: Expression analysis of human neuroblastoma (Agilent)

city: Hiroshima

first: Eiso

last: Hiyama

state: Hiroshima

address: 1-2-3, Kasumi, Minami-ku

department: Natural Science Center for Basic Research and Deve

institute: Hiroshima University

description: Agilent Technologies, Tokyo, Japan), were compared using the same RNA sample extracted from a human neuroblastoma tissue sample.

hyb_protocol: The protocol and conditions used during hybridization, blocking and washing are provided in the following source: AgilentTM Low RNA Input Fluorescent Linear Amplification Kit Protocol.

scan_protocol: The Agilent microarray was scanned using an Agilent™ DNA Microarray Scanner and processed using Agilent™ Feature Extraction software ver. 9.1.

data_processing: Data processing Data were processed using functional ‘ON/OFF’ state of a gene.

source_name: human neuroblastoma tissue

label_protocol: The first-strand cDNA was generated from 0.5 μg of total RNA using reverse transcriptase and a T7 primer supplied in each labeling kit listed in 2-3), and then second-strand cDNA was produced using DNA polymerase mix and RNase H. cRNA (complementary RNA) was generated via an in vitro transcription reaction using T7 RNA polymerase and Cynine 3-CTP for the Agilent array. The synthesized cRNA was quantified by spectrometry and qualified using an Agilent 2100 BioanalyzerTM. The recommended amount of cRNA was then fragmented and hybridized to each array.

extract_protocol: Total RNA was extracted from the frozen tissue sample by the acid-guanidium-phenol chloroform method using RNA isolation kit according to the manufacturer’s instructions (Stratagene, Agilent techonology, Santa Clara , CA), and the quality of the RNA was checked using an Agilent Technologies 2100 Bioanalyzer (Agilent, Palo Alto, CA).

treatment_protocol: At surgery, right adrenal tumor and lymph node metastasis were resected. Then, small peccieces of primary tumor was picked up and frozen immediately until use.

tag: Tissue

tag: Gender

value: female

tag: Age

value: 13 months old

value: stage III unfavorable type neuroblastoma having developed in the adrenal gland

tag: Cells

value: neuroblastoma cells


title: Testis_NOA_ID19


title: Testis_NOA_ID06


title: N limitation NO3 aerial (L1_NO3PAE1)


title: Chicken liver 12th week Sample 10

status: Public on Dec 30 2007

description: Indigenous chicken liver samples hybridized with samll group of genes which related to lipid metabolism.

hyb_protocol: Two pmoles each of Cy3-labelled or Cy5-labelled sample in hybridization buffer was added to per isolated sub-array. cover the droplet with tiny cover slips with forceps, place the slide in a hybridization cassette and incubate the cassette for 16h at 42°C. washed in 2X SSC and 0.1% SDS (5 min, 55°C), 1X SSC and 0.1% SDS (5 min, 55°C), 0.1 X SSC (30sec, 3 X), and dried by centrifugation.

scan_protocol: Fluorescent array images were collected individually in each sub-array area for Cy3 or Cy5 in a GenePix 4000B fluorescent scanner (Axon Instruments, CA)

data_processing: Based on housekeeping genes that are relatively invariant for printed cDNA microarry as positive control, an edited normalization method using Fortran software was used for for all data processing

source_name: chicken Liver 12 weeks of age

label_protocol: For fluorescence labeling, 0.5 μl 1 M NaHCO3 and 1 μl Cy3 and Cy5 mono-reactive dyes (Amersham Pharmacia) in DMSO (Sigma) (10 μg/μl) were added to samples, respectively.  The reaction mixture was then incubated at 37°C for 2 hours in the dark then purified by QIAquick PCR Purification kit to remove unincorporated fluorophores.

extract_protocol: Tissue samples were ground with pestle in a mortar under liquid nitrogen.  Total RNA was extracted by using Trizol reagent from tissue powder, purified by using QIAquick PCR Purification kit.

tag: Breed

value: Beijing-You chicken

value: 12 week


title: Chicken liver 12th week Sample 11


title: Chicken liver 12th week Sample 12


title: Chicken liver 12th week Sample 6


title: Chicken liver 12th week Sample 5


title: Chicken liver 12th week Sample 3


title: Chicken liver 12th week Sample 9


title: Chicken liver 12th week Sample 4


title: Chicken liver 12th week Sample 2


title: Chicken liver 12th week Sample 7

hyb_protocol: Two pmoles each of Cy3-labelled or Cy5-labelled sample in hybridization buffer was added to per isolated sub-array. cover the droplet with tiny cover slips with forceps, place the slide in a hybridization cassette and incubate the cassette for 16h at 42°C.washed in 2X SSC and 0.1% SDS (5 min, 55°C), 1X SSC and 0.1% SDS (5 min, 55°C), 0.1 X SSC (30sec, 3 X), and dried by centrifugation.


title: HT29 resistant cells replicate 1

city: Barcelona

first: Carlos

middle: J

last: Ciudad

state: Barcelona

address: Av. Juan XXIII-27

department: Biochemistry and Molecular Biology

country: Spain

institute: University of Barcelona

description: gene expression profile of HT29 cells resistant to 10e-5M Methotrexate

hyb_protocol: Affymetrix protocol for HG U133 A 2.0

scan_protocol: Affymetrix protocol for HG U133 A 2.0

data_processing: Value generated using MAS 5.0 non-scaled.

source_name: HT29 cells resistant to 10e-5M methotrexate

label_protocol: Affymetrix protocol for HG U133 A 2.0

extract_protocol: RNeasy Mini kit from Qiagen

tag: colon cancer cell line resistant to 10e-5M methotrexate


title: N satisfaction NO3 1 (NO3S2)


title: Chicken liver 12th week Sample 1


title: Chicken liver 12th week Sample 8


title: HT29 resistant cells replicate 2


title: Testis_NOA_ID02


title: HT29 resistant cells replicate 3


title: HT29 sensitive cells replicate 1

description: gene expression profile of HT29 cells sensitive to Methotrexate

source_name: HT29 methotrexate sensitive cells

tag: colon cancer cell line.


