title: VEHICLE_24h_rep3

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 125_S125_L001_R1_001.fastq.gz


title: VEHICLE_24h_rep1

status: Public on Feb 22 2018

type: SRA

city: RALEIGH

first: Dereje

last: Jima

state: NC

address: 850 Main Campus Drive

department: CHHE

country: USA

institute: NCSU

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 121_S121_L001_R1_001.fastq.gz

library_source: transcriptomic

data_processing:
Library strategy: TempOSeq
Detailed in https://github.com/demis001/temposeqcount
Temposeqcount is a pipeline that accepts the probe manifest file (included on the series record) and generates the probe fasta file, indexes it, maps the fastq file against the indexed probe fasta file using the STAR aligner and calculates the read count.
Supplementary_files_format_and_content: txt file with raw read counts

molecule: total RNA

organism: Homo sapiens

source_name: induced PSCs

growth_protocol: iCell cardiomyocytes were plated and maintained according to the  manufacturer’s recommendations (Cellular Dynamics International, Madison, WI) and in accordance with  previously published protocols with minor adjustments (Sirenko et al. 2017; Grimm et al. 2016; Grimm et  al. 2015; Sirenko, Cromwell, et al. 2013; Sirenko, Crittenden, et al. 2013). Individual units of   cardiomyocytes were thawed for 4 min in a 37 °C water bath and subsequently resuspended in 10 ml of   cardiomyocyte plating medium containing 1:500 penicillin/streptomycin solution. Following microscopic   cell counting using the trypan blue exclusion method, the cell density was adjusted to a final plating   density of 2x105 cells/ml. 25μl of cell suspension were then transferred per well to a 384-well microplate,   yielding a final cell density of 5000/well. Tissue-culture treated microplates (cat.no.: 353962, Corning   Life Sciences, Corning, NY) were gelatinized for 2 hours at 37 °C with 25μl 0.1% gelatin in water before   cardiomyocytes were plated. After disposal of the gelatin solution and addition of the cell suspension,   microplates were kept at room temperature for 30 min. Cells were then incubated at 37 °C and 5% CO2   for 48 hours. The plating medium was then exchanged with 40μl of maintenance medium containing   1:500 penicillin/streptomycin solution per well. Maintenance medium was replaced every 48-72 hours   until day 13 post-plating. The maintenance medium was then exchanged with 50μl fresh medium per well   and incubated overnight.

extract_protocol:
RNA was isolated from cells using TRIzol reagent (Invitrogen) and further purified by RNeasy MinElute Cleanup (Qiagen).Differential gene expression patterns and  concentration-response relationships were analyzed using TempO-Seq™ (BioSpyder Technologies, Inc.,  Carlsbad, CA) (Yeakley et al. 2017), a targeted RNA sequencing technology 119 focused on a surrogate  transcriptome panel comprising 2982 transcripts, as described previously (Grimm et al. 2016).
The  sequencing library was prepared according to the manufacturer’s guidelines and as previously described  (Grimm et al. 2015). In brief, RNA in 2μl of each cell lysate were hybridized with the provided detector  oligo pool mix (2μl per sample) using the following thermocycler settings: 10 min at 70°C, followed by  gradual decrease to 45°C over 49 min, and ending with 45°C for 1 min. Subsequent steps included  nuclease digestion (90 min at 37°C) ligation step (60 min at 37°C, followed by heat denaturation at 80°C  for 30 min) following addition of 24μl nuclease mix and 24μl ligation mix. 10μl of each ligation product  were then transferred to a 96-well amplification microplate containing 10μl of PCR mix per well. The  ligation products were then uniquely labeled during product amplification, when well-specific,  “barcoded” primer pairs were introduced to templates. Sequence-based barcoding is an essential step  allowing for correct identification and recognition of transcript-specific sequencing counts. 5μl of sample  amplicons from each well were subsequently pooled into a single sequencing library. The TempO-Seq  library was further processed using a PCR clean-up kit (Clontech, Mountain View, CA) prior to  sequencing at Texas A&M University Genomics & Bioinformatics Services. Sequencing was achieved  using a 50 single-end read mode in a rapid flow cell (2 sequencing lanes for increased sequencing depth)  on a HiSeq 2500 Ultra-High-Throughput Sequencing System (Illumina, San Diego, CA). Sequencing  readouts were demultiplexed to generate FASTQ files, and passed all internal quality controls.

treatment_protocol: Cells were treated the next morning (day 14 post-plating) with 12.5μl 5x  chemical solutions in 0.5% DMSO (v/v) in media (vehicle) in addition to untreated or vehicle-treated  negative control wells, and incubated at 37 °C and 5% CO2. Following 24 hours of incubation, the cell  medium was discarded, and cardiomyocytes were lysed with 10μl 1x lysis buffer provided in the TempO  Seq assay kit (BioSpyder Technologies, Carlsbad, CA). Lysate-containing micro-plates were agitated at  300 rpm using a benchtop microplate shaker and stored at -80°C until further use.

tag: cell type

value: Beating Cardiomyocytes

tag: treatment

value: Vehicle

tag: dose um


title: MEDIA_24h_rep6

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 275_S275_L001_R1_001.fastq.gz

value: Media


title: MEDIA_24h_rep5

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 131_S131_L001_R1_001.fastq.gz


title: MEDIA_24h_rep3

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 271_S271_L001_R1_001.fastq.gz


title: MEDIA_24h_rep2

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 129_S129_L001_R1_001.fastq.gz


title: MEDIA_24h_rep1

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 127_S127_L001_R1_001.fastq.gz


title: Isoproterenol_24h_dose_1

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 004_S4_L001_R1_001.fastq.gz

value: Isopreterenol


title: Dofetilide_24h_dose_0.1

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 229_S229_L001_R1_001.fastq.gz

value: Dofetelide


title: Dofetilide_24h_dose_1

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 231_S231_L001_R1_001.fastq.gz


title: VEHICLE_24h_rep11

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 285_S285_L001_R1_001.fastq.gz


title: Dofetilide_24h_dose_10

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 233_S233_L001_R1_001.fastq.gz


title: VEHICLE_24h_rep10

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 283_S283_L001_R1_001.fastq.gz


title: VEHICLE_24h_rep7

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 277_S277_L001_R1_001.fastq.gz


title: VEHICLE_24h_rep2

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 123_S123_L001_R1_001.fastq.gz


title: MEDIA_24h_rep4

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 273_S273_L001_R1_001.fastq.gz


title: POL_36hr_rep3

status: Public on Sep 26 2017

type: RNA

description:
POL36_3
Gene expression after 36hr in PolyIC Zebrafish larvae

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 Genome Oligo Microarrays (G4112A) 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 (G2505B) 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 8.5 (Agilent) using default parameters  to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Danio rerio

source_name: euthanized larvae, POL, 36hr

label_protocol: Target labeling, hybridization, washing, scanning and data extraction will proceed using established procedures for the analysis of Eukaryotic RNA

extract_protocol: RNA was isolated from euthanized larvae using TRIzol reagent (Invitrogen) and further purified by RNeasy MinElute Cleanup (Qiagen).

treatment_protocol: Zebrafish larvae were exposed to the chemically diverse immune agonists, polyinosine-polycytidylic acid (PolyIC) and synthetic triacylated lipoprotein (Pam3CSK4) and transcriptome analyses completed using microarray analyses. RNA were extracted at 4, 8, 12, 24 and 36 time points after exposure to PolyIC and Pam3CSK4. At each timepoint we  have a untreated controls.

tag: tissue

value: euthanized larvae

tag: agent

value: POL

tag: time


title: PAM_36hr_rep3

description:
PAM36_4
Gene expression after 36hr in Pam3CSK4 Zebrafish larvae

source_name: euthanized larvae, PAM, 36hr

value: PAM


title: Control_36hr_rep4

description:
CNT36_4
Gene expression after 36hr in Untreated Zebrafish larvae

source_name: euthanized larvae, Control, 36hr

value: Control


title: POL_36hr_rep1

description:
POL36_1
Gene expression after 36hr in PolyIC Zebrafish larvae


title: PAM_36hr_rep2

description:
PAM36_3
Gene expression after 36hr in Pam3CSK4 Zebrafish larvae


title: Control_36hr_rep3

description:
CNT36_3
Gene expression after 36hr in Untreated Zebrafish larvae


title: POL_24hr_rep4

description:
POL24_4
Gene expression after 24hr in PolyIC Zebrafish larvae

source_name: euthanized larvae, POL, 24hr


title: Control_36hr_rep1

description:
CNT36_1
Gene expression after 36hr in Untreated Zebrafish larvae


title: POL_36hr_rep2

description:
POL36_2
Gene expression after 36hr in PolyIC Zebrafish larvae


title: POL_24hr_rep3

description:
POL24_3
Gene expression after 24hr in PolyIC Zebrafish larvae


title: Control_36hr_rep2

description:
CNT36_2
Gene expression after 36hr in Untreated Zebrafish larvae


title: POL_36hr_rep4

description:
POL36_4
Gene expression after 36hr in PolyIC Zebrafish larvae


title: PAM_24hr_rep3

description:
PAM24_4
Gene expression after 24hr in Pam3CSK4 Zebrafish larvae

source_name: euthanized larvae, PAM, 24hr


title: POL_24hr_rep1

description:
POL24_1
Gene expression after 24hr in PolyIC Zebrafish larvae


title: Control_24hr_rep3

description:
CNT24_3
Gene expression after 24hr in Untreated Zebrafish larvae

source_name: euthanized larvae, Control, 24hr


title: PAM_24hr_rep1

description:
PAM24_2
Gene expression after 24hr in Pam3CSK4 Zebrafish larvae


title: POL_12hr_rep2

description:
POL12_3
Gene expression after 12hr in PolyIC Zebrafish larvae

source_name: euthanized larvae, POL, 12hr


title: PAM_24hr_rep2

description:
PAM24_3
Gene expression after 24hr in Pam3CSK4 Zebrafish larvae


title: POL_24hr_rep2

description:
POL24_2
Gene expression after 24hr in PolyIC Zebrafish larvae


title: POL_12hr_rep1

description:
POL12_1
Gene expression after 12hr in PolyIC Zebrafish larvae


title: Control_24hr_rep4

description:
CNT24_4
Gene expression after 24hr in Untreated Zebrafish larvae


title: Control_24hr_rep2

description:
CNT24_2
Gene expression after 24hr in Untreated Zebrafish larvae


title: PAM_12hr_rep3

description:
PAM12_3
Gene expression after 12hr in Pam3CSK4 Zebrafish larvae

source_name: euthanized larvae, PAM, 12hr


title: POL_12hr_rep3

description:
POL12_4
Gene expression after 12hr in PolyIC Zebrafish larvae


title: Control_24hr_rep1

description:
CNT24_1
Gene expression after 24hr in Untreated Zebrafish larvae


title: PAM_36hr_rep1

description:
PAM36_2
Gene expression after 36hr in Pam3CSK4 Zebrafish larvae


title: PAM_12hr_rep2

description:
PAM12_2
Gene expression after 12hr in Pam3CSK4 Zebrafish larvae


title: PAM_12hr_rep1

description:
PAM12_1
Gene expression after 12hr in Pam3CSK4 Zebrafish larvae


title: Child_high_cadmium 1859-04

status: Public on Dec 04 2018

description: Whole genome bisulfite sequencing

library_source: genomic

data_processing:
Bisulfite sequencing reads were aligned to the reference human genome (hg38) using BSMAP (Xi & Li 2009), which automatically trims adapters and low-quality sequence reads. For newborn cord blood samples, 460 and 535 million reads were generated for low and high Cd exposure groups, respectively, of which 61.5 % and 61.1 % were uniquely aligned to the reference genome, representing 13x and 15x coverage. For maternal blood samples, 201 million and 188 million reads were generated for low and high Cd exposure groups, respectively, of which 56.2 % and 59.5 % of reads were uniquely aligned to the reference genome, representing 5x and 6x coverage. The percentage of uniquely aligned reads is consistent with data reported in a separate study, in which four alignment tools for genome wide bisulfite sequencing data were compared and yielded 55.5 % uniquely mapped reads, on average (Chatterjee et al. 2012). Model Based Analysis of Bisulfite Sequencing (MOABS, V1.2.2) (Sun et al. 2014) was used to identify differentially methylated CpG dinucleotides and to call Differentially Methylated Regions (DMRs). MOABS uses a beta binomial hierarchical model to capture sampling and biological variation, and generates a credible methylation difference (CDIF) metric. This metric does not require the high coverage necessary for other approaches which mainly implement Fisher’s exact test and typically require >30x coverage. MOABS supports three models to call differentially methylated CpGs and DMRs: Fisher’s exact test, hidden Markov model and CDIF. We used CDIF in this study. DMRs were defined by a minimum of three methylated CpG dinucleotides within a maximum interval of 300 bp, each with an absolute methylation difference of at least 10 % in the same direction (i.e. lower or higher methylation) between low and high Cd exposed groups.
Genome_build: hg38

