title: hTEC_Mock_12 [20091001_01_Hs_Mock_InVitro__0720_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC


title: Chronic lymphocytic leukemia 32

status: Public on Oct 11 2012

type: genomic

city: Ulm

first: Karlheinz

last: Holzmann

address: Helmholtzstreet 8/1

department: Medical Faculty

country: Germany

institute: Ulm University

description: Hybridized to GenomeWide SNP 6.0 array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix® fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
CEL-files were generated using Affymetrix Command console software
CHP-files were generated using Affymetrix Genotyping console (BRLMM2)

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: peripherel blood

label_protocol: As per manufacturer (Affymetrix®)

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations from peripheral blood (CD19 positive and negative fraction after immunomagnetic tumor cell enrichment by Midi MACS, Miltenyi Biotec®; Bergisch Gladbach, Germany) using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

tag: cell type

value: mononuclear cells CD19+

tag: disease state

value: Chronic lymphocytic leukemia

tag: pair


title: Chronic lymphocytic leukemia 30 paired normal

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19-

value: normal


title: hTEC_NC02_16 [20110816_Hs_NC02_InVitro__0960_____hTEC_F_S3_AD_Std_.CEL]

type: RNA

city: Seattle

first: Aderem

last: Lab

state: WA

address: 307 Westlake Avenue North, Suite 500

country: USA

institute: Seattle Children's Research Institute

description: hTEC

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Microarrays were normalized at the gene level using the BrainArray custom CDF (ENST, Version 14) for probeset definitions and RMA as implemented in the justRMA function of the Bioconductor package affy for background adjustment, quantile normalization and summarization [R: 2.15.1 and Bioconductor: 2.11].

label: biotin

molecule: total RNA

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

growth_protocol: Differentiated human airway epithelial (HAE) cultures were obtained from MatTek, Inc. These cultures consist of tracheo-bronchial tissues obtained from healthy donors which are grown in 24-well inserts at the air-liquid interface to generate well-differentiated multi-layers consisting of both ciliated and non-ciliated cells as well as mucous producing goblet cells. The cultures were maintained and subsequent assays were carried out with maintenance media (AIR100 MM, MatTek Corp, Ashland, MA, USA) at 37°C and 5% CO2.

extract_protocol: RNA was extracted from HAE cultures using Trizol (Invitrogen), analyzed for overall quality using an Agilent 2100 Bioanalyzer. mRNA was labeled using the Affymetrix WT Expression kit from Ambion in conjunction with the Affymetrix Gene Chip WT Terminal Labeling kit.. Labeled cRNA was hybridized to an Affymetrix GeneChip Human Exon ST 1.0 Arrays using standard protocols and reagents from Affymetrix. Probe intensities were measured using the Affymetrix GeneChip Scanner 3000 and processed into CEL files using Affymetrix GeneChip Operating Software.

treatment_protocol: HAE and pTEC cultures were rinsed 4 times with normal saline to remove mucous and infected with the respective viruses at an MOI of 0.01 in 140 µl of HBSS at 37°C and 5% CO2. After 1 hour of virus incubation, the inoculum was removed.

value: human trachea epithelial cells

tag: time (hours)

tag: moi


title: hTEC_NC02_16 [20110816_Hs_NC02_InVitro__0960_____hTEC_F_S2_AD_Std_.CEL]

description: hTEC


title: Chronic lymphocytic leukemia 29 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 28 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 29

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 34

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 28

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 26 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 27

description: Hybridized to GenomeWide SNP 6.0 array


title: hTEC_NC02_12 [20110816_Hs_NC02_InVitro__0720_____hTEC_F_S3_AD_Std_.CEL]

description: hTEC


title: Chronic lymphocytic leukemia 27 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Valproic acid(VPA)-treated JEG-3 cell line Replicate 1

city: Seongnam

first: Youn-Jung

last: Kim

address: 212 Yangi-dong Sujeong-gu

department: Department of Food and nutrition

country: South Korea

institute: Eulji University

description: Biological replicate 1 of 3. valproic acid(VPA)-treated JEG-3 cells, 7.83 mM VPA-treated, harvested after 48h treatment.

hyb_protocol: Oligoarray control targets and hybridization buffer (FairPlay microarray labeling kit (Stratagene, Glenville, VA)) were added, and Hybridization was performed in a hybridization oven at 62°C for 12 h. After a series of washes (2×SSC/0.1% SDS for 2 min at 58°C, 1×SSC for 3 min at room temperature, 0.2×SSC for 2 min at room temperature), the slides were dried by centrifugation at 800 rpm for 3 min at room temperature.

scan_protocol: Scanned on an GenePix 4000B microarray scanner (Axon Instruments, Union City, CA) Images were quantified using GenePix 4.1 software (Axon Instruments)

data_processing: The fluorescence intensity of each spot was calculated by local median background subtraction. We then used the robust scatter-plot smoother LOWESS function to perform intensity-dependent normalization of gene expression.

source_name: valproic acid-treated JEG-3 human placental choriocarcinoma cell line

label_protocol: Labeling was performed using a FairPlay microarray labeling kit (Stratagene, Glenville, VA), followed by the coupling of Cy3 (controls) or Cy5 (treated samples) dye.

growth_protocol: The human placental choriocarcinoma cell line (JEG-3 cells) was purchased from Korean Cell Line Bank (KCLB No. 30036, Seoul, Korea) and was maintained under a humidified atmosphere of 5% CO2 and 95% air at 37°C. The culture medium was 90% Dulbecco’s modified Eagle’s medium (GIBCO BRL, Grand Island, NY) supplemented with 10% fetal bovine serum (GIBCO BRL), sodium bicarbonate (Sigma, St. Louis, MO), sodium pyruvate (GIBCO BRL) as well as penicillin and streptomycin (GIBCO BRL). The medium was replaced every 2 to 3 days. JEG-3 cells were seeded in a 100 mm dish at a density of 1.8 × 10^6 cells/ml. After incubation for 24 h at 37°C, the cells were treated with 7.38 mM valproic acid for 48 h.

extract_protocol: Total RNA extracted using Trizol, and was purified using an RNeasy mini kit (Qiagen, Valencia, CA),  following manufacturer's instructions. Genomic DNA was removed using an RNase-free DNase set (Qiagen) during RNA purification.

tag: cell line

tag: tissue

value: placenta

source_name: Control JEG-3 human placental choriocarcinoma cell line


title: hTEC_NC02_12 [20110816_Hs_NC02_InVitro__0720_____hTEC_F_S2_AD_Std_.CEL]

description: hTEC


title: hTEC_NC02_24 [20110816_Hs_NC02_InVitro__1440_____hTEC_F_S2_AD_Std_.CEL]

description: hTEC


title: input_mit1Δ_1

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

country: Sweden

institute: Karolinska Inst

description: mit1Δ mutant S.pombe; input; replicate 1

hyb_protocol: Arrays were hybridized at Gene Center Munich, Research Group Cramer. 200 ul 1x hybridization mixture containing a final concentration of 7.5 ug of fragmented and labeled DNA target, 7% DMSO and 50 pM control oligo B2 (Affymetrix P/N 900301) were prepared according to the Affymetrix Chromatin Immunoprecipitation Assay Protocol. The final DNA target mixture was hybridized onto Affymetrix S. pombe Tiling 1.0FR arrays and incubated in a hybridization oven at 45 °C and 60 rpm for 16 h.

scan_protocol: Arrays were scanned at Gene Center Munich, Research Group Cramer. After hybridization the arrays were washed and stained in an Affymetrix GeneChip Fluidics Station 450 according to the manual of the Affymetrix GeneChip hybridization, wash, and stain kit (#900720).Finally, the arrays were scanned in a Gene Chip 3000 7G scanner, and the signal was quantified with the Affymetrix GeneChip Command Console Software (AGCC) to generate CEL files.

data_processing: Raw data were processed using R/Bioconductor. Data were vsn normalized. Processed data: wig, raw data: CEL

organism: Schizosaccharomyces pombe

source_name: mit1Δ mutant S.pombe

label_protocol: The isolated DNA fragments were fragmented with DNaseI and labelled with terminal deoxynucleotidyl transferase according to Affymetrix GeneChip Mapping 10K Xba Assay Kit (P/N 900441). The purified fragments were diluted to 20 ug of DNA in a volume of 45 ul with 1× fragmentation buffer and freshly prepared fragmentation reagent (DNaseI) was added to a final concentration of 0.048 U/ul. The samples were incubated for 1 h in a preheated thermal cycler at 37 °C. The DNaseI was inactivated by incubating 15 min at 95°C. The samples were immediately placed on ice and the fragments were checked to have a size of about 50 bp with an Agilent bioanalyzer. Next, the fragmented samples were incubated at 37 °C in a thermal cycler with a labeling master mix containing DNA Labeling Reagent (5 mM), terminal deoxynucleotidyl transferase (30 U/ul) and 1× Terminal Deoxynucleotidyl Transferase Buffer as described in the Affymetrix GeneChip Mapping Assay Manual.

growth_protocol: Liquid cultures were grown in YES media. Temperature sensitive strains were grown at the permissive temperature (25 °C) either for ~30 h or for ~24 h followed by 6 h at the nonpermissive temperature (34 °C) before harvesting. All other strains were grown at 30 °C.

extract_protocol: DNAseI fragmented genomic DNA from S. Pombe log phase cells

tag: mutant


title: hTEC_NC02_24 [20110816_Hs_NC02_InVitro__1440_____hTEC_F_S1_AD_Std_.CEL]

description: hTEC


title: hTEC_NC02_12 [20110816_Hs_NC02_InVitro__0720_____hTEC_F_S1_AD_Std_.CEL]

description: hTEC


title: input_WT_2

description: wt S.pombe; input; replicate 2

source_name: wt S.pombe

value: Hu303 (wildtype)


title: Chronic lymphocytic leukemia 26

description: Hybridized to GenomeWide SNP 6.0 array


title: Valproic acid(VPA)-treated JEG-3 cell line Replicate 2

description: Biological replicate 2 of 3. valproic acid(VPA)-treated JEG-3 cells, 7.83 mM VPA-treated , harvested after 48h treatment.


title: input_WT_1

description: wt S.pombe; input; replicate 1


title: Chronic lymphocytic leukemia 25

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 35

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 36 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: nucleosomes_hrp1Δ hrp3Δ_2

description: hrp1Δ hrp3Δ mutant S.pombe; replicate 2

source_name: hrp1Δ hrp3Δ mutant S.pombe

label_protocol: The isolated mononucleosomal DNA fragments were fragmented with DNaseI and labelled with terminal deoxynucleotidyl transferase according to Affymetrix GeneChip Mapping 10K Xba Assay Kit (P/N 900441). The purified fragments were diluted to 20 ug of DNA in a volume of 45 ul with 1× fragmentation buffer and freshly prepared fragmentation reagent (DNaseI) was added to a final concentration of 0.048 U/ul. The samples were incubated for 1 h in a preheated thermal cycler at 37 °C. The DNaseI was inactivated by incubating 15 min at 95°C. The samples were immediately placed on ice and the fragments were checked to have a size of about 50 bp with an Agilent bioanalyzer. Next, the fragmented samples were incubated at 37 °C in a thermal cycler with a labeling master mix containing DNA Labeling Reagent (5 mM), terminal deoxynucleotidyl transferase (30 U/ul) and 1× Terminal Deoxynucleotidyl Transferase Buffer as described in the Affymetrix GeneChip Mapping Assay Manual.