title: HT29 sensitive replicate 2

tag: colon cancer cell line


title: HT29 sensitive replicate 3


title: Chicken liver 10th week Sample 11

source_name: chicken Liver 10 weeks of age

label_protocol: For fluorescence labeling, 0.5 μl 1 M NaHCO3 and 1 μl Cy3 or Cy5 mono-reactive dyes (Amersham Pharmacia) in DMSO (Sigma) (10 μg/μl) were added to samples, respectively.  The reaction mixture was then incubated at 37°C for 2 hours in the dark then purified by QIAquick PCR Purification kit to remove unincorporated fluorophores

value: 10 week


title: Chicken liver 10th week Sample 12


title: Chicken liver 10th week Sample 2


title: Chicken liver 10th week Sample 7


title: Chicken liver 10th week Sample 10


title: Chicken liver 10th week Sample 9


title: Chicken liver 10th week Sample 8


title: Chicken liver 10th week Sample 6


title: Chicken liver 10th week Sample 5


title: Chicken liver 10th week Sample 1


title: Chicken liver 10th week Sample 3


title: Chicken liver 8th week Sample 12

source_name: chicken Liver 8 weeks of age

value: 8 week


title: Chicken liver 10th week Sample 4


title: Chicken liver 8th week Sample 3


title: Chicken liver 8th week Sample 7


title: Chicken liver 8th week Sample 9


title: Chicken liver 8th week Sample 8


title: Chicken liver 8th week Sample 10


title: Chicken liver 8th week Sample 6


title: Chicken liver 6th week Sample 9

source_name: chicken Liver 6 weeks of age

value: 6 week


title: Chicken liver 6th week Sample 12


title: Chicken liver 8th week Sample 1


title: Chicken liver 6th week Sample 10


title: Chicken liver 8th week Sample 2


title: Chicken liver 6th week Sample 8


title: Chicken liver 6th week Sample 11


title: Chicken liver 6th week Sample 5

data_processing: Based onhousekeeping genes that are relatively invariant for printed cDNA microarry as positive control, an edited normalization method using Fortran software was used for for all data processing


title: Chicken liver 6th week Sample 6


title: Chicken liver 8th week Sample 11


title: Chicken liver 6th week Sample 2

label_protocol: For fluorescence labeling, 0.5 μl 1 M NaHCO3 and 1 μl Cy3 and Cy5 mono-reactive dyes (Amersham Pharmacia) in DMSO (Sigma) (10 μg/μl) were added to samples, respectively.  The reaction mixture was then incubated at 37°C for 2 hours in the dark then purified by QIAquick PCR Purification kit to remove unincorporated fluorophores


title: Chicken liver 6th week Sample 4


title: Chicken liver 6th week Sample 7


title: Chicken liver 8th week Sample 5


title: Chicken liver 6th week Sample 3


title: Chicken liver 8th week Sample 4


title: Exp_rpoS_rep2

status: Public on Dec 28 2007

city: Hamilton

first: Herb

middle: E

last: Schellhorn

address: 1280 Main St. W.,

department: Biology

institute: McMaster University

description: This study is to identify the RpoS regulon in MG1655 in early exponential growth. RNA samples from wild type or rpoS mutants were extracted using acidic hot phenol method and hybridized to Affymetrix E. coli Antisense Genome Array.

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: dChip invariant set normalization using (PM-MM) method; log2-transformation

organism: Escherichia coli K-12

source_name: Exponential growth of MG1655 rpoS mutants in LB at OD600 of 0.3

label_protocol: Affymetrix protocol

growth_protocol: Cells were grown in Luria Bertani (LB) media at 37oC at 200 rpm. Overnight cultures were inoculated with single, independent colonies in triplicate, incubated aerobically overnight at 37oC, and sub-cultured to a starting OD600 of 0.0001. Cultures were harvested at an OD600 = 0.3 after being maintained in exponential phase for at least eight generations.

extract_protocol: Acidic Hot Phenol

tag: rpoS mutant


title: Exp_rpoS_rep3


title: Exp_WT_rep3

source_name: Exponential growth of MG1655 wild type in LB at OD600 of 0.3

tag: wild type


title: Exp_rpoS_rep1


title: N limitation NO3 1 (NO3C2)


title: Chicken liver 6th week Sample 1


title: Cont MO

status: Public on Dec 29 2007

city: Wuhan

first: Jie

last: Mei

state: Hubei

address: 7# Donghu South Road

department: Chinese Academy of Sciences

country: China

institute: Institute of Hydrobiology

description: Gene expression data from embryos at 24 hpf injected with control Morpholino (five mismatch DrC1q-like MO)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 37°C on Affymetrix GeneChip Zebrafish Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArrayTM scanner 3000.

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 500.

organism: Danio rerio

source_name: zebrafish embryos at 24 hpf

label_protocol: cRNAs were generated and hybridized on Affymetrix DNA chips according to the Affymetrix protocol, total RNA (8 μg) was used to prepare double-stranded cDNA with the one-cycle cDNA synthesis kit (Affymetrix, USA). The cDNA was then used as a template to synthesize a biotinylated cRNA (16 hr, 37°C) with the IVT kit (Affymetrix, USA). In vitro transcription products were purified with the IVT cleanup module and approximately 35 μg of cRNA were treated with the fragmentation buffer (35' at 94°C).

growth_protocol: A breeding colony of zebrafish (Danio rerio) were maintained at 28.5°C on a 14 h (hour) light/10 h dark cycle

