title: Fruit 147 DAFB replicate1-3

status: Public on Oct 12 2010

city: Tsukuba

first: Chikako

last: Nishitani

state: Ibaraki

institute: National Institutes of Fruit Tree Science

description:
merged replicates:
147DAFB_1
147DAFB_2
147DAFB_3

hyb_protocol: The labeled samples were hybridized to the oligoarray slides using Gene Expression Hybridization Kit (Agilent, Palo Alto, CA) as a hybridization buffer at 65°C for 17 h in a hybridization chamber. After hybridization, arrays were washed with Gene Expression Wash Buffer (Agilent, Palo Alto, CA) according to the manufacturer’s instructions.

scan_protocol: The dried slides were scanned by Agilent scanner. Raw data from scanning of the array was captured using Agilent Feature Extraction Ver. 9.5.1 (with Linear & Lowess normalization).

data_processing: Normalization was performed by GeneSpring Ver. 7.3.1 (Agilent, Palo Alto, CA). Expression for each gene was calculated as the mean value of two to three biological replicates for all time points and the standard error of the mean. Per-chip and per-gene normalization was performed.

organism: Pyrus pyrifolia

source_name: Fruit 147 DAFB

label_protocol: Reverse transcription of mRNA in the total RNA samples and composition of labeled cDNA was performed using Low RNA Input Linear Amplification Kit PLUS, One-Color (Agilent, Palo Alto, CA) according to the manufacturer’s instructions.

growth_protocol: Japanese pear trees (Pyrus pyrifolia Nakai cv. ‘Housui’) were managed according to standard orchard practices.

extract_protocol: Total RNAs were extracted from each sample using the method described in Wan et al. (1994). Isolated RNA was purified using the RNeasy Mini Kit (Qiagen, Hilden, Germany) and the quality and purity were checked using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA). RNA was ethanol precipitated and resuspended to 500 ng/μl.

treatment_protocol: Not treated.

tag: common name

value: Hosui Asian Pear

value: flesh

value: 147 days after full bloom


title: Fruit 133 DAFB replicate1-3

type: RNA

country: Japan

description:
merged replicates:
133DAFB_1
133DAFB_2
133DAFB_3

molecule: total RNA

source_name: Fruit 133 DAFB

tag: tissue

tag: age

value: 133 days after full bloom


title: Fruit 119 DAFB replicate1-2

description:
merged replicates:
119DAFB_1
119DAFB_2

source_name: Fruit 119 DAFB

value: 119 days after full bloom


title: adipose_tissue_calorie-restriction_rep3

city: Tsu

first: oka

last: takehiko

state: Mie

address: 2-174 Edobashi

department: Graduate School of Medicine

institute: mie university

description: Gene expression after 2week calorie-restriction in obesity model zebrafish

hyb_protocol: 1.5 ug of Cy3-labelled cRNA was fragmented following the manufacturers instructions. On completion of the fragmentation reaction, 250 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Zebrafish Whole Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by air spray

scan_protocol: The hybridized microarrays were scanned using a scanner (Agilent G2565BA)

data_processing: The scanned images were analyzed with Feature Extraction software (Agilent). Bad probes were removed based on gIsFeatNonUnifOL,gIsPosAndSignif and gIsWellAboveBG

organism: Danio rerio

source_name: adipose_tissue, 2week calorie-restriction after 8week over-feeding

label_protocol: Three hundred nanograms of total RNA was converted into labeled cRNA using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent) and Cy3-labeled cRNA (1.5 micrograms) were prepared according to manufacture’s protocol

extract_protocol: Visceral adipose tissued were stained by nile red and were collected by surgical manipulation under a fluorescence microscope. These tissue were stored in RNA-later (Ambion). Total RNA were extracted using RNeasy Mini Kit (Qiagen) and were quantified using a spectrophotometer (NanoDrop ND-100)

value: Visceral adipose tissue

tag: gender

value: male


title: adipose_tissue_8week_over-feeding_rep3

description: Gene expression after 8 week over feeding in zebrafish

source_name: adipose_tissue, 8week over-feeding


title: Glycine soja, young leaves, standard condition, replicate 1

status: Public on Oct 13 2010

city: Harbin

first: Yanming

last: Zhu

state: Heilongjiang

address: Wood Street 59

department: Life sciences

country: China

institute: Northeast Agriculture University

description:
Gene expression data from Glycine soja leaves of 21 days old without stress.
0h_leaf_r1

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

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The computation of expression values was conducted using dChip software. Sample wise normalization to the median probe cell intensity (CEL) of all 14 arrays. Model-based gene expression was obtained from normalized CEL intensities based on a Perfect Match-only model.

label: biotin

organism: Glycine soja

source_name: leaf at 0h as control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Glycine soja seeds were grown in a culture room with 60 % relative humidity, 24℃ and a light regime of 12h light/12h dark. Germinated seedlings were grown in the growth boxes containing 1/4 strength Hoagland's solution.

extract_protocol: Total RNA was extracted from frozen leaves with TRIzol (Invitrogen, Carlsbad, CA) according to the instructions from the manufacturer.

treatment_protocol: 21-day-old seedlings were transferred into the growth boxes containing 1/4 strength Hoagland’s solution with 50mmol/L NaHCO3 (pH 8.5).

tag: line

value: leaf

value: 21 days after germination

tag: treatment

value: control

tag: time


title: Fruit 105 DAFB replicate1-3

description:
merged replicates:
105DAFB_1
105DAFB_2
105DAFB_3

source_name: Fruit 105 DAFB

value: 105 days after full bloom


title: Fruit 140 DAFB replicate1-3

description:
merged replicates:
140DAFB_1
140DAFB_2
140DAFB_3

source_name: Fruit 140 DAFB

value: 140 days after full bloom


title: adipose_tissue_8week_over-feeding_rep4


title: AA nucleosomes/Genomic DNA

type: genomic

city: Bethesda

first: Carl

last: Wu

state: MD

address: 37 Convent Dr, 6068

department: LBMB

country: USA

institute: NIH/NCI

description:
normalized/scaled VALUE presented in data table below is AA_raw x 0.82 - 0.344 = AA_Norm
raw' value presented in data table below is direct Alexa555/Alexa647 ratio

hyb_protocol: 0.625 µg of Total DNA (Alexa 555), 0.625 µg of AA DNA (Alexa 555), 0.5 µg of AZ DNA (Alexa 555), 0.25 µg of ZZ DNA (Alexa 555), and 0.25 µg of Z-total DNA (Alexa 555) were hybridized to microarrays in the presence of 1.25 µg of MNase-treated genomic DNA control (Alexa647), 0.045 mg/mL human Cot-1 DNA, 1x Agilent blocking agent, and 1x Agilent hybridization buffer. Hybridization was performed at 65 ˚C for 40 hr. Microarrays were washed with 6% SSPE, 0.005% N-Lauroylsarosine (5 min) and with 0.06% SSPE, 0.005% N-Lauroylsarosine (5 min) before Agilent stabilization solution treatment.

scan_protocol: Microarrays were scanned with the Agilent G2565CA scanner at 2-micron resolution. The feature extraction protocol ChIP_105_Jan09 was used.

data_processing:
The microarray data for the different nucleosomal species vary greatly in their intensity, largely due the vastly different prevalence of the various species. To facilitate direct comparison of the different species we normalized these data as follows. First, an average distribution profile (N=466) of each nucleosomal species in and around the center of +1 nucleosomes was generated (Jiang and Pugh, Genome Biology, 2009). These profiles were transformed by a “leveling factor” such that at the minimum of the NFR region (i.e. 110 bp upstream of the +1 nucleosome center) was set to zero. Second, nonlinear least squares curve fitting (MATLAB function “lsqnonlin”) was used to generate “scaling factors” for both the AA and Z-total profiles such that their sum best fits the Total nucleosome profile. Scaling factors were similarly applied to the AZ and ZZ profiles generating a sum of the two profiles that best fits the Z-total profile.
Raw: direct ratio of green processed signal/red processed signal. Norm: (green processed signal/red processed signal)*scaling factor - leveling factor [see description]

label: Alexa 555

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: G1-arrested yJL036 yeast cells

label_protocol: Nucleosomal DNA and MNase-treated genomic DNA control were amplified by ligation-mediated PCR. Labeling was performed using the BioPrime Plus labeling kit (Invitrogen) according to the manufacturer’s protocol.

growth_protocol: The yeast strain yJL036 (BY4741 htz1::HTZ1-3xFLAG-kanMX bar1∆::hisG) were grown to an OD600 of 0.35 in YPD before arrest with 1 mg/L alpha mating factor for 90 min. Cells were then crosslinked with 3% paraformaldehyde for 15 min at 30˚C and harvested by centrifugation at 2,400 xg.

