title: primordial germ cells female E13.5 biol rep 3

description: PGCs FACSorted for Oct4/GFP+


title: Sante_ConvCropProtection_ConvFertilizer_rep1

status: Public on Jan 31 2012

type: RNA

city: Wageningen

first: Jeroen

last: van Dijk

address: Bornsesteeg 45

country: Netherlands

institute: RIKILT, institute of food safety

description: Biological replicate 1 of 4

hyb_protocol: 1 μl of luciferase RNA (Invitrogen) was added to each sample. Labeled cDNA was dissolved in 80 μl MiliQ water, to which 20 μl Cy3-labelled universal control cDNA was added as well as 4 μl denatured herring sperm DNA and 4 μl dentarued blocker (Agilent, USA). This mix was combined with 100 μl 2x hybridization buffer (Agilent) and hybridization was performed for 17 hrs at 60 degrees Celcius with the Agilent gasket/chamber system in an agilent hybridization oven with rotor. After hybridisation the slides were washed with wash buffer 1, 2 and 3 (Agilent, USA) according to the manufacturer's instructions.

scan_protocol: Microarrays were scanned after excitation of Cy5 dye with 633 nm laser and Cy3 dye with 543 nm laser using scanner ScanArray® Express HT (Perkin Elmer, USA). The microarrays were scanned at constant laser power (90 %) and 10 μm resolution settings.Tiff images were imported into the ArrayVision software (Imaging Research, Waalwijk, The Netherlands) and the fluorescent intensity, background and signal-to-noise ratio were determined for each spot. Photo mulitplier tube (PMT) settings were 80 for the Cy3 channel and 55 for the Cy5 channel.

data_processing: Quality was checked, removal of control and empty spots. The Cy5/Cy3 ratio was calculated and log2 transformed. Normalization was done per array by subtraction from all 3725 remaining spots the median value of the log2(cy3/Cy5) signal of 1080 spots with a target/background ratio of more than 2 on all 16 arrays. R statistical software and Genemaths XT®s software (Applied Maths, St-Martens-Latem, Belgium) were used for analysis.

molecule: total RNA

organism: Solanum tuberosum

source_name: Total RNA, Cy5 labeled, isolated from potato tubers, treatment LadyBalfour_ChickenPellets_Water

label_protocol: 25 µg of total RNA was primed with 2 µl 21-mer oligo-dT primer (1ug/ml) at 25°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 150 U SuperScript II RTase (Invitrogen), and 500 µM each dATP, dTTP, dGTP, with 40 µM dCTP Cy5-labeled

growth_protocol: Potatoes were grown at Nafferton Experimental Farm (University of Newcastle) under organic farming practices in a completely randomised block design with 4 replicate blocks; with all combinations of fertilisation and crop protection being established on one plot in each block (size of individual plots 15 x 6 m)

extract_protocol: Total RNA extraction following a protocol for extraction of RNA from polysaccharide rich tissues  (Chang et al.,2003,Plant Molecular Biology Reporter, 11: 113–116)

treatment_protocol: Organic fertilizer consisted of composted cattle manure, equivalent to 170 kg N/ha. Conventional fertilizer consisted of ammonium nitrate (Nitram), equivalent to 180 kg N/ha and superphosphate and KCl as a compound (0:20:300 fertilizer equivalent to 134 kg P/ha and 200 kg K/ha. Organic crop protection consisted of 2 times mechanical rigging of potato rows (weed control), 2 foliar sprays of copperoxychloride (product: Headland Copper, 15l/ ha + 6 kg Cu/ha) (disease control) and mechanical removal of foliage by flailing to avoid tuber blight. Conventional crop protection consisted of 1 spray of linuron (product: Linuron, 3.5 l/ha) (weed control), pre-planting soil application of aldicarp granules (product: Temik 10G, 67 kg/ha) (pest control), 2 foliar sprays of a mixture of fluazinam (product: Fubol Gold, 2.85 l/ha) and copperoxychloride (product: Headland Copper, 15l/ ha + 6 kg Cu/ha) (disease control) and 1 foliar spray of Oiquat (product: Reglone, 4 l/ha) for removal of foliage to avoid tuber blight.

tag: cultivar

value: Sante

tag: input regime

value: conventional

tag: sample size

value: 4-5 tubers

tag: tissue

value: tuber

tag: treatment

value: Conventional Crop Protection

tag: growth condition

value: Conventional Fertilizer

source_name: Universal control

tag: sample type

value: mixture of PCR products spotted on the microarray in vitro transcribed to RNA


title: Sante_ConvCropProtection_OrgFertilizer_rep4

description: Biological replicate 4 of 4

source_name: Total RNA, Cy5 labeled, isolated from potato tubers, treatment Sante_ChickenPellets_Comcat

value: mixed

value: Organic Fertilizer


title: Sante_ConvCropProtection_OrgFertilizer_rep3

description: Biological replicate 3 of 4

source_name: Total RNA, Cy5 labeled, isolated from potato tubers, treatment LadyBalfour_Compost_CopperOxychloride


title: primordial germ cells mixed E11.5 biol rep 1

city: San Francisco

first: Miguel

last: Ramalho-Santos

state: CA

address: 35 Medical Center Way

department: Eli and Edythe Broad Center of Regeneration Medicine

country: USA

institute: UCSF

description: PGCs FACSorted for Oct4/GFP+

hyb_protocol: Standard Affymetrix hybridization protocols

scan_protocol: Standard Affymetrix scanning protocols

data_processing: intensities of the Affymetrix CEL files were background subtracted, quantile normalized, and summarized for each probe set into a logarithm base two intensity value using the robust multi-array average method (RMA) implemented in the Affymetrix package. Subsequently we applied the mean center global adjustment to remove apparent batch effects across the experiments to facilitate between-experiment comparisons.

label: biotin

organism: Mus musculus

source_name: primordial germ cells E11.5

label_protocol: mRNA was amplified using two-rounds of in vitro transcription, and lableled by incorporation of bio-UTP in the second round.

extract_protocol: total RNA was extracted with Qiagen RNeasy kit with in-column DNAse digestion.

tag: strain

tag: cell type

value: PGCs FAC Sorted for Oct4/GFP+

tag: source age

tag: gender


title: Tumor tissue 1 sl77

city: New Delhi

first: Rakhshan

last: Ihsan

state: Delhi

address: Safdurjung Hospital Campus

country: India

institute: Institute of Pathology(ICMR)

description: Gene expression data of tumor tissue of lung cancer patient

hyb_protocol: 10.0 µg of the labeled aRNA in 100 µl of Ocimum's Hyb buffer was denatured at 95°C for 3 mins and was used for hybridization with the Human 40 K A chip and printed at Ocimum Biosolutions, Hyderabad. Hybridization was performed at 50°C for two hrs on Tecan HS 4800 automated Hyb station. Hybridized chips were scanned using Affymetrix 428TMarray scanner at three different PMT gains (40, 50, 60).

scan_protocol: Scanner Used: AFFYMETRIX, 428 Array. Define scan area: Always set size Y to 0. Use array finder to define the size height (1mm on the array finder » 1mm on the OciChip). Height means the distance from the top of the slide to the end of the spotted array (plus safe distance of 2 mm).Set scan settings: The PMT gain settings of the multiple scanning have to be increased with the same distance (usually a distance of 10 between the settings is used). Set the range of the increasing PMT gain setting to achieve both to avoid saturation of the strongest spots at lowest value and to receive reliable signals from the weak spots at the highest PMT gain setting. Scanning was performed at 40, 50 and 60 PMT gain for the hybridized chips.

data_processing: Initially, the data consisted of 20,160 probes including empty spots and control spots (GPL9365 is a 2 x 20K array). These spots were eliminated, leaving 19,700 genes, which were retained in the downstream analysis. The missing values were imputed by K-nearest neighbor (KNN) method. The resulting data was subjected to normalization. Normalization is performed to overcome the systematic bias incorporated in the experiment while handling multiple arrays. There was differences within control and tumor sample profiles. In order to facilitate comparison across arrays, median centering followed by scale adjustment for each array was performed. Median Absolute Deviation (MAD) scaling technique was used to rescale the data on each array

organism: Homo sapiens

source_name: primary lung cancer

label_protocol: Five microgram of total RNA was used for amplification using Express Art® mRNA amplification Kit by linear transcription based RNA amplification system to produce cRNA. Briefly, mRNA is reverse transcribed followed by second strand synthesis priming with a oligo (dT) primer bearing T7 promoter in a thermal cycler using the conditions described in the manual. The resulting cDNA was then purified and was then transcribed with T7 RNA polymerase to generate multiple copies of aminoallyl antisense RNA (aRNA) at 37°C for 16 hrs. aRNA is then labelled with Cy3TM post-labelling reactive dye pack (GE Healthcare, UK) at room temperature and unincorporated Cy3 molecules were removed by purification process.

extract_protocol: Isolation Kit: RNeasy mini Kit (Qiagen). RNA concentration was evaluated by using a NanoDrop (NanoDrop, USA) and RNA quality was evaluated with Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Total RNA that met the quality standards was released for probe generation.

value: primary lung cancer

tag: patient id

tag: age (y)

value: Male

tag: smoking

value: YES

tag: tobacco chewing

value: NO

tag: betelquid chewing

tag: alcohol

tag: histopathology

value: Squamous cell carcinoma


title: Sante_ConvCropProtection_OrgFertilizer_rep2

description: Biological replicate 2 of 4

source_name: Total RNA, Cy5 labeled, isolated from potato tubers, treatment LadyBalfour_ChickenPellets_CopperOxychloride

tag: cultivar

tag: input regime


title: leaf_LLN_NLN_rep1_ds1

city: Budapest

first: Endre

last: Sebestyén

address: Üllői út 26.

department: 1st Department of Pathology and Experimental Cancer Research

country: Hungary

institute: Semmelweis University

description:
DN-LN-rep1-ds1
rep1_ds1_015_04_SN_vs_FN_v2.txt

hyb_protocol: The cRNA of two biological replicates labeled with Cy3 or Cy5 (dye-swap) were hybridized to the Agilent 4X44K Wheat Chip. The chip contains 43603 unique oligos, besides the positive and negative controls. The cRNA samples of Emese (E) and Nadro (N) plants grown at 18°C under normal (NL) and low (LL) light fluences were compared to each other in a simple loop design and E-NL vs. E-LL; N-NL vs. N-LL; E-NL vs. NLL and E-LL vs. N-LL comparisons were made.

scan_protocol: Scanning was performed, using an Agilent High-Resolution Microarray Scanner. The detection of signal intensities and the grid adjustment were accomplished with the Agilent Feature Extraction Software.

data_processing: Intensity data were imported into the R 2.10.0 statistical programming language. Further analysis was carried out using the LIMMA package of BIOCONDUCTOR. Background correction was done using the normexp method. Normalization of data within arrays was done using the loess method, and to normalize the data between arrays, the quantile method was used.

organism: Triticum aestivum

source_name: leaf, low light, Nadro

label_protocol: The RNA amplification and labeling procedure was done according to the manufacturer’s recommendations (Agilent).

growth_protocol: Seeds of wheat plants (Triticum aestivum L.) winter varieties Mv Emese, with a high level of freezing tolerance, and spring variety Nadro, with a low level of freezing tolerance, were sown in loamy soil and sand, 3:1 (v:v). The plants were grown for 10 d in a Conviron PGR 15 growth chamber with a 16 h/8 h light/dark period, at 20/18°C (day/night) with 75% relative humidity and 250 mmol m-2 s-1 (control, normal light) photosynthetic photon flux density (PPFD) at the leaf level, provided by metal halide lamps. Low temperature hardening was carried out in a chamber of the same type at a constant 5°C either under the light conditions of normal growth (light-hardened plants) or at 20 mmol m-2 s-1 PPFD (low light-hardened plants).

extract_protocol: Two biological replicates with four technical replicates (each replicate consisted of five plants) were harvested. RNA was isolated using TRIzol reagent (Invitrogen) and the samples were DNase I treated and cleaned up with MinElute Kit (Qiagen) according to the manufacturer’s instructions. The RNA Integrity Number (RIN) of the samples was determined using the Agilent BioAnalyzer, and, equal amounts of RNA from the four technical replicates were pooled and used for cRNA amplification.

