title: [6] Photo-Ox IMX-101, 58.2, Rep 2


title: [6] Photo-Ox IMX-101, 30.2, Rep 2

status: Public on Aug 25 2017

type: RNA

city: Vicksburg

first: Kurt

middle: A

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

country: USA

institute: US Army ERDC

hyb_protocol: All samples were hybridized to Agilent 8 x 60K, zebrafish microarrays (AMADID #36575).  Microarray hybridization experimental designs for IMX-101 exposures were completely randomized (using a random number generator) with factorial treatment arrangements contrasting parent versus UV-treated chemicals across each concentration series.  Exposure concentrations were selected to represent both sublethal concentrations and concentrations beyond the threshold of lethality to facilitate identification of mechanisms of toxicity.  The IMX-101 experiment included UV-treated and parent IMX-101 at the measured exposure concentrations:  3.8, 30.2 and 58.2 mg/L (measured concentrations) each including 4 exposure replicates, in addition to 4 control (0 mg/L) exposure replicates.  Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) and with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: An Agilent Surescan Microarray Scanner (G2505 C, Agilent Technologies Inc.) was used to scan microarrays at 2 μm resolution.

data_processing: Data were extracted from microarray images using Agilent Feature Extraction software (Agilent Technologies). Analysis of internal control spikes indicated that signal data was within the linear range of detection.  Microarray data were normalized to the 75th percentile within each array followed by median scaling among all exposures using GeneSpring Software version GX14.5 (Agilent Technologies). GeneSpring was additionally used to conduct ANOVA-based differential transcript expression analyses.  Two-way ANOVA was utilized to test the interactive potential between the UV-treatment and IMX-101 exposures on transcript expression. In the two-way ANOVA tests a p-value cutoff of 0.005 was utilized to identify significantly affected transcripts for the IMX-101 exposure, the UV treatment and the IMX-101 x UV treatment interaction.  In order to identify the specific differences in transcript expression between the parent IMX-101 and the UV-treated IMX-101, post hoc pairwise tests were conducted for all significant targets identified in the UV treatment and the IMX-101 x UV treatment interaction.  The post hoc analysis tested the effects of the UV-treated IMX-101 relative to the parent IMX-101 at each dose-level using a moderated t-test (p = 0.05) and a 1.5 fold change cut-off.

molecule: total RNA

organism: Danio rerio

source_name: whole animal

label_protocol: The Agilent Low-Input Quick Amp, One Color Microarray Hybridization protocol (Agilent Technologies) was utilized following manufacturer’s recommendations where 600 ng of total RNA served as the starting material for each biological replicate.

growth_protocol: Exposure chambers were 300-ml high-form lipless beakers with a test solution volume of 250 ml.  Ten larval fish per beaker were exposed in the parent and UV-treated IMX-101 exposures where all treatments included 4 exposure replicates.  Larval zebrafish were fed newly hatched Artemia nauplii two hours before the initiation of exposures and at the 48-h timepoint.

extract_protocol: Total RNA was extracted from 4 whole fish/replicate for all transcript expression experiments.  All samples were flash frozen upon collection and stored at -80 °C until RNA extraction.  Samples were homogenized in lysis buffer with a FAST Prep-24 instrument (MP Biomedicals, Santa Ana, CA) before RNA isolation with RNeasy kits (Qiagen, Valencia, CA). Total RNA concentrations were measured using a NanoDrop ND-1000 spectrophotometer (NanoDrop technologies, Wilmington, DE, USA). The integrity of total RNA was assessed on an Agilent 2100 Bioanalyzer (Palo Alto, CA).  Criteria for acceptable RNA integrity included a RNA integrity number >7.0 from the Agilent 2100 Bioanalyzer and a 260/280 spectrophotometric reading >2.0.

treatment_protocol: Zebrafish larvae were exposed to IMX-101 at  0, 3.8, 30.2 and 58.2 mg/L (measured concentrations) as the parent or UV-irradiated IMX-101.   Danio rerio larvae were exposed in static nonrenewal acute 96-h bioassays.  Exposure chambers were 300-ml high-form lipless beakers with a test solution volume of 250 ml.  Ten larval fish per beaker were exposed in the parent or UV-treated IMX-101 where all treatments included 4 exposure replicates.  Larval zebrafish were fed newly hatched Artemia nauplii two hours before the initiation of exposures and at the 48-h timepoint.  Surviving fish were enumerated daily and any fish found to be deceased were promptly removed from exposure chambers.

tag: tissue

value: larvae

tag: concentration

tag: treatment

value: Photo-Ox IMX-101


title: Chronic lymphocytic leukemia 32 first treatment

type: genomic

city: London

first: Jennifer

last: Edelmann

address: Charterhouse Square

department: Centre for Haemato-/Oncology

country: United Kingdom

institute: Barts Cancer Institute

description: Hybridized to GenomeWide SNP 6.0 array

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

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

data_processing:
CEL-files and chp-files (generated by Affymetrix GTYPE using the DM algorithm and by the birdseed algorithm in Affymetrix Genotyping Console version 4.0, respectively) were processed by dChip and model-based expression performed using the PM/MM model.
Signal' = Summarized signal; Genotype Call (SNP call): AA, AB, BB, NC, and NoCall

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: peripherel blood

label_protocol: As per manufacturer (Affymetrix®)