extract_protocol: Formaldehyde-fixed nucleosomes prepared from G1-arrested haploid cells bearing the HTZ1-FLAG gene were diluted 10-fold in buffer F [20 mM HEPES-KOH (pH 7.6), 1 mM EDTA, 80 mM KCl, 1x PI] and were incubated with anti-Flag M2 agarose (Sigma) (40 µL bead slurry per mL) for 4 hr. The bead-bound materials, which were enriched for the AZ and ZZ nucleosomes, were washed once with buffer G (buffer F + 220 mM KCl + 0.01% NP-40) and eluted with buffer H [buffer G + 0.5 µg/µL 3x Flag peptides (Sigma) + 0.09% NP-40 + 0.1% deoxycholate] giving the anti-Flag (Z-total) fraction. The flow-through fraction, which was enriched for AA nucleosomes, was subjected to anti-H2A IP (according to Katou et al. Methods Enzymol, 2006) yielding the AA fraction. To separate the AZ nucleosomes from the ZZ nucleosomes, the Z-total fraction was diluted with equal volume of buffer J [25 mM HEPES-KOH (pH 7.6), 1 mM EDTA, 0.01% NP-40, 1x PI] and incubated with one-tenth volume of anti-H2A antibodies (Active Motif) and one-forth slurry volume of nProtein-A sepharose beads (GE Healthcare). After washing with Buffer K (25 mM HEPES-KOH (pH 7.6), 1 mM EDTA, 0.01% NP-40, 150 mM NaCl, 1x Protease inhibitor), the bound materials were eluted with buffer L (400 mM NaCl, 10 mM EDTA, 0.5% SDS, 0.125 µg/µL Glycogen, 0.4 µg/µL Proteinase K) at 55˚C for 1 hr giving the AZ fraction. The DNA from the purified nucleosomal species was decrosslinked by heating at 65˚C overnight and deproteinated by proteinase K (Invitrogen). After RNase treatment, the DNA was purified with the QIAquick column (Qiagen).

treatment_protocol: Fixed cells were pre-incubated with buffer A [100 mM Tris-HCl (pH 9.4), 10 mM DTT] for 10 min and digested with 250 U/mL Lyticase (Sigma) in buffer B [50 mM potassium phosphate at pH 7.5, 0.6 M sorbitol, 10 mM DTT, 2x Complete EDTA-free protease inhibitors (PI, Roche)] at 30˚C for 30 min. After washing in buffer C [100 mM KCl, 50 mM HEPES-KOH (pH 7.6), 2.5 mM MgCl2, 0.4 M sorbitol, 2x PI], the spheroplasts were resuspended in equal volume of ice-cold buffer E [80 mM KCl, 50 mM HEPES-KOH (pH 7.6), 2.5 mM MgCl2, 0.25% Triton X-100, 2x PI] and lysed with a Dounce homogenizer. Crude chromatin was obtained by centrifugation of the lysate over a 30% (w/v) sucrose cushion in buffer E (minus Triton X-100) at 13,000 xg for 10 min and was washed once in buffer E. Nuclease digestion of chromatin was performed in buffer E containing 1 mM CaCl2 and 2 U/µL micrococcal nuclease (MNase, Worthington) at 37 ˚C for ~20 min and was stopped with 10 mM EGTA. Soluble nucleosomes were collected after centrifugation at 20,400 xg for 5 min and were cleared by passage through an Ultrafree-CL, GV 0.22 µm filter unit (Millipore).

tag: strain

tag: sample type

value: Mnase-treated nucleosomal DNA

tag: sample subtype

value: AA nucleosomes

label: Alexa 647

value: Mnase-treated genomic DNA


title: adipose_tissue_calorie-restriction_rep2


title: adipose_tissue_calorie-restriction_rep4


title: adipose_tissue_8week_over-feeding_rep2


title: Total nucleosomes/Genomic DNA

description:
normalized/scaled VALUE presented in data table below is Total_raw x 1 - 0.512 = Total_Norm
raw' value presented in data table below is direct Alexa555/Alexa647 ratio

value: Total nucleosomes


title: ZZ nucleosomes/Genomic DNA

description:
normalized/scaled VALUE presented in data table below is ZZ_raw x 0.036 - 0.074 = ZZ_Norm
raw' value presented in data table below is direct Alexa555/Alexa647 ratio

value: ZZ nucleosomes


title: adipose_tissue_1week_over-feeding_rep1

description: Gene expression after 1 week over feeding in zebrafish

source_name: adipose_tissue, 1week over-feeding


title: adipose_tissue_calorie-restriction_rep1


title: adipose_tissue_1week_over-feeding_rep3


title: adipose_tissue_1week_over-feeding_rep2


title: adipose_tissue_8week_over-feeding_rep1


title: H2A.Z-containing nucleosomes/Genomic DNA

description:
normalized/scaled VALUE presented in data table below is Z-total_raw x 0.14 - 0.151 = Z-total_Norm
raw' value presented in data table below is direct Alexa555/Alexa647 ratio

value: H2A.Z-containing nucleosomes


title: adipose_tissue_1week_over-feeding_rep4


title: AZ nucleosomes/Genomic DNA

description:
normalized/scaled VALUE presented in data table below is AZ_raw x 0.097 - 0.079 = AZ_Norm
raw' value presented in data table below is direct Alexa555/Alexa647 ratio

value: AZ nucleosomes


title: AR113Q-3-Cy5_Vs_Reference-Cy3

city: Mississauga

first: Ashley

last: Monks

state: Ontario

address: 3359 Mississauga Road

department: Dept. of Psychology

country: Canada

institute: University of Toronto

description: This hybridization compared a sample from limb muscles of AR113Q-Knock In transgenic mice with RNA reference from limb muscles of 10 wild type C57BL/6 mice (5 of males and 5 of females).

hyb_protocol: The labelled cDNA was combined with 75 µL of hybridization solution composed of 20:1:1 volume fraction DIG EasyHyb (Roche Diagnostics, Laval, Que.), 10 mg yeast tRNA/mL, and 10 mgsalmon sperm DNA/mL. Target cDNAs were denatured at 65 °C (5 min), allowed to cool slightly, and applied to the microarrays. The arrays were sealed in hybridization chambers (Corning) before incubation in a 37 °C water bath for 18 h. Coverslips were removed after submerging the slides in plastic Coplin jars containing 1× SSC/0.1% SDS at 50 °C. The slides were washed (three times for 15 min each) in Coplin jars containing fresh 1× SSC/ 0.1% SDS in a 50 °C water bath, with occasional swirling. Slides were then repeatedly dipped in 1× SSC and then 0.1× SSC, both at room temperature. Liquid was quickly removed from the slide surface by blowing compressed air at a downward angle onto the vertically held slide.

scan_protocol: Microarrays were scanned at a 10-µm resolution with a ScanArray 4000 system (GSI Lumonics/Perkin Elmer), using both blue and red lasers. The 16-bit TIFF images were saved and pre-processed and quantified with GenePix 5 software (Axon Instruments, Inc., CA). The adaptive quantification algorithm was used.

data_processing: Data analysis was performed with GeneTraffic Duo 2.5 (Iobion Informatics LLC, La Jolla, Calif.). The data were normalized using the Lowess algorithm at the subgrid level while ignoring flagged values. After normalization of data, average values were taken for statistical analysis. Gene lists were filtered in GeneTraffic to include only those genes that displayed at least 1.4-fold difference and whose coefficient of variance was less than 100% and p-value small than 0.05. Hierarchical cluster analysis and significant analysis of microarrays were performed in GeneTraffic DUO using the Pearson algorithm and average linkage.

organism: Mus musculus

source_name: Total RNA from 10 of wild type mice as RNA reference

label_protocol: Cyanine (Cy) dyes were directly incorporated into cDNA synthesized from 40 µg of total RNA. RNA was mixed with 1x SuperScript II first-strand buffer (Invitrogen); 10 mmol/L DTT; 150 pmol dT20VN primer; 50 µmol/L dCTP (Amersham Biosciences); 25 µmol/L Cy3-dCTP (Perkin Elmer); and  RNase-free water, up to a volume of 38 µL. The reactions were heated to 65 °C for 5 min, then 42 °C for 5 min, and SuperScript II reverse transcriptase (400 U, Invitrogen) was added, and cDNA synthesis was carried out for 3 h at 42 °C.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions from limb muscles.

treatment_protocol: Limb muscles from 10 of wild type C57BL/6 mice (5 of males and 5 of females) were used for the extraction of RNA reference

value: Male and Female

value: 70 days

value: Limb Muscles

source_name: Total RNA from AR113Q-Knock In mice-3

label_protocol: Cyanine (Cy) dyes were directly incorporated into cDNA synthesized from 40 µg of total RNA. RNA was mixed with 1x SuperScript II first-strand buffer (Invitrogen); 10 mmol/L DTT; 150 pmol dT20VN primer; 50 µmol/L dCTP (Amersham Biosciences); 25 µmol/L Cy5-dCTP (Perkin Elmer); and  RNase-free water, up to a volume of 38 µL. The reactions were heated to 65 °C for 5 min, then 42 °C for 5 min, and SuperScript II reverse transcriptase (400 U, Invitrogen) was added, and cDNA synthesis was carried out for 3 h at 42 °C.

treatment_protocol: Limb muscles from male transgenic AR113Q-Knock In mice.

value: Transgenic AR113Q-Knock In mice

value: Male

value: 100 days


title: EZH2siRNA_4

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48803 probes on the Human-6 beadChip ver. 3 were used.