tag: variety

value: Nadro

tag: tissue

value: leaf

tag: light condition

value: low light

source_name: leaf, normal light, Nadro

value: normal light


title: Sante_ConvCropProtection_OrgFertilizer_rep1

description: Biological replicate 1 of 4

source_name: Total RNA, Cy5 labeled, isolated from potato tubers, treatment LadyBalfour_ChickenPellets_Comcat

value: Sante

tag: sample size

value: 4-5 tubers

tag: treatment

tag: growth condition

tag: sample type


title: leaf_NLE_LLE_rep1_ds1

description:
LE-DE-rep1-ds1
rep1_ds1_015_02_FE_vs_SE_v2.txt

source_name: leaf, normal light, Mv Emese

value: Mv Emese

source_name: leaf, low light, Mv Emese


title: leaf_LLE_LLN_rep1_ds1

description:
DE-DN-rep1-ds1
rep1_ds1_015_03_SE_vs_SN_v2.txt


title: leaf_LLN_NLN_rep2_ds2

description:
DN-LN-rep2-ds2
rep2_ds2_014_04_SN_vs_FN.txt


title: leaf_NLE_NLN_rep1_ds1

description:
LE-LN-rep1-ds1
rep1_ds1_015_01_FE_vs_FN_v2.txt


title: leaf_LLE_LLN_rep2_ds2

description:
DE-DN-rep2-ds2
rep2_ds2_014_03_SE_vs_SN.txt


title: leaf_NLE_LLE_rep2_ds2

description:
LE-DE-rep2-ds2
rep2_ds2_014_02_FE_vs_SE.txt


title: leaf_LLN_NLN_rep2_ds1

description:
DN-LN-rep2-ds1
rep2_ds1_013_04_SN_vs_FN.txt


title: leaf_NLE_LLE_rep2_ds1

description:
LE-DE-rep2-ds1
rep2_ds1_013_02_FE_vs_SE.txt


title: leaf_NLE_NLN_rep1_ds2

description:
LE-LN-rep1-ds2
rep1_ds2_012_01_FE_vs_FN.txt


title: leaf_LLE_LLN_rep2_ds1

description:
DE-DN-rep2-ds1
rep2_ds1_013_03_SE_vs_SN.txt


title: leaf_NLE_NLN_rep2_ds2

description:
LE-LN-rep2-ds2
rep2_ds2_014_01_FE_vs_FN.txt


title: leaf_NLE_LLE_rep1_ds2

description:
LE-DE-rep1-ds2
rep1_ds2_012_02_FE_vs_SE.txt


title: leaf_NLE_NLN_rep2_ds1

description:
LE-LN-rep2-ds1
rep2_ds1_013_01_FE_vs_FN.txt


title: leaf_LLE_LLN_rep1_ds2

description:
DE-DN-rep1-ds2
rep1_ds2_012_03_SE_vs_SN.txt


title: leaf_LLN_NLN_rep1_ds2

description:
DN-LN-rep1-ds2
rep1_ds2_012_04_SN_vs_FN.txt


title: 5_LS_EPI_Double

status: Public on Jan 30 2012

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

hyb_protocol: Affymetrix protocol

scan_protocol: Hewlett-Packard GeneArray Scanner G25Time: 0Time: 0A.

data_processing: GCRMA (using gcrma package from R/Bioconductor)

source_name: 5, LS, EPI, Double

label_protocol: Affymetrix single and double amplification protocol

extract_protocol: QIAGEN Rneasy Kit

value: lesional psoriatic skin

tag: patient

tag: condition

value: Lesional

tag: region

value: EPI (epidermis)

tag: amplification

value: Double

tag: material

value: sliced section


title: 5_LS_PD_Double

source_name: 5, LS, PD, Double

value: PD (papillary dermis)


title: 5_LS_ICs_Double

source_name: 5, LS, ICs, Double

value: ICs (infiltrated cells)


title: Collection day 25 biological replicate 2, technical replicate 2

city: Oeiras

first: Marta

last: Simões

address: Quinta do Marquês - EAN

country: Portugal

institute: IBET

hyb_protocol: Hybridization and pre and post-hybridization washing steps were performed according to Lorenz et al. (Lorenz et al. Journal of Visualized Experiments 2009, 25) except that 2 μg of Cy-labeled amplified RNA was used to hybridize with the array after fragmentation with Fragmentation Reagent (Ambion, Cat. #AM8740).

scan_protocol: Slides were scanned on a ProScanArray™ confocal scanner (Perkin Elmer) equipped with 532 nm and 635 nm lasers.

data_processing: Numerical signal data was obtained using ImaGene software v6.1 (Biodiscovery). Poor quality spots (i.e. merged, excessively large or small diameter spots) that passed the specified thresholds were flagged manually. Duplicated probes as well as empty spots that were on the array to serve as internal controls were also flagged. Raw microarray data was then filtered using the methods described by Wang et al. (Wang et al. Nucleic Acids Res 2001, 29:e75) and converted into a file adequate to be imported into BRB-Array Tools software v3.7  (http://linus.nci.nih.gov/BRB-ArrayTools.html) by using an in house Perl script. Raw signal intensity data from the 30 slides were Log2 transformed and normalized by the print-tip Lowess method on BRB.  Wang plus ImaGene flagging was used to filter signal spots. Samples were clustered hierarchically using centered correlation and average linkage methods in order to check for hybridization reproducibility. Biological replicate 2 from Day15 (samples Day15_2_1 and Day15_2_2) was excluded from further analyses for not fullfil the clustering requirements. Other users are advised to do the same. To investigate differential expressed gene patterns along embryo development a time course analysis was conducted on BRB with a maximum significance level and false discovery rate (FDR) of 0.001. This plug-in applies a regression model to identify genes whose expression is varying over time, based on BRB normalized Log2 ratio.

organism: Pinus pinaster

label_protocol: Messenger RNA amplification and amino allyl UTP nucleotide incorporation were performed using Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion) after treatment with TURBO DNase (Ambion). One hundred nanograms of DNase-treated total RNA was amplified in two sequential rounds of amplification following instructions provided by the supplier. Sample fluorescent labeling was performed according to Lorenz et al. (Lorenz et al. Journal of Visualized Experiments 2009, 25).

growth_protocol: Maritime pine immature female cones were randomly collected from open-pollinated plus trees growing in a clonal orchard at Escaroupim National Forest, Portugal. Cone collection was performed at five different dates, from 3-5 trees at each date, during July and August 2007. Seeds were removed from cones and opened for isolation of the dominant embryo. Embryos were quickly observed under a dissecting stereomicroscope for evaluation of developmental stage according to the staging system of Pullman and Webb (Pullman and Webb. TAPPI R&D Division Biological Sciences Symposium 1994) as described by Gonçalves et al. (Gonçalves et al. Planta 2005, 222(3):556–563). Embryos were pooled into five different developmental periods according to the collection date, with each collection date containing one or several consecutive embryo developmental stages as follows: Day 0 (stages T0, T1 and T2); Day 5 (stages T3 and T4); Day 11 (stage T4B); Day 15 (stage T5) and Day 25 (stage T7). Embryo samples were kept frozen at -80ºC until total RNA extraction.

extract_protocol: Total RNA extracted using RNeasy Plant Mini Kit (Qiagen). On-column DNaseI digestion was performed with the RNase-Free DNase Set (Qiagen) according to manufacturer’s instructions. In some cases total RNA from different extractions from the same collection date was pooled to reach a total of 60 embryos in each sample.

value: Zygotic embryos

tag: Stage

tag: pool

value: 60 embryos

source_name: Reference sample

value: Reference sample composed by a pool of 200 ng of total RNA from each biological replicate of Day0, Day5, Day11, Day15 and Day25.


title: NSC_3

city: Mansoura

first: Hany

middle: El Sayed

last: Marei

state: Dakahlaya

address: Gomhoraya

department: Histology

country: Egypt

institute: Fac. Vet Med

description: I6 line 29, NIH

hyb_protocol: cRNA samples (750 ng) were hybridized onto Illumina SentrixH HumanHT-12 v3 Expression Bead Chips at 58 °C overnight (19 h).

scan_protocol: Chips were scanned with the Illumina Bead Array Reader (Factor = 1, PMT= 520, Filter = 100%), and the numerical results were extracted with GenomeStudio using the Gene Expression Module v.1.0.6.

data_processing: Raw data were background-subtracted and normalized using the quantile normalization method (Illumina Genome Studio). Normalized data were imported in BRB Array Tools, log2 transformed and filtered for genes with significant detection pvalue (0.05).

source_name: hENSC

label_protocol: Approximately 400 ng of total RNA per each sample served as the input to generate biotin-labeled cRNA using a linear amplification kit (Ambion, Austin, TX, United States). RNA and biotinylated cRNA concentrations were confirmed with Nanodrop ND-1000 and controlled for quality using a BioRad Experion electrophoresis station.

growth_protocol:
The olfactory bulbs (OBs) were harvested from adult patients undergoing craniotomy at the Institute of Neurosurgery, Catholic University, Rome. Informed consent was obtained according to protocols approved by the Ethical Committee of the Catholic University. Immediately after removal, the OBs were dissociated in Papain 0.1% (Sigma-Aldrich, St. Louis, MO) for 30 minutes at 37◦C. Dissociated cells were cultured in the presence of human recombinant EGF (20 ng/ml; PeproTech, Rocky Hill, NJ), human recombinant bFGF (10 ng/ml; PeproTech), and LIF (20 ng/ml; Immunological Sciences, Rome, Italy) in DMEM/F12 (1:1) serum-free medium (Invitrogen, Carlsband, CA) containing L glutamine 2 mM, glucose 0.6%, putrescine 9.6 ug/ml, progesterone 0.025 mg/ml, sodium selenite 5.2 ng/ml, insulin 0.025 mg/ml, apo-transferrin sodium salt 0.1 mg/ml, sodium bicarbonate 3 mM, Hepes 5 mM, BSA 4 mg/ml, heparin 4 ug/ml. Primary neurospheres were dissociated with Accutase (Invitrogen) for 4 minutes at 37◦C, serially diluted and plated one cell per mini-well onto 96-well plates.

Mini-wells containing one single cell were marked after microscopic confirmation and assessed for secondary neurosphere generation after one week. Secondary neurospheres were subsequently dissociated, plated at the density of 10^3 cells/cm2 in serum-free medium containing EGF and bFGF, and passaged up to P30. Between P7 and P10, parallel cultures were established in which cells were grown as adherent monolayers in medium containing EGF and bFGF supplemented with 5% fetal calf serum (Hyclone, Logan, UT). Cells were counted with a hemacytometer every 48 hours. Differentiation assays were performed by 14 days after plating on Matrigel-coated glass coverslips in the absence of EGF and bFGF and in the presence of 1% fetal calf serum (Hyclone) supplemented with 3'-5'-cyclic adenosine monophosphate (cAMP) 50 mM, all-trans retinoic acid 5 mM (Sigma Aldrich), and triiodothyronine (T3) 30 nM (Sigma Aldrich).

extract_protocol: Total cellular RNA was isolated from embryonic NSCs (n=3) and adult human OB-NSCs (n=6) using Trizol (Invitrogen).

tag: cell line

value: I6 line 29

tag: developmental stage

value: embryonic

tag: cell type

value: human embryonic neural stem cells (hENSCs)


title: NSC_1

description: I6 line 29, NIH


title: OB1 P25

source_name: OBNSC, P25

value: olfactory bulb

value: adult

value: olfactory bulb neural stem cells (OBNSCs)

tag: passage


title: NSC_2

description: I6 line 29, NIH


title: OB2 P20

source_name: OBNSC, P20

tag: tissue


title: OB2 P22

source_name: OBNSC, P22


title: OB1 P20


title: Collection day 25 biological replicate 3, technical replicate 1


title: OB1 P9

source_name: OBNSC, P9


title: Collection day 25 biological replicate 3, technical replicate 2


title: OB2 P9


title: 5_NL_RD_Double

source_name: 5, NL, RD, Double

value: non-lesional psoriatic skin

value: Non-Lesional

value: RD (reticular dermis)


title: Collection day 25 biological replicate 1, technical replicate 1


title: 6_NL_RD_Double

source_name: 6, NL, RD, Double


title: 5_NL_EPI_Double

source_name: 5, NL, EPI, Double

value: EPI (epidermis)


title: Collection day 25 biological replicate 1, technical replicate 2


title: Collection day 25 biological replicate 2, technical replicate 1


title: 6_LS_EPI_Double

source_name: 6, LS, EPI, Double

value: lesional psoriatic skin

value: Lesional

value: Double


title: Collection day 15 biological replicate 3, technical replicate 2


title: 6_LS_PD_Double

source_name: 6, LS, PD, Double

value: PD (papillary dermis)

value: sliced section


title: 6_LS_ICs_Double

source_name: 6, LS, ICs, Double

value: ICs (infiltrated cells)


title: Collection day 15 biological replicate 3, technical replicate 1

value: Zygotic embryos

value: 60 embryos

value: Reference sample composed by a pool of 200 ng of total RNA from each biological replicate of Day0, Day5, Day11, Day15 and Day25.