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations from peripheral blood using the Qiagen® DNA Blood Mini Kit (Hilden, Germany). Immunomagnetic tumor cell enrichment was performed for a subset of samples (Midi MACS, Miltenyi Biotec®; Bergisch Gladbach, Germany) so that 98 mononuclear cell fractions, 118 CD19-positive fractions, and 52 CD19-negative fractions were used. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

tag: cell type

value: mononuclear cells CD19+

tag: ighv mutational status

value: IgHV unmutated

tag: tp53 diruption

value: no TP53 disruption detected

tag: atm disruption

value: FCR

tag: best clinical response

value: complete remission


title: non-tumor liver CR562704

city: Philadelphia

first: Moses

middle: Morakortoi

last: Darpolor

state: PA

address: 423 Guardian Drive

department: Radiology

institute: University of Pennsylvania

description: Based on pathologist report of grouping stage IIIA.

hyb_protocol: Target hybridization was performed on Affymetrix Human GeneChip® Gene 1.0 ST Arrays (Affymetrix, Inc., Santa Clara, CA, USA) according to the manufacturer’s procedures in the GeneChip® Hybridization Oven 645, followed by washing and staining in the GeneChip® Fluidics Station 450.

scan_protocol: Data acquired with GeneChip®  Scanner 3000 7G (Affymetrix, Inc., Santa Clara, CA, USA)

data_processing:
The mean absolute deviation of residuals, mean absolute relative log expression, and the positive versus negative Receiver Operator Curve (ROC) Area under Curve (ROC) of the array data were metrics used to assess the overall data quality. The probe-level data (cel files) from all arrays were imported into Partek Genomics Suite software (Partek Incorporated, St. Louis, MO, USA) where RMA normalization was applied yielding log2-transformed expression intensities.
One-way ANOVA was performed on the genes across the 3 groups to provide p-values, and false positive rates were computed using the Benjamini-Hochberg step-up algorithm as implemented in Partek. Pairwise comparisons were made between tissues types providing p-values, log2 ratios, and fold-change values. Within-patient (i.e. tissues from the same human subject) log2 ratios and fold-changes were also calculated for the 3 patient sample pairs.

label: biotin allonamide triphosphate

source_name: non-tumor liver

label_protocol: Biotin Allonamide Triphosphate was used according to the standard Affymetrix protocol provided in 2012. The Ambion® WT Expression kit was used as suggested by the manufacturer to generate sense strand cDNA from 250 ng total RNA followed by fragmentation and labeling of 5.5 ug of sense strand cDNA with the GeneChip® Wt Terminal labeling kit.

extract_protocol: Homogenized lysate of human tissues (i.e. hepatocellular carcinoma, cirrhotic, and liver) were processed to obtain about 5 mg of high-quality total RNA using a RNeasy Midi Kit (QIAGEN, Valencia, CA, USA). The samples were obtained via tissue biorepository (OriGene Technologies, Inc., Rockville, MD, USA).  The RNA integrity and quality control of 2 mL sample was assessed with NanoDrop® ND-1000 UV spectrophotometer and Agilent® 2100 Bioanalyzer at the Molecular Profiling Facility at the University of Pennsylvania. Degraded samples were eliminated from the study based on the OD A260/A280 ratios, electrophoresis results, 28S/18S rRNA ratios, and RNA Integrity Number (RIN).

treatment_protocol: No treatment was involved with any of the patients.

tag: project id

tag: facility id

tag: sample id

value: liver

tag: gender

value: male

tag: age

tag: paired

value: B

tag: rin

tag: disease state

value: non-tumor liver


title: Chronic lymphocytic leukemia 32 post treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells

value: not annotated


title: Chronic lymphocytic leukemia 31 post treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: del(17p) and TP53mut

value: no ATM disruption detected


title: Chronic lymphocytic leukemia 31 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: partial remission


title: Chronic lymphocytic leukemia 32 paired normal

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19-


title: Chronic lymphocytic leukemia 30 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: hepatocellular carcinoma CR560983

source_name: hepatocellular carcinoma

value: C

value: hepatocellular carcinoma


title: [6] Photo-Ox IMX-101, Control, Rep 2

value: larvae

value: Photo-Ox IMX-101


title: [6] Photo-Ox IMX-101, 3.8, Rep 3


title: [6] Photo-Ox IMX-101, 3.8, Rep 1


title: [6] Photo-Ox IMX-101, 30.2, Rep 3


title: Cirrhosis of liver CR561125

source_name: Cirrhosis of liver

value: Cirrhosis of liver


title: [6] IMX-101, Control, Rep 2


title: Chronic lymphocytic leukemia 30 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+

value: IgHV mutated

value: FC


title: Chronic lymphocytic leukemia 29 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: [6] Photo-Ox IMX-101, Control, Rep 1


title: [6] Photo-Ox IMX-101, 3.8, Rep 2


title: [6] IMX-101, 58.2, Rep 3


title: Chronic lymphocytic leukemia 27 post treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: IgHV unmutated


title: [6] IMX-101, 58.2, Rep 4


title: Mock - 24h

city: Curitiba

first: Guilherme

middle: Ferreira

last: Silveira

address: Prof Algacyr Munhoz Máder

country: Brazil

institute: Instituto Carlos Chagas

description: RMA expression value derived from Expression Console software; core-gene analysis

hyb_protocol: Samples were hybridized with GeneChip Human Gene 1.0 ST Arrays (Affymetrix) and scanned at the LNLS- Campinas Brazil facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: The generated files were analyzed for quality by the software Expression Console (Affymetrix, Santa Clara, CA). The same software was used to normalize the data by the RMA method. Log-ratio between DENV3/5532 infected-mdDCs and mock-infected-mdDCs intensity signal values were generated and a list of differential expressed genes was obtained by using a 2 our higher fold-change. Data clustering was performed by the Cluster 3.0 software with a Euclidian’s distance. Tool for Analysis of GO Enrichments (TANGO), in Expander software was used to obtain a GO with statistical enhancer values of 0.05, and, NCBIEntrez Gene database (www.ncbi.nih.gov) and the Gene Ontology database (www.geneontology.org), to define the most relevant cell signaling and metabolic pathways during mdDC infection with DENV3 5532.