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-12 V3.0 expression beadchip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions

data_processing: Array data processing were performed on Illumina BeadStudio software (version 3.2). We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to a data matrix, Sample Gene Profile option of this software was used.

label: Biotin

organism: Homo sapiens

source_name: siRNA-transfected SKOV3 cell line

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina. TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)

tag: protocol

value: EZH2 siRNA


title: WT-2-Cy5_Vs_Reference-Cy3

description: This hybridization compared a sample from limb muscles of wild type mice with RNA reference from limb muscles of 10 wild type C57BL/6 mice (5 of males and 5 of females).

treatment_protocol: Limb muscles from 10 of wild type C57BL/6 mice (5 of males and 5 of females) were used for the extraction of RNA reference.

source_name: Total RNA from WT mice-2

treatment_protocol: Limb muscles from WT mouse were used for the extraction of RNA.

value: Wild type C57BL/6 mice

value: 108 days


title: EZH2siRNA_3


title: AR113Q-2-Cy5_Vs_Reference-Cy3

source_name: Total RNA from AR113Q-Knock In mice-2


title: CTLsiRNA_4

value: scrambled siRNA


title: pupa_adult

city: Shanghai

first: Shuai

last: Zhan

address: 300 Fenglin Road

institute: Shanghai Institutes for Biological Sciences

description: pupa vs adult

hyb_protocol: Agilent 8*15k two-color microarray system

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

organism: Bombyx mori

source_name: pupa

growth_protocol: silkworm reared at 25 degree, feeding fresh mullberry

extract_protocol: total RNA was extracted by Trizol (Invitrogen)

treatment_protocol: natural live, no treatment

tag: developmental stage

value: pupa

source_name: adult

value: adult


title: 13688455 - C4TS-2 vs LVL2-2

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Determine the level of expresison in transgenic plants expressing geminviral gene silencing suppressors.

hyb_protocol: LVL2-2 Cy5 / C4TS-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,500V,laser power 35%, Cy5:635nm,pmt voltage 500V,laser power 30%

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

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: whole plant - Media=soil hygrometry=not controlled Temperature=22:C Light=8h light-16h darkness

treatment_protocol: no treatment

tag: transgene

value: control

tag: ecotype

value: Columbia

tag: harvest date

value: whole plant


title: CTLsiRNA_2


title: EZH2siRNA_1


title: larva_pupa

description: larva vs pupa

scan_protocol: Agilent 8*15k two-color microarray system

source_name: larva

value: larva


title: HSA-AR-1-Cy5_Vs_Reference-Cy3

description: This hybridization compared a sample from limb muscles of HAS-AR transgenic mice with RNA reference from limb muscles of 10 wild type C57BL/6 mice (5 of males and 5 of females).

data_processing: Data analysis was performed with GeneTraffic Duo 2.5 (Iobion Informatics LLC, La Jolla, Calif.). The data were normalized using the Lowess algorithm at the subgrid level while ignoring flagged values. After normalization of data, average values were taken for statistical analysis. Gene lists were filtered in GeneTraffic to include only those genes that displayed at least 2-fold difference and whose coefficient of variance was less than 100% and p-value small than 0.05. Hierarchical cluster analysis and significant analysis of microarrays were performed in GeneTraffic DUO using the Pearson algorithm and average linkage.

source_name: Total RNA from HAS-AR transgenic mice-1

treatment_protocol: Limb muscles from HAS-AR transgenic mice were used for the extraction of RNA.

value: Transgenic L141 mice

value: 129 days


title: EZH2siRNA_2


title: HSA-AR-2-Cy5_Vs_Reference-Cy3

value: Male and Female

value: 70 days

source_name: Total RNA from HAS-AR transgenic mice-2

treatment_protocol: Limb muscles from HAS-AR transgenic mice were used for the extraction of RNA

value: Transgenic L141


title: egg_larva

description: egg vs larva

source_name: egg

label_protocol: Agilent 8*15k two-color microarray system

value: egg


title: 13688456 - LVL2-3 vs V2BC-3

hyb_protocol: V2BC-3 Cy5 / LVL2-3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: CTLsiRNA_3


title: WT-1-Cy5_Vs_Reference-Cy3

value: Limb Muscles

source_name: Total RNA from WT mice-1

value: Male


title: 13756850 - LVL2-1 vs C4TS-1

hyb_protocol: C4TS-1 Cy5 / LVL2-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13756851 - C4TS-1 vs LVL2-1

hyb_protocol: LVL2-1 Cy5 / C4TS-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688453 - LVL2-2 vs C4TS-2

hyb_protocol: C4TS-2 Cy5 / LVL2-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: CTLsiRNA_1


title: 13688457 - V2BC-3 vs LVL2-3

hyb_protocol: LVL2-3 Cy5 / V2BC-3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688454 - C4TS-3 vs LVL2-3

hyb_protocol: LVL2-3 Cy5 / C4TS-3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: SKOV3ip_4

source_name: untransfected SKOV3 cell line

value: no siRNA


title: UACC control

city: Madrid

first: Beatriz

last: Martinez

address: Calle Melchor Fernandez Almagro 3

department: Human Cancer Genetics

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

description: UACC control

hyb_protocol: For each hybridization, Cy 3 labeled cRNA (reference) and 1ug of Cy 5 labeled cRNA (carriers or controls) were mixed, fragmented and hybridized to to an Agilent 44 K Whole Human genome Oligo Microarray . After hybridization, slides were washed sequential

scan_protocol: Microarrays were scanned using an Agilent DNA microarray scanner

data_processing: Agilent feature extraction software (version 9.5.3) was run on all array datasets using the GE2-v5_95_Feb07 protocol.  Lowess  and quantiles were applied for intra-array and  between array normalization respectively.

source_name: pool

label_protocol: 500ng of total RNA was reversed transcribed to double-strand cDNA using a poly dT-T7 promoter primer. At first, template RNA and quality-control transcripts of known concentration and quality were first denatured at 650C for 10 min and incubated for 2 hours at 400C with 5xfirst strand Buffer, 0.1 M DTT, 10 mM dNTP, MMLV RT, and RNase-out. The MMLV RT enzyme was inactivated at 650C for 15 min. cDNA products were then used as templates for in vitro transcription to generate fluorescent cRNA. cDNA products were mixed with a transcription master mix in the presence of T7 RNA  polymerase and Cyanine 5 (Cy5) labeled or Cyanine 3 (Cy3) labeled-CTP and incubated at 400C for 2 hours.

growth_protocol: The breast cancer cell lines were cultured in RPMI-1640 containing 10% fetal bovine serum with the exception of MDA MB 157 normal human fibroblasts being cultured in Dulbecco Modified Eagle’s Medium (DMEM/F12) supplemented with 10% fetal serum  and maintained at 37ºC in 5% CO2. All media were supplemented with fungizone, and penicillin/streptomycin. Cells were routinely grown at 37ºC with 5% CO2 content.

extract_protocol: Total RNA from untreated and 17-AAG treated cell lines at 24 h and 48 h was extracted using the TriReagent  following the manufacturers’ instructions and purified using QIAGEN’s Rneasy mini spin columns

treatment_protocol: Cells were seeded in 10cm dishes  at a moderate density in 20 ml complete medium. At 24h after plating, cells were treated with 17-AAG (500nM) or DMSO (0.1%) as a control. At appropriate intervals 24H, 48H upon treatment with the drug, cells were harvested and cell pellets frozen for downstream experiments

value: Universal Human Reference RNA (from Stratagene, Cat Nr:740000)

source_name: UACC control

tag: cell line

value: UACC

value: Control


title: SKOV3ip_3


title: 13688450 - LVL2-3 vs C4TS-3

hyb_protocol: C4TS-3 Cy5 / LVL2-3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: SKOV3ip_2


title: UACC 24H

description: UACC 24H

source_name: UACC 24H


title: 13688448 - C2TS-3 vs LVL2-3

hyb_protocol: LVL2-3 Cy5 / C2TS-3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: AR97Q-2-Cy5_Vs_WT5-Cy3

description: This hybridization compared a sample from limb muscles of AR97Q transgenic mice with RNA from wild type mice.

source_name: Total RNA from wild type mice-5

treatment_protocol: Limb muscles from wild type mice were used for the extraction of RNA reference.

value: 100 days

source_name: Total RNA from AR97Q transgenic mice-2

treatment_protocol: Limb muscles from male AR97Q transgenic mice.

value: AR97Q transgenic mice


title: SKOV3ip_1


title: T47D Control

description: T47D Control

source_name: T47D Control


title: 13688446 - V2BC-2 vs LVL2-2

hyb_protocol: LVL2-2 Cy5 / V2BC-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: control

value: Columbia


title: Time 50% infection  17XL

city: Barcelona

first: Susana

last: Kalko

state: BARCELONA

address: c/Rosello 153

department: Bioinformatics Platform

institute: IDIBAPS

description:
Gene expression spleen at 50% peripheral parasitemia with the lethal P. yoelii 17XL strain.
Cy5_P50

hyb_protocol: 1.5 ug of Cy3-  (specific activity >10.0 pmol Cy3/ug cRNA) and Cy5-labeled cRNA were fragmented at 60°C for 30 minutes in a reaction volume of 250 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (GPL2872) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the GenePix 4000 scanner.