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

treatment_protocol: For injection, MOs were at a concentration of about 5ng each embryo. After injection, embryos were incubated at 28.5°C in Embryo Medium. The embryos at 24 hpf were washed with PBS and extracted RNA with Trizol

tag: AB line


title: MO

description: Gene expression data from embryos at 24 hpf injected with DrC1q-like Morpholino


title: Exp_WT_rep2


title: Exp_WT_rep1


title: WT_totalRNA_2_R

city: La Jolla

first: Joseph

middle: R.

last: Ecker

address: 10010 N. Torrey Pines Road

department: Genomic Analysis Laboratory

institute: The Salk Institute

description: Empty vector control for estradiol-specific effects

hyb_protocol: Whole Genome Tiling Array  was hybridized for 16 hrs, washed and stained with a streptavidin-phycoerythrin conjugate on the Affymetrix Fluidics Station 450 according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned on Affymetrix Scanner G7

data_processing: Gene chip data files were processed usingTileMap.

organism: Arabidopsis thaliana

source_name: whole plant tissue germinated and grown for ~6 days on 8 uM of 17beta-estradiol (Sigma), added from the 8 mM stock in DMSO

label_protocol: Fifteen ug of total RNA was used to synthesize double-stranded cDNA using the GeneChip One-Cycle cDNA Synthesis Kit (Affymetrix). Biotin-labeled cRNA was generated by in vitro transcription using the GeneChip IVT Labeling Kit (Affymetrix),

growth_protocol: plant tissue germinated and grown for ~6 days on DMSO under 16 hours light, 8 hours dark at 25 degrees C

extract_protocol: total RNA was isolated from whole plant tissues using TRIzol reagent following instructions from the manufacturer (Invitrogen)

treatment_protocol: DMSO

tag: Contains empty vector


title: csl4_totalRNA_2_F

description: csl4-2 mutant plants

source_name: whole plant tissue germinated and grown for ~6 days plant growth medium

growth_protocol: plant tissue germinated and grown for ~6 days on plant growth medium under 16 hours light, 8 hours dark at 25 degrees C

treatment_protocol: plant growth medium

tag: Contains mutation in CSL4 locus


title: rrp41_totalRNA_1_R

description: Mock depleted for RRP41

source_name: whole plant tissue germinated and grown for ~6 days on DMSO as a control

tag: Contains vector that targets exosome subunit RRP41 for RNAi-mediated genetic depletion


title: csl4_totalRNA_1_R

description: csl4-2 mutant plants


title: rrp41_totalRNA_2_F

description: Mock depleted for RRP41


title: rrp4est_totalRNA_2_R

description: Depleted for RRP4

growth_protocol: plant tissue germinated and grown for ~6 days on 8 uM of 17beta-estradiol (Sigma), added from the 8 mM stock in DMSO under 16 hours light, 8 hours dark at 25 degrees C

treatment_protocol: 8 uM of 17beta-estradiol (Sigma)

tag: Contains vector that targets exosome subunit RRP4 for RNAi-mediated genetic depletion


title: rrp41est_totalRNA_1_F

description: Depleted for RRP41


title: rrp41_totalRNA_2_R

description: Mock depleted for RRP41


title: ws_totalRNA_1_R

description: Arabidopsis ecotype WS plants

tag: Arabidopsis ecotype WS plants


title: csl4_totalRNA_1_F

description: csl4-2 mutant plants


title: rrp4_totalRNA_2_F

description: Mock depleted for RRP4


title: ws_totalRNA_2_R

description: Arabidopsis ecotype WS plants


title: csl4_totalRNA_2_R

description: csl4-2 mutant plants


title: WT_totalRNA_1_F


title: rrp41est_totalRNA_2_F

description: Depleted for RRP41


title: WTest_totalRNA_2_F


title: rrp4est_totalRNA_2_F

description: Depleted for RRP4


title: WT_totalRNA_2_F


title: WTest_totalRNA_2_R


title: rrp4_totalRNA_1_R

description: Mock depleted for RRP4


title: BY4742  Non-Quiescent KGD1

status: Public on Dec 27 2007

city: Albuquerque

first: Sushmita

last: Roy

state: NM

institute: Biology, University of New Mexico

description: Yeast

hyb_protocol: The Cy5 and Cy3 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and re-suspended in 30 µl of the hybridization solution.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 6.0 analysis software. After background correction and removal of flagged values, log base 2 expression ratios were normalized to exogonus controls.

data_processing: After background correction based on negative controls and removal of flaged valuse, data was normalized to Arabidopsis thaliana controls.

source_name: BY4742 Non-Quiescent KGD1

label_protocol: RNA (20 µg) was annealed with 2 µg oligo dT, and reverse-transcribed into cDNA with Superscript II reverse transcriptase for 2h at 42°C in the presence of 0.5 mM dGTP, 0.25 mM dCTP, 0.5 mM dATP, 0.5 mM dTTP. RNA was degraded using RNase H and RNase A.

extract_protocol: Cells were collected as quiescent or non-quiescent cell fractions. All RNA isolation was accomplished with a modified Gentra protocol followed by Qiagen RNeasy Mini Kit reagents. As a control, exponential and stationary phase RNA were mixed 1:1.