label: biotin

source_name: Mock-infected

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Monocyte-derived dendritic cells (mdDCs) were generated using peripheral blood from healthy volunteers after informed consent and approval of the FIOCRUZ Research Ethics Committee (number 514/09). Mononuclear cells were separated by density gradient using Lymphocyte Separation Medium (Lonza, Walkersville, USA) and CD14+ cells were purified by magnetic immunosorting (Miltenyi Biotec, Auburn, CA), according to the manufacturer’s recommendations. CD14+ cells were cultured for 6-7 days in RPMI 1640 medium containing 100 ng/mL interleukin-4 (IL-4) and 50 ng/mL granulocyte-monocyte colony stimulating factor (GM-CSF; PeproTech, Rocky Hill, NJ), 10% fetal bovine serum (FBS) and 100 IU/µg/mL of penicillin/streptomycin and 2 mM of L-Glutamine (Gibco-BRL, Grand Island, NY). The cultures were assessed by flow cytometry and only cultures with more than 80% of CD1a+ and less than 5% of CD14+ purity were used. C6/36 cells were grown in Leibovitz-15 medium supplemented with 5% FBS and 0.26% of tryptose and 25 µg/mL of gentamicin (all reagents from Gibco-BRL, Grand Island, NY).

extract_protocol: Cells were collected at 6, 12, 24 and 48 hours post infection (hpi) and used to extract total RNA using RNaesy Mini Kit according to the manufacturer’s recommendations (QIAGEN, Valencia, CA). The RNA of all ten mdDC cultures was pooled (75 µg of each) for microarray experiments and compared to mock infected cells using Human Gene 1.0 st v. 1 array GeneChip slides from Affymetrix (Santa Clara, CA). The RNA pool was processed as according to the manufacturer’s recommendations (Affymetrix, Santa Clara, CA) for the amplification and in vitro transcription, purification, tagging, hybridization and scanning of the slides (GeneChip® Scanner 3000).

treatment_protocol: Ten mdDCs cultures were mock-infected or infected with DENV3/5532 at an MOI of 5 for two hours in the absence of FBS. The viral inoculum was removed and cells were washed and cultured in RPMI 1640 plus 10% of FBS and 100 IU/µg/mL of penicillin/streptomycin (Gibco-BRL, Grand Island, NY).

tag: infection

value: mock

tag: time point

value: Dendrític Cells


title: Chronic lymphocytic leukemia 30 post treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells


title: [6] IMX-101, 58.2, Rep 2

tag: tissue

tag: concentration


title: Mock - 12h

tag: cell type


title: [6] IMX-101, Control, Rep 1

tag: treatment


title: Chronic lymphocytic leukemia 28 post treatment

description: Hybridized to GenomeWide SNP 6.0 array

tag: ighv mutational status

tag: tp53 diruption

value: no TP53 disruption detected

value: del(11q) and ATMmut

value: not annotated


title: Chronic lymphocytic leukemia 31 paired normal

description: Hybridized to GenomeWide SNP 6.0 array

tag: atm disruption

value: no ATM disruption detected

tag: best clinical response


title: Chronic lymphocytic leukemia 29 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: non-response


title: Chronic lymphocytic leukemia 29 paired normal

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19-


title: Chronic lymphocytic leukemia 28 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: FCR

value: partial remission


title: Chronic lymphocytic leukemia 28 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Mock - 06h


title: Mock - 48h


title: [6] IMX-101, 30.2, Rep 3

value: larvae


title: [6] IMX-101, 3.8, Rep 4


title: [6] IMX-101, 58.2, Rep 1


title: 5532 - 24h


title: 5532 - 06h


title: Chronic lymphocytic leukemia 26 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 26 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: 5532 - 48h


title: [6] IMX-101, 30.2, Rep 2


title: Chronic lymphocytic leukemia 27 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: del(17p) and TP53mut


title: [6] IMX-101, 30.2, Rep 1


title: [6] IMX-101, 3.8, Rep 3


title: CUTLL Resveratrol rep 3

city: New York

first: Alberto

last: Ambesi-Impiombato

state: NY

address: 1130 St. Nicholas Avenue

department: ICG

institute: Columbia University

description: replicate 3

hyb_protocol: hybridized to the Illumina HumanT-12v4 Expression BeadChip  Expression BeadChip  according to manufacturer’s protocol

scan_protocol: Standard scan according to manufacturer's protocol

data_processing: Raw gene expression data were log2 transformed and quantile-normalized using MATLAB.

source_name: CUTLL Cell Line

label_protocol: 10 ng of RNA from each sample was amplified using the Ovation PicoSL WTA System (NuGen), labeled by the Encore BiotinIL Module (NuGen)

growth_protocol: CUTLL1 cells were cultured in standard conditions in RPMI 1640 media supplemented with 10% FBS and 1% Penicillin/Streptomycin

extract_protocol: RNA isolation from cell lines was performed in 6 replicates using the RNeasy Micro kit (QIAGEN) according to manufacturer’s protocol.