data_processing: Bioconductor limma package, using background correction (normexp) and quantiles normalization between arrays for final values. Cy3 and Cy5 channels are normalized values as separate channels for every GPR file.

source_name: spleen, 50% parasitemia, lethal 17XL strain

label_protocol: Cyanine-3 (Cy3) or Cyanine-5 (Cy5) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Parasites from either strain were injected IP into Balb/c mice and daily parasitemia was monitored by Giemsa staining.

extract_protocol: Total RNA was extracted using the Trizol reagent as described in (http://www.medsci.uu.se/klinfarm/arrayplatform/TRIzol_Method%20(2).pdf). The protocol includes lysis of red and white blood cells and DNase digestion.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: BALB/c

value: spleen

value: female

value: 6-8 weeks


title: AR97Q-1-Cy5_Vs_WT4-Cy3

source_name: Total RNA from wild type mice-4

treatment_protocol: Limb muscles from wild type mice were used for the extraction of RNA reference

source_name: Total RNA from AR97Q transgenic mice-1


title: AR97Q-3-Cy5_Vs_WT6-Cy3

source_name: Total RNA from wild type mice-6

treatment_protocol: Limb muscles from wild type were used for the extraction of RNA reference

source_name: Total RNA from AR97Q transgenic mice-3


title: T47D 48H

description: T47D 48H


title: K_STA15

city: Stanford

first: Li

last: Li

state: CA

address: 300 pastuer dr.,

department: Pediatric

institute: Stanford University

hyb_protocol: 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays. 2. Equilibrate probe array to room temperature immediately before use. 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block. 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa. 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation. 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes. 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture. 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2). 9. Place probe array into the hybridization oven, set to 45°C. 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm. 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.

scan_protocol: 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run. 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list. 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required. 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner. 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam. • Pixel value = 3 μm • Wavelength = 570 nm If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed. 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode. 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.

data_processing: Dchip MBEI processing, quantile-quantile normalization

source_name: STA15 kidney allograft biopsy, stable

label_protocol: GeneChip One-cycle target labeling and control reagents

extract_protocol: For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).

tag: stable


title: T47D 24H

description: T47D 24H


title: 13688444 - LVL2-2 vs V2BC-2

hyb_protocol: V2BC-2 Cy5 / LVL2-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: whole plant


title: 13688447 - LVL2-3 vs C2TS-3

hyb_protocol: C2TS-3 Cy5 / LVL2-3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: UACC 48H

description: UACC 48H

source_name: UACC 48H


title: MCF7 24H 2

description: MCF7 24H

source_name: MCF7 24H


title: K_STA9

source_name: STA9_ kidney allograft biopsy, stable


title: MCF7 48H 2

description: MCF7 48H

source_name: MCF7 48H


title: K_STA17

source_name: STA17 kidney allograft biopsy, stable


title: WT-3-Cy5_Vs_Reference-Cy3

hyb_protocol: The labelled cDNA was combined with 75 µL of hybridization solution composed of 20:1:1 volume fraction DIG EasyHyb (Roche Diagnostics, Laval, Que.), 10 mg yeast tRNA/mL, and 10 mgsalmon sperm DNA/mL. Target cDNAs were denatured at 65 °C (5 min), allowed to cool slightly, and applied to the microarrays. The arrays were sealed in hybridization chambers (Corning) before incubation in a 37 °C water bath for 18 h. Coverslips were removed after submerging the slides in plastic Coplin jars containing 1× SSC/0.1% SDS at 50 °C. The slides were washed (three times for 15 min each) in Coplin jars containing fresh 1× SSC/ 0.1% SDS in a 50 °C water bath, with occasional swirling. Slides were then repeatedly dipped in 1× SSC and then 0.1× SSC, both at room temperature. Liquid was quickly removed from the slide surface by blowing compressed air at a downward angle onto the vertically held slide.

source_name: Total RNA from 10 of wild type mice as RNA reference

label_protocol: Cyanine (Cy) dyes were directly incorporated into cDNA synthesized from 40 µg of total RNA. RNA was mixed with 1x SuperScript II first-strand buffer (Invitrogen); 10 mmol/L DTT; 150 pmol dT20VN primer; 50 µmol/L dCTP (Amersham Biosciences); 25 µmol/L Cy3- or Cy5-dCTP (Perkin Elmer); and  RNase-free water, up to a volume of 38 µL. The reactions were heated to 65 °C for 5 min, then 42 °C for 5 min, and SuperScript II reverse transcriptase (400 U, Invitrogen) was added, and cDNA synthesis was carried out for 3 h at 42 °C.

value: Male and Female

value: 70 days

source_name: Total RNA from WT mice-3

treatment_protocol: Limb muscles from WT mice were used for the extraction of RNA.


title: Time 10% infection 17XL

description:
Gene expression spleen at 10% peripheral parasitemia with the lethal P. yoelii 17XL strain.
Cy5_P10

source_name: spleen, 10% parasitemia, lethal 17XL strain


title: HSA-AR-3-Cy5_Vs_Reference-Cy3

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

value: Limb Muscles

source_name: Total RNA from HAS-AR transgenic mice-3

value: HAS-AR transgenic L141 mice


title: MCF7 Control

description: MCF7 Control

source_name: pool

source_name: MCF7 Control


title: 13688442 - C2TS-2 vs LVL2-2

hyb_protocol: LVL2-2 Cy5 / C2TS-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: MCF7 24H 1

description: MCF 7 24H

source_name: MCF 7 24H


title: K_STA10

source_name: STA10 kidney allograft biopsy, stable


title: 13688438 - V2BC-1 vs LVL2-1

hyb_protocol: LVL2-1 Cy5 / V2BC-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688441 - LVL2-2 vs C2TS-2

hyb_protocol: C2TS-2 Cy5 / LVL2-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Time 4  17XL

description:
Gene expression spleen after 4 days post-infection with the lethal P. yoelii 17XL strain.
Cy5_D4

source_name: spleen, day 4 post-infection, lethal 17XL strain


title: Time 5  17XL

description:
Gene expression spleen after 5 days post-infection with the lethal P. yoelii 17XL strain.
Cy5_D5

source_name: spleen, day 5 post-infection, lethal 17XL strain


title: MCF7 48H 1

description: MCF 7 48H

source_name: MCF 7 48H


title: K_AR4

source_name: AR4 kidney allograft biopsy, acute rejection

tag: acute rejection

tag: banff classification

value: Grade 1B


title: K_AR10

source_name: AR10 kidney allograft biopsy, acute rejection

value: Grade 11A


title: K_AR3

source_name: AR3 kidney allograft biopsy, acute rejection


title: 13688022 - LVL2-1 vs V2BC-1

hyb_protocol: V2BC-1 Cy5 / LVL2-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: tissue


title: Time 3 17XL

description:
Gene expression spleen after 3 days post-infection with the lethal P. yoelii 17XL strain.
Cy5_D3

source_name: spleen, day 3 post-infection, lethal 17XL strain

tag: gender

tag: age


title: 13688021 - C2TS-1 vs LVL2-1

hyb_protocol: LVL2-1 Cy5 / C2TS-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: whole plant - Media=soil hygrometry=not controlled Temperature=22: Light=8h light-16h darkness


title: MBA MD 436 24H

description: MBA Md 436 24H

value: Universal Human Reference RNA (from Stratagene, Cat Nr:740000)

source_name: MBA Md 436 24H

value: MBA MD 436

tag: treatment


title: K_AR5

source_name: AR5 kidney allograft biopsy, acute rejection


title: 13688020 - LVL2-1 vs C2TS-1

hyb_protocol: C2TS-1 Cy5 / LVL2-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Time 50% infection  17X

description:
Gene expression spleen at 50% peripheral parasitemia with the non-lethal P. yoelii 17X strain.
Cy3_P50

source_name: spleen, 50% parasitemia, non-lethal 17X strain


title: Time 0  17XL

description:
Gene expression normal spleen 0h infection.
Cy5_C0

source_name: spleen, control 2, 0h


title: K_AR15

source_name: AR15 kidney allograft biopsy, acute rejection

value: Grade 1A


title: MBA MD 436 48H

description: MBA MD 436 48H

source_name: MBA MD 436 48H

tag: time


title: K_AR1

source_name: AR1 kidney allograft biopsy, acute rejection


title: K_STA16

source_name: STA16 kidney allograft biopsy, stable


title: rat femur on day 56 post-ablation G9.56D.19-224

city: Chicago

first: Amarjit

middle: S.

last: Virdi

state: IL

address: 600 South Paulina, Armour Academic Facility, Suite 507

department: Anatomy and Cell Biology

institute: Rush University Medical Center

description: Gene expression data from total RNA extracted from rat femur marrow tissue on Day 56 post-ablation

hyb_protocol: Total RNA from the samples was hybridized according to the standard Affymetrix protocol (GeneChip® Expression Analysis Technical Manual, 2005, Affymetrix), using a GeneChip® Hybridization Oven and a GeneChip® Fluidics Station.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 enabled for High-Resolution Scanning. Data acquisition from the microarrays also required the use of Affymetrix GeneChip® Command Console® Software (AGCC).