extract_protocol: Chromatin was prepared from formaldehyde crosslinked log phase cells and digested with micrococcal nuclease (MNase, Sigma-Aldrich) to yield about 90% mononucleosomes. DNA of mononucleosomal size was purified from agarose gels, fragmented to an average size of about 50 bp with DNaseI. DNAseI fragmented genomic DNA from S. pombe was used as hybridization control.


title: nucleosomes_hrp1Δ hrp3Δ_1

description: hrp1Δ hrp3Δ mutant S.pombe; replicate 1


title: nucleosomes_hrp3Δ_2

description: hrp3Δ mutant S.pombe; replicate 2

source_name: hrp3Δ mutant S.pombe


title: Chronic lymphocytic leukemia 24

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 41

description: Hybridized to GenomeWide SNP 6.0 array


title: Valproic acid(VPA)-treated JEG-3 cell line Replicate 3

description: Biological replicate 3 of 3. valproic acid(VPA)-treated JEG-3 cells, 7.83 mM VPA-treated , harvested after 48h treatment.


title: Chronic lymphocytic leukemia 25 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: nucleosomes_hrp3Δ_1

description: hrp3Δ mutant S.pombe; replicate 1


title: hTEC_Mock_24 [20100303_05_Hs_Mock_InVitro__1440_____hTEC_U_S1_PA_Std_.CEL]

description: hTEC

value: Mock


title: hTEC_Mock_16 [20100303_04_Hs_Mock_InVitro__0960_____hTEC_U_S2_PA_Std_.CEL]

description: hTEC


title: Chronic lymphocytic leukemia 24 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: nucleosomes_hrp1Δ_2

description: hrp1Δ mutant S.pombe; replicate 2

source_name: hrp1Δ mutant S.pombe


title: hTEC_Mock_16 [20100303_03_Hs_Mock_InVitro__0960_____hTEC_U_S1_PA_Std_.CEL]

description: hTEC


title: nucleosomes_mit1Δ_2

description: mit1Δ mutant S.pombe; replicate 2


title: Chronic lymphocytic leukemia 30

description: Hybridized to GenomeWide SNP 6.0 array


title: nucleosomes_mit1Δ_1

description: mit1Δ mutant S.pombe; replicate 1


title: nucleosomes_snf21- ts swr1Δ_2

description: snf21- ts swr1Δ mutant S.pombe; replicate 2

source_name: snf21- ts swr1Δ mutant S.pombe


title: hTEC_NC02_24 [20100111_06_Hs_NC02_InVitro__1440_____hTEC_U_SC_PA_Std_.CEL]

description: hTEC


title: hTEC_Mock_24 [20100303_06_Hs_Mock_InVitro__1440_____hTEC_U_S2_PA_Std_.CEL]

description: hTEC


title: Chronic lymphocytic leukemia 23

description: Hybridized to GenomeWide SNP 6.0 array


title: hTEC_NC02_16 [20110816_Hs_NC02_InVitro__0960_____hTEC_F_S1_AD_Std_.CEL]

description: hTEC


title: hTEC_NC02_24 [20100111_05_Hs_NC02_InVitro__1440_____hTEC_U_SC_PA_Std_.CEL]

description: hTEC


title: nucleosomes_snf21- ts_2

description: snf21- ts mutant S.pombe; replicate 2

source_name: snf21- ts mutant S.pombe


title: nucleosomes_set2Δ_2

description: set2Δ mutant S.pombe; replicate 2

source_name: set2Δ mutant S.pombe

extract_protocol: Chromatin was prepared from formaldehyde crosslinked log phase cells and digested with micrococcal nuclease (MNase, Sigma-Aldrich) to yield about 90% mononucleosomes. DNA of mononucleosomal size was purified from agarose gels, fragmented to an average size of about 50 bp with DNaseI.


title: nucleosomes_pht1Δ swr1Δ_2

description: pht1Δ swr1Δ mutant S.pombe; replicate 2

source_name: pht1Δ swr1Δ mutant S.pombe


title: Chronic lymphocytic leukemia 33 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 22 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: hTEC_NC02_24 [20100111_04_Hs_NC02_InVitro__1440_____hTEC_U_SC_PA_Std_.CEL]

description: hTEC


title: nucleosomes_pht1Δ swr1Δ_1

description: pht1Δ swr1Δ mutant S.pombe; replicate 1


title: Chronic lymphocytic leukemia 22

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 21 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: RNA_pht1D_swr1D_rep2

description: RNA from pht1D swr1D S. pombe; replicate 2

hyb_protocol: Hybridised to Affymetrix GeneChip S. pombe Tiling 1.0FR Affymetrix core facility at Novum (http://apt.bea.ki.se) according to standard Affymetrix protocols.

scan_protocol: Scanned at the Affymetrix core facility at Novum (http://apt.bea.ki.se) according to standard Affymetrix protocols.

data_processing: CEL.files were analysed in R (http://www.r-project.org) using the Bioconductor (http://www. bioconductor.org) packages “affy”, “affxparser” and “preprocessCore” with standard parameters.

source_name: RNA from pht1D swr1D S. pombe

label_protocol: RNA was treated according to the Affymetrix total RNA labelling protocol (http://www.affymetrix.com).

extract_protocol: Total RNA was extracted from mid-logarithmic phase cells using the hot-phenol method. Briefly, cells were harvested by centrifugation at RT, resuspended in TES (10 mM TrisHCl pH7.5, 10 mM EDTA and 0.5% SDS) and transferred to preheated acid phenol (65 °C).  After a 45 min shaking incubation at 65 °C, RNA was isolated by phenol-chloroform extraction.


title: RNA_pht1D_swr1D_rep1

description: RNA from pht1D swr1D S. pombe; replicate 1


title: Chronic lymphocytic leukemia 21

description: Hybridized to GenomeWide SNP 6.0 array


title: nucleosomes_snf21- ts_1

description: snf21- ts mutant S.pombe; replicate 1


title: hTEC_NC02_16 [20100111_02_Hs_NC02_InVitro__0960_____hTEC_U_SC_PA_Std_.CEL]

description: hTEC


title: nucleosomes_set2Δ_1

description: set2Δ mutant S.pombe; replicate 1


title: RNA_snf21ts_swr1D_34C_rep1

description: RNA from snf21ts swr1D at 34C S. pombe; replicate 1

source_name: RNA from snf21ts swr1D at 34C S. pombe


title: RNA_snf21ts_swr1D_34C_rep2

description: RNA from snf21ts swr1D at 34C S. pombe; replicate 2


title: RNA_snf21ts_34C_rep2

description: RNA from snf21ts at 34C S. pombe; replicate 2

source_name: RNA from snf21ts at 34C S. pombe


title: Chronic lymphocytic leukemia 31

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 20 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: hTEC_IT95_24 [20091123_10_Hs_IT95_InVitro__1440_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC


title: Chronic lymphocytic leukemia 20

description: Hybridized to GenomeWide SNP 6.0 array


title: RNA_snf21ts_25C_rep1

description: RNA from snf21ts at 25C S. pombe; replicate 1

source_name: RNA from snf21ts at 25C S. pombe


title: nucleosomes_snf21- ts swr1Δ_1

description: snf21- ts swr1Δ mutant S.pombe; replicate 1


title: hTEC_NC02_16 [20100111_01_Hs_NC02_InVitro__0960_____hTEC_U_SC_PA_Std_.CEL]

description: hTEC


title: hTEC_IT95_24 [20091123_11_Hs_IT95_InVitro__1440_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC


title: RNA_snf21ts_swr1D_25C_rep2

description: RNA from snf21ts swr1D at 25C S. pombe; replicate 2

source_name: RNA from snf21ts swr1D at 25C S. pombe


title: RNA_snf21ts_25C_rep2

description: RNA from snf21ts at 25C S. pombe; replicate 2


title: RNA_wt_rep3

description: RNA from wt S. pombe; replicate 3

source_name: RNA from wt S. pombe


title: nucleosomes_hrp1Δ_1

description: hrp1Δ mutant S.pombe; replicate 1


title: RNA_snf21ts_swr1D_25C_rep1

description: RNA from snf21ts swr1D at 25C S. pombe; replicate 1


title: RNA_snf21ts_34C_rep1

description: RNA from snf21ts at 34C S. pombe; replicate 1


title: Chronic lymphocytic leukemia 19

description: Hybridized to GenomeWide SNP 6.0 array

source_name: peripherel blood


title: RNA_wt_rep1

description: RNA from wt S. pombe; replicate 1


title: hTEC_Bsb07_24 [20091123_08_Hs_Bsb07_InVitro__1440_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC

value: A/Brisbane/59/07 (H1N1)


title: RNA_wt_rep2

description: RNA from wt S. pombe; replicate 2


title: RNA_hrp1D_hrp3D_actD_rep2

description: RNA from hrp1Dhrp3D S. pombe, actinomycin D; replicate 2


title: RNA_hrp1D_hrp3D_actD_rep1

description: RNA from hrp1Dhrp3D S. pombe, actinomycin D; replicate 1


title: hTEC_IT95_24 [20091123_09_Hs_IT95_InVitro__1440_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC


title: hTEC_Bsb07_24 [20091123_07_Hs_Bsb07_InVitro__1440_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC


title: Chronic lymphocytic leukemia 18 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: hTEC_NC02_16 [20100111_03_Hs_NC02_InVitro__0960_____hTEC_U_SC_PA_Std_.CEL]

description: hTEC


title: RNA_hrp3D_actD_rep2

description: RNA from hrp3D S. pombe, actinomycin D; replicate 2

source_name: RNA from hrp3D S. pombe, actinomycin D


title: RNA_hrp3D_actD_rep1

description: RNA from hrp3D S. pombe, actinomycin D; replicate 1


title: RNA_hrp1D_actD_rep2

description: RNA from hrp1D S. pombe, actinomycin D; replicate 2

source_name: RNA from hrp1D S. pombe, actinomycin D


title: RNA_hrp1D_actD_rep1

description: RNA from hrp1D S. pombe, actinomycin D; replicate 1


title: RNA_wt_actD_rep2

description: RNA from wt S. pombe, actinomycin D; replicate 2

source_name: RNA from wt S. pombe, actinomycin D


title: RNA_wt_actD_rep1

description: RNA from wt S. pombe, actinomycin D; replicate 1


title: hTEC_TN09_24 [20091123_05_Hs_TN09_InVitro__1440_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC


title: hTEC_TN09_24 [20091123_04_Hs_TN09_InVitro__1440_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC


title: Chronic lymphocytic leukemia 17

description: Hybridized to GenomeWide SNP 6.0 array


title: hTEC_Bsb07_24 [20091123_06_Hs_Bsb07_InVitro__1440_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC


title: Chronic lymphocytic leukemia 17 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: hTEC_TN09_24 [20091123_03_Hs_TN09_InVitro__1440_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC


title: hTEC_CA09_24 [20091123_02_Hs_CA09_InVitro__1440_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC


title: CAKI1 ccRCC cells treated with DMSO

city: Jacksonville

first: John

middle: A

last: Copland

state: Florida

address: 4500 San Pablo Rd

department: Cancer Research

institute: The Mayo Clinic, Jacksonville FL

hyb_protocol: The IVT products were column-purified, fragmented, and hybridized onto Affymetrix U133 Plus 2.0 GeneChips® at 45º C for 16 h.

scan_protocol: Subsequent to hybridization, the arrays were washed and stained with streptavidin-phycoerythrin, then scanned in an Affymetrix GeneChip® Scanner 3000 (Santa Clara, CA). All control parameters were confirmed to be within normal ranges before normalization and data reduction was initiated.