title: 6_NL_EPI_Double

source_name: 6, NL, EPI, Double


title: Collection day 15 biological replicate 2, technical replicate 2


title: 7_LS_ICs_Double

source_name: 7, LS, ICs, Double


title: 7_NL_EPI_Double

source_name: 7, NL, EPI, Double


title: Collection day 15 biological replicate 2, technical replicate 1


title: 7_LS_EPI_Double

source_name: 7, LS, EPI, Double


title: 6_LS_whole_Double

source_name: 6, LS, whole, Double

value: whole


title: 7_NL_RD_Double

source_name: 7, NL, RD, Double


title: 7_NL_whole_Double

source_name: 7, NL, whole, Double


title: 7_LS_PD_Double

source_name: 7, LS, PD, Double


title: Collection day 11 biological replicate 3, technical replicate 1

source_name: Reference sample


title: Collection day 15 biological replicate 1, technical replicate 1


title: Collection day 11 biological replicate 3, technical replicate 2


title: WT vs sigI deletion mutant OD2

city: Baltimore

first: JongHee

last: Lee

state: MD

address: 1550 Orleans St. CRB2

department: Medicine

institute: Johns Hopkins Medical School

hyb_protocol: Slides prehybed for >1 hour in prehyb buffer (5X SSC, 0.1% SDS, 1% BSA), washed 2X for 1 minute in water, 15 seconds in isopropanol, dried by centrifugation. Probes added to slides, sealed in incubation chambers and submerged in 42 degree incubator overnight. Arrays washed in increasingly stringent washes: 5 minutes at 42 degrees low stringency wash (0.2%SDS, 1XSSC), 10 minutes lower stringency wash (0.2%SDS, 0.1XSSC), 4 times 1 minute in 0.1XSSC, 10 seconds in 0.01XSSC. Slides dried by centrifugation.

scan_protocol: Arrays scanned in with a GenePix4000B using GenePix 4 scanning software.

data_processing: Data analysis conducted with Acuity 4 software

organism: Mycobacterium tuberculosis CDC1551

source_name: wild type

label_protocol: standard amino-allyl labelling protocol from TIGR. cDNA made with Superscript III using aminoallyl dUTP

growth_protocol: Grown to phase (OD600 1 and 2) in roller bottles with 200-400 mL Middlebrook 7H9 media+ADC and Tween at 37℃

extract_protocol: Pellets were bead beat in the presence of trizol. Aqueus phase isolated using phase lock gel. RNA precipitated with isopropyl alchol

tag: genotype/variation

value: wild type

source_name: sigma factor sigI deletion mutant

value: sigma factor sigI deletion mutant


title: 5_NL_whole_Double

source_name: 5, NL, whole, Double


title: 4_LS_whole_Double

source_name: 4, LS, whole, Double

value: block


title: 7_LS_whole_Double

source_name: 7, LS, whole, Double


title: Collection day 11 biological replicate 2, technical replicate 2


title: WT vs sigI deletion mutant OD1


title: Collection day 15 biological replicate 1, technical replicate 2


title: 5_LS_whole_Double

source_name: 5, LS, whole, Double


title: 3_LS_whole_Double

source_name: 3, LS, whole, Double


title: 6_NL_whole_Double

source_name: 6, NL, whole, Double

value: non-lesional psoriatic skin


title: Collection day 11 biological replicate 2, technical replicate 1


title: 2_NL_whole_Double

source_name: 2, NL, whole, Double

value: Non-Lesional


title: 3_NL_whole_Double

source_name: 3, NL, whole, Double


title: 4_NL_whole_Double

source_name: 4, NL, whole, Double


title: Collection day 11 biological replicate 1, technical replicate 2


title: Collection day 11 biological replicate 1, technical replicate 1


title: 1_LS_whole_Double

source_name: 1, LS, whole, Double


title: Collection day 5 biological replicate 3, technical replicate 2

tag: stages

value: T3 and T4


title: 2_LS_whole_Double

source_name: 2, LS, whole, Double


title: 1_NL_whole_Double

source_name: 1, NL, whole, Double


title: 2_NL_whole_Single

source_name: 2, NL, whole, Single

value: Single


title: Mammospheres induced to differentiate in serum Affy#863A_--DMS

city: Hamilton

first: Robin

last: Hallett

state: Ontario

address: 1200 Main St W

department: Biochemistry and Biomedical Sciences

country: Canada

institute: McMaster University

description: gene expression data from mammospheres induced to differentiate

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The data was analyzed with Genespring

source_name: mammospheres induced to differentiate (7 days) in serum

label_protocol: RNA from 3 independent tumorsphere, mammosphere, and mammospheres induced to differentiate cell populations was used to prepare cRNA probes for hybridization to MOE430A Gene ChipsTM in accordance with manufacturer’s protocols (Affymetrix, Santa Clara, California)

growth_protocol: tumorspheres and mammospheres were passaged every 7 days in mouse stem cell media and harvested for RNA between passages 3-5. Mammospheres were placed in serum containing media and allowed to differentiate for 7 days.

extract_protocol: Total RNA was isolated from tumorspheres, mammospheres or mammospheres induced to differentiate using an RNAeasy mini prep kit (QIAGEN, Hilden, Germany) according to the manufacturer’s protocol

tag: strain

value: FVB/N

value: mammospheres induced to differentiate in serum


title: Collection day 5 biological replicate 3, technical replicate 1

source_name: Reference sample


title: Collection day 5 biological replicate 2, technical replicate 2


title: Collection day 5 biological replicate 2, technical replicate 1


title: Collection day 5 biological replicate 1, technical replicate 1


title: Mammospheres induced to differentiate in serum Affy#861A_--DMS


title: 3_LS_whole_Single

source_name: 3, LS, whole, Single

value: lesional psoriatic skin

value: Lesional


title: 4_NL_whole_Single

source_name: 4, NL, whole, Single


title: Collection day 5 biological replicate 1, technical replicate 2


title: Collection day 0 biological replicate 3, technical replicate 2

value: T0, T1 and T2


title: 2_LS_whole_Single

source_name: 2, LS, whole, Single


title: Mammospheres Affy#860A_--UMS

description: gene expression data from mammospheres

source_name: mammosphere (passage 3-5)

value: mammospheres


title: hMSC_DMSO_passage 2_donor3

city: Glasgow

first: Claire

middle: Judith

last: Cairney

address: Garscube Estate, Switchback Rd

department: College of Veterinary, Medical and Life Sciences

country: United Kingdom

institute: University of Glasgow

description: Gene expression at passage 2 after expansion with DMSO

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 2x blocking agent and 1x fragmentation buffer (Agilent) following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent hybridisation buffer was added to the fragmentation mixture and 100ul was hybridised to Agilent Whole Human Genome 4x44k Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridisation oven.  After hybridisation, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash Buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analysed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 014850_D_20070207) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Bone marrow MSC, DMSO, passage2, donor3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.8 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: Human MSCs were derived from bone marrow harvested from the iliac crest of patients undergoing osteomy or diagnostic bone marrow.  Mono-nuclear cells (MNC) were seeded at 800000 MNC/cm2 in DMEM supplemented with 10% Foetal bovine serum.

extract_protocol: RNA was extracted using the Nucleospin II RNA extraction kit (Macherey-Nagel, Duren, Germany) following manufacturers instructions.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: hMSCs were expanded in the presence of 10uM 3/689 or DMSO and harvested at passage 2 or passage 8.

value: Iliac crest

value: Human mesenchymal stem cells (hMSC)

tag: age

value: 14 years

tag: gender

value: Male


title: 3_NL_whole_Single

source_name: 3, NL, whole, Single

tag: patient

value: whole


title: hMSC_3/689_passage 8_donor3

description: Gene expression at passage 8 after expansion with 10uM 3/689

source_name: Bone marrow MSC, 3/689, passage8, donor3


title: Mammospheres Affy#859A_--UMS

description: gene expression data from mammospheres

tag: sample type


title: Collection day 0 biological replicate 3, technical replicate 1

value: Zygotic embryos

value: 60 embryos

value: Reference sample composed by a pool of 200 ng of total RNA from each biological replicate of Day0, Day5, Day11, Day15 and Day25.


title: Mammospheres induced to differentiate in serum Affy#862A_--DMS


title: Mammospheres Affy#858A-R_UMS

description: gene expression data from mammospheres


title: hMSC_3/689_passage 2_donor3

description: Gene expression at passage 2 after expansion with 10uM 3/689

source_name: Bone marrow MSC, 3/689, passage2, donor3


title: hMSC_DMSO_passage 8_donor2

description: Gene expression at passage 8 after expansion with DMSO

source_name: Bone marrow MSC, DMSO, passage8, donor2

value: 66 years


title: 4_LS_whole_Single

source_name: 4, LS, whole, Single

tag: condition

tag: region

value: block


title: hMSC_3/689_passage 8_donor2

source_name: Bone marrow MSC, 3/689, passage8, donor2


title: 1_LS_whole_Single

source_name: 1, LS, whole, Single

tag: amplification

value: Single

tag: material


title: hMSC_DMSO_passage 8_donor3

source_name: Bone marrow MSC, DMSO, passage8, donor3


title: Tumorspheres Affy#1100A_-TMS

description: gene expression data from tumorspheres

source_name: tumorspheres (passage 3-5)

value: tumorspheres


title: hMSC_3/689_passage 2_donor2

source_name: Bone marrow MSC, 3/689, passage2, donor2


title: 1_NL_whole_Single

source_name: 1, NL, whole, Single

value: non-lesional psoriatic skin

value: Non-Lesional


title: Collection day 0 biological replicate 2, technical replicate 1

tag: pool

source_name: Reference sample


title: Collection day 0 biological replicate 2, technical replicate 2


title: hMSC_DMSO_passage 2_donor2

source_name: Bone marrow MSC, DMSO, passage2, donor2


title: Tumorspheres Affy#1101A_-TMS

description: gene expression data from tumorspheres


title: intestine_group6_24hpi_chick14

status: Public on Jan 29 2012

first: Dirkjan

last: Schokker

address: Droevendaalsesteeg 1

department: Wageningen Livestock Research

institute: Wageningen UR

hyb_protocol: Total RNA (5 μg) was hybridized using the MICROMAX TSA labeling and detection kit (PerkinElmer, Wellesley, MA, USA) according to suppliers instruction with minor modifications as described by Van Hemert et al. (van Hemert et al., 2007).

scan_protocol: After signal amplification, the microarrays were dried and scanned for Cy5 and Cy3 fluorescence intensities using a Axon GenePix® Microarray Scanner and GenePix Pro 6.1 software (Molecular Devices, Sunnyvale, CA, USA).

data_processing: Bioconductor limma package was used, background correction with normexp, data was log2-transformed, loess normalized (within arrays) and quantile normalized (between arrays)

organism: Gallus gallus

source_name: jejunum, group 6, 24 hours pi

label_protocol: Total RNA (5 μg) was labeled using the MICROMAX TSA labeling and detection kit (PerkinElmer, Wellesley, MA, USA) according to suppliers instruction with minor modifications as described by Van Hemert et al. (van Hemert et al., 2007).