data_processing: The raw gene expression data from Affymetrix were available in the form of binary CEL (Affymetrix cell intensity) files. The open-source integrated software system BRB-ArrayTools (Dr. Richard Simon and BRB-ArrayTools Development Team) was used and the CEL files were collated with RMA (robust multi-array average) method and “affy” R/Bioconductor package to compute probeset summaries. This utilized a three-step approach of background correction on PM (Perfect Match) data, quantile normalization, and Tukey’s median polish algorithm for summarization of probe level data. A univariate F-test (with random variance model) with a significance threshold of p<1×10-3 (an appropriately stringent significant level to reduce the chance of false positives) was performed with BRB-ArrayTools and used to determine differentially expressed gene probe sets over all time points. A univariate two-sample T-test with significance threshold of p<1×10-3 BRB-ArrayTools was further used to determine significant gene lists of gene probe sets differentially expression on each time point (day 1, 3, 7, 10, 14, 28, and 56 vs. day 0 intact control) post-ablation.

organism: Rattus norvegicus

source_name: Total RNA extracted from marrow rat femur on Day 56 post-ablation

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

extract_protocol: For three samples per time point, both the distal and proximal ends of the femurs were cut off in order to exclude the epiphyses and growth plate regions. Diaphyseal marrow tissue and cells from the mid-shaft were flushed out using Trizol®. Following homogenization, 1 ml of solution was transferred to a 1.5 ml Eppendorf tube and centrifuged at 12,000g for 10 minutes at 4°C to remove insoluble material. The supernatant containing RNA was collected, mixed with 0.2 ml of chloroform, and centrifuged at 12,000g for 15 minutes at 4°C. After RNA in the aqueous phase was transferred into a new tube, the RNA was precipitated by mixing 0.5 ml of isopropyl alcohol and recovered by centrifuging the tube at 12,000g for 10 minutes at 4°C. The RNA pellet was washed briefly in 1 ml of 75% ethanol and centrifuged at 7,500g for 5 minutes at 4°C. Finally, the total RNA pellet was dissolved in diethylpyrocarbonate (DEPC) water, and its quantity was assessed by spectrophotometric analysis.

value: femoral marrow (intramedullary) tissue

tag: strain

value: Sprague Dawley

value: adult

value: male

value: day 56 post-ablation


title: MBA MD 231 Control

description: MBA MD 231 C

source_name: pool

tag: sample type

source_name: MBA MD 231 C

value: MBA MD 231

value: Control


title: MBA MD 231 48H

description: MBA MD 231 48H

source_name: MBA MD 231 48H


title: Time 5  17X

description:
Gene expression spleen after 5 days post-infection with the non-lethal P. yoelii 17X strain.
Cy3_D5

source_name: spleen, day 5 post-infection, non-lethal 17X strain

value: BALB/c

value: spleen

value: female

value: 6-8 weeks


title: MBA MD 436 Control

description: MBA Md 436 Control

source_name: MBA Md 436 Control


title: AR113Q-1-Cy5_Vs_Reference-Cy3

source_name: Total RNA from 10 of wild type mice as RNA reference

value: Male and Female

value: 70 days

value: Limb Muscles

source_name: Total RNA from AR113Q-Knock In mice-1

value: AR113Q-Knock In mice

value: Male

value: 100 days


title: rat femur on day 56 post-ablation G9.56D.1-223

value: femoral marrow (intramedullary) tissue


title: Time 3 17X

description:
Gene expression spleen after 3 days post-infection with the non-lethal P. yoelii 17X strain.
Cy3_D3

source_name: spleen, day 3 post-infection, non-lethal 17X strain


title: MBA MD 157 48H 2

description: MBA Md 157 48H-2

value: Universal Human Reference RNA (from Stratagene, Cat Nr:740000)

value: MBA MD 157


title: MBA MD 157 Control 2

description: MBa MD 157 Control 2

source_name: MBa MD 157 Control 2


title: Time 10% infection 17X

description:
Gene expression spleen at 10% peripheral parasitemia with the non-lethal P. yoelii 17X strain.
Cy3_P10

source_name: spleen, 10% parasitemia, non-lethal 17X strain


title: MBA MD 157 Control 1

description: MBA MD 157 Control 1

source_name: MBA MD 157 Control 1


title: MBA MD 231 24H

description: MBA MD 231 24H

source_name: MBA MD 231 24H


title: rat femur on day 56 post-ablation G9.56D.10-225

value: Sprague Dawley

value: adult

value: male


title: K_AR11

source_name: AR11 kidney allograft biopsy, acute rejection

value: Grade 1A


title: K_STA12

source_name: STA12 kidney allograft biopsy, stable


title: Time 4  17X

description:
Gene expression spleen after 4 days post-infection with the non-lethal P. yoelii 17X strain.
Cy3_D4

source_name: spleen, day 4 post-infection, non-lethal 17X strain

value: BALB/c


title: Time 0  17X

description:
Gene expression normal spleen 0h infection.
Cy3_C0

source_name: spleen, control 1, 0h

value: spleen


title: rat femur on day 28 post-ablation G8.28D.20-231

description: Gene expression data from total RNA extracted from rat femur marrow tissue on Day 28 post-ablation

source_name: Total RNA extracted from marrow rat femur on Day 28 post-ablation

value: day 28 post-ablation


title: K_STA14

source_name: STA14 kidney allograft biopsy, stable


title: rat femur on day 28 post-ablation G8.28D.2-232


title: K_AR2

source_name: AR2 kidney allograft biopsy, acute rejection

value: Grade 1B


title: K_AR18

source_name: AR18 kidney allograft biopsy, acute rejection


title: rat femur on day 28 post-ablation G8.28D.11-230


title: MBA MD 157 24H 1

description: MBA MD 157 24H -1

source_name: pool


title: Arabidopsis, root cells, Pericycle, +Fe, replicate 1

city: Durham

first: Terri

middle: Anita

last: Long

state: NC

department: Biology

institute: Duke University

description: Gene expression data from isolated pericycle cells after roots were treated to +Fe media for 24 hours

hyb_protocol: Samples were submitted to Expression Analysis Inc. (Durham, NC) for hybridization to Affymetrix ATH1 microarrays.

data_processing: For the PER study we performed 3 replicates under +Fe and 3 replicates under -Fe. We normalized the expression values from the CEL files using ANOVA, which normalizes all three replicates into one value for each probeset. The ANOVA normalization process we used in described in Levesque et al., PLoS Biol. 4, e143 (2006).

source_name: Protoplasted and FACS sorted root cells

label_protocol: Fragmented cRNA probes were prepared using the two-cycle amplification protocol by Affymetrix.

growth_protocol: Seeds were surface sterilized for 2 minutes in 70% ethanol, the ethanol was removed, then replaced with 30% Bleach and 0.02% Triton X-100 for 15 minutes. Seeds were rinsed 3 times with sterile water, stratified for 4˚C for 2 days, then placed on standard media. Standard media is 1X Murashige and Skoog salt mixture in which ferrous sulfate is replaced with 100mM Fe(III)-EDTA, 0.5g/L MES, 1% sucrose, 1% agar and adjusted to pH 5.7 with KOH.  –Fe media is 1X Murashige and Skoog salt mixture in which ferrous sulfate is replaced with 0.3mM Ferrozine. Nylon mesh was placed on top of the solidified media and seeds were planted at ~20 seeds/cm in two rows.

extract_protocol: RNA was extracted using the RNAeasy Micro Kit (Qiagen GmbH).

treatment_protocol: Samples were prepared as in Birnbaum et al. (2005) Nat. Methods for roots grown under standard conditions. Roots were transferred to +Fe or -Fe media for 24 hours then cut with a razor blade 0.5 mm below the root/hypocotyl junction before protoplasting. Three biological replicates being performed per line.

value: Columbia

value: 7 days after germination

value: seedling roots

tag: gfp-reporter

tag: growth media

value: Standard media for 6 days, transferred to +Fe media for 24 hours before protoplasting


title: Arabidopsis, root cells, Pericycle, -Fe, replicate 1

description: Gene expression data from isolated pericycle cells after roots were treated to -Fe media for 24 hours

scan_protocol: Samples were submitted to Expression Analysis Inc. (Durham, NC) for hybridization to Affymetrix ATH1 microarrays.