molecule: genomic DNA

source_name: Blood (buffy coat)

extract_protocol:
Genomic DNA was isolated from the buffy coat from maternal and newborn cord blood samples using PureGene reagents (Qiagen, Inc., Valencia, CA). DNA was bisulfite converted using Epitect Bisulfite kits (Qiagen, Inc., Valencia, CA) according to manufacturer’s protocols. The bisulfite conversion rate was ~98.0 % across all samples.
Bisulfite converted maternal DNAs were pooled and converted to sequencing libraries using TruSeq DNA Methylation kits (Illumina, Inc., San Diego, CA) according to manufacturer’s protocols. Sequencing libraries from bisulfite converted newborn cord blood DNAs were prepared individually using TruSeq DNA Methylation kits, and index tagged using TruSeq DNA Methylation Index PCR Primers (Illumina, Inc.). The index tagged libraries were quantitated using the ddPCR Library Quantification Kit for Illumina TruSeq (Bio-Rad, Inc., Hercules, CA) according to manufacturer’s protocols, and a QX200 Droplet Digital PCR system at the North Carolina State University Genomic Sciences Laboratory (NCSU GSL). Normalized libraries were pooled, with 4 or 5 libraries per pool. Libraries were sequenced on an Illumina HiSeq 2500 instrument at the NCSU GSL, producing 100 bp single end reads.

treatment_protocol: Study participants were recruited between January 2009 and June 2011 as part of the ongoing Newborn Epigenetics STudy (NEST), a prospective cohort study of women and their children. Details of participant identification, enrollment and data and specimen collection procedures have been described elsewhere (Hoyo et al. 2014). Briefly, English- or Spanish-speaking pregnant women aged 18 years or older visiting Duke prenatal clinics were identified from logs of prenatal clinics in Durham County, NC, United States. From these, women who planned to relinquish custody of the child or had established HIV infection were excluded, as were those who received obstetric care at facilities other than Duke Obstetrics or Durham Regional Hospitals. By December of 2011, 1700 of the 2548 eligible women had been enrolled. From these 115 were excluded because of fetal demise and 281 refused further participation, could not be located for subsequent follow-up, were illiterate and could not reasonably provide informed consent, or were underage, leaving 1304 (77 %). The median gestational age at enrollment was 12 weeks (interquartile range (IQR): 7-14 weeks). The protocol was approved by Duke University, Durham Regional Hospital, and North Carolina State University. At enrollment, 10 ml of peripheral blood was obtained in EDTA vacutainers from all women, of which 1 ml was stored as whole blood in 200 µl aliquots. For the first 310 participants, one 200 µl aliquot was used to measure Cd using established solution-based ICP-MS methods that have been previously described (Vidal et al. 2015; Darrah et al. 2009; McLaughlin et al. 2011). Briefly, the 200 µl frozen samples were equilibrated at room temperature, homogenized and then pipetted into a trace-metal-clean test tube and verified gravimetrically using a calibrated mass balance. These samples were then spiked with internal standards comprising known quantities (10 and 1 ng/g, respectively) of indium and bismuth (SCP Science, Canada) used to correct for instrumental drift. Cd concentrations were measured using a Perkin Elmer DRC II (Dynamic Reaction Cell) axial field ICP-MS at the University of Massachusetts, Boston. The method detection limit (83 pg/g parts per trillion) was calculated using the t99SLLMV method (USEPA, 1993) at 99 % CI (t = 3.71). The limit of detection and the limit of quantification estimated according to (Long & Winefordner 1983) were less than 43 pg/g, and 51 pg/g, respectively. In the current study, we analyzed specimens from 20 pregnant women and their offspring, 10 with the highest blood Cd concentrations in the first trimester of pregnancy and 10 who were selected from the majority of women with blood concentrations close to zero. Participants were selected to minimize confounding by matching on factors shown either to be directly associated with CpG methylation and thus provide a potential explanation for associations observed, or to modify associations between Cd or other toxic metals and CpG methylation. By matching on these factors individuals in the high and low Cd exposure groups were comparable with respect to advanced maternal age, pre-pregnancy obesity, gestational age at delivery and race/ethnicity, among other factors. In this population, only one woman had gestational diabetes, a factor that may also influence CpG methylation.

value: Newborn cord blood


title: Control_12hr_rep3

description:
CNT12_4
Gene expression after 12hr in Untreated Zebrafish larvae

source_name: euthanized larvae, Control, 12hr


title: POL_8hr_rep2

description:
POL8_3
Gene expression after 8hr in PolyIC Zebrafish larvae

source_name: euthanized larvae, POL, 8hr


title: Control_12hr_rep2

description:
CNT12_3
Gene expression after 12hr in Untreated Zebrafish larvae


title: PAM_8hr_rep2

description:
PAM8_3
Gene expression after 8hr in Pam3CSK4 Zebrafish larvae

source_name: euthanized larvae, PAM, 8hr


title: Control_8hr_rep3

description:
CNT8_4
Gene expression after 8hr in Untreated Zebrafish larvae

source_name: euthanized larvae, Control, 8hr


title: PAM_8hr_rep1

description:
PAM8_2
Gene expression after 8hr in Pam3CSK4 Zebrafish larvae


title: POL_8hr_rep3

description:
POL8_4
Gene expression after 8hr in PolyIC Zebrafish larvae


title: Control_8hr_rep1

description:
CNT8_2
Gene expression after 8hr in Untreated Zebrafish larvae


title: Control_12hr_rep1

description:
CNT12_2
Gene expression after 12hr in Untreated Zebrafish larvae


title: POL_4hr_rep2

description:
POL4_3
Gene expression after 4hr in PolyIC Zebrafish larvae

source_name: euthanized larvae, POL, 4hr


title: PAM_12hr_rep4

description:
PAM12_4
Gene expression after 12hr in Pam3CSK4 Zebrafish larvae


title: High BPA group Rep 6

status: Public on Aug 01 2017

city: Ann Arbor

first: Maureen

middle: A

last: Sartor

state: MI

address: 2017 Palmer Commons Bldg., 100 Washtenaw Ave

department: Department of Computational Medicine and Bioinformatics

institute: University of Michigan

description:
Total and Free BPA measured via HPLC
9976

data_processing:
Image data was first processed by Illumina analysis pipeline
reads were aligned using BWA with default parameters.
edgeR (for read counts)
Genomatics RegionMiner (for annotation features)
Genome_build: NCBI build 37 (human)
Supplementary_files_format_and_content: DNA methylation read counts from genomic regions. The column names are included in the file.

source_name: Human Fetal Liver

extract_protocol:
Qiagen kit
Illumina prep kit

treatment_protocol: Methylplex enzymatic enrichment of GC

tag: enzymatic treatment

value: Methyplex treated human fetal liver DNA

tag: bpa exposure

value: High BPA

value: Fetal Liver


title: High BPA group Rep 5

description:
Total and Free BPA measured via HPLC
9837


title: High BPA group Rep 4

description:
Total and Free BPA measured via HPLC
9836


title: PAM_8hr_rep3

description:
PAM8_4
Gene expression after 8hr in Pam3CSK4 Zebrafish larvae


title: Control_4hr_rep2

description:
CNT4_2
Gene expression after 4hr in Untreated Zebrafish larvae

source_name: euthanized larvae, Control, 4hr


title: PAM_4hr_rep1

description:
PAM4_1
Gene expression after 4hr in Pam3CSK4 Zebrafish larvae

source_name: euthanized larvae, PAM, 4hr


title: POL_4hr_rep3

description:
POL4_4
Gene expression after 4hr in PolyIC Zebrafish larvae


title: High BPA group Rep 3

description:
Total and Free BPA measured via HPLC
9831


title: PAM_4hr_rep3

description:
PAM4_3
Gene expression after 4hr in Pam3CSK4 Zebrafish larvae


title: PAM_4hr_rep2

description:
PAM4_2
Gene expression after 4hr in Pam3CSK4 Zebrafish larvae


title: Control_4hr_rep4

description:
CNT4_4
Gene expression after 4hr in Untreated Zebrafish larvae


title: Control_4hr_rep1

description:
CNT4_1
Gene expression after 4hr in Untreated Zebrafish larvae


title: POL_8hr_rep1

description:
POL8_1
Gene expression after 8hr in PolyIC Zebrafish larvae


title: Control_8hr_rep2

description:
CNT8_3
Gene expression after 8hr in Untreated Zebrafish larvae


title: Control_4hr_rep3

description:
CNT4_3
Gene expression after 4hr in Untreated Zebrafish larvae


title: RXRα_24H-Ctl_ChIP-seq

status: Public on Sep 13 2017

city: Ottawa

first: Qiao

last: Li

state: Ontario

address: 451 smyth road

department: Cellular and Molecular Medicine

country: Canada

institute: University of Ottawa

description: chip antibody: RXRα (Santa Cruz_sc-553)

data_processing:
Sequencing reads were mapped to the mouse genome build mm9 using Bowtie, allowing for 3 mismatches and reporting the single best alignment per 50bp read. Picard was used to filter out replicated reads and BAM files were converted into BED files after which aligned reads were extended by 125 bp at their 3’ end, and converted to bedgraph format using the bedtools2 package.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files were generated with the bedtools2 package for ChIP-seq datasets and represent coverage depth of sequencing over the genome.

organism: Mus musculus

source_name: C2C12 myoblasts

growth_protocol: Cells of the murine myoblasts cell line C2C12 (ATCC) were maintained in growth medium (GM), Dulbecco’s Modified Eagle Medium (D-MEM) supplemented with 10% Fetal Bovine Serum, at 37ºC with 5% CO2. To induce differentiation, the medium of 80% confluent cell cultures was changed to differentiation medium (DM), D-MEM supplemented with 2% horse serum and 50 nM of bexarotene was added for treatment conditions.

extract_protocol:
Cells were crosslinked in formaldehyde and sonicated with a Bioruptor (Diagenode). DNA was precipitated with the appropriate antibody and sent for sequencing to the McGill University Genome Quebec Innovation Centre using Illumina HiSeq 2000 platform.
Genomic DNA libraries were prepared for sequencing by McGill University Genome Quebec Innovation Centre using standard Illumina protocols.