data_processing: Raw data was processed by MAS.5 (Affymetrix) and analyzed using GeneSpring GX10

source_name: CAKI1 ccRCC cells treated with DMSO for 24H

label_protocol: The RNA products were column-purified (Affymetrix) and then in vitro transcribed to generate biotin-labeled cRNA.

growth_protocol: RCC cell lines A498, ACHN, Caki1, and Caki2 (ATCC) were maintained in 5% FBS and 1% penicillin-streptomycin supplemented DMEM medium

extract_protocol: RNA from samples was extracted and LiCl precipitation purified using RNAqueous Midi Kit (Ambion) as per manufacturer protocol, and samples were shipped to Advanced Genomic Technology Center Gene Expression Core at the Mayo Clinic in Rochester, MN for further analysis. RNA quality was assessed by Agilent Bioanalyzer (Santa Clara, CA). Reverse transcription to second strand cDNA was generated from 100 ng of good quality total RNA.

treatment_protocol: RCC cells were treated with 75 nM dose of A939572 SCD1 inhibitor for 24 hours (vs. DMSO control)

tag: treatment

value: DMSO


title: A498 ccRCC cells treated with DMSO

source_name: A498 ccRCC cells treated with DMSO for 24H


title: A498 ccRCC cells treated with A939572

source_name: A498 ccRCC cells treated with A939572 for 24H


title: Chronic lymphocytic leukemia 23 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: hTEC_CA09_24 [20091123_01_Hs_CA09_InVitro__1440_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC


title: CAKI2 ccRCC cells treated with A939572

source_name: CAKI2 ccRCC cells treated with A939572 for 24H


title: Chronic lymphocytic leukemia 16 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: hTEC_CA09_24 [20091119_12_Hs_CA09_InVitro__1440_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC


title: CAKI1 ccRCC cells treated with A939572

source_name: CAKI1 ccRCC cells treated with A939572 for 24H


title: hTEC_Mock_24 [20091119_11_Hs_Mock_InVitro__1440_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC


title: CAKI2 ccRCC cells treated with DMSO

source_name: CAKI2 ccRCC cells treated with DMSO for 24H


title: ACHN ccRCC cells treated with DMSO

source_name: ACHN ccRCC cells treated with DMSO for 24H

value: ACHN


title: Chronic lymphocytic leukemia 16

description: Hybridized to GenomeWide SNP 6.0 array


title: ACHN ccRCC cells treated with A939572

source_name: ACHN ccRCC cells treated with A939572 for 24H


title: trophoblast_shRNA_3

city: Fort Collins

first: Katherine

last: Gates

state: CO

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

hyb_protocol: Following fragmentation, 10 ug of aRNA were hybridized for 16 hours at 40C to GeneChip Human Genome U133 Plus 2.0 Arrays.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 7G Scanner using GCOS version 1.4 software and system controls.

data_processing: The data were analyzed in ArrayTrack and normalized to the geometric mean intensities of each chip. Groups were compared by Welch's T-test on log base 2 expression values.

source_name: ACH-3P cells

label_protocol: Biotinylated aRNA were prepared from 500 ng RNA according to the standard Affymetrix protocol (Affymetrix User Manual, GeneChip 3' IVT Express Kit)

growth_protocol: First trimester human trophoblast cells (ACH-3P) were grown in plastic cell culture dishes at 37C.

extract_protocol: RNeasy Mini Kit (Qiagen) was used to extract RNA from cell pellets according to the manufacturer's protocol.

treatment_protocol: ACH-3P cells were infected with lentivirus expressing no shRNA (control) or shRNA to target PRR15 mRNA for degradation (shRNA) at an MOI~100, with three biological replicates per treatment.

value: ACH-3P cells

value: shRNA


title: hTEC_IT95_16 [20091015_03_Hs_IT95_InVitro__0960_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC


title: Chronic lymphocytic leukemia 13 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: hTEC_Mock_24 [20091119_09_Hs_Mock_InVitro__1440_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC


title: hTEC_Mock_24 [20091119_10_Hs_Mock_InVitro__1440_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC


title: trophoblast_shRNA_1


title: Chronic lymphocytic leukemia 14 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: trophoblast_shRNA_2


title: hTEC_IT95_16 [20091015_02_Hs_IT95_InVitro__0960_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC


title: Chronic lymphocytic leukemia 15 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: trophoblast_control_3

value: control


title: trophoblast_control_2


title: Chronic lymphocytic leukemia 15

description: Hybridized to GenomeWide SNP 6.0 array


title: hTEC_Bsb07_16 [20091014_12_Hs_Bsb07_InVitro__0960_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC


title: trophoblast_control_1


title: Chronic lymphocytic leukemia 18

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 19 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: hTEC_Bsb07_16 [20091014_11_Hs_Bsb07_InVitro__0960_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC


title: Chronic lymphocytic leukemia 13

description: Hybridized to GenomeWide SNP 6.0 array


title: hTEC_IT95_16 [20091015_01_Hs_IT95_InVitro__0960_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC


title: Chronic lymphocytic leukemia 12

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 14

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 11

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 12 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: AEPC-KIA rep3

city: Sendai

first: Hiroshi

last: Kubo

state: Miyagi

address: 2-1 Seiryomachi, Aobaku

department: Department of Advanced Preventive Medicine for Infectious Disease, and Regenerative Medicine

country: Japan

institute: Tohoku University Graduate School of Medicine

hyb_protocol: The purified and fragmented cRNA (12.5 μg) was hybridized to GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix). The array was incubated for 16 hours at 45°C, then automatically washed and stained with GeneChip Hybridization, Wash and Stain Kit (Affymetrix).

scan_protocol: The probe array was scanned using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix Expression Console (Affymetrix).

source_name: AEPC-3, treated with KIA

label_protocol: Biotinylated cRNA were prepared from 100 ng total RNA according to the manufacturer's protocol using GeneChip 3' IVT Express Kit (Affymetrix).

growth_protocol: To induce ATII-differentiation, AEPCs were cultured on the mixture of Matrigel and collagen type I gel with medium consiting of DMEM+5%FCS+antiboitics+KGF+cAMP+IBMX.

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen, Carlsbad, CA) and cleaned up using miRNeasy mini kit (Qiagen, Tokyo, Japan).

value: human distal lung

tag: age

value: 59 years old

tag: gender

value: male

tag: number


title: hTEC_TN09_16 [20091014_09_Hs_TN09_InVitro__0960_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC


title: Chronic lymphocytic leukemia 11 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: AEPC-KIA rep1

source_name: AEPC-1, treated with KIA

value: 69 years old

value: female


title: hTEC_Bsb07_16 [20091014_10_Hs_Bsb07_InVitro__0960_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC


title: AEPC-KIA rep2

source_name: AEPC-2, treated with KIA

value: 78 years old


title: Chronic lymphocytic leukemia 9 paired normal

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19-

value: normal


title: hTEC_TN09_16 [20091014_08_Hs_TN09_InVitro__0960_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC

value: human trachea epithelial cells


title: HT1080 cell_10 mM 2-deoxyglucose_10 μM versipelostatin_18h

city: Ariake

first: Akihiro

last: Tomida

state: Koto-ku, Tokyo

department: Cancer Chemotherapy Center

institute: Japanese Foundation for Cancer Research (JFCR)

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

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

data_processing: The data were normalized by the Robust Multichip Average (RMA) methods using the RMAExpress version 1.0.4.

label_protocol: cRNA targets for hybridization to GeneChip were prepared by reverse transcription from 100 ng of total RNA and then labeled with biotin according to standard Affymetrix protocols.

growth_protocol: HT1080 cells were maintained in PRIM1640, containing 2 mg/mL of glucose, supplemented with with 10% FBS and 100 μg/mL of kanamycin, and cultured at 37°C , 5% CO2 as the normal growth condition.

extract_protocol: Total RNA from cultured cells was isolated using the RNeasy RNA purification kit (Qiagen, CA, USA) according to the manufacturer's instructions.

value: fibrosarcoma cell


title: hTEC_TN09_16 [20091014_07_Hs_TN09_InVitro__0960_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC


title: Chronic lymphocytic leukemia 10

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+

value: Chronic lymphocytic leukemia


title: Chronic lymphocytic leukemia 8

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 8 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: hTEC_CA09_16 [20091014_06_Hs_CA09_InVitro__0960_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC


title: Chronic lymphocytic leukemia 10 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: HT1080 cell_10 mM 2-deoxyglucose_10 μM compound C_18h


title: hTEC_CA09_16 [20091014_05_Hs_CA09_InVitro__0960_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC


title: HT1080 cell_10 mM 2-deoxyglucose_18h

source_name: 10 mM 2-deoxyglucose_18h


title: HT1080 cell_10 mM 2-deoxyglucose_100 μM phenformin_18h


title: hepatic inflammatory cells of concanavalin A-injected mice No.985

city: Kanazawa

first: Yoshio

last: Sakai

state: Ishikawa

address: 13-1 Takara-machi

department: Department of Gastroenterology

institute: Kanazawa University

description: Gene expression of the hepatic inflammatory cells in concanavalin A-injected mice

hyb_protocol: The 1.65 microgram of cRNA was fragmented and hybiridized to Whole Mouse Genome 4x44K Array (Agilent) oligo DNA chip using hybridization buffer (Agilent Gene Expression Hybridization Kit) at 60 celcius degree for 17 hours.

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

organism: Mus musculus

source_name: hepatic inflammatory cells, 5 hours after concanavalin A injection, adipose tissue derived stem cell treatment, No.985

label_protocol: cRNA was amplified and labaled with Cy3 fluorescence using Low QuickAmp Labeling Kit (Agilent Techologies, Santa Clara, CA).

growth_protocol: Adipose tissue derived stem cells obtained from inguinal adipose tissue of C57Bl/6 mice were obtained by collagenase digestion and expanded in culture until use.

extract_protocol: RNA was extracted using MicroRNA isolation kit (Stratagene).

treatment_protocol: The mice,  which were injected with 300 microgram of concanavalin A, were treated with 1x10^5 adipose tissue derived stem cells immediately or after 3 hours via tail vein. After 2 hours, the liver or hepatic inflammatory cells were obtained.

tag: strain

value: hepatic inflammatory cells in concanavalin A-injected mice after 5 hours


title: hepatic inflammatory cells of concanavalin A-injected mice No.983

source_name: hepatic inflammatory cells, 5 hours after concanavalin A injection, adipose tissue derived stem cell treatment, No.983


title: HT1080 cell_normal growth condition_100 μM phenformin_18h

description: Phen


title: hepatic inflammatory cells of concanavalin A-injected mice No.989

description: Gene expression of the hepatic inflammatory cells in concanavalin A-injected mice treated with adipose tissue derived stem cells after 3 hours

source_name: hepatic inflammatory cells, concanavalin A injection, adipose tissue derived stem cell treatment after 3 hours, No.989


title: 802T4

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430A_2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: R version 2.11.1 (x86_64-pc-linux-gnu), affyPLM_1.24.0, preprocessCore_1.10.0, gcrma_2.20.0, affy_1.26.0, Biobase_2.8.0

source_name: primary tumor derived cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA using Affymetrix GeneChip WT Sense Target Labelling and Control Reagents kit according to the Affymetrix Expression Analysis Technical Manual.