tag: BY4742 Non-Quiescent KGD1

tag: As a control Yeast stationary phase and Exponental mix 1:1


title: BY4742  Non-Quiescent MDH1

description: Yeast

source_name: BY4742 Non-Quiescent MDH1

tag: BY4742 Non-Quiescent MDH1

source_name: Yeast stationary phase and Exponental mix 1:1


title: rrp4_totalRNA_1_F

description: Mock depleted for RRP4


title: BY4742  Non-Quiescent JEN1

description: Yeast

source_name: BY4742 Non-Quiescent JEN1

tag: BY4742 Non-Quiescent JEN1


title: rrp41est_totalRNA_2_R

description: Depleted for RRP41


title: BY4742  Non-Quiescent HSP26

description: Yeast

source_name: BY4742 Non-Quiescent HSP26

tag: BY4742 Non-Quiescent HSP26


title: BY4742  Non-Quiescent MOH1

description: Yeast

source_name: BY4742 Non-Quiescent MOH1

tag: BY4742 Non-Quiescent MOH1


title: ws_totalRNA_1_F

description: Arabidopsis ecotype WS plants


title: WTest_totalRNA_1_R


title: BY4742  Non-Quiescent MLS1

description: Yeast

source_name: BY4742 Non-Quiescent MLS1

tag: BY4742 Non-Quiescent MLS1


title: BY4742  Non-Quiescent HBT1

description: Yeast

source_name: BY4742 Non-Quiescent HBT1

tag: BY4742 Non-Quiescent HBT1


title: WT_totalRNA_1_R


title: rrp41_totalRNA_1_F

description: Mock depleted for RRP41


title: WTest_totalRNA_1_F


title: BY4742  Non-Quiescent HAP4

description: Yeast

source_name: BY4742 Non-Quiescent HAP4

tag: BY4742 Non-Quiescent HAP4


title: BY4742  Non-Quiescent HSP12

description: Yeast

source_name: BY4742 Non-Quiescent HSP12

tag: BY4742 Non-Quiescent HSP12


title: BY4742  Non-Quiescent GUT2

description: Yeast

source_name: BY4742 Non-Quiescent GUT2

tag: BY4742 Non-Quiescent GUT2


title: BY4742  Non-Quiescent GPG1

description: Yeast

source_name: BY4742 Non-Quiescent GPG1

tag: BY4742 Non-Quiescent GPG1


title: BY4742  Non-Quiescent MPM1

description: Yeast

source_name: BY4742 Non-Quiescent MPM1

tag: BY4742 Non-Quiescent MPM1


title: BY4742  Non-Quiescent GPD1

description: Yeast

source_name: BY4742 Non-Quiescent GPD1

tag: BY4742 Non-Quiescent GPD1


title: BY4742  Non-Quiescent GAT2

description: Yeast

source_name: BY4742 Non-Quiescent GAT2

tag: BY4742 Non-Quiescent GAT2


title: BY4742  Non-Quiescent GAD1

description: Yeast

source_name: BY4742 Non-Quiescent GAD1

tag: BY4742 Non-Quiescent GAD1


title: BY4742  Non-Quiescent GIS1

description: Yeast

source_name: BY4742 Non-Quiescent GIS1

tag: BY4742 Non-Quiescent GIS1


title: rrp4_totalRNA_2_R

description: Mock depleted for RRP4

source_name: whole plant tissue germinated and grown for ~6 days on DMSO as a control

tag: Contains vector that targets exosome subunit RRP4 for RNAi-mediated genetic depletion


title: BY4742  Non-Quiescent GRE1

description: Yeast

source_name: BY4742 Non-Quiescent GRE1

tag: BY4742 Non-Quiescent GRE1

tag: As a control Yeast stationary phase and Exponental mix 1:1


title: rrp41est_totalRNA_1_R

description: Depleted for RRP41

source_name: whole plant tissue germinated and grown for ~6 days on 8 uM of 17beta-estradiol (Sigma), added from the 8 mM stock in DMSO

tag: Contains vector that targets exosome subunit RRP41 for RNAi-mediated genetic depletion