tag: cell line

tag: strain


title: Medium BPA group Rep 4

description:
Total and Free BPA measured via HPLC
9839

value: Medium BPA


title: RXRα_24H-Bex_ChIP-seq

description: chip antibody: RXRα (Santa Cruz_sc-553)


title: High BPA group Rep 1

description:
Total and Free BPA measured via HPLC
9829


title: PAM_4hr_rep4

description:
PAM4_4
Gene expression after 4hr in Pam3CSK4 Zebrafish larvae


title: POL_4hr_rep1

description:
POL4_1
Gene expression after 4hr in PolyIC Zebrafish larvae


title: High BPA group Rep 2

description:
Total and Free BPA measured via HPLC
9830


title: Input_RXRα_ChIP-seq


title: Medium BPA group Rep 3

description:
Total and Free BPA measured via HPLC
9838


title: Medium BPA group Rep 6

description:
Total and Free BPA measured via HPLC
9978


title: Medium BPA group Rep 5

description:
Total and Free BPA measured via HPLC
9977


title: Medium BPA group Rep 1

description:
Total and Free BPA measured via HPLC
9832


title: Low BPA group Rep 6

description:
Total and Free BPA measured via HPLC
9979

value: Low BPA


title: Low BPA group Rep 4

description:
Total and Free BPA measured via HPLC
9841


title: Low BPA group Rep 2

description:
Total and Free BPA measured via HPLC
9835


title: Low BPA group Rep 1

description:
Total and Free BPA measured via HPLC
9834


title: Low BPA group Rep 5

description:
Total and Free BPA measured via HPLC
9842


title: Low BPA group Rep 3

description:
Total and Free BPA measured via HPLC
9840


title: PtenFF_CD_RNAseq_rep8

status: Public on Dec 21 2016

description:
all_sample_raw_count.txt
FF.CD.M.698

data_processing:
Basecalls performed using CASAVA-1.8.2
ChIP-seq and input reads were aligned to the mouse reference genome (mm9) using BWA (version 0.5.9-r16) with default options. PePr(v1.0.9) was used to call peaks with a-value cut-off of 1e-12. Peaks overlapping with ENCODE blacklisted regions were removed.
RNA-Seq reads were aligned to rn4 with tophat2 (v2.0.11) and gene read counts were quantified by HTseq (0.6.1p1) with option “-m intersection-strict” and normalized by edgeR (3.2.4). Differential expression analysis was performed using edgeR with tagwise dispersion.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-Seq peak files were generated by PePr, RNA-Seq read counts were quantified by HTSeq. The column headers for processed peak file are: "chr","start","end","width","p-value","q-value","rank".

extract_protocol: RNA was isolated from thyroid glands using an RNeasy Mini Kit per the manufacturer’s protocol (Qiagen, Valencia, CA). Library construction (Illumina TruSeq RNA kit #RS-122-2001) and sequencing on an Illumina HiSeq2000 using 50 nt paired end reads were per the manufacturer’s protocols, performed by the University of Michigan DNA Sequencing Core.

tag: genotype

value: PtenThy-/-

value: control diet

tag: age

value: 8-10 weeks

value: Thyroid gland


title: Medium BPA group Rep 2

description:
Total and Free BPA measured via HPLC
9833


title: PtenFF_CD_RNAseq_rep5

description:
all_sample_raw_count.txt
FF.CD.F.690


title: PtenFF_CD_RNAseq_rep4

description:
all_sample_raw_count.txt
FF.CD.M.686


title: PtenFF_CD_RNAseq_rep3

description:
all_sample_raw_count.txt
FF.CD.F.689


title: PtenFF_CD_RNAseq_rep1

description:
all_sample_raw_count.txt
FF.CD.F.688


title: PPFP_Pio_RNAseq_rep5

description:
all_sample_raw_count.txt
PPFP.Pio.M.661

value: PPFPThy;PtenThy-/-

value: pioglitazone at a concentration of 200 parts per million in irradiated Purina rodent diet 5001


title: PPFP_Pio_RNAseq_rep4

description:
all_sample_raw_count.txt
PPFP.Pio.F.645


title: PtenFF_CD_RNAseq_rep6

description:
all_sample_raw_count.txt
FF.CD.F.692


title: PPFP_Pio_RNAseq_rep3

description:
all_sample_raw_count.txt
PPFP.Pio.M.633


title: PPFP_Pio_RNAseq_rep2

description:
all_sample_raw_count.txt
PPFP.Pio.F.628


title: PPFP_Pio_RNAseq_rep1

description:
all_sample_raw_count.txt
PPFP.Pio.F.601


title: PPFP_CD_RNAseq_rep5

description:
all_sample_raw_count.txt
PPFP.CD.M.659


title: PPFP_CD_RNAseq_rep6

description:
all_sample_raw_count.txt
PPFP.CD.M.295


title: PPFP_CD_RNAseq_rep4

description:
all_sample_raw_count.txt
PPFP.CD.F.668


title: PPFP_CD_RNAseq_rep2

description:
all_sample_raw_count.txt
PPFP.CD.M.660


title: PPFP_CD_RNAseq_rep1

description:
all_sample_raw_count.txt
PPFP.CD.F.629


title: input_DNA_rep2

extract_protocol: The cells were cross-linked with formaldehyde. The tissue was sheared by gauge needle, and then sonication in a Diagenode Bioruptor (Denville, NJ). Library construction was done with a Rubicon Genomics (Ann Arbor, MI) ThruPlex kit.

tag: chip antibody

value: none (input)


title: input_DNA_rep1

extract_protocol: The cells were cross-linked with formaldehyde. The tissue was sheared by gauge needle, and then sonication in a Diagenode Bioruptor (Denville, NJ).   the library was constructed with WaferGen Biosystems (Fremont, CA) reagent kit #400040


title: PPFP_ChIPseq_rep2

extract_protocol: The cells were cross-linked with formaldehyde. The tissue was sheared by gauge needle, and then sonication in a Diagenode Bioruptor (Denville, NJ). The material was then gently rocked overnight at 4C with 1:100 anti-Myc tag antibody 9B11 (Cell Signaling Technology #2276, Danvers, MA). Library construction was done with a Rubicon Genomics (Ann Arbor, MI) ThruPlex kit.

value: anti-Myc tag antibody 9B11 (Cell Signaling Technology #2276, lot #24)


title: PtenFF_CD_RNAseq_rep7

description:
all_sample_raw_count.txt
FF.CD.F.691


title: PPFP_ChIPseq_rep1

extract_protocol: The cells were cross-linked with formaldehyde. The tissue was sheared by gauge needle, and then sonication in a Diagenode Bioruptor (Denville, NJ). The material was then gently rocked overnight at 4C with 1:100 anti-Myc tag antibody 9B11 (Cell Signaling Technology #2276, Danvers, MA).  the library was constructed with WaferGen Biosystems (Fremont, CA) reagent kit #400040


title: PPFP_CD_RNAseq_rep3

description:
all_sample_raw_count.txt
PPFP.CD.F.647


title: PtenFF_CD_RNAseq_rep2

description:
all_sample_raw_count.txt
FF.CD.M.685


title: PtenFF_Pio_affy_rep5

hyb_protocol: Following fragmentation, 16 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader

data_processing: Data were analyzed using the limma and affy Bioconductor packages implemented in the R-statistical environment version 2.12.2. RMA was used to fit log2 transformed expression values

label: biotin

label_protocol: Biotinylated aRNA were prepared according to the Ambion Premier kit protocol from 250 ng total RNA (MessageAmp Premier RNA Amplification Kit Instruction Manual, 2008, Ambion)

extract_protocol: RNA was isolated from thyroid glands using an RNeasy Mini Kit per the manufacturer’s protocol (Qiagen, Valencia, CA)


title: PtenFF_Pio_affy_rep4


title: EV+Pio_RNAseq_rep3

status: Public on Jan 21 2016

description:
Total RNA was prepared using a Qiagen RNeasy kit. Library preparation was with 1 ug of total RNA and the TruSeq RNA prep kit (Illumina Cat #RS-122-2001) according to Illumina’s instructions. Adapter ligated products were enriched with 12 cycles of pcr.
all_sample_raw_count.txt

data_processing:
Basecalls performed using CASAVA-1.8.2
ChIP-seq and input reads were aligned to the rat reference genome (rn4) using BWA (version 0.5.9-r16) with default options. MACS2 (2.0.10.20131216beta) was used to call peaks. Peaks were then filtered by PePr (1.0.5) to remove artifacts.
RNA-Seq reads were aligned to rn4 with tophat2 (v2.0.11) and gene read counts were quantified by HTseq (0.6.1p1) with option “-m intersection-strict” and normalized by edgeR (3.2.4). Differential expression analysis was performed using edgeR with tagwise dispersion.
Genome_build: rn4
Supplementary_files_format_and_content: ChIP-Seq peak files were generated by MACS2, RNA-Seq read counts were quantified by HTSeq

organism: Rattus norvegicus

source_name: PCCL3 cell line

growth_protocol: PCCL3 cells were grown in Coon’s medium/F-12 high zinc supplemented with 5% fetal bovine serum, 0.3 mg/ml glutamine, 1 mU/ml bovine thyrotropin, 10 ug/ml bovine insulin, 5 ug/ml apo-transferrin, 10 nmol/L hydrocortisone, and penicillin/streptomycin.

extract_protocol: Total RNA was prepared using a Qiagen RNeasy kit. Library preparation was with 1 ug of total RNA and the TruSeq RNA prep kit (Illumina Cat #RS-122-2001) according to Illuminas instructions. Adapter ligated products were enriched with 12 cycles of pcr.

treatment_protocol: 16 hours prior to harvest, pioglitazone was added to achieve 1 uM (from a 1 mM stock in DMSO), or vehicle was added as the control.

tag: transfected

value: empty vector

value: 1 μM pioglitazone for 16 hours

tag: growth protocol

value: EV cells were cultured in 60 mm Petri dishes until 80% confluent


title: EV+Pio_RNAseq_rep2


title: EV+Pio_RNAseq_rep1


title: EV-Pio_RNAseq_rep2

value: DMSO for 16 hours


title: PPFP_Pio_affy_rep5


title: PtenFF_CD_affy_rep6


title: PPFP_Pio_affy_rep3


title: PtenFF_Pio_affy_rep1


title: PtenFF_CD_affy_rep3


title: PtenFF_CD_affy_rep2


title: PPFP_Pio_affy_rep1


title: PPFP_Pio_affy_rep4


title: PPFP_Pio_affy_rep2


title: PtenFF_CD_affy_rep4


title: PPFP_CD_affy_rep5


title: PPFP_CD_affy_rep6


title: PtenFF_CD_affy_rep5


title: PtenFF_Pio_affy_rep2


title: PPFP_CD_affy_rep2


title: PPFP_CD_affy_rep3


title: PPFP_Pio_affy_rep6


title: PtenFF_Pio_affy_rep6


title: PPFP_CD_affy_rep4


title: EV-Pio_RNAseq_rep3


title: PtenFF_CD_affy_rep1


title: PtenFF_Pio_affy_rep3


title: PPFP_CD_affy_rep1


title: PPFP+Pio_RNAseq_rep2

value: PAX8-PPARG fusion protein, myc-tagged

value: PPFP  cells were cultured in 60 mm Petri dishes until 80% confluent


title: PPFP+Pio_RNAseq_rep3


title: PPFP-Pio_RNAseq_rep2


title: PPFP_ChIPseq

description: The cells were cross-linked with formaldehyde, extracts were sheared by sonication to an average DNA size of ~300bp, and the chromatin fragments were immunoprecipitated with anti-myc tag antibody (Cell Signaling Technology cat#2276). 10ng of DNA was used for the library prep. The libraries were prepared on an Apollo 324 robot (Wafergen) using the ChIPseq library prep script and Wafergen reagents (Cat #400040). The adapter ligated products were enriched with 15 cycles of pcr.