value: Standard media for 6 days, transferred to -Fe media for 24 hours before protoplasting


title: K_STA5

source_name: STA5 kidney allograft biopsy, stable


title: MBA MD 157 24H 2

description: MBA MD 157 24H-2

hyb_protocol: For each hybridization, Cy 3 labeled cRNA (reference) and 1ug of Cy 5 labeled cRNA (carriers or controls) were mixed, fragmented and hybridized to to an Agilent 44 K Whole Human genome Oligo Microarray . After hybridization, slides were washed sequential


title: HCC 1937 Control 2

description: HCC Control 2

source_name: HCC Control 2

value: Control


title: MBA MD 157 48H 1

description: MBA MD 157 48H-1


title: K_STA11

source_name: STA11 kidney allograft biopsy, stable


title: rat femur on day 14 post-ablation G7.14D.12-236

description: Gene expression data from total RNA extracted from rat femur marrow tissue on Day 14 post-ablation

source_name: Total RNA extracted from marrow rat femur on Day 14 post-ablation

value: femoral marrow (intramedullary) tissue

value: day 14 post-ablation


title: Arabidopsis, pye, -Fe, replicate 2

description: Gene expression data from whole roots after 24 hours of treatment with -Fe media

data_processing: MAS5 algorithm

source_name: Whole roots

label_protocol: Fragmented cRNA probes were prepared using the one-cycle amplification protocol by Affymetrix.

treatment_protocol: Samples were prepared as in Birnbaum et al. (2005) Nat. Methods for roots grown under standard conditions. Roots were transferred to +Fe or -Fe media for 24 hours. Roots were then cut with a razor blade 0.5 mm below the root/hypocotyl junction and collected into RNA extraction buffer.  Approximately 320 roots were collected per replicate, with two biological replicates being performed per line.

tag: genotype

value: whole roots

value: Standard media, transferred to -Fe media  for 24 hours prior to harvesting tissue


title: Arabidopsis, pye, -Fe, replicate 1


title: rat femur on day 10 post-ablation G6.10D.4-244

description: Gene expression data from total RNA extracted from rat femur marrow tissue on Day 10 post-ablation

source_name: Total RNA extracted from marrow rat femur on Day 10 post-ablation

value: Sprague Dawley

value: adult

value: day 10 post-ablation


title: HCC 1937 Control 1

description: HCC 1937 Control

value: Universal Human Reference RNA (from Stratagene, Cat Nr:740000)

source_name: HCC 1937 Control


title: HCC 1937 48H

description: HCC 1937 48H


title: rat femur on day 14 post-ablation G7.14D.3-238

value: male


title: Arabidopsis, pye, +Fe, replicate 1

description: Gene expression data from whole roots after 24 hours of treatment with +Fe media

value: Standard media, transferred to +Fe media  for 24 hours prior to harvesting tissue


title: Arabidopsis, WT, -Fe, replicate 2

value: Wild-type


title: Arabidopsis, pye, +Fe, replicate 2

value: Columbia


title: rat femur on day 10 post-ablation G6.10D.22-243


title: rat femur on day 7 post-ablation G5.7D.5-250

description: Gene expression data from total RNA extracted from rat femur marrow tissue on Day 7 post-ablation

source_name: Total RNA extracted from marrow rat femur on Day 7 post-ablation

value: day 7 post-ablation


title: Arabidopsis, WT, +Fe, replicate 2

value: 7 days after germination


title: HCC 1937 24H

description: HCC 1937 24H


title: K_STA8

source_name: STA8 kidney allograft biopsy, stable


title: 578 Control

description: 578 Control

source_name: 578 Control


title: Arabidopsis, WT, -Fe, replicate 1


title: K_STA6

source_name: STA6 kidney allograft biopsy, stable


title: rat femur on day 10 post-ablation G6.10D.13-242


title: 578 48H

description: 578 48H


title: rat femur on day 7 post-ablation G5.7D.23-249


title: K_STA4

source_name: STA4 kidney allograft biopsy, stable


title: 578 24H

description: 578 24H


title: rat femur on day 7 post-ablation G5.7D.14-247


title: Arabidopsis, WT, +Fe, replicate 1


title: K_AR7

source_name: AR7 kidney allograft biopsy, acute rejection


title: ΔacuM vs. ΔacuM ::acuM 24 hour Replicate 2

city: Rockville

first: Natalie

last: Fedorova

address: 9704 Medical Center Dr

department: Infectious Disease

institute: JCVI

description: Analysis used Aspergillus fumigatus ΔacuM RNA as control samples for comparison to RNA from ΔacuM ::acuM complemented strain.

hyb_protocol: Hybridizations were performed as per JCVI PFGRC SOP m008 (http://pfgrc.jcvi.org/index.php/microarray/protocols.html) Briefly:  Hybridizations were incubated for 18 h at 42C.  Post hybridization washes included (twice each) 55C in 2x ssc, 0.1% SDS, RT in 0.1x SSC, 0.1% SDS and RT 0.1x SSC.

scan_protocol: After washing, slides were scanned with a GenePix 4000b scanner using  GenePix Pro 3.0 software.   PMT gains were changed in order to generate images with red:green ratios of as close to 1:1 as possible.  Images were saved as .TIF files and TIGR Spotfinder (Saeed et al, 2003) was used to quantitate fluorescent intensities.  Poor quality spots were identified manually and flagged. After Spotfinder analysis, resulst were exported as TIGR software compatible MEV files following local background subtraction.

data_processing: MEV files were loaded into the JCVI MIDAS array normalization program where they were first normalized by block locally-weighted scatter plot smoothing (LOWESS).   After LOWESS, the flip-dye pairs were combined a consistency check was applied to remove any spots that do not fall within a specified deviation of the array-wide average log2  ratio of the fluorescence values for spot on both slides.   After the flip-dye consistency check the values underwent inter-slide standard deviation regularisation by averaging the values of the replicate spots for each gene.

organism: Aspergillus fumigatus

source_name: Mycelium cultured in RPMI for 24 hours [control]

label_protocol: cDNA synthesis and labeling were performed as per JCVI PFGRC SOP m007 (http://pfgrc.jcvi.org/index.php/microarray/protocols.html)  Briefly:  cDNA were generated using Invitrogen Superscript II, incorporating aminoallyl-dUTP.  cDNA Samples were labeled with Cy3 or Cy5 during a 2 hour room temperature incubation followed by purification with a Qiagen PCR purification column to remove unbound dye.

growth_protocol: To obtain mycelium, conida of the various strains were used to inoculate PRMI 1640 medium buffered with 4-morpholinepropanesulphonicacid to pH7.0.  For the 8 h time point, a 1 L flask containing 500 ml of medium was used. For the 18 h and 24 h time point, 250 ml flasks containing 100 ml of medium were used. The concentration of condia in these flasks was 500000 cells per ml.

extract_protocol: Total RNA extraction was performed using the filamentous fungi protocol of the Rneasy mini Kit (Qiagen)

treatment_protocol: All the strains were grown in PRMI 1640. After incubating the organisms in a shaking incubator at 37 centrigrade for 8, 18 and 24 h, the resulting hyphae were harvested by filtration.

tag: genotype/variation

value: ΔacuM

value: 24 hours

value: control

source_name: Mycelium cultured in RPMI for 24 hours [experimental]

value: ΔacuM ::acuM

value: experimental


title: K_STA1

source_name: STA1 kidney allograft biopsy, stable


title: rat femur on day 5 post-ablation G4.5D.25-261

description: Gene expression data from total RNA extracted from rat femur marrow tissue on Day 5 post-ablation

source_name: Total RNA extracted from marrow rat femur on Day 5 post-ablation

value: femoral marrow (intramedullary) tissue

value: day 5 post-ablation


title: K_STA2

source_name: STA2 kidney allograft biopsy, stable


title: ΔacuM vs. ΔacuM ::acuM 24 hour Replicate 1


title: K_AR12

source_name: AR12 kidney allograft biopsy, acute rejection

value: Grade 1B


title: ΔacuM vs. ΔacuM ::acuM 18 hour Replicate 2

source_name: Mycelium cultured in RPMI for 18 hours [control]

value: 18 hours

source_name: Mycelium cultured in RPMI for 18 hours [experimental]


title: K_STA13

source_name: STA13 kidney allograft biopsy, stable


title: Tumor2_replicate_2

city: Montreal

first: Sean

last: Cory

state: QC

address: 3649 Promenade Sir William Osler

department: Bioinformatics

institute: McGill University

hyb_protocol: Labeled aRNA (825 ng) was hybridized onto Microarrays using the Agilent in situ Hybridization Plus Kit Large for 17 h at 65°C

scan_protocol: Microarray slides were scanned using a Microarray Scanner (Model G2565BA, Agilent Technologies) at 10-mm resolution according to manufacturer’s instructions

data_processing: Raw probe intensities were background-corrected, within and between each array normalized using the normexp, loess and quantile methods respectively in Bioconductor

source_name: Pooled NIC tumor

label_protocol: A total of 500 ng of total RNA was subjected to one round of T7 linear amplification using the Amino Allyl MessageAmp aRNA Kit (Ambion)

extract_protocol: Total RNA was isolated from samples using the RNeasy Midi Kit (Qiagen)

value: Pooled NIC tumor

source_name: SHC null tumor 2

value: ShcA-null mammary tumor


title: ΔacuM vs. ΔacuM ::acuM 18 hour Replicate 1


title: rat femur on day 5 post-ablation G4.5D.7-262

value: Sprague Dawley

value: adult

value: male


title: Tumor3_replicate_2

source_name: SHC null tumor 3


title: rat femur on day 3 post-ablation G3.3D.6-256

description: Gene expression data from total RNA extracted from rat femur marrow tissue on Day 3 post-ablation

source_name: Total RNA extracted from marrow rat femur on Day 3 post-ablation

value: day 3 post-ablation


title: rat femur on day 5 post-ablation G4.5D.16-260


title: Tumor4_replicate_2

source_name: SHC null tumor 4


title: rat femur on day 14 post-ablation G7.14D.21-237

source_name: Total RNA extracted from marrow rat femur on Day 14 post-ablation

value: day 14 post-ablation


title: K_AR17

source_name: AR17 kidney allograft biopsy, acute rejection

value: Grade 1A


title: rat femur on day 3 post-ablation G3.3D.15-254


title: rat femur on day 3 post-ablation G3.3D.24-255


title: ΔacuM vs. ΔacuM ::acuM 8 hour Replicate 1

source_name: Mycelium cultured in RPMI for 8 hours [control]

value: ΔacuM

value: 8 hours

source_name: Mycelium cultured in RPMI for 8 hours [experimental]


title: Af293 vs. ΔacuM 24 hour Replicate 2

description: Analysis used Aspergillus fumigatus wild type Af293 RNA as control samples for comparison to RNA from ΔacuM mutant.