extract_protocol: Frozen jejunum samples were homogenized in liquid nitrogen using a mortar and pestle. 50-100 mg of the homogenized tissue samples were dissolved in 1 ml of TRIzol reagent (Invitrogen, Breda, The Netherlands) using a syringe and 21-G needle passing the lysate for 10 times. After centrifugation the supernatant was transferred to a fresh tube and phase separation with chloroform was performed. The RNA was precipitated using 500 μl 2-propanol and used for microarray analysis.

tag: infection

value: Salmonella

value: intestine

tag: group

source_name: total RNA from pooled intestine all samples

tag: reference

value: RNA reference pool (from pooled intestine all samples)


title: intestine_group6_48hpi_chick27

source_name: jejunum, group 6, 48 hours pi


title: intestine_group6_24hpi_chick17


title: intestine_group6_48hpi_chick23


title: hMSC_DMSO_passage 2_donor1

source_name: Bone marrow MSC, DMSO, passage2, donor1

value: Iliac crest

tag: cell type

value: 11 years


title: hMSC_DMSO_passage 8_donor1

source_name: Bone marrow MSC, DMSO, passage8, donor1

tag: tissue

value: Human mesenchymal stem cells (hMSC)


title: Tumorspheres Affy#1099A_-TMS

description: gene expression data from tumorspheres


title: Collection day 0 biological replicate 1, technical replicate 2

value: T0, T1 and T2


title: hMSC_3/689_passage 2_donor1

source_name: Bone marrow MSC, 3/689, passage2, donor1

value: Male


title: Collection day 0 biological replicate 1, technical replicate 1

value: Zygotic embryos


title: intestine_group6_8hpi_chick9

source_name: jejunum, group 6, 8 hours pi


title: hMSC_3/689_passage 8_donor1

source_name: Bone marrow MSC, 3/689, passage8, donor1


title: intestine_group5_24hpi_chick12

source_name: jejunum, group 5, 24 hours pi


title: intestine_group5_24hpi_chick20


title: intestine_group6_48hpi_chick26


title: intestine_group6_48hpi_chick24


title: intestine_group6_24hpi_chick18


title: intestine_group6_24hpi_chick16


title: intestine_group5_8hpi_chick2

source_name: jejunum, group 5, 8 hours pi


title: intestine_group5_48hpi_chick23

source_name: jejunum, group 5, 48 hours pi


title: intestine_group6_8hpi_chick6


title: intestine_group5_24hpi_chick16


title: intestine_group6_8hpi_chick5


title: intestine_group6_8hpi_chick4


title: intestine_group5_8hpi_chick5


title: intestine_group4_48hpi_chick24

source_name: jejunum, group 4, 48 hours pi


title: intestine_group5_48hpi_chick29


title: intestine_group5_48hpi_chick22


title: intestine_group5_48hpi_chick25


title: intestine_group4_48hpi_chick29


title: intestine_group4_24hpi_chick14

source_name: jejunum, group 4, 24 hours pi


title: intestine_group5_8hpi_chick1


title: Control_3

city: Omaha

first: Jessica

last: Winkler

address: 985800 Nebraska Medical Center- DRC I

department: Pharmacology and Experimental Neuroscience

institute: University of Nebraska Medical Center

description:
Monkey_332
Gene expression data from the frontal lobe of control Rhesus brain

hyb_protocol: After fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45oC on Human U95Av2 GeneChips were washed and stained.

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

data_processing: The data were analyzed with GeneSring 7.0 software (Agilent Technologies, Palo Alto, CA.)

organism: Macaca mulatta

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

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

treatment_protocol: Intravenously incoculated with a cell-free stock of SIVmac182.

value: Frontal Lobe

tag: phenotype

value: Control

tag: age at sacrafice

value: 92-114 weeks postinoculation


title: intestine_group4_24hpi_chick13


title: intestine_group4_24hpi_chick17


title: intestine_group4_48hpi_chick25


title: intestine_group5_8hpi_chick7


title: SIV infected_3

description:
Monkey_291
Gene expression data from the frontal lobe of SIV infected Rhesus brain

source_name: brain_frontal_lobe_SIV infected

value: Chronic SIV Infection


title: intestine_group5_24hpi_chick17


title: SIV infected_4

description:
Monkey_304
Gene expression data from the frontal lobe of SIV infected Rhesus brain


title: Control_4

description:
Monkey_357
Gene expression data from the frontal lobe of control Rhesus brain


title: MEFs_4hr_1 mM H2O2_rep1

city: Bunkyo-ku

first: Hiroyasu

last: Nakano

state: Tokyo

address: 2-1-1 Hongo

department: School of Medicine

country: Japan

institute: Juntendo University

description: Gene expression after 4 hr in 1 mM of H2O2-treated MEFs.

hyb_protocol: According to standard Agilent protocol.

scan_protocol: Agilent scanner and Agilent Feature Extraction software.

data_processing: gProcessedSignal; processed Cy3 signal.

source_name: MEFs, 4 hr, 1 mM H2O2

label_protocol: Labeled with Cy3 according to standard protocol.

growth_protocol: Primary murine embryonic fibroblasts (MEFs) were cultured in 10% FCS containing DMEM at 37 ºC in a humidified incubator with CO2.

extract_protocol: RNAs were extracted from MEFs with Trizol (Tel-Test) according to the manufacturer's instructions.

treatment_protocol: MEFs were untreated or stimulated with H202 (1 mM) for 2 or 4 hrs.

value: murine embryonic fibroblasts (MEFs)

tag: treatment

tag: treatment time

value: 4 hours


title: MEFs_4hr_1 mM H2O2_rep2


title: Control_2

description:
Monkey_331
Gene expression data from the frontal lobe of control Rhesus brain


title: intestine_group4_48hpi_chick22

tag: age


title: MEFs_2hr_1 mM H2O2_rep2

description: Gene expression after 2 hr in 1 mM of H2O2-treated MEFs.

source_name: MEFs, 2 hr, 1 mM H2O2

value: 2 hours


title: Control_6

description:
Monkey_393
Gene expression data from the frontal lobe of control Rhesus brain


title: Control_5

description:
Monkey_382
Gene expression data from the frontal lobe of control Rhesus brain


title: intestine_group4_24hpi_chick12


title: Control_1

description:
Monkey_298
Gene expression data from the frontal lobe of control Rhesus brain


title: intestine_group4_48hpi_chick21


title: SIV infected_1

description:
Monkey_227
Gene expression data from the frontal lobe of SIV infected Rhesus brain


title: intestine_group4_8hpi_chick7

source_name: jejunum, group 4, 8 hours pi


title: MEFs_0hr_rep2

description: Gene expression of untreated MEFs.

source_name: MEFs, 0 hr

value: untreated

value: 0 hour


title: intestine_group4_24hpi_chick11

value: Salmonella

value: intestine

source_name: total RNA from pooled intestine all samples


title: intestine_group4_8hpi_chick4

value: RNA reference pool (from pooled intestine all samples)


title: E_coli_negativ_control_right_chamber_rep2

status: Public on Jan 28 2012

city: Leipzig

first: Simona

middle: Gabriele

last: Huwiler

address: Bruederstr. 34

department: Institute of Biochemistry

country: Germany

institute: University of Leipzig

description:
E_coli_neg_right_rep2
E. coli K-12 grown aerobically in continous cultivation, unexposed sample from right chamber/bioreactor

hyb_protocol: Hybridization, washing and staining were done on an Affymetrix gene chip processing platform at the Functional Genomics Centre Zurich (FGCZ, Switzerland) following in principal the GeneChip® Expression Analysis Technical Manual of Affymetrix (Appendix C & D). GeneChip® E. coli Genome 2.0 Arrays (Affymetrix) were hybridized with 2.2 – 2.6 µg labeled cDNA for 16 h at 45°C and 60 rpm. The washing and staining was done according to the protocol Mini_prok2v1_450 on the GeneChip® Fluidics Station 450 (Affymetrix).

scan_protocol: Scanning was done with the GeneChip® Scanner 3000 7G (Affymetrix) using the Affymetrix Command Console as instrument control software.

data_processing: Quality control and microarray data analysis of all 60 chips was done using R/Bioconductor (http://www.bioconductor.org/). Signal intensity files (CEL files) of all 60 chips were summarized using RMA (robust multi array average) as processing algorithm and quantile normalization. A modified t-test using limma was performed for comparison of experimental conditions. See also additional files containing only E.coli K-12 MG1655 probes with P-values and ratio.

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

label_protocol: 3’-terminal labeling of cDNA was performed in a 30-µl reaction containing 2.2 - 3 µg fragmented cDNA, 6 µl 5x terminal transferase reaction buffer, 2.4 µl GeneChip® DNA labeling reagent (7.5 mM, Affymetrix), 2.4 µl terminal desoxynucleotide transferase (Promega) and nuclease-free water. The reaction was incubated for 75 min at 37°C and stopped by adding 2 µl 0.2 M EDTA (Gibco).

growth_protocol: Escherichia coli K-12 strain MG1655 was cultivated aerobically (~0.5 l/min air supply) in a defined mineral medium containing 1 g/l glucose in continous cultures growing in a chemostat (dilution rate = 0.4 h-1, working volume = 100 ml).

extract_protocol: Samples of ~7.2 ml bacterial culture were mixed with 0.8 ml stop solution, pelleted and total RNA was purified using RNeasy Mini Kit (Qiagen). DNase treatment was done twice with RQ1 DNase (Promega) to remove genomic DNA. cDNA synthesis was done according to the GeneChip® Expression Analysis Technical Manual of Affymetrix using M-MLV reverse transcriptase (Promega), without DTT addition. 13 µl of EB buffer were used for elution of cDNA after its clean-up with the MiniElute CR purification Kit (Qiagen). cDNA fragmentation was done in a 20-µl reaction containing 3.5 µg cDNA, 2 µl 10x One Phor-All buffer, 2 µl DNase I (diluted to 0.2 U/ µl, Amersham Pharmacia Biotech) in nuclease-free water. After incubation for 4 min at 37°C, DNase I was heat inactivated at 98°C for 10 min.

treatment_protocol: Samples of magnetic field-treated or sham-treated cells were withdrawn as fast as possible from the bioreactor (not later than 3 min) after the specified treatement period. Samples taken during intermittent exposure were withdrawn in the 4 min exposure break. Unexposed samples were withdrawn as fast as possible during steady-state conditions in the chemostat. In the response control experiment, samples were withdrawn 10 min after addition of 1 mM H2O2 (treated culture) or the equivalent water volume (reference culture).

value: unexposed, right chamber/bioreacator

tag: treatment duration

tag: growth condition

value: steady-state continuous cultivation (dilution rate of 0.4 h-1), aerobic

tag: medium

value: defined mineral medium with 1 g/l glucose


title: E_coli_negativ_control_right_chamber_rep3

description:
E_coli_neg_right_rep3
E. coli K-12 grown aerobically in continous cultivation, unexposed sample from right chamber/bioreactor


title: E_coli_response_control_1mM_H2O2_added_rep3

description:
E_coli_resp_H2O2_rep3
E. coli K-12 grown aerobically in continous cultivation, unexposed sample treated with 1mM H2O2 for 10min

value: unexposed, treated with 1mM H2O2

value: 10 min


title: E_coli_negativ_control_left_chamber_rep3

description:
E_coli_neg_left_rep3
E. coli K-12 grown aerobically in continous cultivation, unexposed sample from left chamber/bioreactor

value: unexposed, left chamber/bioreacator


title: E_coli_negativ_control_right_chamber_rep1

description:
E_coli_neg_right_rep1
E. coli K-12 grown aerobically in continous cultivation, unexposed sample from right chamber/bioreactor


title: MEFs_2hr_1 mM H2O2_rep1


title: MEFs_0hr_rep1

description: Gene expression of untreated MEFs.