extract_protocol: The cells were cross-linked with formaldehyde, extracts were sheared by sonication to an average DNA size of ~300bp. 10ng of DNA was used for the library prep. The libraries were prepared on an Apollo 324 robot (Wafergen) using the ChIPseq library prep script and Wafergen reagents (Cat #400040). The adapter ligated products were enriched with 15 cycles of pcr.

value: PPFP cells were cultured in four 150 mm Petri dishes until 80% confluent


title: PPFP-Pio_RNAseq_rep3


title: PPFP-Pio_RNAseq_rep1


title: PPFP+Pio_RNAseq_rep1


title: EV-Pio_RNAseq_rep1


title: input_DNA

description: The cells were cross-linked with formaldehyde, extracts were sheared by sonication to an average DNA size of ~300bp. 10ng of DNA was used for the library prep. The libraries were prepared on an Apollo 324 robot (Wafergen) using the ChIPseq library prep script and Wafergen reagents (Cat #400040). The adapter ligated products were enriched with 15 cycles of pcr.


title: input, InVitroCistromics

status: Public on Jun 25 2015

city: Philadelphia

first: David

middle: J

last: Steger

state: PA

address: 12-193 SCTR 3400 Civic Center Blvd

department: Institute of Diabetes, Obesity, and Metabolism

institute: University of Pennsylvania

data_processing:
Reads were mapped to the hg19 genome using Bowtie. Ambiguous alignments were excluded for TF ChIP-seq tracks. For H3K27Ac, reads were included with alignment locations of up to 3 possible loci.
Redundant reads were removed from TF ChIP-seq datasets using the makeTagDirectory script in HOMER. Redundant reads were preserved only for the H3K27Ac dataset.
Bed files for TF ChIP-Seq peaks were generated using the FindPeaks script in HOMER.
Bedgraph file for H3K27Ac was generated using the makeUCSCfile script in HOMER.
RNAPII.peaks.bed file was produced using a slope-based feature detection algorithm in Galaxy, see Cohen et al. ELife for details.
Input bias regions were manually curated from genomic regions showing strong ChIP enrichment on the genome browser independently of ChIP antibody.
Genome_build: hg19
Supplementary_files_format_and_content: 1 )TF ChIP-seq peak files in BED format 2) H3K27Ac in BEDGRAPH format

source_name: hMSC

growth_protocol: hMSCs were cultured in low glucose DMEM supplemented with 1% glutamine, and 10% FBS. For cell seeding density experiments, low cell density refers to 3000 cells/cm2, and high density to 35000 cells/cm2.

extract_protocol:
Cell pellets were prepared from 1.8x106 cells, crosslinked in 1 % formaldehyde for 15 minutes. A 5 minute quench was performed with 125mM glycine. Cells were harvested from 10 or 15cm dishes in DPBS using a cell scraper. To prepare ChIP extracts, nuclei were suspended SDS lysis buffer (50 mM HEPES/NaOH pH 7.5, 1% SDS, 10 mM EDTA, Complete protease inhibitor), incubated at 4 C for 10 min, and subjected to microtip probe sonication under conditions optimized for IP efficiency.
ChIP-Seq libraries were produced and sequenced according to Illumina protocols. Libraries were multiplexed for sequencing.

treatment_protocol: hMSCs were treated with DMI adipogenic induction medium for 24 hours (RNAPII) or 6 hrs (CEBPb, GR).

value: Human Mesenchymal Stem Cells


title: Burkitt lymphomas_EB2

status: Public on Jul 01 2013

description: mRNA expression

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip human Genome Array version 1. GeneChips were washed and stained in the Affymetrix Fluidics Station 400. The chips were scanned by the Affymetrix scanner.

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

data_processing: The data were analyzed using Affymetrix Expression Console™ Software (version 1.1) default analysis settings and RMA (Robust Multi-Array) summarization and normalization options. The data were imported into Matlab in order to develop the predictors.

source_name: Burkitt lymphomas_EB2

label_protocol: 1 μg of total RNA was reverse transcribed, using oligo(dT) primer to synthesize cDNA. T7 primer was used for in vitro transcription, resulting in labeled cRNA, which was fragmented and hybridized to Affymetrix Whole-Genome Gene 1.0 ST microarrays.

extract_protocol: Total RNA was extracted using a filter-based method from a Norgen Biotek kit.


title: Burkitt lymphomas_EB3

description: mRNA expression

source_name: Burkitt lymphomas_EB3


title: Burkitt lymphomas_677

description: mRNA expression

source_name: Burkitt lymphomas_677

value: Lymph


title: Burkitt lymphomas_747

description: mRNA expression

source_name: Burkitt lymphomas_747


title: Burkitt lymphomas_Ramos

description: mRNA expression

source_name: Burkitt lymphomas_Ramos

value: Ramos


title: Burkitt lymphomas_516

description: mRNA expression

source_name: Burkitt lymphomas_516


title: Burkitt lymphomas_670

description: mRNA expression

source_name: Burkitt lymphomas_670


title: Burkitt lymphomas_475

description: mRNA expression

source_name: Burkitt lymphomas_475


title: Burkitt lymphomas_CA46

description: mRNA expression

source_name: Burkitt lymphomas_CA46


title: Burkitt lymphomas_512

description: mRNA expression

source_name: Burkitt lymphomas_512


title: Burkitt lymphomas_513

description: mRNA expression

source_name: Burkitt lymphomas_513


title: Burkitt lymphomas_515

description: mRNA expression

source_name: Burkitt lymphomas_515


title: Burkitt lymphomas_Raji

description: mRNA expression

source_name: Burkitt lymphomas_Raji

value: Raji


title: Burkitt lymphomas_Namalwa

description: mRNA expression

source_name: Burkitt lymphomas_Namalwa

value: Namalwa


title: Burkitt lymphomas_Jijoye

description: mRNA expression

source_name: Burkitt lymphomas_Jijoye

value: Jijoye


title: Burkitt lymphomas_667

description: mRNA expression

source_name: Burkitt lymphomas_667


title: Burkitt lymphomas_510

description: mRNA expression

source_name: Burkitt lymphomas_510


title: Burkitt lymphomas_479

description: mRNA expression

source_name: Burkitt lymphomas_479


title: Burkitt lymphomas_BL41

description: mRNA expression

source_name: Burkitt lymphomas_BL41


title: WSU-NHL

status: Public on Jan 23 2013

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

data_processing: The data were analyzed using Affymetrix Expression Concole Software (version 1.1) default analysis settings and RMA (Robust Multi-Array) summarization and normalization options. The data were imported into Matlab in order to run the predictors.

source_name: cell line

label_protocol: Total RNA was amplified into sense-strand cDNA using the Ambion WT Expression kit. 5.5 ug of cDNA was fragmented and labeled with biotin using the Affymetrix GeneChip WT Terminal Labeling kit.

value: WSU-NHL

value: diffuse large B-cell lymphoma (DLBCL)


title: Toledo

value: Toledo


title: SUDHL4


title: SKI

value: SKI


title: SUDHL7


title: Burkitt lymphomas_745

description: mRNA expression

source_name: Burkitt lymphomas_745


title: RL

value: RL


title: U2932


title: Burkitt lymphomas_508

description: mRNA expression

source_name: Burkitt lymphomas_508


title: TMD8


title: Ly7


title: DLBCL1057

source_name: Diffuse large B-cell lymphoma


title: Farage

value: Farage


title: Karpas422


title: RCK8


title: HT

value: HT


title: SCI-1


title: Pfieffer

value: Pfieffer


title: BJAB

value: BJAB


title: Ly3


title: Ly10


title: Ly8


title: DLBCL1055


title: Ly1


title: DLBCL1051


title: DLBCL1021


title: Ly19


title: DLBCL894


title: DLBCL797


title: DLBCL738


title: DLBCL895


title: DLBCL923


title: DLBCL922


title: DLBCL899


title: DLBCL733


title: DLBCL905


title: splenic MZL (Splenic414)

status: Public on Aug 26 2010

description: size fractionated small RNA

data_processing:
Sequence mapped to the genome, flanking sequence retrieved and biogenesis characteristics of miRNA checked.

The supplementary *_seq.txt file is an intermediate data file that was used to map the sequences to the reference genome.

source_name: Lymphoid organ

extract_protocol: Total RNA (typically 5ug) from each sample was run on denaturing  polyacrylamide-urea gels. The 18-30 nucleotide RNAs were excised from  the gel, reverse transcribed, and ligated to sequencing adaptors on  the 5’ and 3’ ends. The resulting cDNA library was PCR-amplified for  15 cycles and gel purified on 6% acrylamide gel. The gel-purified  amplicon quality and quantity were analyzed on a 6% acrylamide gel  relative to oligonucleotides of known concentration and size. 120 μl  of 1-4 pM library were loaded on to the Illumina cluster station,  where DNA molecules were attached to high-density universal adaptors  in the flow cells and amplified. The DNA clusters generated via this  process were sequenced with sequencing-by-synthesis technology, where  successive high-resolution images were captured of the four-color  fluorescence excitation dependent on the base incorporated during each  cycle.

tag: b cell type

value: Marginal Zone lymphoma (Primary human)


title: Lymphoblastic (ALL411)

description: size fractionated small RNA

value: Lymphoblastic lymphoma (Primary human)


title: MALT (MALT413)

description: size fractionated small RNA


title: bjab cell line (bjab103)

description: size fractionated small RNA

value: Diffuse Large B cell lymphoma (Bjab Cell Line)


title: h929 Cell line (h929)

description: size fractionated small RNA

value: Multiple Myeloma (H929 human cell line)


title: DLBCL823


title: HIV-positive DL (HIV412)

description: size fractionated small RNA

value: HIV lymphoma (Primary human)


title: Mututated CLL (CLLM633)

description: size fractionated small RNA

value: Chronic lymphocytic Leukemia (Primary human)


title: L428 cell line (L428)

description: size fractionated small RNA

value: Hodkgin lymphoma (L428 human cell line)


title: B Cell + EBV 1

status: Public on Apr 20 2012

description: miRNA microarray expression

hyb_protocol: Labeled miRNAs were hybridized to a miRNA microarray (Exiqon V.10) at 65 degrees Celcius for 16 hours in a nitrogen environment.

scan_protocol: The microarray slides were scanned using the GenePix 4100 scanner (Axon Instruments).

data_processing: The quantified signals were normalized using the global Lowess algorithm, using Genespring (Agilent Technologies, Santa Clara, CA) software. The intensity values for multiple spots were averaged and the normalized values were log2-transformed. Differentially expressed microRNAs (false discovery rate<5%) were identified using SAM that were differentially expressed among the 3 groups (resting B cell, proliferating B cells and LCLs).

source_name: CFSE stained, proliferating, CD19+ cells from EBV-infected PBMCs

label_protocol: Control (Human lymph node RNA from Ambion) and test miRNA was labeled with Hy3 and Hy5, respectively, and mixed with spike-in control miRNA's.