source_name: Mycelium cultured in RPMI for 24 hours [control]

value: wildtype Af293

value: 24 hours

value: control

source_name: Mycelium cultured in RPMI for 24 hours [experimental]


title: ΔacuM vs. ΔacuM ::acuM 8 hour Replicate 2

value: ΔacuM ::acuM

value: experimental


title: K_AR14

source_name: AR14 kidney allograft biopsy, acute rejection


title: rat femur on day 1 post-ablation G2.1D.8-268

description: Gene expression data from total RNA extracted from rat femur marrow tissue on Day 1 post-ablation

source_name: Total RNA extracted from marrow rat femur on Day 1 post-ablation

value: femoral marrow (intramedullary) tissue

value: day 1 post-ablation


title: rat femur on day 1 post-ablation G2.1D.26-267


title: K_STA7

source_name: STA7 kidney allograft biopsy, stable


title: Tumor8_replicate_1

source_name: SHC null tumor 8

tag: reference

value: Pooled NIC tumor


title: Af293 vs. ΔacuM 18 hour Replicate 2

source_name: Mycelium cultured in RPMI for 18 hours [control]

value: 18 hours

source_name: Mycelium cultured in RPMI for 18 hours [experimental]


title: Tumor1_replicate_2

source_name: Pooled NIC tumor

source_name: SHC null tumor 1

value: ShcA-null mammary tumor


title: Tumor6_replicate_1

source_name: SHC null tumor 6


title: K_STA3

source_name: STA3 kidney allograft biopsy, stable


title: rat femur on day 1 post-ablation G2.1D.17-266

value: Sprague Dawley

value: adult


title: Tumor7_replicate_1

source_name: SHC null tumor 7


title: Af293 vs. ΔacuM 24 hour Replicate 1


title: Tumor5_replicate_1

source_name: SHC null tumor 5


title: Af293 vs. ΔacuM 8 hour Replicate 2


title: K_AR13

source_name: AR13 kidney allograft biopsy, acute rejection

value: Grade 1B


title: K_AR16

source_name: AR16 kidney allograft biopsy, acute rejection


title: Tumor4_replicate_1

source_name: SHC null tumor 4


title: K_AR6

source_name: AR6 kidney allograft biopsy, acute rejection


title: intact (control) rat femur on day 0 G1.0D.9-274

description: Gene expression data from total RNA extracted from marrow tissue of intact (control) rat femur on Day 0

source_name: Total RNA extracted from marrow of intact (control) rat femur on Day 0

value: male

value: day 0


title: Tumor3_replicate_1

source_name: SHC null tumor 3


title: K_AR9

source_name: AR9 kidney allograft biopsy, acute rejection


title: Af293 vs. ΔacuM 18 hour Replicate 1

value: ΔacuM


title: Af293 vs. ΔacuM 8 hour Replicate 1

source_name: Mycelium cultured in RPMI for 8 hours [control]

value: 8 hours

source_name: Mycelium cultured in RPMI for 8 hours [experimental]


title: Tumor2_replicate_1

source_name: SHC null tumor 2


title: intact (control) rat femur on day 0 G1.0D.18-272


title: K_AR8

hyb_protocol: 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays. 2. Equilibrate probe array to room temperature immediately before use. 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block. 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa. 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation. 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes. 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture. 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2). 9. Place probe array into the hybridization oven, set to 45°C. 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm. 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining step required immediately after completion of hybridization.

source_name: AR8 kidney allograft biopsy, acute rejection

label_protocol: GeneChip one cycle target labeling and control reagents


title: M. trossulus_13-degrees control, 32-degree-time-point_replicate 5

status: Public on Oct 11 2010

city: Pacific Grove

first: Brent

middle: L

last: Lockwood

address: 120 Oceanview Blvd.

institute: Hopkins Marine Station of Stanford University

description: Biological replicate 5 of 6. M. trossulus control, 13 degrees-C, 32-degree time-point in heat ramp.

hyb_protocol: Competitive hybridization (experimental - AlexaFluor 647 versus reference - AlexaFluor 555). We followed the recommended protocols from Agilent Technologies, Inc for all hybridization and washing steps.

scan_protocol: Microarrays were scanned with an AXON GenePix 4000B scanner (Axon Instruments, Molecular Devices, Sunnyvale, CA, USA).

data_processing:
Fluorescent signal intensities for each spot on the microarray were extracted and Lowess normalized within each microarray using Feature Extraction software (version 9.5.3.1; Agilent Technologies, Inc.). Only spots that Feature Extraction Software measured to have good hybridization among all samples were included in further analysis. We then computed the log2-ratios of the experimental channel divided by the reference channel and normalized these expression values to the median log2-ratio of the control samples of the same species from the same temperature-point on the heat ramp (i.e. 13°C, 24°C, 28°C and 32°C). Log2-ratios of the samples from the 13°C temperature-point were normalized to the median log2-ratio within that group, separately for each species.
Used data only from those probes that performed well for both species in our comparison.

label: Alexa Fluor 647

organism: Mytilus trossulus

source_name: 13-degrees control, 32-degree-time-point, M. trossulus

label_protocol: Total RNA was reverse-transcribed and amplified with the AminoAllyl MessageAmp II kit (Ambion; Foster City, CA, USA). To reduce problems in transcript binding due to sequence differences between species, we employed a reference design that used separate pools of reference RNA for each species. Reference amplified RNA (aRNA) was created for each species by pooling RNA before and after amplification. The reference pool was made up of RNA from six different samples: one control sample from the beginning of the experiment, one treatment sample from each temperature-point, and one control sample from each temperature-point. aRNAs from reference and experimental samples were separately labeled with Alexa Fluor fluorescent dyes (Invitrogen, Carlsbad, CA, USA), 555 for reference and 647 for control or treatment.

growth_protocol: We collected mussels from floating boat docks: Mytilus trossulus (Gould 1850) from Newport Harbor, Newport, OR, USA (44°38’25” N, 124°03’10” W) and Mytilus galloprovincialis (Lamarck 1819) from Santa Barbara Harbor, Santa Barbara, CA, USA (34°24’15” N, 119°41’30” W). All specimens thus were acclimatized to conditions of continuous immersion. Care was taken to collect animals of similar size (5 – 7 cm) to avoid potential artifacts from size-related influences on gene expression. Specimens were returned to the laboratory at California Polytechnic State University San Luis Obispo and placed in a re-circulating seawater tank in which they were common-garden acclimated at 13°C for 4 weeks, in order to limit the effects of past thermal history. We chose both collection sites to be well outside of the hybrid zone (McDonald, 1988; Braby and Somero, 2006a) to ensure no hybrid individuals were included in our study. We confirmed the species identification by genotyping each mussel using published methods (Heath et al., 1995; Rawson et al., 1996). The 13°C acclimation temperature mimicked an ecologically realistic thermal environment for both species.

extract_protocol: Total RNA was extracted from gill tissues with a TissueLyser homogenizer (Qiagen; Valencia, CA, USA) and RNeasy kit (Qiagen).

treatment_protocol: Treatment animals were transferred from the common-garden aquarium to a tank in which they were exposed to a heat-ramp of +6°C h-1, from 13°C to 32°C, to simulate thermal heating on a hot day during falling tide. Control animals were simultaneously transferred to a separate tank that remained at 13°C. At designated temperature-points on the heat-ramp (24°C, 28°C and 32°C), six treatment mussels from each species were transferred to a separate tank and maintained at each respective temperature for an additional hour. Treatment and control mussels corresponding to each temperature-point were then sacrificed and their gill tissues dissected and frozen on liquid nitrogen. Tissues were stored at -70°C prior to RNA extraction.

tag: stress

value: CONTROL, transferred to 13-degrees from 32-degree-time-point

label: Alexa Fluor 555

source_name: M. trossulus pooled: Time-point zero, 24-control, 24-heat-shock, 28-control, 28-heat-shock, 32-control, 32-heat-shock

value: pooled samples

value: gill


title: M. trossulus_32-degree heat shock_replicate 6

description: Biological replicate 6 of 6. M. trossulus heat shock, 32 degrees-C, 32-degree time-point in heat ramp.