treatment_protocol: CUTLL1 cells were treated with Withaferin A or DMSO for 24 hours.

tag: cell line

value: TALL Leukemia

value: Resveratrol 24h


title: wt Col inflorescence sRNA seq

type: SRA

city: Columbus

first: R. Keith

last: Slotkin

state: OH

address: 500 Aronoff Laboratory, 318 W. 12th Ave.

department: Molecular Genetics

institute: The Ohio State University

library_source: transcriptomic

data_processing:
Illumina software was used for basecalling. Sequenced reads were de-multiplexed and trimmed for adaptor sequence. Sequences were masked for low-quality sequence and filtered for reads 18-28 nt in size (UEA small RNA tool v 2.5.0 used).
Wig files represent bowtie alignments of siRNA to the transgene T-DNA sequence, normalized to reads per milllion, at each base.  Tracks were created for combined 21 and 22 nt size class as well as 24 nt size class for both sense and antisense strand.
Genome_build: TAIR10 + iTto transgene sequence
Supplementary_files_format_and_content: First column: small RNA sequence. Second column: normalized abundance (Reads per million) of the small RNA.

organism: Arabidopsis thaliana

source_name: stage 1-12 inflorescence

growth_protocol: Plants were grown on soil in 18 hour long days at 23ºC.

extract_protocol: For the total RNA libraries, total RNA was extracted using Trizol reagent and enriched using the MirVana microRNA isolation kit. Cloning of small RNAs was performed using the Illumina TruSeq RNA Sample Preparation Kit

treatment_protocol: No estradiol spraying protocol was used for this control

tag: ecotype

value: Col


title: Chronic lymphocytic leukemia 27 pre treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: IgHV unmutated


title: [6] IMX-101, 30.2, Rep 4


title: Chronic lymphocytic leukemia 26 pre treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Photo-Ox IMX-101, 58.2, Rep 4

hyb_protocol: All samples were hybridized to Agilent 8 x 60K, zebrafish microarrays (AMADID #36575).  Microarray hybridization experimental designs for UV-treated IMX-101 exposures were completely randomized (using a random number generator).  Exposure concentrations were selected to represent both sublethal concentrations and concentrations beyond the threshold of lethality to facilitate identification of mechanisms of toxicity.  The UV-treated IMX-101 experiment included the measured exposure concentrations:  3.8, 30.2 and 85.2 mg/L (measured concentrations) each including 4 replicates, in addition to 4 control (0 mg/L) exposure replicates.  Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) and with 37°C GE Wash buffer 2 (Agilent).

data_processing: Data were extracted from microarray images using Agilent Feature Extraction software (Agilent Technologies). Analysis of internal control spikes indicated that signal data was within the linear range of detection.  Microarray data were normalized to the 75th percentile within each array followed by median scaling among all exposures using GeneSpring Software version GX14.5 (Agilent Technologies). GeneSpring was additionally used to conduct statistical analyses including gene set enrichment analysis (GSEA) and ANOVA-based differential transcript expression analyses.  For the GSEA analysis, the “50 hallmark gene sets” developed and curated by the Broad Institute (Liberzon et al 2015) were used to provide exploratory screening for biological processes affected by the UV-treated IMX-101 exposure.  Algorithm parameters included a minimum of 15 matching genes within a gene set, a maximum number of 100 permutations and a false discovery rate q-value cut off ≤ 0.3.  In order to rank the importance of significant gene sets identified by GSEA, composite scores were developed using four criteria derived from the GSEA output where significant p-value (p = 0.05), significant q-value (p = 0.3), an enrichment score > |0.5|, and a normalized enrichment score > |1.5| each received scores of 0 or 1 depending if the criteria were met. Additionally, ANOVA-based differential transcript expression was also conducted where one-way was used to ANOVA assess the effects of UV-treated IMX-101 exposure on transcript expression relative to controls.  In the one-way ANOVA test, a p-value cutoff of 0.005 was utilized to identify significantly affected transcripts followed by post hoc pairwise tests comparing expression for each dose-level relative to controls by moderated t-test (p = 0.05) and a 1.5 fold change cut-off.

growth_protocol: Exposure chambers were 300-ml high-form lipless beakers with a test solution volume of 250 ml.  Ten larval fish per beaker were exposed in the IMX-101 exposures where all treatments included 4 exposure replicates.  Larval zebrafish were fed newly hatched Artemia nauplii two hours before the initiation of exposures and at the 48-h timepoint.

treatment_protocol: Zebrafish larvae were exposed to UV-treated IMX-101 at  0, 3.8, 30.2 and 58.2 mg/L (initial measured concentrations prior to UV-treatment).  Danio rerio larvae were exposed in static nonrenewal acute 96-h bioassays.  Exposure chambers were 300-ml high-form lipless beakers with a test solution volume of 250 ml.  Ten larval fish per beaker were exposed to UV-treated IMX-101 where all treatments included 4 exposure replicates.  Larval zebrafish were fed newly hatched Artemia nauplii two hours before the initiation of exposures and at the 48-h timepoint.  Surviving fish were enumerated daily and any fish found to be deceased were promptly removed from exposure chambers.