growth_protocol: Human peripheral blood mononuclear cells (PBMCs) were  obtained by Ficoll purification (Histopaque-1077 column, Sigma) of buffy coats from normal donors (Carolina Red Cross) and kept in RPMI 1640 medium (Invitrogen) supplemented with 15% Fetal Bovine serum (100-500 Gemini Bio Product), 100 U/ml Penicillin, and 2mM L-Glutamine (G6784, Invitrogen). B cells were separated using the Human B Lymphocyte Enrichment set-DM (Imag, BD) as recommended by the manufacturer. PBMCs were infected with limiting amounts of B95-8 virus for 1h at 37°C (0.4-12 μl EBV B95-8 Z-HT supernatant/1x106 PBMC) in the presence of Cyclosporine A (0.5 μg/ml). The cells were washed once in PBS and then re-suspended in fresh medium. For each condition of infection, 105 cells were plated in to 96-well plate (in total 10 wells) to grow out as LCLs. Microarray samples were generated from monoclonal LCLs produced from the lowest amount of virus used For the purification of EBV-positive and proliferating B cells, 1.5x108 PBMC were stained with 4 μM 6-carboxyfluorescein succinimidyl ester (CFSE) for 3 minutes and washed three times in washing buffer (PBS + 5% fetal bovine serum). Stained PBMC (106/ml) were infected with 25 μl/1x106PBMC of B95-8 virus as already described.The cells were washed once in PBS and then re-suspended in fresh medium. At 6 days post-infection, CFSE-labeled PBMCs were washed in washing buffer and stained with APC-labeled α-CD19 (555415-BD Biosciences) (2μl/3x105) for 30 minutes on ice. After 3 washes in washing buffer, CD19+/CFSElow cells were sorted on a FACSVantage cell sorter flow cytometer.

extract_protocol: mir-Vana miRNA isolation kit (Ambion) according to the manufacturer’s instructions

value: B Cell

tag: status

value: infected, proliferating


title: B Cell 1

description: miRNA microarray expression

source_name: Purified B Cells from PBMCs

treatment_protocol: The cells were washed once in PBS and then re-suspended in fresh medium.

tag: cell type

value: uninfected


title: LCL 1

description: miRNA microarray expression

source_name: Monoclonal LCL derived by limited EBV dilution on PBMCs

value: lymphoblastoid cell lines

value: infected, immortalized


title: LCL 2

description: miRNA microarray expression


title: LCL 3

description: miRNA microarray expression


title: B Cell 3

description: miRNA microarray expression


title: DLBCL1000

value: diffuse large B-cell lymphoma (DLBCL)


title: B Cell 2

description: miRNA microarray expression


title: Ly3 cell line (Ly3)

description: size fractionated small RNA

value: Diffuse Large B cell lymphoma (LY3 Cell Line)


title: KMS12 cell line (KMS12)

description: size fractionated small RNA

value: Multiple Myeloma (KMS12 human cell line)


title: EBV activated B cell line (EBV159)

description: size fractionated small RNA

value: EBV-transformed B cell (primary human)


title: B Cell + EBV 2

description: miRNA microarray expression


title: B Cell + EBV 3

description: miRNA microarray expression


title: DLBCL721

data_processing: The data were analyzed using Affymetrix Expression Concole Software (version 1.1) default analysis settings and RNA (Robust Multi-Array) summarization and normalization options. The data were imported into Matlab in order to run the predictors.


title: L1236 cell line (L1236)

description: size fractionated small RNA

value: Hodkgin lymphoma (L1236 human cell line)


title: DLBCL998


title: Multiple Myeloma (U266)

description: size fractionated small RNA

value: Multiple Myeloma (U266 human cell line)


title: Burkitt Lymphoma (BL134)

description: size fractionated small RNA

value: Burkitt Lymphoma (Daudi human Cell Line)


title: Mentle Cell Lymphoma (MCL112)

description: size fractionated small RNA

value: Mantle cell Lymphoma (Primary Human)


title: Burkitt Lymphoma (BL510)

description: size fractionated small RNA

value: Burkitt Lymphoma (Primary Human)


title: Burkitt Lymphoma (BL115)

description: size fractionated small RNA

value: Burkitt Lymphoma (Ramos Cell Line)


title: 6hr Activated B cell line (ABC158)

description: size fractionated small RNA

value: Activated B cell (Primary human)


title: Mentle Cell Lymphoma (MCL114)

description: size fractionated small RNA

value: Mantle cell lymphoma (Primary Human)


title: Mantle Cell Lymphoma (Mino122)

description: size fractionated small RNA

value: Mantle cell Lymphoma (Mino cell line)


title: GCB DLBCL (GCB110)

description: size fractionated small RNA

value: Diffuse Large B cell lymphoma (Primary Human)


title: Memory B cells (MM55)

description: size fractionated small RNA

value: Memory (FACS sorted primary human)


title: Germinal Center B cell (GC40)

description: size fractionated small RNA

value: Germinal Center (FACS sorted primary human)


title: Plasma B cells (PC44)

description: size fractionated small RNA

value: Plasma cell (FACS sorted primary human)


title: Plasma B cells (PC137)

description: size fractionated small RNA


title: GCB DLBCL (GCB385)

description: size fractionated small RNA

value: Transformed follicular lymphoma (Primary Human)


title: Naïve B Cell (Naive39)

description: size fractionated small RNA

value: Naive (FACS sorted primary human)


title: Memory B cells (MM139)

description: size fractionated small RNA


title: Germinal Center B cell (GC136)

description: size fractionated small RNA


title: Naïve B Cell (Naive138)

description: size fractionated small RNA


title: 784_DLBCL Sample

description:
2026_4305_23361_105-13-784_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip human Genome Array version 1. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.  The chips were scanned by the Affymetrix scanner.

label_protocol: Total RNA was amplified into sense-strand cDNA using the Ambion WT Expression kit.  5.5 ug of cDNA was fragmented and labeled with biotin using the Affymetrix GeneChip WT Terminal Labeling kit.

value: diffuse large B-cell lymphoma (DLBCL)


title: 701_DLBCL Sample

description:
2002_4279_23210_103-25-701_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 705_DLBCL Sample

description:
2002_4279_23218_104-5-705_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 655_DLBCL Sample

description:
2002_4253_22612_102-4-655_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 830_DLBCL Sample

description:
2026_4305_23345_104-14-830_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 832_DLBCL Sample

description:
2026_4305_23347_104-16-832_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 759_DLBCL Sample

description:
2002_4279_23225_104-24-759_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 833_DLBCL Sample

description:
2026_4305_23348_104-17-833_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 684_DLBCL Sample

description:
2014_4268_22766_103-16-684_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 666_DLBCL Sample

description:
2014_4268_22762_103-12-666_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 663_DLBCL Sample

description:
2002_4279_23217_104-4-663_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 829_DLBCL Sample

description:
2022_4294_23248_104-13-829_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 810_DLBCL Sample

description:
2031_4315_23489_106-6-810_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 685_DLBCL Sample

description:
2002_4253_22615_102-7-685_HuGene-1+0-st-v1

Gene expression data from DLBCL patient

extract_protocol: Total RNA was extracted using a filter based method from a Norgen Biotek kit.


title: 818_DLBCL Sample

description:
2031_4315_23497_106-14-818_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 763_DLBCL Sample

description:
2051_4350_23866_107-29-763_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 875_DLBCL Sample

description:
2071_4406_24368_110-18-875_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 859_DLBCL Sample

description:
2071_4391_24281_108-28-859_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 649_DLBCL Sample

description:
2002_4279_23215_104-2-649_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 480_DLBCL Sample

description:
2051_4350_23876_108-11-480_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 683_DLBCL Sample

description:
2002_4253_22614_102-6-683_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 831_DLBCL Sample

description:
2026_4305_23346_104-15-831_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 855_DLBCL Sample

description:
2071_4391_24277_108-24-855_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 690_DLBCL Sample

description:
2002_4279_23204_103-20-690_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 813_DLBCL Sample

description:
2031_4315_23492_106-9-813_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 804_DLBCL Sample

description:
2031_4315_23483_105-32-804_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 538_DLBCL Sample

description:
2002_4253_22618_102-10-538_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 891_DLBCL Sample

description:
2071_4429_24495_111-24-891_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 770_DLBCL Sample

description:
2026_4305_23352_105-2-770_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 756_DLBCL Sample

description:
2002_4279_23222_104-21-756_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 487_DLBCL Sample

description:
2051_4350_23883_108-18-487_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 858_DLBCL Sample

description:
2071_4391_24280_108-27-858_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 782_DLBCL Sample

description:
2026_4305_23359_105-11-782_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 492_DLBCL Sample

description:
2051_4350_23886_108-21-492_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 835_DLBCL Sample

description:
2026_4305_23350_104-19-835_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 10a_DLBCL Sample

description:
2051_4350_23887_108-22-610a_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 824_DLBCL Sample

description:
2002_4279_23221_104-8-824_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 707_DLBCL Sample

description:
2002_4279_23219_104-6-707_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 878_DLBCL Sample

description:
2071_4406_24371_110-21-878_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 702_DLBCL Sample

description:
2002_4279_23211_103-28-702_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 491_DLBCL Sample

description:
2051_4350_23885_108-20-491_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 812_DLBCL Sample

description:
2031_4315_23491_106-8-812_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 871_DLBCL Sample

description:
2071_4406_24364_110-14-871_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: DLBCL1052


title: 816_DLBCL Sample

description:
2031_4315_23495_106-12-816_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 773_DLBCL Sample

description:
2026_4305_23353_105-5-773_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 694_DLBCL Sample

description:
2002_4279_23205_103-21-694_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 727_DLBCL Sample

description:
2038_4334_23637_107-11-727_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 798_DLBCL Sample

description:
2031_4315_23477_105-26-798_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 486_DLBCL Sample

description:
2051_4350_23882_108-17-486_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 484_DLBCL Sample

description:
2051_4350_23880_108-15-484_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 648_DLBCL Sample

description:
2002_4279_23214_104-1-648_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 805_DLBCL Sample

description:
2031_4315_23484_106-1-805_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 814_DLBCL Sample

description:
2031_4315_23493_106-10-814_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 846_DLBCL Sample

description:
2038_4334_23627_106-28-846_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 791_DLBCL Sample

description:
2026_4305_23367_105-19-791_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 347_DLBCL Sample

description:
2014_4268_22770_103-32-347_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 781_DLBCL Sample

description:
2026_4305_23358_105-10-781_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 483_DLBCL Sample

description:
2051_4350_23879_108-14-483_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 857_DLBCL Sample

description:
2071_4391_24279_108-26-857_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 704_DLBCL Sample

description:
2002_4279_23213_103-30-704_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 790_DLBCL Sample

description:
2026_4305_23366_105-18-790_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 856_DLBCL Sample

description:
2071_4391_24278_108-25-856_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 789_DLBCL Sample

description:
2026_4305_23365_105-17-789_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 825_DLBCL Sample

description:
2022_4294_23250_104-9-825_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 800_DLBCL Sample

description:
2031_4315_23479_105-28-800_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 689_DLBCL Sample

description:
2002_4279_23203_103-19-689_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 834_DLBCL Sample

description:
2026_4305_23349_104-18-834_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 890_DLBCL Sample

description:
2071_4429_24494_111-23-890_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 503_DLBCL Sample

description:
2014_4268_22769_103-31-503_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 778_DLBCL Sample

description:
2026_4305_23356_105-8-778_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 780_DLBCL Sample

description:
2026_4305_23357_105-9-780_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 481_DLBCL Sample

description:
2051_4350_23877_108-12-481_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 827_DLBCL Sample

description:
2022_4294_23252_104-11-827_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 737_DLBCL Sample

description:
2038_4334_23642_107-16-737_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: Unmutated CLL (CLLU626)

description: size fractionated small RNA

value: Chronic lymphocytic leukemia (Primary human)


title: 809_DLBCL Sample

description:
2031_4315_23488_106-5-809_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 777_DLBCL Sample

description:
2026_4305_23355_105-7-777_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 787_DLBCL Sample

description:
2026_4305_23364_105-16-787_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 844_DLBCL Sample

description:
2038_4334_23625_106-26-844_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 729_DLBCL Sample

description:
2038_4334_23638_107-12-729_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 811_DLBCL Sample

description:
2031_4315_23490_106-7-811_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 792_DLBCL Sample

description:
2026_4305_23368_105-20-792_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 785_DLBCL Sample

description:
2026_4305_23362_105-14-785_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 808_DLBCL Sample

description:
2031_4315_23487_106-4-808_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 842_DLBCL Sample

description:
2038_4334_23624_106-25-842_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 490_DLBCL Sample

description:
2051_4350_23884_108-19-490_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 485_DLBCL Sample

description:
2051_4350_23881_108-16-485_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 817_DLBCL Sample

description:
2031_4315_23496_106-13-817_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 793_DLBCL Sample

description:
2031_4315_23472_105-21-793_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 482_DLBCL Sample

description:
2051_4350_23878_108-13-482_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 806_DLBCL Sample

description:
2031_4315_23485_106-2-806_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 783_DLBCL Sample

description:
2026_4305_23360_105-12-783_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 807_DLBCL Sample

description:
2031_4315_23486_106-3-807_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 801_DLBCL Sample

description:
2031_4315_23480_105-29-801_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 658_DLBCL Sample

description:
2002_4279_23216_104-3-658_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 803_DLBCL Sample

description:
2031_4315_23482_105-31-803_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 720_DLBCL Sample

description:
2038_4334_23634_107-8-720_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 794_DLBCL Sample

description:
2031_4315_23473_105-22-794_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: Germinal Center-like Diffuse large B cell lymphoma DLBCL GCB 542

status: Public on Mar 17 2009

description: micro RNA expression

hyb_protocol: Exiqon protocol;  The fluorescently labeled samples were combined and hybridized to a miRNA microarray (v.10.0, Exiqon, Denmark), in a nitrogen atmosphere.