source_name: 32-degree heat shock, M. trossulus

value: 32-degree heat shock


title: intact (control) rat femur on day 0 G1.0D.08022006-1-271


title: Tumor1_replicate_1

source_name: SHC null tumor 1

source_name: Pooled NIC tumor


title: M. trossulus_13-degrees control, 32-degree-time-point_replicate 4

description: Biological replicate 4 of 6. M. trossulus control, 13 degrees-C, 32-degree time-point in heat ramp.


title: M. trossulus_32-degree heat shock_replicate 5

description: Biological replicate 5 of 6. M. trossulus heat shock, 32 degrees-C, 32-degree time-point in heat ramp.


title: M. trossulus_13-degrees control, 32-degree-time-point_replicate 6

description: Biological replicate 6 of 6. M. trossulus control, 13 degrees-C, 32-degree time-point in heat ramp.


title: M. trossulus_32-degree heat shock_replicate 2

description: Biological replicate 2 of 6. M. trossulus heat shock, 32 degrees-C, 32-degree time-point in heat ramp.


title: M. trossulus_32-degree heat shock_replicate 3

description: Biological replicate 3 of 6. M. trossulus heat shock, 32 degrees-C, 32-degree time-point in heat ramp.


title: M. trossulus_32-degree heat shock_replicate 4

description: Biological replicate 4 of 6. M. trossulus heat shock, 32 degrees-C, 32-degree time-point in heat ramp.


title: M. trossulus_32-degree heat shock_replicate 1

description: Biological replicate 1 of 6. M. trossulus heat shock, 32 degrees-C, 32-degree time-point in heat ramp.


title: M. trossulus_13-degrees control, 32-degree-time-point_replicate 2

description: Biological replicate 2 of 6. M. trossulus control, 13 degrees-C, 32-degree time-point in heat ramp.


title: M. trossulus_13-degrees control, 32-degree-time-point_replicate 1

description: Biological replicate 1 of 6. M. trossulus control, 13 degrees-C, 32-degree time-point in heat ramp.


title: M. trossulus_28-degree heat shock_replicate 4

description: Biological replicate 4 of 6. M. trossulus heat shock, 28 degrees-C, 28-degree time-point in heat ramp.

source_name: 28-degree heat shock, M. trossulus

value: 28-degree heat shock


title: M. trossulus_13-degrees control, 32-degree-time-point_replicate 3

description: Biological replicate 3 of 6. M. trossulus control, 13 degrees-C, 32-degree time-point in heat ramp.


title: M. trossulus_28-degree heat shock_replicate 5

description: Biological replicate 5 of 6. M. trossulus heat shock, 28 degrees-C, 28-degree time-point in heat ramp.


title: M. trossulus_28-degree heat shock_replicate 3

description: Biological replicate 3 of 6. M. trossulus heat shock, 28 degrees-C, 28-degree time-point in heat ramp.


title: M. trossulus_28-degree heat shock_replicate 6

description: Biological replicate 6 of 6. M. trossulus heat shock, 28 degrees-C, 28-degree time-point in heat ramp.


title: M. trossulus_28-degree heat shock_replicate 1

description: Biological replicate 1 of 6. M. trossulus heat shock, 28 degrees-C, 28-degree time-point in heat ramp.


title: M. trossulus_28-degree heat shock_replicate 2

description: Biological replicate 2 of 6. M. trossulus heat shock, 28 degrees-C, 28-degree time-point in heat ramp.


title: M. trossulus_13-degrees control, 28-degree-time-point_replicate 6

description: Biological replicate 6 of 6. M. trossulus control, 13 degrees-C, 28-degree time-point in heat ramp.

source_name: 13-degrees control, 28-degree-time-point, M. trossulus

value: CONTROL, transferred to 13-degrees from 28-degree-time-point


title: M. trossulus_13-degrees control, 28-degree-time-point_replicate 5

description: Biological replicate 5 of 6. M. trossulus control, 13 degrees-C, 28-degree time-point in heat ramp.


title: M. trossulus_13-degrees control, 28-degree-time-point_replicate 2

description: Biological replicate 2 of 6. M. trossulus control, 13 degrees-C, 28-degree time-point in heat ramp.


title: M. trossulus_13-degrees control, 28-degree-time-point_replicate 3

description: Biological replicate 3 of 6. M. trossulus control, 13 degrees-C, 28-degree time-point in heat ramp.


title: M. trossulus_13-degrees control, 28-degree-time-point_replicate 4

description: Biological replicate 4 of 6. M. trossulus control, 13 degrees-C, 28-degree time-point in heat ramp.


title: M. trossulus_24-degree heat shock_replicate 4

description: Biological replicate 4 of 6. M. trossulus heat shock, 24 degrees-C, 24-degree time-point in heat ramp.

source_name: 24-degree heat shock, M. trossulus

value: 24-degree heat shock


title: M. trossulus_24-degree heat shock_replicate 3

description: Biological replicate 3 of 6. M. trossulus heat shock, 24 degrees-C, 24-degree time-point in heat ramp.


title: M. trossulus_24-degree heat shock_replicate 1

description: Biological replicate 1 of 6. M. trossulus heat shock, 24 degrees-C, 24-degree time-point in heat ramp.


title: M. trossulus_24-degree heat shock_replicate 6

description: Biological replicate 6 of 6. M. trossulus heat shock, 24 degrees-C, 24-degree time-point in heat ramp.


title: M. trossulus_13-degrees control, 24-degree-time-point_replicate 5

description: Biological replicate 5 of 6. M. trossulus control, 13 degrees-C, 24-degree time-point in heat ramp.

source_name: 13-degrees control, 24-degree-time-point, M. trossulus

value: CONTROL, transferred to 13-degrees from 24-degree-time-point


title: M. trossulus_13-degrees control, 24-degree-time-point_replicate 1

description: Biological replicate 1 of 6. M. trossulus control, 13 degrees-C, 24-degree time-point in heat ramp.


title: M. trossulus_13-degrees control, 28-degree-time-point_replicate 1

description: Biological replicate 1 of 6. M. trossulus control, 13 degrees-C, 28-degree time-point in heat ramp.


title: M. galloprovincialis_32-degree heat shock_replicate 5

description: Biological replicate 5 of 6. M. galloprovincialis heat shock, 32 degrees-C, 32-degree time-point in heat ramp.

organism: Mytilus galloprovincialis

source_name: 32-degree heat shock, M. galloprovincialis

source_name: M. galloprovincialis pooled: Time-point zero, 24-control, 24-heat-shock, 28-control, 28-heat-shock, 32-control, 32-heat-shock


title: M. galloprovincialis_32-degree heat shock_replicate 6

description: Biological replicate 6 of 6. M. galloprovincialis heat shock, 32 degrees-C, 32-degree time-point in heat ramp.


title: M. trossulus_13-degrees control, 24-degree-time-point_replicate 6

description: Biological replicate 6 of 6. M. trossulus control, 13 degrees-C, 24-degree time-point in heat ramp.


title: M. galloprovincialis_32-degree heat shock_replicate 3

description: Biological replicate 3 of 6. M. galloprovincialis heat shock, 32 degrees-C, 32-degree time-point in heat ramp.


title: M. galloprovincialis_32-degree heat shock_replicate 4

description: Biological replicate 4 of 6. M. galloprovincialis heat shock, 32 degrees-C, 32-degree time-point in heat ramp.


title: M. trossulus_24-degree heat shock_replicate 5

description: Biological replicate 5 of 6. M. trossulus heat shock, 24 degrees-C, 24-degree time-point in heat ramp.


title: M. trossulus_13-degrees control, 24-degree-time-point_replicate 3

description: Biological replicate 3 of 6. M. trossulus control, 13 degrees-C, 24-degree time-point in heat ramp.


title: M. galloprovincialis_32-degree heat shock_replicate 2

description: Biological replicate 2 of 6. M. galloprovincialis heat shock, 32 degrees-C, 32-degree time-point in heat ramp.


title: M. trossulus_24-degree heat shock_replicate 2

description: Biological replicate 2 of 6. M. trossulus heat shock, 24 degrees-C, 24-degree time-point in heat ramp.


title: M. galloprovincialis_13-degrees control, 32-degree-time-point_replicate 3

description: Biological replicate 3 of 6. M. galloprovincialis control, 13 degrees-C, 32-degree time-point in heat ramp.

source_name: 13-degrees control, 32-degree-time-point, M. galloprovincialis


title: M. trossulus_13-degrees control, 24-degree-time-point_replicate 4

description: Biological replicate 4 of 6. M. trossulus control, 13 degrees-C, 24-degree time-point in heat ramp.


title: M. galloprovincialis_13-degrees control, 32-degree-time-point_replicate 5

description: Biological replicate 5 of 6. M. galloprovincialis control, 13 degrees-C, 32-degree time-point in heat ramp.


title: M. galloprovincialis_13-degrees control, 32-degree-time-point_replicate 6

description: Biological replicate 6 of 6. M. galloprovincialis control, 13 degrees-C, 32-degree time-point in heat ramp.