growth_protocol: Tumours were initiated by intratracheal infection of KrasLSL-G12D/+;p53flox/flox mice with a lentiviral vector expressing Cre-recombinase.  The MIT Institutional Animal Care and Use Committee approved all animal studies and procedures. Cell lines were created from individual lung tumours and metastases harvested from mice 8-14 months after tumour initiation. Tumours were cut into small pieces and then digested for 30 minutes at 37°C in 2ml of HBSS-free containing Trypsin, Collagenase IV, and Dispase in a 15ml conical tube. Following digestion, 4mL of Quench Solution (L15 media with 400μl of FBS and 15μl of 5mg/ml DNase) was added. Digested tumour samples were then pressed through 40μm cell strainers (BD). Finally, samples were centrifuged at 1,000 r.p.m. for 5 minutes, resuspended in culture media (DMEM, 10% FBS, pen/strep, glutamine), and plated in a 12-well plate. Cells were washed and culture media was changed every day for a week until stable cell lines were formed. In general we were able to derive cell lines from approximately 50% of tumours and metastases without a noticeable difference in the frequency of cell line generation from metastases from different site relative to the primary lung tumours.

extract_protocol: Cell lysates were harvested using Trizol (Sigma). Chloroform extraction was performed followed by RNA purification using Qiagen RNeasy spin columns. Lysates were analyzed for RNA integrity.

treatment_protocol: Cell lines were cultured in DMEM, 10% FBS, penicillin/streptomycin, and glutamine.

value: primary tumor derived cell line

tag: genotype/variation


title: hTEC_Mock_16 [20091014_03_Hs_Mock_InVitro__0960_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC

value: Mock


title: hepatic inflammatory cells of concanavalin A-injected mice No.987

source_name: hepatic inflammatory cells, concanavalin A injection, adipose tissue derived stem cell treatment after 3 hours, No.987

value: hepatic inflammatory cells in concanavalin A-injected mice treated with adipose tissue derived stem cells after 3 hours


title: HT1080 cell_normal growth condition_10 μM versipelostatin_18h

description: VST


title: hTEC_CA09_16 [20091014_04_Hs_CA09_InVitro__0960_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC


title: 482N1

source_name: metastasis derived cell line (from lymph node metastasis)


title: liver of concanavalin A-injected mice No.6

description: Gene expression of the liver in concanavalin A-injected mice

source_name: liver, 5 hours after concanavalin A injection, No.6

value: liver in concanavalin A-injected mice after 5 hours


title: 2691n1

value: metastasis derived cell line (from lymph node metastasis)


title: hTEC_Mock_16 [20091014_01_Hs_Mock_InVitro__0960_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC


title: HT1080 cell_normal growth condition_10 μM compound C_18h

description: CC


title: hTEC_TN09_12 [20091012_01_Hs_TN09_InVitro__0720_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC


title: 389T2


title: Chronic lymphocytic leukemia 9

description: Hybridized to GenomeWide SNP 6.0 array

source_name: peripherel blood


title: Chronic lymphocytic leukemia 7

description: Hybridized to GenomeWide SNP 6.0 array


title: hTEC_IT95_12 [20091001_14_Hs_IT95_InVitro__0720_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC


title: hTEC_Mock_16 [20091014_02_Hs_Mock_InVitro__0960_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC


title: liver of concanavalin A-injected mice No.5

source_name: liver, 5 hours after concanavalin A injection, No.5


title: 389t2_b


title: HT1080 cell_normal growth condition_18h

description: Control

source_name: normal growth condition_18h


title: hTEC_IT95_12 [20091001_13_Hs_IT95_InVitro__0720_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC


title: 393m1

source_name: metastasis derived cell line (from liver metastasis)


title: Chronic lymphocytic leukemia 7 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: ATII non-COPD rep2

extract_protocol: Total RNA was isolated using miRNeasy mini kit (Qiagen, Tokyo, Japan)

value: human distal lung

value: 70 years old

tag: smoking history (pack-years)

tag: smoking cessation

value: 0 yr

tag: fev1 (% pred)

value: non-COPD

value: Alveolar epithelial type II


title: liver of concanavalin A-injected mice No.4

source_name: liver, 5 hours after concanavalin A injection, No.4

value: female


title: hTEC_IT95_12 [20091001_12_Hs_IT95_InVitro__0720_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC

tag: cell type


title: Chronic lymphocytic leukemia 6 paired normal

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19-

tag: disease state

value: normal


title: liver of concanavalin A-injected mice No.2

description: Gene expression of the liver in concanavalin A-injected mice treated with adipose tissue derived stem cells after 3 hours

source_name: liver, concanavalin A injection, adipose tissue derived stem cell treatment after 3 hours, No.2


title: Chronic lymphocytic leukemia 5

description: Hybridized to GenomeWide SNP 6.0 array

tag: pair


title: liver of concanavalin A-injected mice No.3

source_name: liver, concanavalin A injection, adipose tissue derived stem cell treatment after 3 hours, No.3

value: liver in concanavalin A-injected mice treated with adipose tissue derived stem cells after 3 hours


title: ATII non-COPD rep1

value: 44 years old

value: male

value: 20 yr


title: 368t1

value: primary tumor derived cell line


title: Chronic lymphocytic leukemia 6

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+

value: Chronic lymphocytic leukemia


title: hTEC_Bsb07_12 [20091001_11_Hs_Bsb07_InVitro__0720_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC

value: human trachea epithelial cells

tag: time (hours)

value: A/Brisbane/59/07 (H1N1)


title: hTEC_Bsb07_12 [20091001_10_Hs_Bsb07_InVitro__0720_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC

tag: moi


title: 393t5


title: ATII COPD rep2

value: human distal lung

value: 69 years old

value: 1 yr

value: COPD


title: Chronic lymphocytic leukemia 4 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 5 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: liver of concanavalin A-injected mice No.13

source_name: liver, 2 hours after concanavalin A injection, No.13

value: liver in concanavalin A-injected mice after 2 hours


title: ATII non-COPD rep3

value: 81 years old

value: 0 yr

value: non-COPD

value: Alveolar epithelial type II


title: hTEC_Bsb07_12 [20091001_09_Hs_Bsb07_InVitro__0720_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC


title: 394t4


title: liver of concanavalin A-injected mice No.12

source_name: liver, 2 hours after concanavalin A injection, No.12

value: female


title: ATII COPD rep3

value: 70 years old

value: male


title: 389n1

value: metastasis derived cell line (from lymph node metastasis)


title: liver of concanavalin A-injected mice No.11

source_name: liver, 2 hours after concanavalin A injection, No.11


title: 482t1

value: primary tumor derived cell line


title: ATII COPD rep1

value: 59 years old

value: 15 yr

tag: fev1 (%pred)


title: hTEC_TN09_12 [20091001_07_Hs_TN09_InVitro__0720_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC

value: human trachea epithelial cells


title: Chronic lymphocytic leukemia 3 paired normal

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19-

value: normal


title: Chilli_PepLCV susceptible_treated_rep1

city: Varanasi

first: Ved

middle: Prakash

last: Rai

state: Uttar Pradesh

address: Lanka

department: Genetics and Plant Breeding

country: India

institute: Banaras Hindu University, Varanasi

description: Gene expression data from chilli PepLCV susceptible treated plants

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

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G3000) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3 (Agilent) using default parameters to  obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Capsicum annuum

source_name: Leaves at three leaf stage, artificially infected with PepLCV

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

growth_protocol: Plantlets were grown in plastic pots in polyhouse at optimal conditions for chilli plants.

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

treatment_protocol: To infect with PepLCV, plantlets were artificially inoculated with virulified white flies vectors using microcages.

tag: tissue

value: leaves at three leaf stage

tag: infectious agent

value: PepLCV

tag: genotype

value: PepLCV susceptible


title: Chilli_PepLCV susceptible_treated_rep2


title: C. elegans grown without a-SWCNT treatment for 48 hr at 22°C.

city: Chiayi

first: Cheng

middle: Chung

last: Chou

state: International

address: 168 University Road, Minhsiung Township

country: Taiwan

institute: ChungCheng university

description: control

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

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

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

organism: Caenorhabditis elegans

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

growth_protocol: Wild-type N2 was used in all experiments. This strain was maintained at 13°C on Nematode Growth Medium (NGM) agar. Before seeding, the E. coli strain OP50 was allowed to grow overnight. The preparation of synchronized worms was performed using the alkaline hypochlorite method. In brief, adult worms were collected by washing the NGM plates with sterile d2H2O to remove the supernatant, and the worms were subjected to shaking for 3-5 min in a solution containing 1:1 1 M NaOH/bleach. After washing twice with sterile d2H2O, the eggs were kept in M9 buffer until hatching. The hatched worms (L1 stage larvae) were transferred to fresh agar plates and cultured at 22°C for phenotype analysis.

treatment_protocol: Exposure of synchronized L1 worms to different concentrations of a-SWCNTs for 48 hr at 22°C.

value: whole organism

tag: age

value: L4 stage

tag: treatment

value: control


title: hTEC_TN09_12 [20091001_08_Hs_TN09_InVitro__0720_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC


title: hTEC_CA09_12 [20091001_06_Hs_CA09_InVitro__0720_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC


title: Chronic lymphocytic leukemia 2

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+

value: Chronic lymphocytic leukemia


title: Chronic lymphocytic leukemia 4

description: Hybridized to GenomeWide SNP 6.0 array


title: liver of concanavalin A-injected mice No.8

description: Gene expression of the liver in concanavalin A-injected mice immediately treated with adipose tissue derived stem cells

source_name: liver, concanavalin A injection, adipose tissue derived stem cell immediate treatment, No.8

tag: gender

value: female


title: liver of concanavalin A-injected mice No.10

source_name: liver, concanavalin A injection, adipose tissue derived stem cell immediate treatment, No.10

tag: strain

value: liver in concanavalin A-injected mice immediately treated with adipose tissue derived stem cells


title: liver of concanavalin A-injected mice No.1

source_name: liver, concanavalin A injection, adipose tissue derived stem cell treatment after 3 hours, No.1

value: liver in concanavalin A-injected mice treated with adipose tissue derived stem cells after 3 hours


title: Chronic lymphocytic leukemia 1 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: liver of concanavalin A-injected mice No.9

source_name: liver, concanavalin A injection, adipose tissue derived stem cell immediate treatment, No.9


title: Chronic lymphocytic leukemia 2 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: temperature: 25-25 C - rep2

status: Public on Oct 10 2012

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

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

department: Virtual Reality Application Center

institute: Iowa State University

hyb_protocol: Affymetrix vitis vinifera Genechips

scan_protocol: CNB Grapegen Affymetrix scanning

data_processing: The MAS5.0 Normalization was performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org, Version: 2.12.1). The target value is 500 for all cases. The code was developed using R2.4.1 to 2.13.0, Bioconductor 1.9 to 2.12.1, and simpleaffy 2.8.0. to 2.28.0 The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html.