title: intestine_group4_8hpi_chick3


title: E_coli_response_control_1mM_H2O2_added_rep1

description:
E_coli_resp_H2O2_rep1
E. coli K-12 grown aerobically in continous cultivation, unexposed sample treated with 1mM H2O2 for 10min


title: E_coli_response_control_1mM_H2O2_added_rep2

description:
E_coli_resp_H2O2_rep2
E. coli K-12 grown aerobically in continous cultivation, unexposed sample treated with 1mM H2O2 for 10min


title: E_coli_response_control_water_added_rep2

description:
E_coli_resp_water_rep2
E. coli K-12 grown aerobically in continous cultivation, unexposed sample treated with water

value: unexposed, treated with water


title: E_coli_response_control_water_added_rep1

description:
E_coli_resp_water_rep1
E. coli K-12 grown aerobically in continous cultivation, unexposed sample treated with water


title: E_coli_response_control_water_added_rep3

description:
E_coli_resp_water_rep3
E. coli K-12 grown aerobically in continous cultivation, unexposed sample treated with water


title: E_coli_treated_powerline_interm_15h_rep3

description:
E_coli_Tpi_15h_rep3
E. coli K-12 grown aerobically in continous cultivation treated with power line intermittent (2 min on, 4 min off) magnetic field for 15 h

value: treated power line intermittent (2 min on, 4 min off) magnetic field


title: E_coli_sham_powerline_interm_2.5h_rep3

description:
E_coli_Spi_2.5h_rep3
E. coli K-12 grown aerobically in continous cultivation sham-treated with power line intermittent (2 min on, 4 min off) magnetic field for 2,5 h

value: sham-treated power line intermittent (2 min on, 4 min off) magnetic field


title: E_coli_sham_powerline_interm_15h_rep3

description:
E_coli_Spi_15h_rep3
E. coli K-12 grown aerobically in continous cultivation sham-treated with power line intermittent (2 min on, 4 min off) magnetic field for 15 h


title: E_coli_negativ_control_left_chamber_rep1

description:
E_coli_neg_left_rep1
E. coli K-12 grown aerobically in continous cultivation, unexposed sample from left chamber/bioreactor


title: E_coli_negativ_control_left_chamber_rep2

description:
E_coli_neg_left_rep2
E. coli K-12 grown aerobically in continous cultivation, unexposed sample from left chamber/bioreactor


title: E_coli_sham_powerline_interm_15h_rep2

description:
E_coli_Spi_15h_rep2
E. coli K-12 grown aerobically in continous cultivation sham-treated with power line intermittent (2 min on, 4 min off) magnetic field for 15 h


title: E_coli_treated_powerline_interm_15h_rep1

description:
E_coli_Tpi_15h_rep1
E. coli K-12 grown aerobically in continous cultivation treated with power line intermittent (2 min on, 4 min off) magnetic field for 15 h


title: E_coli_sham_powerline_interm_2.5h_rep2

description:
E_coli_Spi_2.5h_rep2
E. coli K-12 grown aerobically in continous cultivation sham-treated with power line intermittent (2 min on, 4 min off) magnetic field for 2,5 h


title: E_coli_treated_powerline_interm_15h_rep2

description:
E_coli_Tpi_15h_rep2
E. coli K-12 grown aerobically in continous cultivation treated with power line intermittent (2 min on, 4 min off) magnetic field for 15 h


title: E_coli_sham_powerline_interm_2.5h_rep1

description:
E_coli_Spi_2.5h_rep1
E. coli K-12 grown aerobically in continous cultivation sham-treated with power line intermittent (2 min on, 4 min off) magnetic field for 2,5 h


title: E_coli_treated_powerline_interm_2.5h_rep1

description:
E_coli_Tpi_2.5h_rep1
E. coli K-12 grown aerobically in continous cultivation treated with power line intermittent (2 min on, 4 min off) magnetic field for 2,5 h


title: E_coli_sham_powerline_interm_8min_rep3

description:
E_coli_Spi_8min_rep3
E. coli K-12 grown aerobically in continous cultivation sham-treated with power line intermittent (2 min on, 4 min off) magnetic field for 8 min

value: 8 min


title: E_coli_treated_powerline_interm_2.5h_rep2

description:
E_coli_Tpi_2.5h_rep2
E. coli K-12 grown aerobically in continous cultivation treated with power line intermittent (2 min on, 4 min off) magnetic field for 2,5 h


title: E_coli_sham_sinusoidal_interm_15h_rep3

description:
E_coli_Ssi_15h_rep3
E. coli K-12 grown aerobically in continous cultivation sham-treated with sinusoidal intermittent (2 min on, 4 min off) magnetic field for 15 h

value: sham-treated sinusoidal intermittent (2 min on, 4 min off) magnetic field


title: E_coli_treated_powerline_interm_8min_rep3

description:
E_coli_Tpi_8min_rep3
E. coli K-12 grown aerobically in continous cultivation treated with power line intermittent (2 min on, 4 min off) magnetic field for 8 min


title: E_coli_sham_powerline_interm_15h_rep1

description:
E_coli_Spi_15h_rep1
E. coli K-12 grown aerobically in continous cultivation sham-treated with power line intermittent (2 min on, 4 min off) magnetic field for 15 h


title: E_coli_sham_powerline_interm_8min_rep1

description:
E_coli_Spi_8min_rep1
E. coli K-12 grown aerobically in continous cultivation sham-treated with power line intermittent (2 min on, 4 min off) magnetic field for 8 min


title: E_coli_treated_powerline_interm_8min_rep2

description:
E_coli_Tpi_8min_rep2
E. coli K-12 grown aerobically in continous cultivation treated with power line intermittent (2 min on, 4 min off) magnetic field for 8 min


title: E_coli_sham_powerline_interm_8min_rep2

description:
E_coli_Spi_8min_rep2
E. coli K-12 grown aerobically in continous cultivation sham-treated with power line intermittent (2 min on, 4 min off) magnetic field for 8 min


title: E_coli_treated_powerline_interm_2.5h_rep3

description:
E_coli_Tpi_2.5h_rep3
E. coli K-12 grown aerobically in continous cultivation treated with power line intermittent (2 min on, 4 min off) magnetic field for 2,5 h


title: E_coli_treated_powerline_interm_8min_rep1

description:
E_coli_Tpi_8min_rep1
E. coli K-12 grown aerobically in continous cultivation treated with power line intermittent (2 min on, 4 min off) magnetic field for 8 min


title: E_coli_sham_sinusoidal_interm_2.5h_rep1

description:
E_coli_Ssi_2.5h_rep1
E. coli K-12 grown aerobically in continous cultivation sham-treated with sinusoidal intermittent (2 min on, 4 min off) magnetic field for 2,5 h


title: E_coli_treated_sinusoidal_interm_15h_rep3

description:
E_coli_Tsi_15h_rep3
E. coli K-12 grown aerobically in continous cultivation treated with sinusoidal intermittent (2 min on, 4 min off) magnetic field for 15 h

value: treated sinusoidal intermittent (2 min on, 4 min off) magnetic field


title: E_coli_sham_sinusoidal_interm_15h_rep2

description:
E_coli_Ssi_15h_rep2
E. coli K-12 grown aerobically in continous cultivation sham-treated with sinusoidal intermittent (2 min on, 4 min off) magnetic field for 15 h


title: E_coli_treated_sinusoidal_interm_15h_rep1

description:
E_coli_Tsi_15h_rep1
E. coli K-12 grown aerobically in continous cultivation treated with sinusoidal intermittent (2 min on, 4 min off) magnetic field for 15 h


title: E_coli_treated_sinusoidal_interm_15h_rep2

description:
E_coli_Tsi_15h_rep2
E. coli K-12 grown aerobically in continous cultivation treated with sinusoidal intermittent (2 min on, 4 min off) magnetic field for 15 h


title: E_coli_sham_sinusoidal_interm_2.5h_rep3

description:
E_coli_Ssi_2.5h_rep3
E. coli K-12 grown aerobically in continous cultivation sham-treated with sinusoidal intermittent (2 min on, 4 min off) magnetic field for 2,5 h


title: E_coli_sham_sinusoidal_interm_2.5h_rep2

description:
E_coli_Ssi_2.5h_rep2
E. coli K-12 grown aerobically in continous cultivation sham-treated with sinusoidal intermittent (2 min on, 4 min off) magnetic field for 2,5 h


title: E_coli_treated_sinusoidal_interm_2.5h_rep1

description:
E_coli_Tsi_2.5h_rep1
E. coli K-12 grown aerobically in continous cultivation treated with sinusoidal intermittent (2 min on, 4 min off) magnetic field for 2,5 h


title: E_coli_treated_sinusoidal_interm_2.5h_rep3

description:
E_coli_Tsi_2.5h_rep3
E. coli K-12 grown aerobically in continous cultivation treated with sinusoidal intermittent (2 min on, 4 min off) magnetic field for 2,5 h


title: E_coli_sham_sinusoidal_cont_15h_rep3

description:
E_coli_Ssc_15h_rep3
E. coli K-12 grown aerobically in continous cultivation sham-treated with sinusoidal continous magnetic field for 15 h

value: sham-treated sinusoidal continous magnetic field


title: E_coli_treated_sinusoidal_interm_2.5h_rep2

description:
E_coli_Tsi_2.5h_rep2
E. coli K-12 grown aerobically in continous cultivation treated with sinusoidal intermittent (2 min on, 4 min off) magnetic field for 2,5 h


title: E_coli_sham_sinusoidal_interm_15h_rep1

description:
E_coli_Ssi_15h_rep1
E. coli K-12 grown aerobically in continous cultivation sham-treated with sinusoidal intermittent (2 min on, 4 min off) magnetic field for 15 h


title: E_coli_sham_sinusoidal_cont_15h_rep2

description:
E_coli_Ssc_15h_rep2
E. coli K-12 grown aerobically in continous cultivation sham-treated with sinusoidal continous magnetic field for 15 h


title: E_coli_treated_sinusoidal_cont_15h_rep1

description:
E_coli_Tsc_15h_rep1
E. coli K-12 grown aerobically in continous cultivation treated with sinusoidal continous magnetic field for 15 h

value: treated sinusoidal continous magnetic field


title: E_coli_treated_sinusoidal_cont_15h_rep2

description:
E_coli_Tsc_15h_rep2
E. coli K-12 grown aerobically in continous cultivation treated with sinusoidal continous magnetic field for 15 h


title: E_coli_treated_sinusoidal_cont_15h_rep3

description:
E_coli_Tsc_15h_rep3
E. coli K-12 grown aerobically in continous cultivation treated with sinusoidal continous magnetic field for 15 h


title: E_coli_sham_sinusoidal_cont_15h_rep1

description:
E_coli_Ssc_15h_rep1
E. coli K-12 grown aerobically in continous cultivation sham-treated with sinusoidal continous magnetic field for 15 h


title: E_coli_sham_sinusoidal_cont_2.5h_rep3

description:
E_coli_Ssc_2.5h_rep3
E. coli K-12 grown aerobically in continous cultivation sham-treated with sinusoidal continous magnetic field for 2,5 h


title: E_coli_sham_sinusoidal_cont_2.5h_rep1

description:
E_coli_Ssc_2.5h_rep1
E. coli K-12 grown aerobically in continous cultivation sham-treated with sinusoidal continous magnetic field for 2,5 h


title: E_coli_sham_sinusoidal_cont_2.5h_rep2

description:
E_coli_Ssc_2.5h_rep2
E. coli K-12 grown aerobically in continous cultivation sham-treated with sinusoidal continous magnetic field for 2,5 h


title: E_coli_treated_sinusoidal_cont_2.5h_rep3

description:
E_coli_Tsc_2.5h_rep3
E. coli K-12 grown aerobically in continous cultivation treated with sinusoidal continous magnetic field for 2,5 h


title: E_coli_sham_sinusoidal_cont_8min_rep3

description:
E_coli_Ssc_8min_rep3
E. coli K-12 grown aerobically in continous cultivation sham-treated with sinusoidal continous magnetic field for 8 min


title: E_coli_treated_sinusoidal_cont_2.5h_rep1

description:
E_coli_Tsc_2.5h_rep1
E. coli K-12 grown aerobically in continous cultivation treated with sinusoidal continous magnetic field for 2,5 h


title: E_coli_treated_sinusoidal_cont_8min_rep2

description:
E_coli_Tsc_8min_rep2
E. coli K-12 grown aerobically in continous cultivation treated with sinusoidal continous magnetic field for 8 min


title: E_coli_treated_sinusoidal_cont_8min_rep3

description:
E_coli_Tsc_8min_rep3
E. coli K-12 grown aerobically in continous cultivation treated with sinusoidal continous magnetic field for 8 min


title: E_coli_treated_sinusoidal_cont_2.5h_rep2

description:
E_coli_Tsc_2.5h_rep2
E. coli K-12 grown aerobically in continous cultivation treated with sinusoidal continous magnetic field for 2,5 h


title: FadR-rep4

city: Emeryville

first: Mario

last: Ouellet

address: 5885 Hollis St., 4th Floor

institute: Joint BioEnergy Institute

hyb_protocol: As recommended [NimbleGen Arrays User's Guide - Gene Expression Analysis v.3.0.] simultaneously for all arrays

scan_protocol: Individual arrays were scanned independently using a GenePix Professional 4200A scanner (Axon Instruments), adjusting the PMT gain for each array as recommended [NimbleGen Arrays User's Guide - Gene Expression Analysis v.3.0.]. Image analysis was performed with the NimbleScan software and features intensities were exported as .pair files

data_processing: ArrayStar 3.0 (DNASTAR) was used for probe summarization and normalization (RMA algorithm, quantile normalization) and data analysis

organism: Escherichia coli

source_name: FRT-ΔfadE

label_protocol: Direct Random labeling as previously described in Ouellet et al., BMC Biotechnology 2009, 9:97.