value: Photo-Ox IMX-101


title: CUTLL Resveratrol rep 1

description: replicate 1


title: [6] IMX-101, 3.8, Rep 2


title: CUTLL Wortmannin rep 1

description: replicate 1

value: Wortmannin 24h


title: [6] IMX-101, 3.8, Rep 1


title: CUTLL Wortmannin rep 2

description: replicate 2


title: Photo-Ox IMX-101, 58.2, Rep 2


title: CUTLL Resveratrol rep 2

description: replicate 2


title: CUTLL Wortmannin rep 3

description: replicate 3


title: 5532 - 12h

value: Dendrític Cells


title: Photo-Ox IMX-101, 58.2, Rep 1


title: Photo-Ox IMX-101, 58.2, Rep 3


title: Chronic lymphocytic leukemia 25 paired normal

description: Hybridized to GenomeWide SNP 6.0 array

value: no TP53 disruption detected


title: Photo-Ox IMX-101, 30.2, Rep 4


title: Chronic lymphocytic leukemia 25 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+


title: CUTLL Phenoxibenzamine rep 1

description: replicate 1

value: Phenoxibenzamine 24h


title: Photo-Ox IMX-101, 30.2, Rep 3


title: Photo-Ox IMX-101, 30.2, Rep 2


title: PC3 EV exp2_rep4

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The bead-level data were preprocessed using BASH (Cairns et al. (2008) Bioinformatics 24(24):2921-2), a function from the beadarray package (Dunning et al (2007) Bioinformatics 23(16):2183-4) in Bioconductor, and also log base 2 transformed and quantile normalised using the beadarray package.

source_name: PC3_over-expressing empty vector EV

label_protocol: cRNA was generated and biotin labelled using the Illumina TotalPrep RNA Amplification Kit

growth_protocol: Cells were grown in RPMI medium supplemented with 10% Foetal Bovine Serum and 100 µg/ml geneticin, and passaged at 70% confluence using 0.25% Trypsin EDTA.

extract_protocol: RNA was extracted using RiboPure kits (Ambion), according to instructions.

treatment_protocol: Stable cell lines were grown to max 70 % confluence and then harvested for RNA extraction.

tag: genotype/variation

value: over-expressing empty vector EV


title: CUTLL Phenoxibenzamine rep 3

description: replicate 3


title: PC3 EV exp2_rep3


title: PC3 HNF1B exp2_rep2

source_name: PC3_over-expressing HNF1B

value: over-expressing HNF1B


title: Photo-Ox IMX-101, 30.2, Rep 1


title: CUTLL Trifluoperazine rep 3

description: replicate 3

value: Trifluoperazine 24h


title: CUTLL Phenoxibenzamine rep 2

description: replicate 2


title: Chronic lymphocytic leukemia 25 pre treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells

value: no ATM disruption detected

value: not annotated


title: CUTLL Trifluoperazine rep 2

description: replicate 2


title: Chronic lymphocytic leukemia 24 paired normal

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19-


title: CUTLL Trifluoperazine rep 1

description: replicate 1

value: TALL Leukemia


title: Photo-Ox IMX-101, 3.8, Rep 4

value: larvae


title: CUTLL Thioridazine rep 3

description: replicate 3

value: Thioridazine 24h


title: Photo-Ox IMX-101, 3.8, Rep 3


title: Chronic lymphocytic leukemia 25 post treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: IgHV unmutated


title: Chronic lymphocytic leukemia 23 pre treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: PC3 HNF1B exp2_rep1


title: Chronic lymphocytic leukemia 23 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: FC

value: missing response


title: Chronic lymphocytic leukemia 24 pre treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: PC3 HNF1B exp2_rep3


title: Chronic lymphocytic leukemia 22 post treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: del(17p) and TP53mut


title: Photo-Ox IMX-101, 3.8, Rep 2

value: Photo-Ox IMX-101


title: CUTLL Thioridazine rep 1

description: replicate 1


title: PC3 EV exp2_rep1


title: Chronic lymphocytic leukemia 24 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+

value: no TP53 disruption detected

value: FCR

value: partial remission


title: CUTLL Thioridazine rep 2

description: replicate 2


title: Photo-Ox IMX-101, 3.8, Rep 1


title: PC3 EV exp2_rep2

value: over-expressing empty vector EV


title: Chronic lymphocytic leukemia 22 pre treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells


title: Chronic lymphocytic leukemia 23 post treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: no ATM disruption detected


title: PC3 EV exp1_rep2


title: CUTLL Valproic acid rep 3

description: replicate 3

value: Valproic acid 24h


title: Photo-Ox IMX-101, Control, Rep 4


title: Photo-Ox IMX-101, Control, Rep 3


title: PC3 HNF1B exp2_rep4

value: over-expressing HNF1B


title: PC3 HNF1B exp1_rep2


title: CUTLL Valproic acid rep 1

description: replicate 1

value: TALL Leukemia


title: PC3 EV exp1_rep1


title: Photo-Ox IMX-101, Control, Rep 2

value: larvae


title: PC3 EV exp1_rep3


title: CUTLL Valproic acid rep 2

description: replicate 2


title: Photo-Ox IMX-101, Control, Rep 1


title: Chronic lymphocytic leukemia 21 post treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: IgHV mutated

value: not annotated


title: Chronic lymphocytic leukemia 24 post treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: IgHV unmutated


title: Chronic lymphocytic leukemia 21 paired normal

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19-


title: Chronic lymphocytic leukemia 21 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: FC


title: PC3 HNF1B exp1_rep3


title: CUTLL Parthenolide rep 2

description: replicate 2

value: Parthenolide 24h


title: IMX-101, Control, Rep 4

hyb_protocol: All samples were hybridized to Agilent 8 x 60K, zebrafish microarrays (AMADID #36575).  Microarray hybridization experimental designs for IMX-101 exposures were completely randomized (using a random number generator).  Exposure concentrations were selected to represent both sublethal concentrations and concentrations beyond the threshold of lethality to facilitate identification of mechanisms of toxicity.  The IMX-101 experiment included the measured exposure concentrations:  3.8, 30.2 and 85.2 mg/L (measured concentrations) each including 4 replicates, in addition to 4 control (0 mg/L) exposure replicates.  Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) and with 37°C GE Wash buffer 2 (Agilent).