title: BY4742  Non-Quiescent FMP21

description: Yeast

source_name: BY4742 Non-Quiescent FMP21

tag: BY4742 Non-Quiescent FMP21

source_name: Yeast stationary phase and Exponental mix 1:1


title: BY4742  Non-Quiescent ETR1

description: Yeast

source_name: BY4742 Non-Quiescent ETR1

tag: BY4742 Non-Quiescent ETR1


title: BY4742  Non-Quiescent FMP16

description: Yeast

source_name: BY4742 Non-Quiescent FMP16

tag: BY4742 Non-Quiescent FMP16


title: BY4742  Non-Quiescent DOA4

description: Yeast

source_name: BY4742 Non-Quiescent DOA4

tag: BY4742 Non-Quiescent DOA4


title: BY4742  Non-Quiescent GTT1

description: Yeast

source_name: BY4742 Non-Quiescent GTT1

tag: BY4742 Non-Quiescent GTT1


title: BY4742  Non-Quiescent HXT5

description: Yeast

source_name: BY4742 Non-Quiescent HXT5

tag: BY4742 Non-Quiescent HXT5


title: BY4742  Non-Quiescent FAA1

description: Yeast

source_name: BY4742 Non-Quiescent FAA1

tag: BY4742 Non-Quiescent FAA1


title: BY4742  Non-Quiescent DDR2

description: Yeast

source_name: BY4742 Non-Quiescent DDR2

tag: BY4742 Non-Quiescent DDR2


title: BY4742  Non-Quiescent FBP1

description: Yeast

source_name: BY4742 Non-Quiescent FBP1

tag: BY4742 Non-Quiescent FBP1


title: BY4742  Non-Quiescent CTA1

description: Yeast

source_name: BY4742 Non-Quiescent CTA1

tag: BY4742 Non-Quiescent CTA1


title: BY4742  Non-Quiescent FMP45

description: Yeast

source_name: BY4742 Non-Quiescent FMP45

tag: BY4742 Non-Quiescent FMP45


title: BY4742  Non-Quiescent CTT1

description: Yeast

source_name: BY4742 Non-Quiescent CTT1

tag: BY4742 Non-Quiescent CTT1


title: BY4742  Non-Quiescent COR1

description: Yeast

source_name: BY4742 Non-Quiescent COR1

tag: BY4742 Non-Quiescent COR1


title: BY4742  Non-Quiescent CIT2

description: Yeast

source_name: BY4742 Non-Quiescent CIT2

tag: BY4742 Non-Quiescent CIT2


title: BY4742  Non-Quiescent COX7

description: Yeast

source_name: BY4742 Non-Quiescent COX7

tag: BY4742 Non-Quiescent COX7


title: BY4742  Non-Quiescent ATP2

description: Yeast

source_name: BY4742 Non-Quiescent ATP2

tag: BY4742 Non-Quiescent ATP2

tag: As a control Yeast stationary phase and Exponental mix 1:1


title: BY4742  Non-Quiescent COX6

description: Yeast

source_name: BY4742 Non-Quiescent COX6

tag: BY4742 Non-Quiescent COX6


title: BY4742  Non-Quiescent HSP30

description: Yeast

source_name: BY4742 Non-Quiescent HSP30

tag: BY4742 Non-Quiescent HSP30

source_name: Yeast stationary phase and Exponental mix 1:1


title: BY4742  Non-Quiescent CIT1

description: Yeast

source_name: BY4742 Non-Quiescent CIT1

tag: BY4742 Non-Quiescent CIT1


title: BY4742  Non-Quiescent ALD4

description: Yeast

source_name: BY4742 Non-Quiescent ALD4

tag: BY4742 Non-Quiescent ALD4


title: BY4742  Non-Quiescent ATP1

description: Yeast

source_name: BY4742 Non-Quiescent ATP1

tag: BY4742 Non-Quiescent ATP1


title: BY4742  Non-Quiescent ALD3

description: Yeast

source_name: BY4742 Non-Quiescent ALD3

tag: BY4742 Non-Quiescent ALD3


title: BY4742  Non-Quiescent ATP3

description: Yeast

source_name: BY4742 Non-Quiescent ATP3

tag: BY4742 Non-Quiescent ATP3


title: BY4742  Non-Quiescent ADH2

description: Yeast

source_name: BY4742 Non-Quiescent ADH2

tag: BY4742 Non-Quiescent ADH2


title: BY4742  Non-Quiescent ALD2

description: Yeast

source_name: BY4742 Non-Quiescent ALD2

tag: BY4742 Non-Quiescent ALD2


title: BY4742  Non-Quiescent YLR327C

description: Yeast

source_name: BY4742 Non-Quiescent YLR327C

tag: BY4742 Non-Quiescent YLR327C


title: ws_totalRNA_2_F

description: Arabidopsis ecotype WS plants

source_name: whole plant tissue germinated and grown for ~6 days plant growth medium

tag: Arabidopsis ecotype WS plants


title: BY4742  Non-Quiescent AGX1

description: Yeast

source_name: BY4742 Non-Quiescent AGX1

tag: BY4742 Non-Quiescent AGX1


title: BY4742  Non-Quiescent YGR043C

description: Yeast

source_name: BY4742 Non-Quiescent YGR043C

tag: BY4742 Non-Quiescent YGR043C


title: BY4742  Non-Quiescent YLR312C

description: Yeast

source_name: BY4742 Non-Quiescent YLR312C

tag: BY4742 Non-Quiescent YLR312C


title: BY4742  Non-Quiescent YDR262W

description: Yeast

source_name: BY4742 Non-Quiescent YDR262W

tag: BY4742 Non-Quiescent YDR262W


title: BY4742  Non-Quiescent COX8

description: Yeast

source_name: BY4742 Non-Quiescent COX8

tag: BY4742 Non-Quiescent COX8


title: BY4742  Non-Quiescent YBR230C

description: Yeast

source_name: BY4742 Non-Quiescent YBR230C

tag: BY4742 Non-Quiescent YBR230C

tag: As a control Yeast stationary phase and Exponental mix 1:1


title: BY4742  Non-Quiescent YHR097C

description: Yeast

source_name: BY4742 Non-Quiescent YHR097C

tag: BY4742 Non-Quiescent YHR097C


title: BY4742  Non-Quiescent YHR138C

description: Yeast

source_name: BY4742 Non-Quiescent YHR138C

tag: BY4742 Non-Quiescent YHR138C

source_name: Yeast stationary phase and Exponental mix 1:1


title: BY4742  Non-Quiescent YPL230W

description: Yeast

source_name: BY4742 Non-Quiescent YPL230W

tag: BY4742 Non-Quiescent YPL230W


title: BY4742  Non-Quiescent YDL218W

description: Yeast

source_name: BY4742 Non-Quiescent YDL218W

tag: BY4742 Non-Quiescent YDL218W


title: BY4742  Non-Quiescent ADY2

description: Yeast

source_name: BY4742 Non-Quiescent ADY2

tag: BY4742 Non-Quiescent ADY2


title: BY4742  Non-Quiescent ACS1

description: Yeast

source_name: BY4742 Non-Quiescent ACS1

tag: BY4742 Non-Quiescent ACS1


title: BY4742  Non-Quiescent YBR056W

description: Yeast

source_name: BY4742 Non-Quiescent YBR056W

tag: BY4742 Non-Quiescent YBR056W


title: BY4742  Non-Quiescent YBL048W

description: Yeast

source_name: BY4742 Non-Quiescent YBL048W

tag: BY4742 Non-Quiescent YBL048W


title: rrp4est_totalRNA_1_F

description: Depleted for RRP4

source_name: whole plant tissue germinated and grown for ~6 days on 8 uM of 17beta-estradiol (Sigma), added from the 8 mM stock in DMSO

tag: Contains vector that targets exosome subunit RRP4 for RNAi-mediated genetic depletion