growth_protocol: Single colonies of each strain were inoculated into 5 mL LB media (containing 50 mg/L ampicillin and 30 mg/L chloramphenicol) and incubated at 37C overnight. The overnight cultures were used to inoculate 5 mL minimal media (M9 medium supplemented with 75 mM MOPS, 2 mM MgSO4, 1 mg/L thiamine, 10 nM FeSO4, 0.1 mM CaCl2 and micronutrients including 3 μM (NH4)6Mo7O24, 0.4 mM boric acid, 30 μM CoCl2, 15 μM CuSO4, 80 μM MnCl2, 10 μM ZnSO4, 2% glucos, 50 mg/L ampicillin and 30 mg/L chloramphenicol) and incubated at 37C until OD600 reached 0.8. Production was induced with 1 mM IPTG and cultures were incubated at 37C with shaking for 12h before sampling.

extract_protocol: Cells where rapidly harvested after 12h of induction and frozen in liquid nitrogen. Total RNA was extracted using the RNEasy Mini kit (Qiagen) following lyzozyme treatment. RNA was quantified by spectrophotometry with a Nanodrop ND-1000 (Thermo Scientific) and its integrity verified on a 2100 Bioanalyzer (Agilent).

tag: strain

value: FRT-ΔfadE

tag: expected approximate fatty acids (c12-c20) titer (mg/l culture)


title: Control-rep2

source_name: LT-ΔfadE

value: LT-ΔfadE


title: Control-rep1


title: E_coli_sham_sinusoidal_cont_8min_rep1

description:
E_coli_Ssc_8min_rep1
E. coli K-12 grown aerobically in continous cultivation sham-treated with sinusoidal continous magnetic field for 8 min


title: E_coli_sham_sinusoidal_cont_8min_rep2

description:
E_coli_Ssc_8min_rep2
E. coli K-12 grown aerobically in continous cultivation sham-treated with sinusoidal continous magnetic field for 8 min


title: Control-rep3


title: Furfural-tolerant IrrE mutant F1-37, biological rep1

city: Beijing

first: Jianqing

last: Wang

state: Beijing

address: One Tsinghua Graden Road

department: Chemical Engineering

country: China

institute: Tsinghua University

description: Gene expression data from cells in exponential phase under furfural stress

hyb_protocol: E. coli genome 2.0 arrays (Affymetrix, Santa Clara, CA, USA) were used for hybridization, and arrays were run in triplicate with biological replicates to allow for statistical confidence in differential gene expression

scan_protocol: GeneChips were scanned using a GeneChip Scanner 3000 (Affymetrix)

data_processing: Data were analyzed using GeneChip Operating Software Version 1.4 (Affymetrix)

source_name: Cells in log phase under furfural stress

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol

growth_protocol: Cells were grown at 37°C in Luria-Bertani (LB) medium supplemented with 50 μg/ml ampicillin overnight, then inoculated into LB medium supplemented with 0.095% (v/v) furfural and 50 μg/ml ampicillin at an initial OD600 value of 0.02, and grown at 37°C.

extract_protocol: Total RNA was isolated from the cells stored in liquid nitrogen using TRIzol Reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) and RNeasy MinElute Cleanup Kits (Qiagen, Valencia, CA, USA)

treatment_protocol: The cells were centrifuged when they reached the log phase, and then rapidly chilled and stored in liquid nitrogen until used for the DNA microarray assay

tag: genotype

value: furfural-tolerant mutant F1-37 of IrrE


title: Wild-type IrrE, biological rep1

value: wild type IrrE


title: Furfural-tolerant IrrE mutant F1-37, biological rep2


title: FadR-rep3


title: FadR-rep1


title: FadR-rep2


title: SIV infected_2

description:
Monkey_290
Gene expression data from the frontal lobe of SIV infected Rhesus brain

value: Frontal Lobe

value: Chronic SIV Infection

value: 92-114 weeks postinoculation


title: Wild-type IrrE, biological rep2


title: Furfural-tolerant IrrE mutant F1-37, biological rep3


title: E_coli_treated_sinusoidal_cont_8min_rep1

description:
E_coli_Tsc_8min_rep1
E. coli K-12 grown aerobically in continous cultivation treated with sinusoidal continous magnetic field for 8 min

value: steady-state continuous cultivation (dilution rate of 0.4 h-1), aerobic

value: defined mineral medium with 1 g/l glucose


title: intestine_group4_8hpi_chick9

value: Salmonella

value: intestine

value: RNA reference pool (from pooled intestine all samples)


title: Wild-type IrrE, biological rep3


title: Primary tumor 4

city: Heidelberg

first: Gustavo

last: Acuna

address: INF 280

institute: DKFZ

description: labelled by method described in Eberwine et al., 1992

hyb_protocol: Hybridization was performed at 58°C, in GEX-HCB buffer (Illumina Inc.) at a concentration of 100 ng/µl cRNA, unsealed in a wet chamber for 20 hours

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: Biotin

source_name: primary tumor of the oral cavity

label_protocol: labelled by method described by Eberwine et al., 1992

growth_protocol: SCC-7 cell line was cultured in MEM supplemented with 10% FCS prior injection into the oral cavity.

extract_protocol: The RNA extraction from mouse tumors and murine SCC cell line was performed according to the manufacturer´s intruction using peqGOLG RNA Pure reagent.

treatment_protocol: The tumors were embedded in OCT media and kept at -80°C.

value: primary tumor


title: [RV+]-[control]-rep3

first: Kurtis

last: Haro

address: 1275 York Ave

institute: MSKCC

description:
gene expression collected on day3
J3

hyb_protocol: Following fragmentation, cRNA were hybridized for Illumina GX human HT12 Array. Slides were washed and stained in the Illumina instrument.

scan_protocol: Slides were scanned using Illumina iScanner.

data_processing: The data were analyzed with GenomeStudio using Illumina default analysis settings. No normalization and background correction are performed.

source_name: RV+_unirradiated (0Gy)_control

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA.

growth_protocol: cells were split to 2.5E5 cells/mL in standard growth medium 24h prior to irradiation

extract_protocol: Total RNA extraction was performed with Qiagen RNeasy kit per manufacturer's protocol with ~1E6 cells/sample.

treatment_protocol: cells were irradiated with 0, 8Gy gamma IR (1.9Gy/m) or ~2Gy alpha IR (~1Gy/m) in special aluminum dishes for 241Am alpha particle source and cultured 4h under standard cell culture conditions prior to harvesting of RNA

value: RV+

value: vincristine-resistant HL60 derivative

value: unirradiated


title: Primary tumor 5


title: Recurrence 3

source_name: recurrent tumor after removal of the primary tumor 3

value: recurrent tumor


title: Recurrence 4

source_name: recurrent tumor after removal of the primary tumor 4


title: [RA11]-[gammaIR]-rep3

description:
gene expression collected on day3
E3

source_name: RA11_4h following gamma ionizing radiation (IR) exposure

value: alpha particle-resistant HL60 derivative

value: 8Gy gamma IR


title: [RA11]-[control]-rep3

description:
gene expression collected on day3
D3

source_name: RA11_unirradiated (0Gy)_control


title: SCC-7 (1)

source_name: squamous cell carcinoma cell line

value: squamous cell carcinoma cell line SCC-7


title: Primary tumor 3


title: Recurrence 5

source_name: recurrent tumor after removal of the primary tumor 5


title: [RG8]-[control]-rep3

description:
gene expression collected on day3
G3

source_name: RG8_unirradiated (0Gy)_control

value: gamma-resistant HL60 derivative


title: [RV+]-[gammaIR]-rep3

description:
gene expression collected on day3
K3

source_name: RV+_4h following gamma ionizing radiation (IR) exposure


title: [RG8]-[alphaIR]-rep3

description:
gene expression collected on day3
I3

source_name: RG8_4h following alpha ionizing radiation (IR) exposure

value: 7.5 alpha particle traversals per nucleus (~2Gy)


title: Recurrence 2

source_name: recurrent tumor after removal of the primary tumor 2


title: [RA11]-[alphaIR]-rep3

description:
gene expression collected on day3
F3

source_name: RA11_4h following alpha ionizing radiation (IR) exposure


title: [RV+]-[alphaIR]-rep3

description:
gene expression collected on day3
L3

source_name: RV+_4h following alpha ionizing radiation (IR) exposure


title: [HL60]-[alphaIR]-rep3

description:
gene expression collected on day3
C3

source_name: HL60_4h following alpha ionizing radiation (IR) exposure

value: naïve


title: [HL60]-[gammaIR]-rep3

description:
gene expression collected on day3
B3

source_name: HL60_4h following gamma ionizing radiation (IR) exposure


title: SCC-7 (2)


title: [HL60]-[control]-rep3

description:
gene expression collected on day3
A3

source_name: HL60_unirradiated (0Gy)_control


title: [RG8]-[gammaIR]-rep3

description:
gene expression collected on day3
H3

source_name: RG8_4h following gamma ionizing radiation (IR) exposure


title: [RG8]-[alphaIR]-rep2

description:
gene expression collected on day2
I2


title: [RV+]-[alphaIR]-rep2

description:
gene expression collected on day2
L2


title: Primary tumor 1

source_name: primary tumor of the oral cavity


title: Ubx

type: protein

city: Boston

first: Leila

last: Shokri

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Brigham and Women's Hospital and Harvard Medical School

hyb_protocol: Double-stranded microarrays were first pre-moistened in PBS / 0.01% Triton X-100 for 5 min and blocked with PBS / 2% (wt/vol) nonfat dried milk (Sigma) under LifterSlip cover slips (Erie Scientific) for 1 h. Microarrays were then washed once with PBS / 0.1% (vol/vol) Tween-20 for 5 min and once with PBS / 0.01% Triton X-100 for 2 min. Proteins were diluted to final concentration (100-200 nM) in a 175-μl protein binding reaction containing PBS / 2% (wt/vol) milk / 51.3 ng/μl salmon testes DNA (Sigma) / 0.2 μg/μl bovine serum albumin (New England Biolabs). Preincubated protein binding mixtures were applied to individual chambers of a four-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 1 h at 20°C. Microarrays were again washed once with PBS / 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS / 0.01% Triton X-100 for 2 min. Alexa488-conjugated rabbit polyclonal antibody to GST (Invitrogen) was diluted to 50 μg/ml in PBS / 2% milk and applied to a four-chamber gasket cover slip (Agilent), and the assembled microarrays were again incubated for 1 h at 20°C. Finally, microarrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min. After each hour-long incubation step, microarrays and cover slips were disassembled in a staining dish filled with 500 ml of the first wash solution. All washes were performed in Coplin jars at 20°C on an orbital shaker at 125 r.p.m. Immediately following each series of washes, microarrays were rinsed in PBS (slowly removed over approximately 10 seconds) to ensure removal of detergent and uniform drying.

scan_protocol: Protein-bound microarrays were scanned to detect Alexa488-conjugated antibody (488 nm ex, 522 nm em) using at least three different laser power settings to best capture a broad range of signal intensities and ensure signal intensities below saturation for all spots. Separately, slides were scanned after primer extension to quantify the amount of incorporated Cy3-conjugated dUTP (543 nm ex, 570 nm em). Microarray TIF images were analyzed using GenePix Pro version 6.0 software (Molecular Devices), bad spots were manually flagged and removed, and data from multiple Alexa488 scans of the same slide were combined using masliner (MicroArray LINEar Regression) software.