scan_protocol: GenePix Pro 6.0.1.25. The microarray slides were scanned with GenePix 4100 Scanner.

data_processing: The GPR file was extracted  and exported to Genespring 7.3.1. The raw data were normalized using Data transformation: set measurements less than 0.01 to 0.01, per spot and per chip: Intensity dependent (Lowess) normalization, and per gene: normalize to median

source_name: DLBCL GCB 542

label_protocol: MiRNA expression profiling from human B cell lymphomas was conducted using  up to 1 ug of total RNA from sample and reference (normal lymph node), which were labeled with Cy3 or Cy5 fluorescent dyes, using the miRNA/LNA labeling kit (Exiqon, Denmark).

extract_protocol: Exiqon

value: Frozen Biopsy Specimen; Germinal Center-like Diffuse large B cell lymphoma

source_name: Human Normal Lymph node total RNA (Ambion)

value: Normal lymph node


title: Germinal Center-like Diffuse large B cell lymphoma DLBCL GCB 534

description: micro RNA expression

source_name: DLBCL GCB 534


title: Germinal Center-like Diffuse large B cell lymphoma DLBCL GCB 547

description: micro RNA expression

source_name: DLBCL GCB 547


title: Germinal Center-like Diffuse large B cell lymphoma DLBCL GCB 541

description: micro RNA expression

source_name: DLBCL GCB 541


title: Germinal Center-like Diffuse large B cell lymphoma DLBCL GCB 538

description: micro RNA expression

source_name: DLBCL GCB 538


title: Germinal Center-like Diffuse large B cell lymphoma DLBCL GCB 480

description: micro RNA expression

source_name: DLBCL GCB 480


title: Germinal Center-like Diffuse large B cell lymphoma DLBCL GCB 501

description: micro RNA expression

source_name: DLBCL GCB 501


title: Germinal Center-like Diffuse large B cell lymphoma DLBCL GCB 498

description: micro RNA expression

source_name: DLBCL GCB 498


title: Germinal Center-like Diffuse large B cell lymphoma DLBCL GCB 486

description: micro RNA expression

source_name: DLBCL GCB 486


title: 802_DLBCL Sample

description:
2031_4315_23481_105-30-802_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: 799_DLBCL Sample

description:
2031_4315_23478_105-27-799_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.


title: Germinal Center-like Diffuse large B cell lymphoma DLBCL GCB 497

description: micro RNA expression

source_name: DLBCL GCB 497


title: Germinal Center-like Diffuse large B cell lymphoma DLBCL GCB 490

description: micro RNA expression

source_name: DLBCL GCB 490


title: Germinal Center-like Diffuse large B cell lymphoma DLBCL GCB 386

description: micro RNA expression

source_name: DLBCL GCB 386


title: Germinal Center-like Diffuse large B cell lymphoma DLBCL GCB 385

description: micro RNA expression

source_name: DLBCL GCB 385


title: Germinal Center-like Diffuse large B cell lymphoma DLBCL GCB 367

description: micro RNA expression

source_name: DLBCL GCB 367


title: Germinal Center-like Diffuse large B cell lymphoma DLBCL GCB 494

description: micro RNA expression

source_name: DLBCL GCB 494


title: Germinal Center-like Diffuse large B cell lymphoma DLBCL GCB 365

description: micro RNA expression

source_name: DLBCL GCB 365


title: Germinal Center-like Diffuse large B cell lymphoma DLBCL GCB 342

description: micro RNA expression

source_name: DLBCL GCB 342


title: Germinal Center-like Diffuse large B cell lymphoma DLBCL GCB 343

description: micro RNA expression

source_name: DLBCL GCB 343

source_name: Human Normal Lymph node total RNA (Ambion)


title: Germinal Center-like Diffuse large B cell lymphoma DLBCL GCB 318

description: micro RNA expression

source_name: DLBCL GCB 318


title: Germinal Center-like Diffuse large B cell lymphoma DLBCL GCB 340

description: micro RNA expression

source_name: DLBCL GCB 340


title: Activated B cell-like Diffuse large B cell lymphoma DLBCL ABC 543

description: micro RNA expression

source_name: DLBCL ABC 543

value: Frozen Biopsy Specimen; Activated B cell-like Diffuse large B cell lymphoma


title: Activated B cell-like Diffuse large B cell lymphoma DLBCL ABC 551

description: micro RNA expression

source_name: DLBCL ABC 551


title: Activated B cell-like Diffuse large B cell lymphoma DLBCL ABC 546

description: micro RNA expression

source_name: DLBCL ABC 546


title: Activated B cell-like Diffuse large B cell lymphoma DLBCL ABC 485

description: micro RNA expression

source_name: DLBCL ABC 485


title: Activated B cell-like Diffuse large B cell lymphoma DLBCL ABC 523

description: micro RNA expression

source_name: DLBCL ABC 523


title: Activated B cell-like Diffuse large B cell lymphoma DLBCL ABC 383

description: micro RNA expression

source_name: DLBCL ABC 383


title: Activated B cell-like Diffuse large B cell lymphoma DLBCL ABC 496

description: micro RNA expression

source_name: DLBCL ABC 496


title: Activated B cell-like Diffuse large B cell lymphoma DLBCL ABC 351

description: micro RNA expression

source_name: DLBCL ABC 351


title: Activated B cell-like Diffuse large B cell lymphoma DLBCL ABC 384

description: micro RNA expression

source_name: DLBCL ABC 384


title: Activated B cell-like Diffuse large B cell lymphoma DLBCL ABC 448

description: micro RNA expression

source_name: DLBCL ABC 448


title: 815_DLBCL Sample

description:
2031_4315_23494_106-11-815_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.

source_name: Diffuse large B-cell lymphoma


title: Activated B cell-like Diffuse large B cell lymphoma DLBCL ABC 349

description: micro RNA expression

source_name: DLBCL ABC 349


title: Activated B cell-like Diffuse large B cell lymphoma DLBCL ABC 464

description: micro RNA expression

source_name: DLBCL ABC 464


title: Activated B cell-like Diffuse large B cell lymphoma DLBCL ABC 366

description: micro RNA expression

source_name: DLBCL ABC 366


title: Activated B cell-like Diffuse large B cell lymphoma DLBCL ABC 350

description: micro RNA expression

source_name: DLBCL ABC 350

source_name: Human Normal Lymph node total RNA (Ambion)


title: Activated B cell-like Diffuse large B cell lymphoma DLBCL ABC 346

description: micro RNA expression

source_name: DLBCL ABC 346


title: Activated B cell-like Diffuse large B cell lymphoma DLBCL ABC 319

description: micro RNA expression

source_name: DLBCL ABC 319


title: Activated B cell-like Diffuse large B cell lymphoma DLBCL ABC 315

description: micro RNA expression

source_name: DLBCL ABC 315


title: Activated B cell-like Diffuse large B cell lymphoma DLBCL ABC 344

description: micro RNA expression

source_name: DLBCL ABC 344


title: Activated B cell-like Diffuse large B cell lymphoma DLBCL ABC 345

description: micro RNA expression

source_name: DLBCL ABC 345


title: Activated B cell-like Diffuse large B cell lymphoma DLBCL ABC 461

description: micro RNA expression

source_name: DLBCL ABC 461


title: Chronic Lymphocytic Leukemia (Unmutated) CLL UM 630

description: micro RNA expression

source_name: CLL UM 630

value: Frozen Biopsy Specimen; Chronic Lymphocytic Leukemia (Unmutated)


title: Chronic Lymphocytic Leukemia (Unmutated) CLL UM 629

description: micro RNA expression

source_name: CLL UM 629


title: Chronic Lymphocytic Leukemia (Unmutated) CLL UM 628

description: micro RNA expression

source_name: CLL UM 628


title: Chronic Lymphocytic Leukemia (Unmutated) CLL UM 626

description: micro RNA expression

source_name: CLL UM 626


title: Chronic Lymphocytic Leukemia (Unmutated) CLL UM 623

description: micro RNA expression

source_name: CLL UM 623


title: Chronic Lymphocytic Leukemia (Unmutated) CLL UM 622

description: micro RNA expression

source_name: CLL UM 622


title: Chronic Lymphocytic Leukemia (Mutated) CLL M 640

description: micro RNA expression

source_name: CLL M 640

value: Frozen Biopsy Specimen; Chronic Lymphocytic Leukemia (Mutated)


title: Chronic Lymphocytic Leukemia (Unmutated) CLL UM 621

description: micro RNA expression

source_name: CLL UM 621


title: Chronic Lymphocytic Leukemia (Unmutated) CLL UM 624

description: micro RNA expression

source_name: CLL UM 624


title: Chronic Lymphocytic Leukemia (Mutated) CLL M 639

description: micro RNA expression

source_name: CLL M 639


title: Chronic Lymphocytic Leukemia (Mutated) CLL M 636

description: micro RNA expression

source_name: CLL M 636

source_name: Human Normal Lymph node total RNA (Ambion)


title: Chronic Lymphocytic Leukemia (Mutated) CLL M 637

description: micro RNA expression

source_name: CLL M 637


title: Chronic Lymphocytic Leukemia (Mutated) CLL M 635

description: micro RNA expression

source_name: CLL M 635


title: Chronic Lymphocytic Leukemia (Mutated) CLL M 638

description: micro RNA expression

source_name: CLL M 638


title: Chronic Lymphocytic Leukemia (Mutated) CLL M 634

description: micro RNA expression

source_name: CLL M 634


title: Chronic Lymphocytic Leukemia (Mutated) CLL M 631

description: micro RNA expression

source_name: CLL M 631


title: Chronic Lymphocytic Leukemia (Unmutated) CLL UM 627

description: micro RNA expression

source_name: CLL UM 627


title: Burkitt Lymphoma BL479

description: micro RNA expression

value: Frozen Biopsy Specimen; Burkitt Lymphoma


title: Chronic Lymphocytic Leukemia (Mutated) CLL M 633

description: micro RNA expression

source_name: CLL M 633


title: Burkitt Lymphoma BL406

description: micro RNA expression


title: Chronic Lymphocytic Leukemia (Mutated) CLL M 632

description: micro RNA expression

source_name: CLL M 632


title: Burkitt Lymphoma BL475

description: micro RNA expression


title: Burkitt Lymphoma BL404

description: micro RNA expression


title: Chronic Lymphocytic Leukemia (Unmutated) CLL UM 625

description: micro RNA expression

source_name: CLL UM 625


title: Burkitt Lymphoma BL 515

description: micro RNA expression


title: Burkitt Lymphoma BL 513

description: micro RNA expression


title: Burkitt Lymphoma BL 510

description: micro RNA expression


title: Burkitt Lymphoma BL320

description: micro RNA expression


title: Burkitt Lymphoma BL403

description: micro RNA expression


title: Burkitt Lymphoma BL 508

description: micro RNA expression


title: Human Tonsil Naïve Bcells rep2

status: Public on Sep 19 2008

description: Gene expression data from Naïve B cells

hyb_protocol: standard Affymetreix protocol

scan_protocol: standard Affymetreix protocol

data_processing: The CEL file extracted and normalized using Robust Multi-array Average(GCRMA) prob summarization algorithms (perform background correction, Normalization, and probe summarization) while exported to GeneSpring 7.3.1.  Normalization to median was applied in geneSpring as an additional normalization.

source_name: Human Tonsil Naïve Bcells

label_protocol: standard Affymetreix protocol

extract_protocol: standard Affymetreix protocol

tag: Human Tonsil Naïve Bcells


title: intestine, rag1+/- and rag1-/- , biological rep2, technical rep2

status: Public on Jan 05 2009

description: Biological replicate 2; technical replicate 2 (dye swap)

hyb_protocol: Equal amounts of Cy5- and Cy3-labeled cRNA (750ng) from two different samples were hybridized to Agilent Zebrafish Genome Oligonucleotide Microarrays.