data_processing: Data were extracted from microarray images using Agilent Feature Extraction software (Agilent Technologies). Analysis of internal control spikes indicated that signal data was within the linear range of detection.  Microarray data were normalized to the 75th percentile within each array followed by median scaling among all exposures using GeneSpring Software version GX14.5 (Agilent Technologies). GeneSpring was additionally used to conduct statistical analyses including gene set enrichment analysis (GSEA) and ANOVA-based differential transcript expression analyses.  GSEA was conducted for IMX-101.  The “50 hallmark gene sets” developed and curated by the Broad Institute (Liberzon et al 2015) were used to provide exploratory screening for biological processes affected by the IMX-101 exposure.  Algorithm parameters included a minimum of 15 matching genes within a gene set, a maximum number of 100 permutations and a false discovery rate q-value cut off ≤ 0.3.  In order to rank the importance of significant gene sets identified by GSEA, composite scores were developed using four criteria derived from the GSEA output where significant p-value (p = 0.05), significant q-value (p = 0.3), an enrichment score > |0.5|, and a normalized enrichment score > |1.5| each received scores of 0 or 1 depending if the criteria were met. Additionally, one-way ANOVA was conducted to assess the effects on transcript expression relative to controls.  In the one-way ANOVA tests a p-value cutoff of 0.005 was utilized to identify significantly affected transcripts followed by post hoc pairwise tests comparing expression for each dose-level relative to controls by moderated t-test (p = 0.05) and a 1.5 fold change cut-off.

treatment_protocol: Zebrafish larvae were exposed to IMX-101 at 0, 3.8, 30.2 and 58.2 mg/L (measured concentrations).  Danio rerio larvae were exposed in static nonrenewal acute 96-h bioassays.  Exposure chambers were 300-ml high-form lipless beakers with a test solution volume of 250 ml.  Ten larval fish per beaker were exposed to IMX-101 where all treatments included 4 exposure replicates.  Larval zebrafish were fed newly hatched Artemia nauplii two hours before the initiation of exposures and at the 48-h timepoint.  Surviving fish were enumerated daily and any fish found to be deceased were promptly removed from exposure chambers.


title: CUTLL Parthenolide rep 1

description: replicate 1


title: IMX-101, Control, Rep 2


title: PC3 HNF1B exp1_rep1


title: Chronic lymphocytic leukemia 20 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: IMX-101, Control, Rep 3


title: CUTLL Rapamycin rep 3

description: replicate 3

value: Rapamycin 24h


title: CUTLL Rapamycin rep 2

description: replicate 2


title: IMX-101, Control, Rep 1


title: CUTLL Parthenolide rep 3

description: replicate 3


title: Humanized 3F8 -- Anti-GD2 Antibody hu3F8_5

type: protein

city: Frederick

first: Jeff

last: Gildersleeve

state: MD

address: 376 Boyles St.

institute: National Cancer Institute

hyb_protocol: Arrays were blocked with BSA overnight, and serum samples (diluted 1:50) was incubated on the array for 4 hours at 37 C and gentle agitation (100 RPM).  Slides were then washed with PBS contain 0.05% Tween (PBST).  After washing, bound antibodies were detected with fluorescently labeled secondary antibodies.  Slides were then washed with PBST, spun dry in a centrifuge, and scanned.

scan_protocol: Slides were scanned with a Genepix 4000A fluorescence scanner at two gain settings (typically 430 and 520) in order to increase dynamic range.  Signal from ch1 (532 nm) was analyzed to determine the level of bound DyLight 549 conjugated secondary antibody specific for human IgG.  Signal from ch2 (635nm) was analyzed to determine the level of bound DyLight 649 secondary antibody specific for human IgM.  Scanned images were analyzed with Genepix Pro (v6.0) to determine the fluorescence and background signal for each array component.

data_processing: First, median pixel intensity of each feature was background subtracted.  Second, signals for features that were saturated at the high photomultipler tube (PMT) setting were calculated by proportionally scaling the value from the low PMT setting according to a correction factor, which was calculated based on mid-intensity signals measured at the high and low PMT settings.  To account for slide-to-slide variations in array processing, microarray data were normalized by median centering based on a reference serum sample analyzed on each slide.  Additionally, a minimum signal of 150 was set as the floor.  Since array features were printed in duplicate and all samples were analyzed on two slides, pre-processing averaged normalized data from 4 technical replicates.  Final data are reported on a log 2 scale.

molecule: protein

label_protocol: After serum was incubated on the array, bound anti-glycan antibodies were labeled for 2 hours with a combination of DyLight549 conjugated anti-human IgG (Jackson 109-505-008) and DyLight 649 conjugated anti-human IgM  (Jackson Immuno, 109-495-043).