organism: Vitis vinifera

source_name: Leaves & Stems (temperature: 25-25 C)

label_protocol: Affymetrix one-cycle target labeling

extract_protocol: Total RNA extraction

tag: germplasm name

value: Cabernet Sauvignon

tag: organism part

value: Leaves & Stems

tag: development stage

value: leaf development stages ('PO:0001050')

tag: growth media

value: peat/perlite/soil

tag: temperature


title: temperature: 25-25 C - rep3

tag: cell type


title: temperature: 25 C - rep3

source_name: Leaves & Stems (temperature: 25 C)


title: temperature: 25-25 C - rep1


title: temperature: 45-25 C - rep2

source_name: Leaves & Stems (temperature: 45-25 C)


title: Chronic lymphocytic leukemia 3

description: Hybridized to GenomeWide SNP 6.0 array

source_name: peripherel blood

tag: disease state

tag: pair


title: Chilli_PepLCV resistant_treated_rep2

description: Gene expression data from chilli PepLCV resistant treated plants

organism: Capsicum chinense x Capsicum frutescens

value: PepLCV resistant


title: temperature: 45-25 C - rep1


title: 2691m1

value: metastasis derived cell line (from liver metastasis)

tag: genotype/variation


title: temperature: 45 C - rep3

source_name: Leaves & Stems (temperature: 45 C)


title: temperature: 45-25 C - rep3


title: temperature: 25 C - rep2


title: Chronic lymphocytic leukemia 1

description: Hybridized to GenomeWide SNP 6.0 array


title: temperature: 45 C - rep2


title: temperature: 45 C - rep1


title: temperature: 25 C - rep1


title: Chilli_PepLCV resistant_treated_rep1

value: leaves at three leaf stage


title: genotype: PI459025B - pathogen inoculation: Hawaii 94-1 - time: 144 hai - rep2

description: PI459025B Hawaii 94-1(avir) treatment 144 hours

hyb_protocol: Affy- Eukaryotic Target Hybridization

scan_protocol: Affy- Array Scanning

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

organism: Glycine max

source_name: leaf (genotype: PI459025B - pathogen inoculation: Hawaii 94-1 - time: 144 hai)

label_protocol: Affy-Eukaryotic Target Preparation

extract_protocol: QIAGEN RNeasy Plant Mini Kit

tag: pathogen isolates

value: Hawaii 94-1 (avir)

tag: time

value: williams

value: UD:0000051 vegetative


title: genotype: PI459025B - pathogen inoculation: Hawaii 94-1 - time: 144 hai - rep1


title: genotype: PI459025B - pathogen inoculation: Hawaii 94-1 - time: 216 hai - rep3

description: PI459025B Hawaii 94-1(avir) treatment 216 hours

source_name: leaf (genotype: PI459025B - pathogen inoculation: Hawaii 94-1 - time: 216 hai)


title: genotype: PI459025B - pathogen inoculation: Hawaii 94-1 - time: 144 hai - rep3


title: genotype: PI459025B - pathogen inoculation: Hawaii 94-1 - time: 288 hai - rep2

description: PI459025B Hawaii 94-1(avir) treatment 288 hours

source_name: leaf (genotype: PI459025B - pathogen inoculation: Hawaii 94-1 - time: 288 hai)


title: genotype: PI459025B - pathogen inoculation: Hawaii 94-1 - time: 216 hai - rep2


title: genotype: PI459025B - pathogen inoculation: Hawaii 94-1 - time: 288 hai - rep1


title: genotype: PI459025B - pathogen inoculation: Hawaii 94-1 - time: 216 hai - rep1


title: C. elegans exposed to 500 μg/mL of a-SWCNT for 48 hr at 22°C.

description: Expression data from C. elegans exposed to amide single-walled carbon nanotubes (500 μg/mL) for 48 hr at 22°C.

tag: tissue

value: whole organism

value: L4 stage

value: 500 μg/mL of a-SWCNT for 48 hr


title: genotype: PI459025B - pathogen inoculation: Hawaii 94-1 - time: 288 hai - rep3


title: genotype: PI459025B - pathogen inoculation: Hawaii 94-1 - time: 12 hai - rep2

description: PI459025B Hawaii 94-1(avir) treatment 12 hours

source_name: leaf (genotype: PI459025B - pathogen inoculation: Hawaii 94-1 - time: 12 hai)

value: 12 hr


title: genotype: PI459025B - pathogen inoculation: Hawaii 94-1 - time: 24 hai - rep3

description: PI459025B Hawaii 94-1(avir) treatment 24 hours

source_name: leaf (genotype: PI459025B - pathogen inoculation: Hawaii 94-1 - time: 24 hai)

value: 24 hr


title: genotype: PI459025B - pathogen inoculation: Mock - time: 216 hai - rep3

description: PI459025B mock treatment 216 hours

source_name: leaf (genotype: PI459025B - pathogen inoculation: Mock - time: 216 hai)

value: Mock


title: genotype: PI459025B - pathogen inoculation: Mock - time: 216 hai - rep2

description: PI459025B mock treatment 216 hours


title: genotype: PI459025B - pathogen inoculation: Hawaii 94-1 - time: 72 hai - rep2

description: PI459025B Hawaii 94-1(avir) treatment 72 hours

source_name: leaf (genotype: PI459025B - pathogen inoculation: Hawaii 94-1 - time: 72 hai)

value: 72 hr


title: genotype: PI459025B - pathogen inoculation: Hawaii 94-1 - time: 72 hai - rep1


title: genotype: PI459025B - pathogen inoculation: Hawaii 94-1 - time: 12 hai - rep1


title: genotype: PI459025B - pathogen inoculation: Mock - time: 288 hai - rep3

description: PI459025B mock treatment 288 hours

source_name: leaf (genotype: PI459025B - pathogen inoculation: Mock - time: 288 hai)


title: genotype: PI459025B - pathogen inoculation: Mock - time: 288 hai - rep1

description: PI459025B mock treatment 288 hours


title: genotype: PI459025B - pathogen inoculation: Hawaii 94-1 - time: 72 hai - rep3


title: genotype: PI459025B - pathogen inoculation: Hawaii 94-1 - time: 24 hai - rep1


title: genotype: PI459025B - pathogen inoculation: Hawaii 94-1 - time: 24 hai - rep2


title: genotype: PI459025B - pathogen inoculation: Mock - time: 144 hai - rep1

description: PI459025B mock treatment 144 hours

source_name: leaf (genotype: PI459025B - pathogen inoculation: Mock - time: 144 hai)


title: genotype: PI459025B - pathogen inoculation: Mock - time: 216 hai - rep1

description: PI459025B mock treatment 216 hours


title: genotype: PI459025B - pathogen inoculation: Mock - time: 144 hai - rep2

description: PI459025B mock treatment 144 hours


title: genotype: PI459025B - pathogen inoculation: Mock - time: 72 hai - rep1

description: PI459025B mock treatment 72 hours

source_name: leaf (genotype: PI459025B - pathogen inoculation: Mock - time: 72 hai)


title: genotype: PI459025B - pathogen inoculation: Mock - time: 288 hai - rep2

description: PI459025B mock treatment 288 hours


title: genotype: PI459025B - pathogen inoculation: Mock - time: 144 hai - rep3

description: PI459025B mock treatment 144 hours


title: genotype: PI459025B - pathogen inoculation: Mock - time: 24 hai - rep2

description: PI459025B mock treatment 24 hours

source_name: leaf (genotype: PI459025B - pathogen inoculation: Mock - time: 24 hai)


title: genotype: PI459025B - pathogen inoculation: Hawaii 94-1 - time: 12 hai - rep3


title: genotype: PI459025B - pathogen inoculation: Mock - time: 24 hai - rep1

description: PI459025B mock treatment 24 hours


title: genotype: PI459025B - pathogen inoculation: Mock - time: 72 hai - rep3

description: PI459025B mock treatment 72 hours


title: genotype: PI459025B - pathogen inoculation: Mock - time: 24 hai - rep3

description: PI459025B mock treatment 24 hours


title: genotype: Williams - pathogen inoculation: Hawaii 94-1 - time: 288 hai - rep2

description: Williams Hawaii 94-1(vir) treatment 288 hours

source_name: leaf (genotype: Williams - pathogen inoculation: Hawaii 94-1 - time: 288 hai)


title: genotype: PI459025B - pathogen inoculation: Mock - time: 12 hai - rep3

description: PI459025B mock treatment 12 hours

source_name: leaf (genotype: PI459025B - pathogen inoculation: Mock - time: 12 hai)


title: genotype: Williams - pathogen inoculation: Hawaii 94-1 - time: 288 hai - rep3


title: genotype: PI459025B - pathogen inoculation: Mock - time: 12 hai - rep2

description: PI459025B mock treatment 12 hours


title: genotype: PI459025B - pathogen inoculation: Mock - time: 12 hai - rep1

description: PI459025B mock treatment 12 hours


title: LaminA in ACs (rep 2)

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

hyb_protocol: Hybridisation was performed as described: Peric-Hupkes, Meuleman et al., Mol. Cell (2010).

scan_protocol: Scanning was performed as described: Peric-Hupkes, Meuleman et al., Mol. Cell (2010).

data_processing: Data were normalized using quantile normalisation on the single channel data, after which channels are re-combined into M- and A-values.

source_name: LaminA in ACs (rep 2)

label_protocol: Material was labelled as described: Peric-Hupkes, Meuleman et al., Mol. Cell (2010).

growth_protocol: A lentiviral Dam-lamin A expressing construct was made through gateway cloning as described in (Vogel et al., 2006), and correct subnuclear localization to the NL of the fusion protein was confirmed by immunofluorescence microscopy using an antibody against the v5 epitope-tag (data not shown).

extract_protocol: Cells were grown and material was extracted as described: Peric-Hupkes, Meuleman et al., Mol. Cell (2010).

value: Acs

tag: dam status

value: Dam-fusion

value: Dam-only


title: genotype: Williams - pathogen inoculation: Hawaii 94-1 - time: 216 hai - rep2

description: Williams Hawaii 94-1(vir) treatment 216 hours

source_name: leaf (genotype: Williams - pathogen inoculation: Hawaii 94-1 - time: 216 hai)

tag: age

value: peat/perlite/soil


title: genotype: Williams - pathogen inoculation: Hawaii 94-1 - time: 288 hai - rep1


title: genotype: Williams - pathogen inoculation: Hawaii 94-1 - time: 216 hai - rep1


title: genotype: Williams - pathogen inoculation: Hawaii 94-1 - time: 216 hai - rep3


title: LaminB1 in wt MEFs (rep 2)

source_name: LaminB1 in wt MEFs (rep 2)

growth_protocol: Oct1-/- MEFs and matching isogenic wildtype MEFs were obtained from D. Tantin and cultured as described (Kang et al., 2009).

value: MEFs

tag: genotype

value: WT


title: genotype: Williams - pathogen inoculation: Hawaii 94-1 - time: 144 hai - rep3

description: Williams Hawaii 94-1(vir) treatment 144 hours

source_name: leaf (genotype: Williams - pathogen inoculation: Hawaii 94-1 - time: 144 hai)


title: genotype: Williams - pathogen inoculation: Hawaii 94-1 - time: 144 hai - rep1


title: genotype: Williams - pathogen inoculation: Hawaii 94-1 - time: 72 hai - rep3

description: Williams Hawaii 94-1(vir) treatment 72 hours

source_name: leaf (genotype: Williams - pathogen inoculation: Hawaii 94-1 - time: 72 hai)


title: LaminB1 in Oct1-/- MEFs (rep 2)

source_name: LaminB1 in Oct1-/- MEFs (rep 2)


title: genotype: Williams - pathogen inoculation: Hawaii 94-1 - time: 12 hai - rep1

description: Williams Hawaii 94-1(vir) treatment 12 hours

source_name: leaf (genotype: Williams - pathogen inoculation: Hawaii 94-1 - time: 12 hai)


title: genotype: Williams - pathogen inoculation: Hawaii 94-1 - time: 24 hai - rep3

description: Williams Hawaii 94-1(vir) treatment 24 hours

source_name: leaf (genotype: Williams - pathogen inoculation: Hawaii 94-1 - time: 24 hai)


title: genotype: Williams - pathogen inoculation: Hawaii 94-1 - time: 72 hai - rep1


title: genotype: Williams - pathogen inoculation: Hawaii 94-1 - time: 12 hai - rep2


title: genotype: Williams - pathogen inoculation: Hawaii 94-1 - time: 24 hai - rep1


title: genotype: Williams - pathogen inoculation: Hawaii 94-1 - time: 72 hai - rep2