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 8.5).

data_processing: The following data processing steps were applied to the data while importing to GeneSpring:  1) Data Transformation: Dye swap applied to Samples in which test sample (rag1 -/-) was labeled with Cy3.  2) Data Transformation: Set measurements less than 0.01 to 0.01.  3) Per Spot and Per Chip: Intensity-dependent (Lowess) normalization.  4) Per Gene: Normalize to median.

source_name: Zebrafish, intestine, rag1 heterozygous siblings

label_protocol: 1 microgram of total RNA was converted into labeled cRNA with nucleotides coupled to a fluorescent dye (either Cy3 or Cy5) using the  Low RNA Input Linear Amplification Kit (Agilent Technologies, Palo Alto,CA)  following the manufacturer's protocol.

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

tag: Intestine

tag: Adult zebrafish

tag: Biological replicate 2

source_name: Zebrafish, intestine, homozygous for rag1 mutant allele


title: intestine, rag1-/- and rag1+/- , biological rep2, technical rep1

description: Biological replicate 2; technical replicate 1


title: Human Tonsil Dark Zone -GC Bcells rep1

description: Gene expression data from Memory B cells

source_name: Human Tonsil Dark Zone -GC Bcells

tag: Human Tonsil Dark Zone -GC Bcells


title: kidney, rag1+/- and rag1-/- , biological rep2, technical rep2

source_name: Zebrafish, kidney, rag1 heterozygous siblings

tag: Kidney

source_name: Zebrafish, kidney, homozygous for rag1 mutant allele


title: Human Tonsil Dark Zone -GC Bcells rep3


title: Human Tonsil Naïve Bcells rep3

description: Gene expression data from Naïve B cells


title: kidney, rag1-/- and rag1+/- , biological rep1, technical rep1

description: Biological replicate 1; technical replicate 1

tag: Biological replicate 1


title: Human Tonsil Pre-GC Bcells rep2

source_name: Human Tonsil Pre-GC Bcells

tag: Human Tonsil Pre-GC Bcells


title: Human Tonsil Dark Zone -GC Bcells rep2


title: Human Tonsil Naïve Bcells rep1

description: Gene expression data from Naïve B cells


title: Human Blood Bcells CD19+ IgD- rep2

description: Gene expression data from Plasma B cells

source_name: Human Blood Bcells CD19+ IgD-

tag: Human Blood Bcells CD19+ IgD-


title: kidney, rag1-/- and rag1+/- , biological rep2, technical rep1


title: Human Blood Bcells CD19+ IgD+ rep2

description: Gene expression data from Germinal Center B cells

source_name: Human Blood Bcells CD19+ IgD+

tag: Human Blood Bcells CD19+ IgD+


title: Human Blood Bcells CD19+ IgD- rep3


title: kidney, rag1+/- and rag1-/- , biological rep1, technical rep2

description: Biological replicate 1; technical replicate 2 (dye swap)


title: Human Blood Bcells CD19+ IgD+ rep1


title: 795_DLBCL Sample

description:
2031_4315_23474_105-23-795_HuGene-1+0-st-v1

Gene expression data from DLBCL patient.

source_name: Diffuse large B-cell lymphoma

tag: tissue


title: Naïve B Cells; Naïve_48

status: Public on Aug 07 2008

description: Gene expression data from Naïve B cells

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

source_name: Naïve B cells

label_protocol: Affymetrix protocol

extract_protocol: CD19 selected B cells were sorted using flow cytometry

tag: Acutly resected tonsils from young patients undergoing routine tonsillectomy


title: Naïve B Cells; Naïve_41

description: Gene expression data from Naïve B cells


title: Human Tonsil Pre-GC Bcells rep 1


title: Memory B cells; MM_36

source_name: Memory B cells


title: intestine, rag1-/- and rag1+/- , biological rep1, technical rep1


title: intestine, rag1+/- and rag1-/- , biological rep1, technical rep2


title: Human Blood Bcells CD19+ IgD+ rep3


title: Memory B cells; MM_38


title: Human Blood Bcells CD19+ IgD- rep1


title: Memory B cells; MM_28


title: Naïve B Cells; Naïve_39

description: Gene expression data from Naïve B cells


title: Plasma B Cells; PC_33

source_name: Plasma B cells


title: Plasma B Cells; PC_44


title: HMVEC Control of TSP

status: Public on Dec 31 2005

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

description:
Control RNA was extracted from untreated HMVEC. Total RNA was isolated using TRIZOL solution (Invitrogen, Carlsbad, CA). Briefly, after treatment, cells were washed twice in PBS and incubated with TRIZOL for 5 minutes at room temperature. RNA was extracted with 200 ul chloroform per ml TRIZOL and precipitated with 100% isopropanol at -20ºC. The RNA pellet was resuspended in DEPC-treated water and stored at –80ºC until further use. Human cDNA microarrays (Research Genetics/Invitrogen, Carlsbad, CA) consisted of nylon membranes containing 4,132 named genes EST’s (GF211). The array also contained 192 spots of total genomic DNA that served as reference points for the image analysis software Pathways 2.0 (Research Genetics/Invitrogen, Carlsbad, CA) for normalization purposes and to verify the homogeneity of the hybridization. cDNA probes were made from 5 micro-g total RNA with α[33P]-dATP (Amersham Biosciences, Piscataway, NJ) by oligo dT-primed polymerization using SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA). Probes were purified by gel chromatography (BioSpin 6; BioRad Laboratories, Hercules, CA), boiled for about 3 min and allowed to cool to room temperature. The microarrays were pre-hybridized for no less than 2 hr and then hybridized overnight at 42 oC. Filters were washed with 2xSSC and 1 % SDS for 15 min at 50 oC, and then with 0.5xSSC and 1% SDS twice for a total of 30 min at room temperature. Washed filters were then exposed to phosphor imager screens, which were scanned by a Molecular Dynamics Storm Imager (Packard Instruments, Meriden, CT) at 600 dpi resolution. Scanned files containing the microarray were analyzed with Pathways software (Invitrogen/Research Genetics, Carlsbad, CA). Pathways 2.0 (Research Genetics, Carlsbad, CA) and Bioconductor packages (http://www.bioconductor.org) were used to quantify the background intensity, normalize data (loess normalization), and determine actually expressed genes.
Keywords = Homo sapiens
Keywords = human micro vascular endothelial cell
Keywords = thrombospondin-1
Keywords = angiogenesis

source_name: Untreated human micro vascular endothelial cells


title: HMVEC treated with TSP

description:
Total RNA was first isolated from HMVEC’s that had been incubated with Thrombospondin-1  (Dr. Noel Bouck, Northwestern University) at IC50 concentration (TSP, 0.5 nM) for 4 hr. Total RNA was isolated using TRIZOL solution (Invitrogen, Carlsbad, CA). Briefly, after treatment, cells were washed twice in PBS and incubated with TRIZOL for 5 minutes at room temperature. RNA was extracted with 200 ul chloroform per ml TRIZOL and precipitated with 100% isopropanol at -20ºC. The RNA pellet was resuspended in DEPC-treated water and stored at –80ºC until further use. Human cDNA microarrays (Research Genetics/Invitrogen, Carlsbad, CA) consisted of nylon membranes containing 4,132 named genes EST’s (GF211). The array also contained 192 spots of total genomic DNA that served as reference points for the image analysis software Pathways 2.0 (Research Genetics/Invitrogen, Carlsbad, CA) for normalization purposes and to verify the homogeneity of the hybridization. cDNA probes were made from 5 micro-g total RNA with α[33P]-dATP (Amersham Biosciences, Piscataway, NJ) by oligo dT-primed polymerization using SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA). Probes were purified by gel chromatography (BioSpin 6; BioRad Laboratories, Hercules, CA), boiled for about 3 min and allowed to cool to room temperature. The microarrays were pre-hybridized for no less than 2 hr and then hybridized overnight at 42 oC. Filters were washed with 2xSSC and 1 % SDS for 15 min at 50 oC, and then with 0.5xSSC and 1% SDS twice for a total of 30 min at room temperature. Washed filters were then exposed to phosphor imager screens, which were scanned by a Molecular Dynamics Storm Imager (Packard Instruments, Meriden, CT) at 600 dpi resolution. Scanned files containing the microarray were analyzed with Pathways software (Invitrogen/Research Genetics, Carlsbad, CA). Pathways 2.0 (Research Genetics, Carlsbad, CA) and Bioconductor packages (http://www.bioconductor.org) were used to quantify the background intensity, normalize data (loess normalization), and determine actually expressed genes.
Keywords = Homo sapiens
Keywords = human micro vascular endothelial cell
Keywords = thrombospondin-1
Keywords = angiogenesis

source_name: Human micro vascular endothelial cells treated with TSP


title: HMVEC treated with Endostatin

description:
Total RNA was first isolated from HMVEC’s that had been incubated with endostatin (National Cancer Institute) at IC50 concentration (ENDO, 3 nM) for 4 hr. Total RNA was isolated using TRIZOL solution (Invitrogen, Carlsbad, CA). Briefly, after treatment, cells were washed twice in PBS and incubated with TRIZOL for 5 minutes at room temperature. RNA was extracted with 200 ul chloroform per ml TRIZOL and precipitated with 100% isopropanol at -20ºC. The RNA pellet was resuspended in DEPC-treated water and stored at –80ºC until further use. Human cDNA microarrays (Research Genetics/Invitrogen, Carlsbad, CA) consisted of nylon membranes containing 4,132 named genes EST’s (GF211). The array also contained 192 spots of total genomic DNA that served as reference points for the image analysis software Pathways 2.0 (Research Genetics/Invitrogen, Carlsbad, CA) for normalization purposes and to verify the homogeneity of the hybridization. cDNA probes were made from 5 micro-g total RNA with α[33P]-dATP (Amersham Biosciences, Piscataway, NJ) by oligo dT-primed polymerization using SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA). Probes were purified by gel chromatography (BioSpin 6; BioRad Laboratories, Hercules, CA), boiled for about 3 min and allowed to cool to room temperature. The microarrays were pre-hybridized for no less than 2 hr and then hybridized overnight at 42 oC. Filters were washed with 2xSSC and 1 % SDS for 15 min at 50 oC, and then with 0.5xSSC and 1% SDS twice for a total of 30 min at room temperature. Washed filters were then exposed to phosphor imager screens, which were scanned by a Molecular Dynamics Storm Imager (Packard Instruments, Meriden, CT) at 600 dpi resolution. Scanned files containing the microarray were analyzed with Pathways software (Invitrogen/Research Genetics, Carlsbad, CA). Pathways 2.0 (Research Genetics, Carlsbad, CA) and Bioconductor packages (http://www.bioconductor.org) were used to quantify the background intensity, normalize data (loess normalization), and determine actually expressed genes.
Keywords = Homo sapiens
Keywords = human micro vascular endothelial cell
Keywords = endostatin
Keywords = angiogenesis