extract_protocol: Serum was obtained from peripheral blood samples

tag: antibody concentration [nm]

tag: antibody

value: IgG

label: DyLight 649

value: IgM


title: Humanized 3F8 -- Anti-GD2 Antibody hu3F8_7


title: Chronic lymphocytic leukemia 21 pre treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: no TP53 disruption detected


title: Chronic lymphocytic leukemia 20 post treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 20 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+

value: FCR

value: complete remission


title: Humanized 3F8 -- Anti-GD2 Antibody hu3F8_3


title: Humanized 3F8 -- Anti-GD2 Antibody hu3F8_4


title: Humanized 3F8 -- Anti-GD2 Antibody hu3F8_6


title: Humanized 3F8 -- Anti-GD2 Antibody hu3F8_2


title: CUTLL Rapamycin rep 1

description: replicate 1


title: IMX-101, 58.2, Rep 3


title: IMX-101, 58.2, Rep 2


title: CUTLL Trichostatin A rep 2

description: replicate 2

value: Trichostatin A 24h


title: CUTLL Trichostatin A rep 3

description: replicate 3


title: Chronic lymphocytic leukemia 19 paired normal

description: Hybridized to GenomeWide SNP 6.0 array

value: no ATM disruption detected


title: Humanized 3F8 -- Anti-GD2 Antibody hu3F8_1


title: IMX-101, 58.2, Rep 4


title: IMX-101, 58.2, Rep 1


title: Germline 14.18 -- Anti-GD2 Antibody gl14.18_7

description: Chimeric mouse-human

organism:
Homo sapiens
Mus musculus


title: Chronic lymphocytic leukemia 19 post treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells

value: ATMmut


title: CUTLL Trichostatin A rep 1

description: replicate 1

value: TALL Leukemia


title: Chronic lymphocytic leukemia 22 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: del(17p) and TP53mut

value: partial remission


title: Germline 14.18 -- Anti-GD2 Antibody gl14.18_6

description: Chimeric mouse-human


title: IMX-101, 30.2, Rep 4

value: larvae


title: Chronic lymphocytic leukemia 20 pre treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: IgHV mutated

value: not annotated


title: Germline 14.18 -- Anti-GD2 Antibody gl14.18_4

description: Chimeric mouse-human


title: CUTLL DMSO rep 2

description: replicate 2

value: DMSO 24h


title: IMX-101, 30.2, Rep 3


title: IMX-101, 30.2, Rep 2


title: Chronic lymphocytic leukemia 18 post treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: IgHV unmutated

value: del(11q) and ATMmut


title: CUTLL DMSO rep 3

description: replicate 3


title: CUTLL Mefloquine rep 3

description: replicate 3

value: Mefloquine 24h


title: Chronic lymphocytic leukemia 19 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+

value: no TP53 disruption detected

value: FC


title: CUTLL DMSO rep 1

description: replicate 1


title: Germline 14.18 -- Anti-GD2 Antibody gl14.18_3

description: Chimeric mouse-human

value: IgG

value: IgM


title: Germline 14.18 -- Anti-GD2 Antibody gl14.18_5

description: Chimeric mouse-human


title: Germline 14.18 -- Anti-GD2 Antibody gl14.18_1

description: Chimeric mouse-human


title: Chronic lymphocytic leukemia 18 pre treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells


title: IMX-101, 3.8, Rep 4


title: IMX-101, 30.2, Rep 1


title: CUTLL Astemizole rep 3

description: replicate 3

value: Astemizole 24h


title: Germline 14.18 -- Anti-GD2 Antibody gl14.18_2

description: Chimeric mouse-human


title: Chronic lymphocytic leukemia 16 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: no ATM disruption detected

value: FCR


title: IMX-101, 3.8, Rep 2


title: Chronic lymphocytic leukemia 16 pre treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 17 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: CUTLL Mefloquine rep 2

description: replicate 2

value: TALL Leukemia


title: IMX-101, 3.8, Rep 1

value: larvae


title: CUTLL Mefloquine rep 1

description: replicate 1


title: Chronic lymphocytic leukemia 18 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: partial remission


title: Germline 3F8 -- Anti-GD2 Antibody gl3F8_7

description: Chimeric mouse-human


title: Germline 3F8 -- Anti-GD2 Antibody gl3F8_6

description: Chimeric mouse-human


title: CUTLL Astemizole rep 2

description: replicate 2


title: IMX-101, 3.8, Rep 3


title: CUTLL Astemizole rep 1

description: replicate 1


title: [3] Photo ox NQ, 90.4, Rep 4

hyb_protocol: All samples were hybridized to Agilent 8 x 60K, zebrafish microarrays (AMADID #36575).  Microarray hybridization experimental designs for NQ exposures were completely randomized (using a random number generator) with factorial treatment arrangements contrasting parent versus UV-treated NQ across each concentration series.  Exposure concentrations were selected to represent both sublethal concentrations and concentrations beyond the threshold of lethality to facilitate identification of mechanisms of toxicity.  The NQ experiment included UV-treated and parent NQ at the measured exposure concentrations:  5.5, 45.6 and 90.4 mg/L each including at least 4 replicates, in addition to 6 control (0 mg/L) exposure replicates.  Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) and with 37°C GE Wash buffer 2 (Agilent).