title: rrp4est_totalRNA_1_R

description: Depleted for RRP4


title: BY4742  Non-Quiescent SSP100

description: Yeast

source_name: BY4742 Non-Quiescent SSP100

tag: BY4742 Non-Quiescent SSP100


title: BY4742  Quiescent YMR31

description: Yeast

source_name: BY4742 Quiescent YMR31

tag: BY4742 Quiescent YMR31


title: BY4742  Quiescent SPI1

description: Yeast

source_name: BY4742 Quiescent SPI1

tag: BY4742 Quiescent SPI1


title: BY4742  Quiescent YAT1

description: Yeast

source_name: BY4742 Quiescent YAT1

tag: BY4742 Quiescent YAT1


title: BY4742  Quiescent SIP18

description: Yeast

source_name: BY4742 Quiescent SIP18

tag: BY4742 Quiescent SIP18


title: BY4742  Quiescent RTN2

description: Yeast

source_name: BY4742 Quiescent RTN2

tag: BY4742 Quiescent RTN2


title: BY4742  Quiescent SPS100

description: Yeast

source_name: BY4742 Quiescent SPS100

tag: BY4742 Quiescent SPS100


title: BY4742  Quiescent SFA1

description: Yeast

source_name: BY4742 Quiescent SFA1

tag: BY4742 Quiescent SFA1

tag: As a control Yeast stationary phase and Exponental mix 1:1


title: BY4742  Quiescent SPG1

description: Yeast

source_name: BY4742 Quiescent SPG1

tag: BY4742 Quiescent SPG1


title: BY4742  Quiescent POR1

description: Yeast

source_name: BY4742 Quiescent POR1

tag: BY4742 Quiescent POR1

source_name: Yeast stationary phase and Exponental mix 1:1


title: BY4742  Quiescent SPG3

description: Yeast

source_name: BY4742 Quiescent SPG3

tag: BY4742 Quiescent SPG3


title: BY4742  Quiescent SNA2

description: Yeast

source_name: BY4742 Quiescent SNA2

tag: BY4742 Quiescent SNA2


title: BY4742  Quiescent SDH2

description: Yeast

source_name: BY4742 Quiescent SDH2

tag: BY4742 Quiescent SDH2


title: BY4742  Quiescent POT1

description: Yeast

source_name: BY4742 Quiescent POT1

tag: BY4742 Quiescent POT1


title: BY4742  Quiescent SNZ1

description: Yeast

source_name: BY4742 Quiescent SNZ1

tag: BY4742 Quiescent SNZ1


title: BY4742  Quiescent QCR8

description: Yeast

source_name: BY4742 Quiescent QCR8

tag: BY4742 Quiescent QCR8


title: BY4742  Quiescent SPG5

description: Yeast

source_name: BY4742 Quiescent SPG5

tag: BY4742 Quiescent SPG5


title: BY4742  Quiescent SPG4

description: Yeast

source_name: BY4742 Quiescent SPG4

tag: BY4742 Quiescent SPG4


title: BY4742  Quiescent PBI2

description: Yeast

source_name: BY4742 Quiescent PBI2

tag: BY4742 Quiescent PBI2


title: BY4742  Quiescent PNC1

description: Yeast

source_name: BY4742 Quiescent PNC1

tag: BY4742 Quiescent PNC1


title: BY4742  Quiescent SDS24

description: Yeast

source_name: BY4742 Quiescent SDS24

tag: BY4742 Quiescent SDS24


title: BY4742  Quiescent PST2

description: Yeast

source_name: BY4742 Quiescent PST2

tag: BY4742 Quiescent PST2


title: BY4742  Quiescent OM45

description: Yeast

source_name: BY4742 Quiescent OM45

tag: BY4742 Quiescent OM45


title: BY4742  Quiescent PCK1

description: Yeast

source_name: BY4742 Quiescent PCK1

tag: BY4742 Quiescent PCK1


title: BY4742  Quiescent NAT1

description: Yeast

source_name: BY4742 Quiescent NAT1

tag: BY4742 Quiescent NAT1

tag: As a control Yeast stationary phase and Exponental mix 1:1


title: BY4742  Quiescent MLS1

description: Yeast

source_name: BY4742 Quiescent MLS1

tag: BY4742 Quiescent MLS1


title: BY4742  Quiescent JEN1

description: Yeast

source_name: BY4742 Quiescent JEN1

tag: BY4742 Quiescent JEN1

source_name: Yeast stationary phase and Exponental mix 1:1


title: BY4742  Quiescent MSC1

description: Yeast

source_name: BY4742 Quiescent MSC1

tag: BY4742 Quiescent MSC1


title: BY4742  Quiescent HSP104

description: Yeast

source_name: BY4742 Quiescent HSP104

tag: BY4742 Quiescent HSP104


title: BY4742  Quiescent MPM1

description: Yeast

source_name: BY4742 Quiescent MPM1

tag: BY4742 Quiescent MPM1


title: BY4742  Quiescent NGR1

description: Yeast

source_name: BY4742 Quiescent NGR1

tag: BY4742 Quiescent NGR1


title: BY4742  Quiescent GUT2

description: Yeast

source_name: BY4742 Quiescent GUT2

tag: BY4742 Quiescent GUT2


title: BY4742  Quiescent MOH1

description: Yeast

source_name: BY4742 Quiescent MOH1

tag: BY4742 Quiescent MOH1


title: BY4742  Quiescent HSP12

description: Yeast

source_name: BY4742 Quiescent HSP12

tag: BY4742 Quiescent HSP12


title: BY4742  Quiescent ODC1

description: Yeast

source_name: BY4742 Quiescent ODC1

tag: BY4742 Quiescent ODC1


title: BY4742  Quiescent HAP4

description: Yeast

source_name: BY4742 Quiescent HAP4

tag: BY4742 Quiescent HAP4


title: BY4742  Quiescent HSP30

description: Yeast

source_name: BY4742 Quiescent HSP30

tag: BY4742 Quiescent HSP30


title: BY4742  Quiescent HSP26

description: Yeast

source_name: BY4742 Quiescent HSP26

tag: BY4742 Quiescent HSP26


title: BY4742  Quiescent HXT5

description: Yeast