title: genotype: Williams - pathogen inoculation: Mock - time: 288 hai - rep3

description: Williams mock treatment 288 hours

source_name: leaf (genotype: Williams - pathogen inoculation: Mock - time: 288 hai)


title: genotype: Williams - pathogen inoculation: Hawaii 94-1 - time: 144 hai - rep2


title: genotype: Williams - pathogen inoculation: Hawaii 94-1 - time: 12 hai - rep3


title: genotype: Williams - pathogen inoculation: Mock - time: 216 hai - rep2

description: Williams mock treatment 216 hours

source_name: leaf (genotype: Williams - pathogen inoculation: Mock - time: 216 hai)


title: genotype: Williams - pathogen inoculation: Mock - time: 288 hai - rep2

description: Williams mock treatment 288 hours


title: genotype: Williams - pathogen inoculation: Mock - time: 216 hai - rep1

description: Williams mock treatment 216 hours


title: genotype: Williams - pathogen inoculation: Hawaii 94-1 - time: 24 hai - rep2


title: genotype: Williams - pathogen inoculation: Mock - time: 216 hai - rep3

description: Williams mock treatment 216 hours


title: LaminA in ACs (rep 1)

source_name: LaminA in ACs (rep 1)


title: genotype: Williams - pathogen inoculation: Mock - time: 288 hai - rep1

description: Williams mock treatment 288 hours


title: LaminA in NPCs (rep 1)

source_name: LaminA in NPCs (rep 1)

value: NPCs


title: genotype: Williams - pathogen inoculation: Mock - time: 144 hai - rep3

description: Williams mock treatment 144 hours

source_name: leaf (genotype: Williams - pathogen inoculation: Mock - time: 144 hai)


title: genotype: Williams - pathogen inoculation: Mock - time: 72 hai - rep3

description: Williams mock treatment 72 hours

source_name: leaf (genotype: Williams - pathogen inoculation: Mock - time: 72 hai)


title: genotype: Williams - pathogen inoculation: Mock - time: 72 hai - rep2

description: Williams mock treatment 72 hours


title: genotype: Williams - pathogen inoculation: Mock - time: 144 hai - rep1

description: Williams mock treatment 144 hours


title: genotype: Williams - pathogen inoculation: Mock - time: 72 hai - rep1

description: Williams mock treatment 72 hours


title: genotype: Williams - pathogen inoculation: Mock - time: 144 hai - rep2

description: Williams mock treatment 144 hours


title: LaminA in NPCs (rep 2)

source_name: LaminA in NPCs (rep 2)


title: LaminB1 in Oct1-/- MEFs (rep 1)

source_name: LaminB1 in Oct1-/- MEFs (rep 1)


title: LaminB1 in wt MEFs (rep 1)

source_name: LaminB1 in wt MEFs (rep 1)


title: genotype: PI459025B - pathogen inoculation: Mock - time: 72 hai - rep2

description: PI459025B mock treatment 72 hours

source_name: leaf (genotype: PI459025B - pathogen inoculation: Mock - time: 72 hai)


title: genotype: Williams - pathogen inoculation: Mock - time: 24 hai - rep2

description: Williams mock treatment 24 hours

source_name: leaf (genotype: Williams - pathogen inoculation: Mock - time: 24 hai)


title: genotype: Williams - pathogen inoculation: Mock - time: 24 hai - rep3

description: Williams mock treatment 24 hours


title: genotype: Williams - pathogen inoculation: Mock - time: 24 hai - rep1

description: Williams mock treatment 24 hours


title: genotype: Williams - pathogen inoculation: Mock - time: 12 hai - rep2

description: Williams mock treatment 12 hours

source_name: leaf (genotype: Williams - pathogen inoculation: Mock - time: 12 hai)


title: ravS Replicate 1

city: Beijing

first: jun

last: tao

address: Beichen west road

country: China

institute: institute of microbiology, Chinese academy of sciences

hyb_protocol: standard CapitalBio Methods

scan_protocol: Luxscan 10KA (CapitalBio)

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed. For each test and control sample, two hybridizations were performed by using a reversal fluorescent strategy,the geometric mean  of lowess normalized log2 ratio (test/control) of two dye-swap slides was calculated.

organism: Xanthomonas campestris pv. campestris

source_name: ravS mutant

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP, Amersham Pharmacia Biotech, Piscataway, NJ) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction. the amplified RNA (aRNA) was purified with NucleoSpin Extract II (MN). We took a cDNA labeling approach with Klenow enzyme after reverse transcription.

growth_protocol: Xcc was grown in NYGB liquid medium for 1 day.

extract_protocol: RNA was isolated by Trizol (Invitrogen) per the manufacturer's protocol

treatment_protocol: When the OD600 reached 1.0, bacterial cells were collected by centrifugation at 25°C

value: ΔravS

source_name: wild type


title: HNSCC_primary_9005369

first: Paul

last: Roepman

address: Science Park 406

institute: Agendia

scan_protocol: Scanned on an Agilent G2565AA scanner

data_processing: Background subtracted data for the Cy5 (reference) and Cy3 (sample) channel were obtained using Agilent Feature Extraction software (version 9.5) based on MedianSignal calls. Lowess-normalization.

label_protocol: Low Input RNA Fluorescent Linear Amplification. Agilent's recommended procedures for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis 1). Convert mRNA primed with an oligo (d)T-T7 primer into dsDNA with MMLV-RT. 2) amplify sample using T7 RNA Polymerase [http://www.chem.agilent.com/temp/rad6D82C/00056953.pdf]  Agilent recommended procedure for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis. Publication Number: G4140-90050 V4.0  Last Updated: 2/2006 Number of Pages: 70

extract_protocol:
RNA isolation. We used 2-5 sections of 20-µm thickness for total RNA isolation. Total RNA was isolated with Trizol, and finally dissolved in RNase-free H2O and treated with DNase using the Qiagen RNase-free DNase kit and RNeasy spin columns.
Sample reference protocol: A reference sample was made by processing of the Universal Human Reference cell line (Stratagene) similarly as the test samples.

tag: gender

value: male

value: head-neck

tag: tumor type

value: HNSCC

tag: location

value: oral cavity

tag: ct

tag: cn (clinical n-status = lymph node metastasis status)

tag: pt

tag: pn (pathological n-status = lymph node metastasis status)

tag: grade

tag: hpv

source_name: UHR

tag: sample type

value: Stratagene Universal human reference cell line (UHR)


title: ravA Replicate 2

tag: strain

source_name: ravA mutant

value: ΔravA


title: ravR Replicate 1

source_name: ravR mutant

value: ΔravR


title: genotype: Williams - pathogen inoculation: Mock - time: 12 hai - rep1

description: Williams mock treatment 12 hours

tag: pathogen isolates

value: Mock

value: 12 hr

tag: germplasm name

value: williams

tag: organism part

tag: development stage

value: UD:0000051 vegetative

tag: growth media


title: ravS Replicate 2


title: ravR Replicate 2


title: HNSCC_primary_9005370

hyb_protocol: Agilent recommended procedure for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis. Publication Number: G4140-90050 V4.0  Last Updated: 2/2006 Number of Pages: 70

value: female

tag: tissue

tag: age


title: ravA Replicate 1


title: HNSCC_primary_9005363

tag: gender

tag: tumor type


title: HNSCC_primary_9005365

tag: location

tag: ct


title: genotype: Williams - pathogen inoculation: Mock - time: 12 hai - rep3

description: Williams mock treatment 12 hours

tag: time

value: peat/perlite/soil


title: HNSCC_primary_9005354

tag: cn (clinical n-status = lymph node metastasis status)

tag: pt

tag: pn (pathological n-status = lymph node metastasis status)


title: HNSCC_primary_9005351

tag: grade

tag: hpv

tag: sample type


title: HNSCC_primary_9005352


title: HNSCC_primary_9005358


title: HNSCC_primary_9005359


title: HNSCC_primary_9005349


title: HNSCC_primary_9005357


title: HNSCC_primary_9005347


title: HNSCC_primary_9005350


title: HNSCC_primary_9004861


title: HNSCC_primary_9004856


title: HNSCC_primary_9004860


title: HNSCC_primary_9004858


title: HNSCC_primary_9004854


title: HNSCC_primary_9004847


title: HNSCC_primary_9004853


title: HNSCC_primary_9004851


title: HNSCC_primary_9004836


title: HNSCC_primary_9004834


title: HNSCC_primary_9004830


title: HNSCC_primary_9004841


title: HNSCC_primary_9004844


title: HNSCC_primary_9004827


title: HNSCC_primary_9004839


title: HNSCC_primary_9004826


title: HNSCC_primary_9004822


title: HNSCC_primary_9004818


title: HNSCC_primary_9004698

value: oropharynx


title: HNSCC_primary_9004796


title: HNSCC_primary_9004707


title: HNSCC_primary_9004710


title: HNSCC_primary_9004793


title: HNSCC_primary_9004693


title: HNSCC_primary_9004772


title: HNSCC_primary_9004786


title: HNSCC_primary_9004762


title: HNSCC_primary_9004769


title: HNSCC_primary_9004763


title: HNSCC_primary_9004743


title: HNSCC_primary_9004752


title: HNSCC_primary_9004760


title: HNSCC_primary_9004683


title: HNSCC_primary_9004729


title: HNSCC_primary_9004732


title: HNSCC_primary_9004692


title: HNSCC_primary_9004808


title: HNSCC_primary_9004737


title: HNSCC_primary_9004790


title: HNSCC_primary_9004682


title: HNSCC_primary_9004800


title: HNSCC_primary_9004677


title: HNSCC_primary_9004660


title: HNSCC_primary_9004661


title: HNSCC_primary_9004666


title: HNSCC_primary_9004659


title: HNSCC_primary_9004657


title: HNSCC_primary_9004658


title: HNSCC_primary_9004671


title: HNSCC_primary_9004650


title: HNSCC_primary_9004649


title: HNSCC_primary_9004740


title: HNSCC_primary_9004640


title: HNSCC_primary_9004646


title: HNSCC_primary_9004638


title: HNSCC_primary_9004629


title: HNSCC_primary_9004630


title: HNSCC_primary_9004631


title: HNSCC_primary_9004628


title: HNSCC_primary_9004634


title: HNSCC_primary_9004627


title: HNSCC_primary_9004636


title: Human HT1080 LaminA replicate1

hyb_protocol: The labeled MePCR DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, 60 μg per sample was combined into 33.6 μl water, and mixed with 2.4 μl Alignment oligo, 24 μl hybridization component A, and 60 μl 2x Hybridization Buffer. The entire 120 μl was used for hybridization in Tecan hybridization stations for 16-18 h at 42C. Arrays were then washed in 42 °C Nimblegen washbuffer1, and room temperature Nimblegen washbuffer 2 and 3. All buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Microarrays were scanned in a Agilent Scanner (Model G2505C, Serial number US22502518), which uses Scan Control software (Version A.8.1.3). Slides were first placed in a slide holder before putting it in the Scanner Carousel, which was installed in the scanner. Slides were double-pass scanned at maximum PMT for each channel, at a 2 um per pixel resolution.

data_processing:
Arrays were quantified with NimbleScan 2.5. Raw .pair files were read with the Ringo package for R and the loess normalized. Subsequently, single channel data was obtained and subjected to quantile-quantile normalisation over all available cell types and replicates.
The score was calculated as the log2 Dam-LaminB1: Dam ratio of the loess-quantile normalized data.

source_name: Dam-LaminA DamID DNA from HT1080 Cells

label_protocol: 1.5 µg MePCR DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3/Cy5 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html). Labeling time was extended to 12 hours to increase yield.