data_processing: First, we normalize Alexa488 signal by the Cy3 signal for each spot to account for differences in the total amount of double-stranded DNA. Because Cy3-dUTP incorporation is influenced both by the total number of adenines and the sequence context of each adenine, we perform a linear regression over all 41,944 variable spots to compute the relative contributions to the total signal of all trinucleotide combinations (followed by adenine). Using these regression coefficients, we calculate the ratio of observed-to-expected Cy3 intensity and use that as a normalization factor. Second, to correct for any possible non-uniformities in protein binding, we further adjust the Cy3-normalized Alexa488 signals according to their positions on the microarray. We calculate the median normalized intensity of the 15 x 15 block centered on each spot and divide the spot’s signal by the ratio of the median within the block to the median over the entire chamber. Every non-palindromic 8-mer occurs on at least 32 spots in each chamber of our universal PBM and we provide several scores for each 8-mer in each experiment: (1) Median Intensity, (2) Z-Score, and (3) Enrichment Score (E-Score).

molecule: protein

organism: Drosophila melanogaster

source_name: D. melanogaster Ubx

label_protocol: Protein-bound arrays were incubated with Alexa488-conjugated rabbit polyclonal antibody to GST (Invitrogen).  For details, see Hybridization protocol below.

extract_protocol: The DNA binding domains (DBDs) of selected Drosophila HD TFs were cloned into Gateway-compatible Entry (pENTR/D-TOPO) and pDEST15 (N-terminal GST-tag) expression vector. Slou, Msh and Lbl DBDs were cloned into pGEX-5X-1. Slou, Msh and Lbl TFs were produced from E. coli over-expression cultures followed by purification with GSTrapTM FF affinity columns (GE Healthcare) using an AKTAprime plus FPLC (GE Healthcare). All other proteins were produced from purified plasmids by in vitro transcription and translation using the PURExpress® In Vitro Protein Synthesis Kit according to manufacturer’s instructions. Glycerol was added to a final concentration of 28%, and proteins were stored at -20°C until further use. Western blots were performed for each protein to assess quality and to approximate protein concentration by visual inspection relative to a dilution series of recombinant GST standard.

tag: drosophila transcription factor

value: Ubx


title: [RV+]-[control]-rep2

description:
gene expression collected on day2
J2

source_name: RV+_unirradiated (0Gy)_control


title: Ptx1

source_name: D. melanogaster Ptx1


title: control for Glut4 knockout 2

first: Mark

last: Herman

state: MA

address: 330 Brookline Avenue

department: Medicine / Endocrine

institute: Beth Israel Deaconess Medical Center

hyb_protocol: standard Affy protocols as performed at the Genomics Core Facility of the Beth Israel Deaconess Medical Center.

data_processing: The data were processed using dChip.  Model based expression values were calculated using a PM/MM difference model

source_name: perigonadal adipose tissue

extract_protocol: RNeasy mini kit (Qiagen)

tag: gender

value: female

value: 6 months

value: C57B6/FVB/SV129 mix

tag: genotype/variation

value: Glut4 knockout

tag: fed-fasted state

value: ad libitum fed


title: [RA11]-[alphaIR]-rep2

description:
gene expression collected on day2
F2

tag: cell type


title: [RG8]-[control]-rep2

description:
gene expression collected on day2
G2


title: Six4

source_name: D. melanogaster Six4


title: Primary tumor 2

value: primary tumor


title: [RV+]-[gammaIR]-rep2

description:
gene expression collected on day2
K2

value: RV+


title: [RG8]-[gammaIR]-rep2

description:
gene expression collected on day2
H2


title: Recurrence 1

source_name: recurrent tumor after removal of the primary tumor 1


title: Tin

source_name: D. melanogaster Tin

value: Tin


title: [HL60]-[alphaIR]-rep2

description:
gene expression collected on day2
C2


title: [RA11]-[gammaIR]-rep2

description:
gene expression collected on day2
E2

source_name: RA11_4h following gamma ionizing radiation (IR) exposure


title: control for Glut4 knockout 3

scan_protocol: standard Affy protocols as performed at the Genomics Core Facility of the Beth Israel Deaconess Medical Center.


title: [HL60]-[gammaIR]-rep2

description:
gene expression collected on day2
B2


title: adipose-specific Glut4 knockout 3

label_protocol: standard Affy protocols as performed at the Genomics Core Facility of the Beth Israel Deaconess Medical Center.


title: [RA11]-[control]-rep2

description:
gene expression collected on day2
D2

source_name: RA11_unirradiated (0Gy)_control

value: unirradiated


title: Eve

source_name: D. melanogaster Eve

value: Eve


title: Lbl

source_name: D. melanogaster Lbl

value: Lbl


title: Slou

source_name: D. melanogaster Slou

value: Slou


title: Bap

source_name: D. melanogaster Bap

value: Bap


title: control for Glut4 knockout 1


title: [RV+]-[gammaIR]-rep1

description:
gene expression collected on day1
K1

source_name: RV+_4h following gamma ionizing radiation (IR) exposure

value: vincristine-resistant HL60 derivative

value: 8Gy gamma IR


title: Msh

source_name: D. melanogaster Msh

value: Msh


title: [RG8]-[alphaIR]-rep1

description:
gene expression collected on day1
I1

source_name: RG8_4h following alpha ionizing radiation (IR) exposure

value: gamma-resistant HL60 derivative

value: 7.5 alpha particle traversals per nucleus (~2Gy)


title: [RV+]-[alphaIR]-rep1

description:
gene expression collected on day1
L1

source_name: RV+_4h following alpha ionizing radiation (IR) exposure


title: [HL60]-[control]-rep2

description:
gene expression collected on day2
A2

source_name: HL60_unirradiated (0Gy)_control

value: naïve


title: adipose-specific Glut4 knockout 1

value: female

value: 6 months

value: C57B6/FVB/SV129 mix


title: adipose-specific Glut4 knockout 2

value: Glut4 knockout

value: ad libitum fed


title: [RG8]-[gammaIR]-rep1

description:
gene expression collected on day1
H1

source_name: RG8_4h following gamma ionizing radiation (IR) exposure


title: [RA11]-[alphaIR]-rep1

description:
gene expression collected on day1
F1

source_name: RA11_4h following alpha ionizing radiation (IR) exposure

value: alpha particle-resistant HL60 derivative


title: [RV+]-[control]-rep1

description:
gene expression collected on day1
J1

source_name: RV+_unirradiated (0Gy)_control

value: RV+

value: unirradiated


title: control for Glut4 overexpressor 2

source_name: perigonadal adipose tissue

value: FVB

value: Glut4 overexpressor


title: control for Glut4 overexpressor 3


title: [RG8]-[control]-rep1

description:
gene expression collected on day1
G1

source_name: RG8_unirradiated (0Gy)_control


title: [HL60]-[alphaIR]-rep1

description:
gene expression collected on day1
C1

source_name: HL60_4h following alpha ionizing radiation (IR) exposure


title: AbdB

source_name: D. melanogaster AbdB

value: AbdB


title: [RA11]-[control]-rep1

description:
gene expression collected on day1
D1

source_name: RA11_unirradiated (0Gy)_control


title: [RA11]-[gammaIR]-rep1

description:
gene expression collected on day1
E1

source_name: RA11_4h following gamma ionizing radiation (IR) exposure


title: [HL60]-[gammaIR]-rep1

description:
gene expression collected on day1
B1

source_name: HL60_4h following gamma ionizing radiation (IR) exposure


title: [HL60]-[control]-rep1

description:
gene expression collected on day1
A1


title: adipose-specific Glut4 overexpressor 1


title: Left arm biopsy EMS patient

city: Lebanon

first: Tammara

last: Wood

state: NH

address: WTRB 674

department: Biomedical Data Science

institute: Dartmouth Medical School

hyb_protocol: Fragmentation Buffer and Hybridization Buffer (Agilent Gene Expression Hybridization Kit) were added, and samples applied to Whole Human Genome microarrays

scan_protocol: Scanned on Axon scanner

data_processing: Images were quantified using GenePixPro 5.1

source_name: Human Tissue biopsy LA

label_protocol: 150ng of total RNA was reversed transcribed using Agilent Quick Amp Kit and labeled with Perkin Elmer Cy3

extract_protocol: Total RNA extracted using RNeasy Fibrous Tissue Mini following manufacturers protocol

treatment_protocol: Storage of human tissue in RNAlater

tag: tissue

value: skin tissue

tag: disease status

value: Eosinophilia–myalgia syndrome (EMS) patient

source_name: Universal Human Reference

value: cell lines (UHR)


title: CP stromal cells, cultured

city: Seattle

first: Alvin

middle: Y

last: Liu

state: WA

address: 815 Mercer Street Box 358056

department: Urology

institute: University of Washington

description:
primary cell line
stromal mesenchyme

hyb_protocol: Following fragmentation, ten micrograms of adjusted cRNA from each sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip

scan_protocol: Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.

data_processing: Raw CEL intensity data were RMA normalized using R/Bioconductor

source_name: prostate

label_protocol: GeneChip® Two-Cycle Target Labeling Kit

growth_protocol: Cells were isolated after overnight tissue digestion with collagenase in serum-free RPMI1640 media. Cells were transfected to produce induced pluripotent stem cells.

extract_protocol: Sorted and cultured cell populations were lysed in RLT buffer for RNA isolation.

treatment_protocol: Cells were labeled with dye conjugated-antiCD monoclonal antibodies and sorted by MACS. Infected with lentiviral vectors containing NANOG, SOX2, LIN28 and POU5F1/OCT4 constructs.

value: cultured CD90+ prostate cancer-associated (CP) stromal cells


title: Left arm biopsy EMS patient replicate #2


title: Control human tissue biopsy 06

value: normal control


title: CP stromal cells, sorted 2

description:
primary tumor
stromal mesenchyme

value: sorted CD90+ prostate cancer-associated (CP) stromal cells


title: Control human tissue biopsy 05


title: iPS cells from CP stromal

description:
induced pluripotent cells
iPS cells

label_protocol: GeneChip® One-Cycle Target Labeling Kit

value: iPS cells from CP stromal cells

value: transfected with NANOG, SOX2, POU5F1, LIN28


title: control for Glut4 overexpressor 1

value: female

value: 6 months


title: adipose-specific Glut4 overexpressor 2

value: ad libitum fed


title: Control human tissue biopsy 01


title: CP stromal cells, sorted 1

description:
primary tumor
stromal mesenchyme


title: Embryonal carcinoma cell line NCCIT

description:
germ cell tumor line
EC stem-like cells

source_name: testis

tag: cell line

value: NCCIT


title: Human embryonic stem cells

description:
human stem cell XY
ES cells

source_name: embryo

value: embryonic stem cells


title: adipose-specific Glut4 overexpressor 3


title: Left arm biopsy EMS patient replicate #3


title: MZL080

status: Public on Jan 27 2012

city: Scottsdale

first: Esteban

last: Braggio

state: AZ

address: 13400 E. Shea Blvd, MCCRB-300

institute: Mayo Clinic Arizona

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on HG-U133A Plus2.0 GeneChip.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings  as normalization method.

source_name: Spleen

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA.

extract_protocol: Total RNA extraction was performed according to the manufacturer's instructions (Qiagen).

tag: pathology

value: SMZL

tag: organ

value: Spleen


title: MZL068


title: MZL108


title: MZL107


title: MZL106


title: MZL064


title: MZL056


title: MZL072


title: MZL060


title: MZL084


title: MZL092


title: MZL096


title: MZL048


title: MZL052


title: MZL076


title: MZL104


title: MZL040


title: MZL088


title: MZL006


title: MZL044


title: MZL036


title: MZL024


title: MZL012


title: MZL018


title: MZL032


title: MZL100


title: MZL028

source_name: Spleen + hilar + portal LN

value: Spleen + hilar + portal LN


title: Fibroblast NOF #626

city: Chicago

first: Youjia

last: Hua

state: IL

address: 303 East Superior Street, Lurie 6-220

institute: Northwestern University

data_processing: Normalization method: MAS5.0

label: standard Affymetrix protocol

source_name: Normal omental fibroblast, patient #626

label_protocol: standard Affymetrix protocol

extract_protocol: standard Affymetrix protocol

value: human normal omental fibroblast

tag: patient no.