source_name: BY4742 Quiescent HXT5

tag: BY4742 Quiescent HXT5


title: BY4742  Non-Quiescent ATG8

description: Yeast

source_name: BY4742 Non-Quiescent ATG8

tag: BY4742 Non-Quiescent ATG8


title: BY4742  Quiescent GTT1

description: Yeast

source_name: BY4742 Quiescent GTT1

tag: BY4742 Quiescent GTT1


title: BY4742  Non-Quiescent ATP18

description: Yeast

source_name: BY4742 Non-Quiescent ATP18

tag: BY4742 Non-Quiescent ATP18

tag: As a control Yeast stationary phase and Exponental mix 1:1


title: BY4742  Quiescent HBT1

description: Yeast

source_name: BY4742 Quiescent HBT1

tag: BY4742 Quiescent HBT1


title: BY4742  Quiescent HXK1

description: Yeast

source_name: BY4742 Quiescent HXK1

tag: BY4742 Quiescent HXK1

source_name: Yeast stationary phase and Exponental mix 1:1


title: BY4742  Quiescent GID8

description: Yeast

source_name: BY4742 Quiescent GID8

tag: BY4742 Quiescent GID8


title: BY4742  Quiescent GPD1

description: Yeast

source_name: BY4742 Quiescent GPD1

tag: BY4742 Quiescent GPD1


title: BY4742  Quiescent GPG1

description: Yeast

source_name: BY4742 Quiescent GPG1

tag: BY4742 Quiescent GPG1


title: BY4742  Quiescent GAT2

description: Yeast

source_name: BY4742 Quiescent GAT2

tag: BY4742 Quiescent GAT2


title: BY4742  Quiescent GLK1

description: Yeast

source_name: BY4742 Quiescent GLK1

tag: BY4742 Quiescent GLK1


title: BY4742  Quiescent GRE1

description: Yeast

source_name: BY4742 Quiescent GRE1

tag: BY4742 Quiescent GRE1


title: BY4742  Quiescent GIS1

description: Yeast

source_name: BY4742 Quiescent GIS1

tag: BY4742 Quiescent GIS1


title: BY4742  Quiescent FAA1

description: Yeast

source_name: BY4742 Quiescent FAA1

tag: BY4742 Quiescent FAA1


title: BY4742  Quiescent DDR2

description: Yeast

source_name: BY4742 Quiescent DDR2

tag: BY4742 Quiescent DDR2


title: BY4742  Quiescent CTA1

description: Yeast

source_name: BY4742 Quiescent CTA1

tag: BY4742 Quiescent CTA1


title: BY4742  Quiescent ATG8

description: Yeast

source_name: BY4742 Quiescent ATG8

tag: BY4742 Quiescent ATG8


title: BY4742  Quiescent DOA4

description: Yeast

source_name: BY4742 Quiescent DOA4

tag: BY4742 Quiescent DOA4


title: BY4742  Quiescent GAD1

description: Yeast

source_name: BY4742 Quiescent GAD1

tag: BY4742 Quiescent GAD1


title: BY4742  Quiescent COX8

description: Yeast

source_name: BY4742 Quiescent COX8

tag: BY4742 Quiescent COX8


title: BY4742  Quiescent ATP18

description: Yeast

source_name: BY4742 Quiescent ATP18

tag: BY4742 Quiescent ATP18

tag: As a control Yeast stationary phase and Exponental mix 1:1


title: BY4742  Quiescent ETR1

description: Yeast

source_name: BY4742 Quiescent ETR1

tag: BY4742 Quiescent ETR1


title: BY4742  Quiescent FBP1

description: Yeast

source_name: BY4742 Quiescent FBP1

tag: BY4742 Quiescent FBP1

source_name: Yeast stationary phase and Exponental mix 1:1


title: BY4742  Quiescent CTT1

description: Yeast

source_name: BY4742 Quiescent CTT1

tag: BY4742 Quiescent CTT1


title: BY4742  Quiescent FMP45

description: Yeast

source_name: BY4742 Quiescent FMP45

tag: BY4742 Quiescent FMP45


title: BY4742  Quiescent ATP2

description: Yeast

source_name: BY4742 Quiescent ATP2

tag: BY4742 Quiescent ATP2


title: BY4742  Quiescent CIT2

description: Yeast

source_name: BY4742 Quiescent CIT2

tag: BY4742 Quiescent CIT2


title: BY4742  Quiescent ADY2

description: Yeast

source_name: BY4742 Quiescent ADY2

tag: BY4742 Quiescent ADY2


title: BY4742  Quiescent AGX1

description: Yeast

source_name: BY4742 Quiescent AGX1

tag: BY4742 Quiescent AGX1


title: BY4742  Quiescent TIP1

description: Yeast

source_name: BY4742 Quiescent TIP1

tag: BY4742 Quiescent TIP1


title: BY4742  Non-Quiescent HSP104

description: Yeast

source_name: BY4742 Non-Quiescent HSP104

tag: BY4742 Non-Quiescent HSP104


title: BY4742  Quiescent ALD2

description: Yeast

source_name: BY4742 Quiescent ALD2

tag: BY4742 Quiescent ALD2


title: BY4742  Quiescent ADH2

description: Yeast

source_name: BY4742 Quiescent ADH2

tag: BY4742 Quiescent ADH2


title: BY4742  Quiescent YPL230W

description: Yeast

source_name: BY4742 Quiescent YPL230W

tag: BY4742 Quiescent YPL230W


title: BY4742  Quiescent XBP1

description: Yeast

source_name: BY4742 Quiescent XBP1

tag: BY4742 Quiescent XBP1


title: BY4742  Quiescent ALD3

description: Yeast

source_name: BY4742 Quiescent ALD3

tag: BY4742 Quiescent ALD3


title: BY4742  Quiescent YLR327C

description: Yeast

source_name: BY4742 Quiescent YLR327C

tag: BY4742 Quiescent YLR327C


title: BY4742  Quiescent YLR312C

description: Yeast

source_name: BY4742 Quiescent YLR312C

tag: BY4742 Quiescent YLR312C

tag: As a control Yeast stationary phase and Exponental mix 1:1


title: BY4742  Quiescent YHR138C

description: Yeast

source_name: BY4742 Quiescent YHR138C