extract_protocol: 1-2x10e5 cells were infected with lenti-virus expressing either Dam-LaminA or only Dam. After 48 hours gDNA was isolated with the Qiagen Blood and Tissue kit per the manufacturers protocol. 2.5 μg of gDNA was digested with DpnI (New England Biolabs)), adapters were ligated with T4 ligase ((New England Biolabs)), and the ligation reaction was subsequently digested with DpnII ((New England Biolabs)). 500 ng of the DpnII digested material was used as input for a PCR amplification of methylated fragments (MePCR), see Vogel et al., 2008, Nature Protocols for details. MePCR fragments were purified by Qiaquick Spin columns (Qiagen).

tag: cell line

tag: treatment protocol

value: infection with lentivirus expressing Dam-LaminA

source_name: Dam-only DamID DNA from HT1080 Cells

value: infection with lentivirus expressing Dam only


title: Human HT1080 LaminB1 replicate2

extract_protocol: 1-2x10e5 cells were infected with lenti-virus expressing either Dam-LaminB1 or only Dam. After 48 hours gDNA was isolated with the Qiagen Blood and Tissue kit per the manufacturers protocol. 2.5 μg of gDNA was digested with DpnI (New England Biolabs)), adapters were ligated with T4 ligase ((New England Biolabs)), and the ligation reaction was subsequently digested with DpnII ((New England Biolabs)). 500 ng of the DpnII digested material was used as input for a PCR amplification of methylated fragments (MePCR), see Vogel et al., 2008, Nature Protocols for details. MePCR fragments were purified by Qiaquick Spin columns (Qiagen).

source_name: Dam-LaminB1 DamID DNA from HT1080 Cells

value: infection with lentivirus expressing Dam-LaminB1


title: HNSCC_primary_9004676

value: male


title: HNSCC_primary_9004622

value: head-neck


title: Human HT1080 LaminA replicate2


title: HNSCC_primary_9004619

value: HNSCC


title: Human HT1080 LaminB1 replicate1


title: Human ESC LaminB1 replicate2

hyb_protocol: The labeled MePCR DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, 80 μg per sample was combined into 33.6 μl water, and mixed with 2.4 μl Alignment oligo, 24 μl hybridization component A, and 60 μl 2x Hybridization Buffer. The entire 120 μl was used for hybridization in Tecan hybridization stations for 16-18 h at 42C. Arrays were then washed in 42 °C Nimblegen washbuffer1, and room temperature Nimblegen washbuffer 2 and 3. All buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

source_name: Dam-only DamID DNA from Embryonic Stem Cells

source_name: Dam-LaminB1 DamID DNA from Embryonic Stem Cells


title: HNSCC_primary_9004615

value: oral cavity


title: Human ESC LaminB1 replicate1


title: HNSCC_primary_9004618

value: Stratagene Universal human reference cell line (UHR)


title: HNSCC_primary_9004603


title: HNSCC_primary_9004614


title: HNSCC_primary_9004612


title: HNSCC_primary_9004608


title: HNSCC_primary_9004611


title: HNSCC_primary_9004601


title: HNSCC_primary_9004600


title: U2OS_21a

city: Berlin

first: Philip

last: Groth

address: Muellerstr. 178

department: Therapeutic Research Group Oncology

institute: Bayer Pharma AG

description:
gene expression profiling of 21 cell lines
U-2 OS, replicate 1

hyb_protocol: 15 ug of cleaned cRNA is fragmented and then hybridized for 16 hr at 45°C on GeneChip U133 Plus 2.0 probe array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Scanning parameters: pixel size: 1.56 μm, wavelength: 570 nm.

data_processing:
Signal intensities were extracted with Affymetrix GeneChip Operating software (GCOS, version 1.4.0.036; Instrument control version: 6.0.1.002).
Expression values for all .CEL files were computed using MAS5.0.

source_name: U-2 OS

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).

growth_protocol: Cell lines were obtained from ATCC and DSMZ and cultivated in appropriate media according to supplier recommendations. Isolation of total RNA was performed after 72h growth using Qiagen

treatment_protocol: Cell lines were not treated.

tag: organ

value: Bone

tag: disease

value: osteosarcoma

tag: morphology

value: epithelial

value: no

value: not tested

value: U-2 OS


title: T47D_20b

description:
gene expression profiling of 21 cell lines
T47D, replicate 2

value: female

value: Breast

value: ductal carcinoma

value: yes

value: pleural fluid


title: U2OS_21c

description:
gene expression profiling of 21 cell lines
U-2 OS, replicate 3


title: SW480_19b

description:
gene expression profiling of 21 cell lines
SW480, replicate 2

value: Colon

value: Dukes' type B; colorectal adenocarcinoma


title: SW480_19c

description:
gene expression profiling of 21 cell lines
SW480, replicate 3


title: HNSCC_primary_9004598

value: male

tag: tissue

value: head-neck

tag: age

value: oropharynx


title: HNSCC_primary_9004596

tag: gender

tag: tumor type

value: HNSCC

value: Stratagene Universal human reference cell line (UHR)


title: HNSCC_primary_9004594

tag: location

value: oral cavity

tag: ct


title: T47D_20c

description:
gene expression profiling of 21 cell lines
T47D, replicate 3

value: epithelial


title: U2OS_21b

description:
gene expression profiling of 21 cell lines
U-2 OS, replicate 2

value: Bone

value: osteosarcoma

value: no


title: HNSCC_primary_9004593

tag: cn (clinical n-status = lymph node metastasis status)


title: HNSCC_primary_9004616

tag: pt


title: T47D_20a

description:
gene expression profiling of 21 cell lines
T47D, replicate 1

value: female


title: HNSCC_primary_9004586

tag: pn (pathological n-status = lymph node metastasis status)


title: HNSCC_primary_9004595

tag: grade


title: SKOV3_18c

description:
gene expression profiling of 21 cell lines
SK-OV-3, replicate 3

value: Ovary

value: adenocarcinoma

value: ascites


title: HNSCC_primary_9004585

tag: hpv


title: HNSCC_primary_9004583

tag: sample type


title: HNSCC_primary_9004581


title: HNSCC_primary_9004582


title: HNSCC_primary_9004584


title: HNSCC_primary_9004575


title: SKOV3_18a

description:
gene expression profiling of 21 cell lines
SK-OV-3, replicate 1

value: yes

tag: cell line


title: SKMEL28_17b

description:
gene expression profiling of 21 cell lines
SK-MEL-28, replicate 2

value: Skin

value: malignant melanoma

value: polygonal


title: SKOV3_18b

description:
gene expression profiling of 21 cell lines
SK-OV-3, replicate 2


title: SW480_19a

description:
gene expression profiling of 21 cell lines
SW480, replicate 1

value: Colon

value: Dukes' type B; colorectal adenocarcinoma


title: PC3_16c

description:
gene expression profiling of 21 cell lines
PC-3, replicate 3

value: male

value: Prostate

value: Gleason Grade 4; adenocarcinoma

value: bone


title: PC3_16a

description:
gene expression profiling of 21 cell lines
PC-3, replicate 1

value: epithelial


title: HNSCC_primary_9004574

value: head-neck

value: HNSCC

value: oral cavity

value: Stratagene Universal human reference cell line (UHR)


title: SKMEL28_17a

description:
gene expression profiling of 21 cell lines
SK-MEL-28, replicate 1

value: no


title: HNSCC_primary_9004573

value: female


title: NCIH460_15b

description:
gene expression profiling of 21 cell lines
NCI-H460, replicate 2

value: Lung

value: large cell carcinoma

value: yes

value: pleural fluid


title: PC3_16b

description:
gene expression profiling of 21 cell lines
PC-3, replicate 2


title: NCIH460_15c

description:
gene expression profiling of 21 cell lines
NCI-H460, replicate 3


title: HNSCC_primary_9004570


title: HNSCC_primary_9004572


title: HNSCC_primary_9004568


title: SKMEL28_17c

description:
gene expression profiling of 21 cell lines
SK-MEL-28, replicate 3

value: Skin

value: malignant melanoma

value: polygonal


title: HNSCC_primary_9004567

value: male


title: MIAPACA2_14c

description:
gene expression profiling of 21 cell lines
Mia PaCa-2, replicate 3

source_name: Mia PaCa-2

value: Pancreas

value: carcinoma

value: attached epithelial with floating rounded cells

value: Mia PaCa-2


title: NCIH460_15a

description:
gene expression profiling of 21 cell lines
NCI-H460, replicate 1

value: epithelial


title: MIAPACA2_14a

description:
gene expression profiling of 21 cell lines
Mia PaCa-2, replicate 1


title: MIAPACA2_14b

description:
gene expression profiling of 21 cell lines
Mia PaCa-2, replicate 2


title: HNSCC_primary_9004564

value: head-neck

value: HNSCC

value: oral cavity


title: HNSCC_primary_9004566

value: female

value: Stratagene Universal human reference cell line (UHR)


title: MDAMB231_13a

description:
gene expression profiling of 21 cell lines
MDA-MB-231, replicate 1

value: Breast

value: adenocarcinoma

value: not tested


title: MDAMB231_13c

description:
gene expression profiling of 21 cell lines
MDA-MB-231, replicate 3

value: yes

value: pleural fluid


title: MDAMB231_13b

description:
gene expression profiling of 21 cell lines
MDA-MB-231, replicate 2


title: HNSCC_primary_9004557


title: HNSCC_primary_9004555

value: oropharynx


title: HNSCC_primary_9004563

value: male


title: MCF7_12c

description:
gene expression profiling of 21 cell lines
MCF7, replicate 3

value: intraductal adenocarcinoma


title: HNSCC_primary_9004562


title: MCF7_12b

description:
gene expression profiling of 21 cell lines
MCF7, replicate 2


title: MCF10A_11b

description:
gene expression profiling of 21 cell lines
MCF 10A, replicate 2

source_name: MCF 10A

value: non-tumorigenic; Fibrocystic Breast disease

value: no

value: MCF 10A


title: MCF7_12a

description:
gene expression profiling of 21 cell lines
MCF7, replicate 1

value: epithelial


title: HNSCC_primary_9004554

value: head-neck


title: MCF10A_11c

description:
gene expression profiling of 21 cell lines
MCF 10A, replicate 3


title: HNSCC_primary_9004553

value: HNSCC


title: HNSCC_primary_9004552

value: oral cavity


title: HNSCC_primary_9004549


title: CGH ZGR3 vs. BYZ1

city: Hangzhou

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

institute: College of Life Sciences, Zhejiang University

hyb_protocol: Competitively hybed ~10ug channel 1 and 2 DNA on NimbleGen 385k whole genome arrays using Maui SL mixers in Maui hybridization chamber. Washed as per NimbleGen hybridization protocol.

scan_protocol: Axon GenePix 4000B microarray scanner

data_processing: Raw data were extracted as pair files by NimbleScan software. Log2-ratio data were calculated and normalized by spatial correction and qspline fit normalization.