source_name: Human micro vascular endothelial cells treated with Endostatin


title: HMVEC Control of Angiostatin

description:
Control RNA was extracted from untreated HMVEC. Total RNA was isolated using TRIZOL solution (Invitrogen, Carlsbad, CA). Briefly, after treatment, cells were washed twice in PBS and incubated with TRIZOL for 5 minutes at room temperature. RNA was extracted with 200 ul chloroform per ml TRIZOL and precipitated with 100% isopropanol at -20ºC. The RNA pellet was resuspended in DEPC-treated water and stored at –80ºC until further use. Human cDNA microarrays (Research Genetics/Invitrogen, Carlsbad, CA) consisted of nylon membranes containing 4,132 named genes EST’s (GF211). The array also contained 192 spots of total genomic DNA that served as reference points for the image analysis software Pathways 2.0 (Research Genetics/Invitrogen, Carlsbad, CA) for normalization purposes and to verify the homogeneity of the hybridization. cDNA probes were made from 5 micro-g total RNA with α[33P]-dATP (Amersham Biosciences, Piscataway, NJ) by oligo dT-primed polymerization using SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA). Probes were purified by gel chromatography (BioSpin 6; BioRad Laboratories, Hercules, CA), boiled for about 3 min and allowed to cool to room temperature. The microarrays were pre-hybridized for no less than 2 hr and then hybridized overnight at 42 oC. Filters were washed with 2xSSC and 1 % SDS for 15 min at 50 oC, and then with 0.5xSSC and 1% SDS twice for a total of 30 min at room temperature. Washed filters were then exposed to phosphor imager screens, which were scanned by a Molecular Dynamics Storm Imager (Packard Instruments, Meriden, CT) at 600 dpi resolution. Scanned files containing the microarray were analyzed with Pathways software (Invitrogen/Research Genetics, Carlsbad, CA). Pathways 2.0 (Research Genetics, Carlsbad, CA) and Bioconductor packages (http://www.bioconductor.org) were used to quantify the background intensity, normalize data (loess normalization), and determine actually expressed genes.
Keywords = Homo sapiens
Keywords = human micro vascular endothelial cell
Keywords = angiostatin
Keywords = angiogenesis


title: Germinal Center B cells; GC_40

source_name: Germinal Center B cells


title: HMVEC treated with RA

description:
Total RNA was first isolated from HMVEC’s that had been incubated with all trans-retinoic acid (Sigma, St. Louis, MO) at IC50 concentration (RA, 1 uM) for 4 hr.
Total RNA was isolated using TRIZOL solution (Invitrogen, Carlsbad, CA). Briefly, after treatment, cells were washed twice in PBS and incubated with TRIZOL for 5 minutes at room temperature. RNA was extracted with 200 ul chloroform per ml TRIZOL and precipitated with 100% isopropanol at -20ºC. The RNA pellet was resuspended in DEPC-treated water and stored at –80ºC until further use. Human cDNA microarrays (Research Genetics/Invitrogen, Carlsbad, CA) consisted of nylon membranes containing 4,132 named genes EST’s (GF211). The array also contained 192 spots of total genomic DNA that served as reference points for the image analysis software Pathways 2.0 (Research Genetics/Invitrogen, Carlsbad, CA) for normalization purposes and to verify the homogeneity of the hybridization. cDNA probes were made from 5 µg total RNA with α[33P]-dATP (Amersham Biosciences, Piscataway, NJ) by oligo dT-primed polymerization using SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA). Probes were purified by gel chromatography (BioSpin 6; BioRad Laboratories, Hercules, CA), boiled for about 3 min and allowed to cool to room temperature. The microarrays were pre-hybridized for no less than 2 hr and then hybridized overnight at 42 oC. Filters were washed with 2SSC and 1 % SDS for 15 min at 50 oC, and then with 0.5SSC and 1% SDS twice for a total of 30 min at room temperature. Washed filters were then exposed to phosphor imager screens, which were scanned by a Molecular Dynamics Storm Imager (Packard Instruments, Meriden, CT) at 600 dpi resolution. Scanned files containing the microarray were analyzed with Pathways software (Invitrogen/Research Genetics, Carlsbad, CA).
Keywords = Homo sapiens
Keywords = human micro vascular endothelial cell
Keywords = retinoic acid
Keywords = angiogenesis

source_name: Human micro vascular endothelial cells treated with RA


title: HMVEC Control of IFN

description:
Control RNA was extracted from untreated HMVEC. Total RNA was isolated using TRIZOL solution (Invitrogen, Carlsbad, CA). Briefly, after treatment, cells were washed twice in PBS and incubated with TRIZOL for 5 minutes at room temperature. RNA was extracted with 200 ul chloroform per ml TRIZOL and precipitated with 100% isopropanol at -20ºC. The RNA pellet was resuspended in DEPC-treated water and stored at –80ºC until further use. Human cDNA microarrays (Research Genetics/Invitrogen, Carlsbad, CA) consisted of nylon membranes containing 4,132 named genes EST’s (GF211). The array also contained 192 spots of total genomic DNA that served as reference points for the image analysis software Pathways 2.0 (Research Genetics/Invitrogen, Carlsbad, CA) for normalization purposes and to verify the homogeneity of the hybridization. cDNA probes were made from 5 micro-g total RNA with α[33P]-dATP (Amersham Biosciences, Piscataway, NJ) by oligo dT-primed polymerization using SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA). Probes were purified by gel chromatography (BioSpin 6; BioRad Laboratories, Hercules, CA), boiled for about 3 min and allowed to cool to room temperature. The microarrays were pre-hybridized for no less than 2 hr and then hybridized overnight at 42 oC. Filters were washed with 2xSSC and 1 % SDS for 15 min at 50 oC, and then with 0.5xSSC and 1% SDS twice for a total of 30 min at room temperature. Washed filters were then exposed to phosphor imager screens, which were scanned by a Molecular Dynamics Storm Imager (Packard Instruments, Meriden, CT) at 600 dpi resolution. Scanned files containing the microarray were analyzed with Pathways software (Invitrogen/Research Genetics, Carlsbad, CA). Pathways 2.0 (Research Genetics, Carlsbad, CA) and Bioconductor packages (http://www.bioconductor.org) were used to quantify the background intensity, normalize data (loess normalization), and determine actually expressed genes.
Keywords = Homo sapiens
Keywords = human micro vascular endothelial cell
Keywords = interferon
Keywords = angiogenesis


title: HMVEC treated with IFN

description:
Total RNA was first isolated from HMVEC’s that had been incubated with recombinant interferon-alpha (Biosource International, Camarillo, CA) at IC50 concentration (IFN, 50 IU/ml) for 4 hr.. Total RNA was isolated using TRIZOL solution (Invitrogen, Carlsbad, CA). Briefly, after treatment, cells were washed twice in PBS and incubated with TRIZOL for 5 minutes at room temperature. RNA was extracted with 200 ul chloroform per ml TRIZOL and precipitated with 100% isopropanol at -20ºC. The RNA pellet was resuspended in DEPC-treated water and stored at –80ºC until further use. Human cDNA microarrays (Research Genetics/Invitrogen, Carlsbad, CA) consisted of nylon membranes containing 4,132 named genes EST’s (GF211). The array also contained 192 spots of total genomic DNA that served as reference points for the image analysis software Pathways 2.0 (Research Genetics/Invitrogen, Carlsbad, CA) for normalization purposes and to verify the homogeneity of the hybridization. cDNA probes were made from 5 micro-g total RNA with α[33P]-dATP (Amersham Biosciences, Piscataway, NJ) by oligo dT-primed polymerization using SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA). Probes were purified by gel chromatography (BioSpin 6; BioRad Laboratories, Hercules, CA), boiled for about 3 min and allowed to cool to room temperature. The microarrays were pre-hybridized for no less than 2 hr and then hybridized overnight at 42 oC. Filters were washed with 2xSSC and 1 % SDS for 15 min at 50 oC, and then with 0.5xSSC and 1% SDS twice for a total of 30 min at room temperature. Washed filters were then exposed to phosphor imager screens, which were scanned by a Molecular Dynamics Storm Imager (Packard Instruments, Meriden, CT) at 600 dpi resolution. Scanned files containing the microarray were analyzed with Pathways software (Invitrogen/Research Genetics, Carlsbad, CA). Pathways 2.0 (Research Genetics, Carlsbad, CA) and Bioconductor packages (http://www.bioconductor.org) were used to quantify the background intensity, normalize data (loess normalization), and determine actually expressed genes.
Keywords = Homo sapiens
Keywords = human micro vascular endothelial cell
Keywords = interferon
Keywords = angiogenesis

source_name: Human micro vascular endothelial cells treated with IFN


title: HMVEC treated with Angiostatin

description:
Total RNA was first isolated from HMVEC’s that had been incubated with angiostatin (Dr. L. Holmgren, Karolinska Institute) at IC50 concentration (ANGIO, 50 nM) for 4 hr. Total RNA was isolated using TRIZOL solution (Invitrogen, Carlsbad, CA). Briefly, after treatment, cells were washed twice in PBS and incubated with TRIZOL for 5 minutes at room temperature. RNA was extracted with 200 ul chloroform per ml TRIZOL and precipitated with 100% isopropanol at -20ºC. The RNA pellet was resuspended in DEPC-treated water and stored at –80ºC until further use. Human cDNA microarrays (Research Genetics/Invitrogen, Carlsbad, CA) consisted of nylon membranes containing 4,132 named genes EST’s (GF211). The array also contained 192 spots of total genomic DNA that served as reference points for the image analysis software Pathways 2.0 (Research Genetics/Invitrogen, Carlsbad, CA) for normalization purposes and to verify the homogeneity of the hybridization. cDNA probes were made from 5 micro-g total RNA with α[33P]-dATP (Amersham Biosciences, Piscataway, NJ) by oligo dT-primed polymerization using SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA). Probes were purified by gel chromatography (BioSpin 6; BioRad Laboratories, Hercules, CA), boiled for about 3 min and allowed to cool to room temperature. The microarrays were pre-hybridized for no less than 2 hr and then hybridized overnight at 42 oC. Filters were washed with 2xSSC and 1 % SDS for 15 min at 50 oC, and then with 0.5xSSC and 1% SDS twice for a total of 30 min at room temperature. Washed filters were then exposed to phosphor imager screens, which were scanned by a Molecular Dynamics Storm Imager (Packard Instruments, Meriden, CT) at 600 dpi resolution. Scanned files containing the microarray were analyzed with Pathways software (Invitrogen/Research Genetics, Carlsbad, CA). Pathways 2.0 (Research Genetics, Carlsbad, CA) and Bioconductor packages (http://www.bioconductor.org) were used to quantify the background intensity, normalize data (loess normalization), and determine actually expressed genes.
Keywords = Homo sapiens
Keywords = human micro vascular endothelial cell
Keywords = angiostatin
Keywords = angiogenesis

source_name: Human micro vascular endothelial cells treated with Angiostatin