tag: transfection

value: scrambled


title: Fibroblast NOF #612

source_name: Normal omental fibroblast, patient #612


title: Fibroblast coCAF 7d #609

source_name: Normal omental fibroblast co-cultured with ovarian cancer cells, 7d, patient #609

value: human cancer-associated fibroblast co-cultured with ovarian cancer cells, 7d

tag: time


title: Fibroblast coCAF 7d #612

source_name: Normal omental fibroblast co-cultured with ovarian cancer cells, 7d, patient #612


title: Fibroblast coCAF 7d #603

source_name: Normal omental fibroblast co-cultured with ovarian cancer cells, 7d, patient #603


title: Fibroblast NOF #474

source_name: Normal omental fibroblast, patient #474


title: Fibroblast iCAF 4d #626

source_name: Normal omental fibroblast transfected with 3 miRNAs, 4d, patient #626

value: human cancer-associated fibroblast transfected with 3 miRNAs, 4d

value: miR-155, anti-miR-31 and anti-miR-214


title: Fibroblast aNOF #225

source_name: Adjacent normal omental fibroblast, patient #225


title: Fibroblast aNOF #248

source_name: Adjacent normal omental fibroblast, patient #248


title: Fibroblast NOF #609

source_name: Normal omental fibroblast, patient #609


title: Fibroblast CAF #225

source_name: Cancer-associated fibroblast, patient #225

value: human cancer-associated fibroblast


title: Fibroblast CAF #248

source_name: Cancer-associated fibroblast, patient #248


title: Fibroblast NOF #603

source_name: Normal omental fibroblast, patient #603


title: Fibroblast iCAF 2d #474

source_name: Normal omental fibroblast transfected with 3 miRNAs, 2d, patient #474

value: human cancer-associated fibroblast transfected with 3 miRNAs, 2d


title: Myo5:9Myc IP (#29) with 9E11, crosslinked 20' formaldehyde, Dynal

city: Stanford

first: Jason

last: Casolari

address: 279 Campus Drive

department: Dept. of Biochemistry

institute: Stanford University

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72352.gif

hyb_protocol: not provided

scan_protocol: Scanner Model: GenePix 4200A

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

organism: Saccharomyces cerevisiae

source_name: whole cell extract, amino-allyl amplified

label_protocol: not provided

extract_protocol: not provided

tag: reference

source_name: IP from JCY39, amino-allyl amplified

extract_protocol: Latrunculin B purification of motors; Immunopurifications of 9Myc- or GFP-tagged motor proteins from cultures treated with latrunculin B were carried out in a manner similar to that described for crosslinking cells with some modifications.  250 ml cultures were grown to mid-log phase, harvested by centrifugation, and washed with 25 mls and then 10 mls of cold Tris-buffered saline.  Pellets were placed on ice and resuspended in 600 ul of lysis buffer with the addition of 2 ug/ml latrunculin B, then mechanically disrupted by a beadbeater.  Lysates were cleared by centrifugation at 4,000g for 1 min at 4 oC, the volume was brought up to 1.4 ml using lysis buffer, and 200 ul was removed for reference RNA isolation.  100 ul of pan-mouse IgG Dynal magnetic beads pre-incubated with antibody (see above) was combined with the remaining lysate and incubated for 4 h at 4 oC with gentle rotation.  Washes were performed as described above.Protein/RNA complexes were eluted with elution buffer (see above), incubation at 70 oC for 10 min, and vigorous vortexing.  Immunopurified and total lysate RNA were extracted with phenol:chloroform:isoamyl alcohol (25:24:1; Invitrogen) twice and chloroform once using 2.0 ml Phase Lock Heavy tubes (Eppendorf) followed by ethanol precipitation in the presence of 7.5 ug Glycoblue (Ambion) as carrier

tag: compound based treatment

value: formaldehyde

tag: tag used for ip


title: Myo4:9Myc IP (#5) with 9E11, crosslinked 20' formaldehyde, Dynal

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72343.gif

value: whole cell extract, amino-allyl amplified

source_name: IP from JCY19, amino-allyl amplified


title: Kar3:GFP IP rep #3 crosslinked 10' 1% formaldehyde

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74458.gif

source_name: whole cell extract, decrosslinked, amino-allyl amplified RNA

source_name: IP anti-GFP , Dynal pan-mouse IgG beads, decrosslinked, JCY 46, amino-allyl amplified

value: GFP


title: Kip3:GFP IP rep #3 crosslinked 10' 1% formaldehyde

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74448.gif

value: whole cell extract, decrosslinked, amino-allyl amplified RNA

source_name: IP anti-GFP , Dynal pan-mouse IgG beads, decrosslinked, JCY 41, amino-allyl amplified


title: mock IP #4, 20' crosslink, Dynal beads

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72431.gif

source_name: mock IP, amino-allyl amplified


title: myo3:9Myc IP JCY38-4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71265.gif

source_name: aa-amplified reference, whole cell extract

source_name: IP of JCY38 (myo3:9Myc strain), aa-amplified


title: Myo5:9Myc IP #31 20' crosslink, Dynal beads

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72446.gif

source_name: Myo5:9Myc IP, amino-allyl amplified


title: myo5:9Myc IP JCY39-4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71269.gif

value: aa-amplified reference, whole cell extract

source_name: IP of JCY30 (she2:9Myc strain), aa-amplified


title: cultured with 5-aza-2'-cytidine and trichostatin A

city: Kanazawa

first: Yo

last: Niida

state: Ishikawa

address: 13-1 Takaramachi

institute: Kanazawa Univ.

description: This sample is normal male derived LCLs cultured with 5-aza-2' cytidine and trichostatin A.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: human lymphoblastoid cell lines

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol:
LCLs were established from normal adults male with B95-8 supernatant. LCLs were maintained in culture with RPMI1640 medium with 10% FCS with chemicals.
At day 0, 5-Aza-2' cytidine was added to medium with 5μM. Then at day 5, trichostatin A was added to medium with 300nM. LCL was harvested at day 7.
LCLs were established from normal adults male with B95-8 supernatant. LCLs were maintained in culture with RPMI1640 medium with 10% FCS with or without 5-aza-2'-cytidine.
5-Aza-2' cytidine was added to medium with 5μM for 5 days.

extract_protocol: Total RNA was isolated by Trizol Reagents (invitrogen).

value: human lymphoblastoid cell lines established from normal adults male

tag: treatment


title: B_Sep_male_rep2

city: Barcelona

first: Anna

last: Navarro Cuenca

state: Barcelona

address: C/Jordi Girona 18-26

department: Environmental Toxicology

country: Spain

institute: IDAEA-CSIC

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of the fragmentation mixture was added to 25 ul of GEx hybridization buffer. Final volumen of 40ul of each mix was dispensed into a costum array for D. Polymorpha (GPL15152) and placed in a rotating Agilent hybridization oven for 17 hours at 65°C After the hybridization, microarrays slides were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), and a last step of 1 minute in acid nitril bath, then dried and placed in a holder.

scan_protocol: The slides were scanned using Agilent G2565CA and signals were extracted using the Agilent Feature Extraction Software v9.5.

data_processing: Normalized signal intensity using Loess normalization protocol by JMP Software v5.

organism: Dreissena polymorpha

label_protocol: The preparations of the samples were performed according the Agilent One-Color Microarray –Based Gene Expression Analysis protocol using Cyanine 3 (Cy3) dye. A total 500ng of total RNA for each sample was used as starter material. After the amplification, labeling and purification procedure, samples were evaluated for yield and effectiveness of Cy3 dye incorporation using the NanoDrop spectrophotometer..

extract_protocol: Total RNA was isolated from the samples using Trizol reagent® protocol (Invitrogene). RNA concentration was measured by spectrophotometric absorption at 260 nm in a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Delaware, DE) and it was treated with DNAseI to remove genomic DNA contamination. RNA quality was checked by Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara CA). The samples that did not show degradation were used in the process of microarray analysis

value: Half Body

value: male

tag: season

value: September_gonad resorption


title: cultured with trichostatin A

description: This sample is normal male derived LCLs cultured withtrichostatin A.

growth_protocol:
LCLs were established from normal adults male with B95-8 supernatant. LCLs were maintained in culture with RPMI1640 medium with 10% FCS with trichostatin A.
Trichostatin A was added to medium with 300nM for 48h.
LCLs were established from normal adults male with B95-8 supernatant. LCLs were maintained in culture with RPMI1640 medium with 10% FCS with or without 5-aza-2'-cytidine.
5-Aza-2' cytidine was added to medium with 5μM for 5 days.

value: cultured with trichostatin A


title: mock 9Myc IP JCY18-1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71270.gif

source_name: mock IP of JCY18 (untagged strain), aa-amplified


title: control

description: This sample is normal male derived LCLs for control.

growth_protocol:
LCLs were established from normal adults male with B95-8 supernatant. LCLs were maintained in culture with RPMI1640 medium with 10% FCS without treatment.
LCLs were established from normal adults male with B95-8 supernatant. LCLs were maintained in culture with RPMI1640 medium with 10% FCS with or without 5-aza-2'-cytidine.
5-Aza-2' cytidine was added to medium with 5μM for 5 days.

value: control


title: Myo3:9Myc IP rep #4 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74441.gif

source_name: whole cell extract, uncrosslinked lysate, amino-allyl amplified RNA

source_name: IP 9E11 anti-c-myc, Dynal pan-mouse IgG beads, JCY 38, amino-allyl amplified

value: LatB


title: Kar3:GFP IP rep #1 crosslinked 10' 1% formaldehyde

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74454.gif


title: Myo4:GFP IP rep #2 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76093.gif

value: whole cell extract, uncrosslinked lysate, amino-allyl amplified RNA

source_name: IP anti-GFP, Dynal pan-mouse IgG beads, JCY 33, amino-allyl amplified


title: cultured with 5-aza-2'-cytidine

description: This sample is normal male derived LCLs cultured with 5-aza-2' cytidine.

growth_protocol:
LCLs were established from normal adults male with B95-8 supernatant. LCLs were maintained in culture with RPMI1640 medium with 10% FCS with 5-aza-2'-cytidine.
5-Aza-2' cytidine was added to medium with 5μM for 5 days.
LCLs were established from normal adults male with B95-8 supernatant. LCLs were maintained in culture with RPMI1640 medium with 10% FCS with or without 5-aza-2'-cytidine.
5-Aza-2' cytidine was added to medium with 5μM for 5 days.

value: cultured with 5-aza-2'-cytidine


title: Myo5:GFP IP rep #3 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76102.gif

source_name: IP anti-GFP, Dynal pan-mouse IgG beads, JCY 45, amino-allyl amplified


title: B_Sep_male_rep1

tag: gender


title: B_Sep_fem_rep1

value: female


title: B_Sep_fem_rep2


title: Myo5:9Myc IP #32 20' crosslink, Dynal beads

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72447.gif

source_name: whole cell extract, amino-allyl amplified


title: dyn1:9Myc IP JCY37-4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71263.gif

source_name: IP of JCY37 (dyn1:9Myc strain), aa-amplified


title: Las17:GFP IP rep #1 crosslinked 10' 1% formaldehyde

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74226.gif

source_name: IP anti-GFP, Dynal pan-mouse IgG beads, decrosslinked, JCY 44, amino-allyl amplified


title: Myo3:9Myc IP rep #2 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74216.gif


title: kip2:9Myc IP JCY36-4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71261.gif

source_name: IP of JCY36 (kip2:9Myc strain), aa-amplified


title: B_Jun_male_rep2


title: Myo4:GFP IP 5' crosslink, Dynal beads

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72448.gif

source_name: Myo4:GFP IP, amino-allyl amplified


title: Vrp1:GFP IP rep #1 crosslinked 10' 1% formaldehyde

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74225.gif

source_name: whole cell extract, decrosslinked, amino-allyl amplified RNA

source_name: IP anti-GFP, Dynal pan-mouse IgG beads, decrosslinked, JCY 43, amino-allyl amplified


title: Myo4:GFP IP rep #4 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76095.gif