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae ZGR3

label_protocol: NimbleGen amplification and labeling.

extract_protocol: Total genomic DNA from yeast cells was isolated with the OMEGA Yeast DNA kit.

tag: strain

value: ZTW1, a wild type strain

source_name: S. cerevisiae BYZ1

label_protocol: NimbleGen amplification and labeling

value: BYZ1 (MATa/MATalpha his3delta1/his3delta1 leu2delta0/leu2delta0 lys2delta0/+ met15delta0/+ ura3delta0/ura3delta0)

tag: genetic background


title: MCF10A_11a

description:
gene expression profiling of 21 cell lines
MCF 10A, replicate 1

value: female

tag: organ

value: Breast

tag: disease


title: KPL4_10c

description:
gene expression profiling of 21 cell lines
KPL-4, replicate 3

value: invasive ductal carcinoma; inflammatory skin metastasis

tag: morphology


title: KPL4_10b

description:
gene expression profiling of 21 cell lines
KPL-4, replicate 2

value: yes


title: HT29_9c

description:
gene expression profiling of 21 cell lines
HT-29, replicate 3

value: Colon

value: colorectal adenocarcinoma


title: HNSCC_primary_9004547

value: male

tag: tissue

tag: age

value: oropharynx

value: Stratagene Universal human reference cell line (UHR)


title: HNSCC_primary_9004548

tag: gender

tag: tumor type


title: HNSCC_primary_9004546

tag: location

tag: ct


title: HNSCC_primary_9004550

tag: cn (clinical n-status = lymph node metastasis status)

tag: pt


title: HNSCC_primary_9004532

tag: pn (pathological n-status = lymph node metastasis status)

tag: grade


title: HNSCC_primary_9004542

tag: hpv

tag: sample type


title: HNSCC_primary_9004533


title: HNSCC_primary_9004541


title: HNSCC_primary_9004527


title: HNSCC_primary_9004529


title: HT29_9b

description:
gene expression profiling of 21 cell lines
HT-29, replicate 2

value: no

tag: cell line


title: HS68_8c

description:
gene expression profiling of 21 cell lines
Hs68, replicate 3

value: Skin

value: non-tumorigenic; aspartoacylase deficiency; possible Canavan disease

value: fibroblast

value: not tested


title: HT29_9a

description:
gene expression profiling of 21 cell lines
HT-29, replicate 1

value: epithelial


title: HS68_8b

description:
gene expression profiling of 21 cell lines
Hs68, replicate 2


title: HELA_7c

description:
gene expression profiling of 21 cell lines
HeLa, replicate 3

source_name: HeLa

value: Cervix

value: adenocarcinoma

value: HeLa


title: HNSCC_primary_9004526

value: head-neck

value: HNSCC

value: oral cavity


title: HELA_7b

description:
gene expression profiling of 21 cell lines
HeLa, replicate 2

value: female


title: HELA_7a

description:
gene expression profiling of 21 cell lines
HeLa, replicate 1


title: HS68_8a

description:
gene expression profiling of 21 cell lines
Hs68, replicate 1


title: HCT116_6b

description:
gene expression profiling of 21 cell lines
HCT 116, replicate 2

source_name: HCT 116

value: Colon

value: colorectal carcinoma

value: yes

value: HCT 116


title: HCT116_6c

description:
gene expression profiling of 21 cell lines
HCT 116, replicate 3

value: male

value: no


title: HNSCC_primary_9004524

value: oropharynx

value: Stratagene Universal human reference cell line (UHR)


title: HNSCC_primary_9004521


title: HNSCC_primary_9004525


title: HNSCC_primary_9004523


title: HNSCC_primary_9004519


title: HNSCC_primary_9004516


title: HNSCC_primary_9004517


title: HNSCC_primary_9004512


title: HACAT_5b

description:
gene expression profiling of 21 cell lines
HaCaT, replicate 2

source_name: HaCaT

value: Skin

value: non-tumorigenic; spontaneously immortilized keratinocytes

value: HaCaT


title: HNSCC_primary_9004514


title: HCT116_6a

description:
gene expression profiling of 21 cell lines
HCT 116, replicate 1

value: epithelial


title: HACAT_5c

description:
gene expression profiling of 21 cell lines
HaCaT, replicate 3


title: HNSCC_primary_9004513


title: HNSCC_primary_9004511


title: HACAT_5a

description:
gene expression profiling of 21 cell lines
HaCaT, replicate 1


title: DU145_4b

description:
gene expression profiling of 21 cell lines
DU 145, replicate 2

value: Prostate

value: brain


title: A549_2b

description:
gene expression profiling of 21 cell lines
A549, replicate 2

value: Lung

value: non-small cell carcinoma


title: HNSCC_primary_9004510

value: female

value: head-neck

value: HNSCC

value: oral cavity


title: CACO2_3b

description:
gene expression profiling of 21 cell lines
Caco-2, replicate 2

value: Colon

value: colorectal adenocarcinoma

value: not tested


title: A549_2c

description:
gene expression profiling of 21 cell lines
A549, replicate 3

value: male

value: no

value: yes


title: DU145_4c

description:
gene expression profiling of 21 cell lines
DU 145, replicate 3


title: 786O_1c

description:
gene expression profiling of 21 cell lines
786-O, replicate 3

value: Kidney

value: renal cell adenocarcinoma


title: CACO2_3a

description:
gene expression profiling of 21 cell lines
Caco-2, replicate 1

value: epithelial


title: 786O_1b

description:
gene expression profiling of 21 cell lines
786-O, replicate 2


title: DU145_4a

description:
gene expression profiling of 21 cell lines
DU 145, replicate 1

value: Prostate


title: CACO2_3c

description:
gene expression profiling of 21 cell lines
Caco-2, replicate 3


title: HNSCC_primary_9004509

value: Stratagene Universal human reference cell line (UHR)


title: HNSCC_primary_9004515

value: oropharynx


title: HNSCC_primary_9004520


title: HNSCC_primary_9004506


title: HNSCC_primary_9004507


title: 786O_1a

description:
gene expression profiling of 21 cell lines
786-O, replicate 1


title: HNSCC_primary_9004508


title: HNSCC_primary_9004500


title: HNSCC_primary_9004502


title: HNSCC_primary_9004505


title: HNSCC_primary_9004504


title: HNSCC_primary_9004498


title: HNSCC_primary_9004499


title: HNSCC_primary_9004503


title: HNSCC_primary_9004497


title: KPL4_10a

description:
gene expression profiling of 21 cell lines
KPL-4, replicate 1

value: Breast

value: invasive ductal carcinoma; inflammatory skin metastasis

value: pleural fluid


title: A549_2a

description:
gene expression profiling of 21 cell lines
A549, replicate 1

value: Lung

value: non-small cell carcinoma


title: HNSCC_primary_9004493

value: head-neck

value: HNSCC

value: oral cavity


title: HNSCC_primary_9004495

value: male


title: normal melanocyte HEMa-LP exosome, mRNA biological rep 2

city: Louisville

first: Hongying

last: Hao

state: KY

address: 505 South Hancock Street

department: Surgery

institute: University of Louisville

description: Gene expression data from HEMa-LP exosomes.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome HG-U133Plus2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using Fluidics Protocol FS450-0001.

scan_protocol: GeneChips were scanned using Affymetrix' GeneChip Scanner GCS3000 7G and Command Console Version 1.0

data_processing: The data were analyzed with Partek Genomics Suite 6.5 using RMA default analysis settings as normalization method and a 2-Way ANOVA was set-up to determine differentially expressed genes.

source_name: HEMa-LP exosome

label_protocol: Biotinylated cRNA were prepared according to the standard protocol for Affymetrix' IVT Express kit from 100 ng total RNA.

growth_protocol: normal melanocytes HEMa-LP cells were cultured in Medium 254 supplemented with Human Melanocyte Growth Supplement-2 (HMGS-2) in a 5% CO2 incubator at 37C. Malignant melanoma A375 cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% exosome-depleted fetal bovine serum (FBS). FBS was depleted of exosomes by ultracentrifugation at 100,000 x g for 16h at 4C.

extract_protocol: Total RNA from cells and exosomes were isolated using mirVana total RNA isolation kit according to the manufacturer’s guidelines.

treatment_protocol: Cells were trypsinized and harvested for RNA isolation. Exosomes were purified from cell culture supernatants by a combination of ultrafiltration and ultracentrifugation.

value: exosome

tag: cancer status

value: Normal Melanocytes

value: HEMa-LP


title: HNSCC_primary_9004492

source_name: UHR


title: normal melanocyte HEMa-LP exosome, mRNA biological rep 1


title: HNSCC_primary_9004480

value: female


title: G spring SITJ 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: Fragmentation of the cDNA was performed in the recommended blocking agent and volume of 2x GE Hybridization Blocking Buffer (Agilent, Gene Expression Hybridization Kit) using 600ng of Cy3-labelled cRNA. A final volume of 40μl containing the fragmented cDNA was added to the 8x15 arrays and the hybridization proceeded for 17h at 65ºC. Microarrays slides were washed according the supplemental Agilent protocol (“One-color Microarray-Based Gene expression analysis”).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner G2565CA and signals were extracted using the Agilent Feature Extraction Software v9.5.

data_processing: default Agilent Feature Extraction Software v9.5 normalization

organism: Dreissena polymorpha

source_name: gills, Spring, Sitjar site, replicate 2

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 prepared from 500ng of total RNA for each sample, with a amplification and purification steps. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 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 DNAse I to remove genomic DNA contamination. RNA quality was checked in an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara CA). The samples that did not show degradation were used in the process of microarray analysis.

treatment_protocol: Zebra mussel were collected form 5 different sites along the Ebro River and 1 extra site located at 200km from the Ebro river, Sitjar Dam, during spring (on March). 2 replicates, containing the RNA of half a body of  5 individuals, were used for each sites to see differences among populations.

value: gills

tag: time

value: spring

tag: population

value: Sitjar


title: G spring FAIO Rep2

source_name: gills, Spring, Faio site, replicate 2

value: Faio


title: G spring FAIO Rep1

source_name: gills, Spring, Faio site, replicate 1


title: melanoma exosome A375, mRNA biological rep 2

description: Gene expression data from A375 exosomes.

source_name: A375 exosome

value: Melanoma


title: HNSCC_primary_9004479

value: Stratagene Universal human reference cell line (UHR)


title: HNSCC_primary_9004501


title: G spring SITJ Rep1

source_name: gills, Spring, Sitjar site, replicate 1


title: HNSCC_primary_9004478


title: G spring MQ Rep2

source_name: gills, Spring, Mequinenza site, replicate 2

value: Mequinenza


title: G spring MQ Rep1

source_name: gills, Spring, Mequinenza site, replicate 1


title: melanoma exosome A375, mRNA biological rep 1


title: normal melanocyte HEMa-LP, mRNA biological rep 2

description: Gene expression data from HEMa-LP cells.

source_name: HEMa-LP cell

value: cell


title: HNSCC_primary_9004476


title: HNSCC_primary_9004470


title: HNSCC_primary_9004474


title: normal melanocyte HEMa-LP, mRNA biological rep 1


title: G spring FF Rep2

source_name: gills, Spring, Flix Factory site, replicate 2

value: Flix Factory


title: melanoma cell A375, mRNA biological rep 1

description: Gene expression data from A375 cells.

source_name: A375 cell


title: HNSCC_primary_9004469

value: head-neck


title: G spring FR Rep2

source_name: gills, Spring, Flix Reservoir site, replicate 2

value: Flix Reservoir


title: HNSCC_primary_9004472

value: HNSCC

value: oral cavity


title: HNSCC_primary_9004475


title: HNSCC_primary_9004468


title: G spring FF Rep1

source_name: gills, Spring, Flix Factory site, replicate 1


title: G spring RR Rep2

source_name: gills, Spring, Riba Roja site, replicate 2

value: Riba Roja


title: HNSCC_primary_9004466

value: male


title: G spring RR Rep1

source_name: gills, Spring, Riba Roja site, replicate 1


title: HNSCC_primary_9004465


title: HNSCC_primary_9004463


title: HNSCC_primary_9004461


title: HNSCC_primary_9004462


title: HNSCC_primary_9004460


title: HNSCC_primary_9004459


title: G spring FR Rep1

source_name: gills, Spring, Flix Reservoir site, replicate 1