tag: BY4742 Quiescent YHR138C


title: BY4742  Quiescent YDR262W

description: Yeast

source_name: BY4742 Quiescent YDR262W

tag: BY4742 Quiescent YDR262W

source_name: Yeast stationary phase and Exponental mix 1:1


title: BY4742  Quiescent YGR043C

description: Yeast

source_name: BY4742 Quiescent YGR043C

tag: BY4742 Quiescent YGR043C


title: BY4742  Quiescent YDL218W

description: Yeast

source_name: BY4742 Quiescent YDL218W

tag: BY4742 Quiescent YDL218W


title: BY4742  Quiescent FMP16

description: Yeast

source_name: BY4742 Quiescent FMP16

tag: BY4742 Quiescent FMP16


title: BY4742  Quiescent YBR056W

description: Yeast

source_name: BY4742 Quiescent YBR056W

tag: BY4742 Quiescent YBR056W


title: BY4742  Quiescent YHR097C

description: Yeast

source_name: BY4742 Quiescent YHR097C

tag: BY4742 Quiescent YHR097C


title: BY4742  Quiescent YBL048W

description: Yeast

source_name: BY4742 Quiescent YBL048W

tag: BY4742 Quiescent YBL048W


title: BY4742 Non-quiescent time   (Replicate 10)

description: Yeast

source_name: BY4742 Non-quiescent time

tag: BY4742 Non-quiescent


title: BY4742 Non-quiescent time   (Replicate 2)

description: Yeast


title: BY4742  Quiescent YBR230C

description: Yeast

source_name: BY4742 Quiescent YBR230C

tag: BY4742 Quiescent YBR230C


title: BY4742 Non-quiescent time   (Replicate 6)

description: Yeast


title: BY4742 Non-quiescent time   (Replicate 7)

description: Yeast


title: BY4742 Non-quiescent time   (Replicate 9)

description: Yeast


title: BY4742 Non-quiescent time   (Replicate 4)

description: Yeast


title: BY4742 Non-quiescent time   (Replicate 5)

description: Yeast


title: BY4742 Non-quiescent time   (Replicate 3)

description: Yeast


title: BY4742 Non-quiescent time   (Replicate 8)

description: Yeast


title: BY4742 Quiescent time   (Replicate 10)

description: Yeast

source_name: BY4742 Quiescent time

tag: BY4742 Quiescent


title: BY4742 Quiescent time   (Replicate 5)

description: Yeast


title: BY4742 Non-quiescent time   (Replicate 1)

description: Yeast


title: BY4742 Quiescent time   (Replicate 8)

description: Yeast


title: BY4742 Quiescent time   (Replicate 6)

description: Yeast


title: BY4742 Quiescent time   (Replicate 9)

description: Yeast


title: BY4742 Quiescent time   (Replicate 2)

description: Yeast


title: BY4742 Quiescent time   (Replicate 7)

description: Yeast


title: BY4742 Quiescent time   (Replicate 4)

description: Yeast


title: BY4742 Quiescent time   (Replicate 3)

description: Yeast


title: BY4742  Non-Quiescent-Replicate YMR31

description: Yeast

source_name: BY4742 Non-Quiescent-Replicate YMR31

tag: BY4742 Non-Quiescent-Replicate YMR31


title: BY4742  Non-Quiescent-Replicate YLR327C

description: Yeast

source_name: BY4742 Non-Quiescent-Replicate YLR327C

tag: BY4742 Non-Quiescent-Replicate YLR327C


title: BY4742  Non-Quiescent-Replicate YHR097C

description: Yeast

source_name: BY4742 Non-Quiescent-Replicate YHR097C

tag: BY4742 Non-Quiescent-Replicate YHR097C


title: BY4742  Quiescent ALD4

description: Yeast

source_name: BY4742 Quiescent ALD4

tag: BY4742 Quiescent ALD4


title: BY4742  Non-Quiescent-Replicate YPL230W

description: Yeast

source_name: BY4742 Non-Quiescent-Replicate YPL230W

tag: BY4742 Non-Quiescent-Replicate YPL230W


title: BY4742 Quiescent time   (Replicate 1)

description: Yeast

tag: As a control Yeast stationary phase and Exponental mix 1:1


title: BY4742  Non-Quiescent-Replicate YHR138C

description: Yeast

source_name: BY4742 Non-Quiescent-Replicate YHR138C

tag: BY4742 Non-Quiescent-Replicate YHR138C


title: BY4742  Non-Quiescent-Replicate YLR312C

description: Yeast

source_name: BY4742 Non-Quiescent-Replicate YLR312C

tag: BY4742 Non-Quiescent-Replicate YLR312C


title: BY4742  Non-Quiescent-Replicate YBL048W

description: Yeast

source_name: BY4742 Non-Quiescent-Replicate YBL048W

tag: BY4742 Non-Quiescent-Replicate YBL048W

source_name: Yeast stationary phase and Exponental mix 1:1


title: BY4742  Non-Quiescent-Replicate YDR262W

description: Yeast

source_name: BY4742 Non-Quiescent-Replicate YDR262W

tag: BY4742 Non-Quiescent-Replicate YDR262W


title: BY4742  Non-Quiescent-Replicate YAT1

description: Yeast

source_name: BY4742 Non-Quiescent-Replicate YAT1

tag: BY4742 Non-Quiescent-Replicate YAT1


title: BY4742  Non-Quiescent-Replicate YDL218W

description: Yeast

source_name: BY4742 Non-Quiescent-Replicate YDL218W

tag: BY4742 Non-Quiescent-Replicate YDL218W


title: BY4742  Non-Quiescent-Replicate SPS100

description: Yeast

source_name: BY4742 Non-Quiescent-Replicate SPS100

tag: BY4742 Non-Quiescent-Replicate SPS100


title: BY4742  Non-Quiescent-Replicate TIP1

description: Yeast

source_name: BY4742 Non-Quiescent-Replicate TIP1

tag: BY4742 Non-Quiescent-Replicate TIP1