data_processing: Data were extracted from microarray images using Agilent Feature Extraction software (Agilent Technologies). Analysis of internal control spikes indicated that signal data was within the linear range of detection.  Microarray data were normalized to the 75th percentile within each array followed by median scaling among all exposures using GeneSpring Software version GX14.5 (Agilent Technologies). GeneSpring was additionally used to conduct statistical analyses including ANOVA-based differential transcript expression analyses.  Two-way ANOVA was utilized to test the interactive potential between the UV-treatment NQ and parent NQ exposures on transcript expression.  In the two-way ANOVA test, a p-value cutoff of 0.005 was utilized to identify significantly affected transcripts for the NQ exposure, the UV treatment and the NQ x UV treatment interaction.  In order to identify the specific differences in transcript expression between the parent NQ and the UV-treated NQ, post hoc pairwise tests were conducted for all significant targets identified in the UV treatment and the NQ x UV treatment interaction.  The post hoc analysis tested the effects of the UV-treated NQ relative to the parent NQ at each dose-level using a moderated t-test (p = 0.05) and a 1.5 fold change cut-off.

growth_protocol: Exposure chambers were 300-ml high-form lipless beakers with a test solution volume of 250 ml.  Eight larval fish per beaker were exposed in the parent or UV-treated NQ treatments each including at least 4 exposure replicates and 6 control exposure replicates.  Larval zebrafish were fed newly hatched Artemia nauplii two hours before the initiation of exposures and at the 48-h timepoint.

treatment_protocol: Zebrafish larvae were exposed to NQ at 0, 5.5, 45.6, and 90.4 mg/L (measured concentrations) as the parent or UV-irradiated IMX-101.   Danio rerio larvae were exposed in static nonrenewal acute 96-h bioassays.  Exposure chambers were 300-ml high-form lipless beakers with a test solution volume of 250 ml.  Eight larval fish per beaker were exposed in the parent or UV-treated NQ treatments each including at least 4 exposure replicates and 6 control replicates.  Larval zebrafish were fed newly hatched Artemia nauplii two hours before the initiation of exposures and at the 48-h timepoint.  Surviving fish were enumerated daily and any fish found to be deceased were promptly removed from exposure chambers.

value: Photo ox NQ


title: Germline 3F8 -- Anti-GD2 Antibody gl3F8_4

description: Chimeric mouse-human


title: Germline 3F8 -- Anti-GD2 Antibody gl3F8_3

description: Chimeric mouse-human


title: CUTLL Prochlorperazine rep 3

description: replicate 3

value: Prochlorperazine 24h


title: [3] Photo ox NQ, 90.4, Rep 3


title: CUTLL Prochlorperazine rep 2

description: replicate 2


title: [3] Photo ox NQ, 90.4, Rep 1


title: [3] Photo ox NQ, 90.4, Rep 2


title: Chronic lymphocytic leukemia 15 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: IgHV mutated

value: not annotated


title: [3] Photo ox NQ, 45.6, Rep 5


title: Chronic lymphocytic leukemia 16 paired normal

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19-


title: Germline 3F8 -- Anti-GD2 Antibody gl3F8_2

description: Chimeric mouse-human


title: Germline 3F8 -- Anti-GD2 Antibody gl3F8_1

description: Chimeric mouse-human


title: CUTLL Withaferin A rep 3

description: replicate 3

value: Withaferin A 24h


title: CUTLL Withaferin A rep 2

description: replicate 2


title: Affinity Mature 3F8 -- Anti-GD2 Antibody ch3F8_7

description: Chimeric mouse-human


title: Chronic lymphocytic leukemia 14 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+

value: no TP53 disruption detected


title: Chronic lymphocytic leukemia 19 pre treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: IgHV unmutated

value: ATMmut


title: Chronic lymphocytic leukemia 14 pre treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells


title: CUTLL Withaferin A rep 1

description: replicate 1


title: [3] Photo ox NQ, 45.6, Rep 4


title: Chronic lymphocytic leukemia 13 pre treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: CUTLL Lanatoside C rep 3

description: replicate 3

value: Lanatoside C 24h


title: Affinity Mature 3F8 -- Anti-GD2 Antibody ch3F8_6

description: Chimeric mouse-human

value: IgG

value: IgM


title: [3] Photo ox NQ, 45.6, Rep 2


title: Chronic lymphocytic leukemia 12 pre treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: no ATM disruption detected


title: Affinity Mature 3F8 -- Anti-GD2 Antibody ch3F8_5

description: Chimeric mouse-human


title: Germline 3F8 -- Anti-GD2 Antibody gl3F8_5

description: Chimeric mouse-human


title: Affinity Mature 3F8 -- Anti-GD2 Antibody ch3F8_4

description: Chimeric mouse-human


title: Chronic lymphocytic leukemia 15 pre treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: CUTLL Lanatoside C rep 2

description: replicate 2

value: TALL Leukemia


title: [3] Photo ox NQ, 45.6, Rep 1

value: larvae


title: Chronic lymphocytic leukemia 13 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: del(11q) and ATMmut

value: FC


title: Chronic lymphocytic leukemia 10 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: IgHV mutated


title: Affinity Mature 3F8 -- Anti-GD2 Antibody ch3F8_3

description: Chimeric mouse-human


title: [3] Photo ox NQ, 45.6, Rep 3

value: Photo ox NQ


title: CUTLL Lanatoside C rep 1

description: replicate 1


title: [3] Photo ox NQ, 5.5, Rep 4


title: [3] Photo ox NQ, 5.5, Rep 3


title: CUTLL Geldanamycin rep 3

description: replicate 3

value: Geldanamycin 24h


title: Affinity Mature 3F8 -- Anti-GD2 Antibody ch3F8_1

description: Chimeric mouse-human


title: Chronic lymphocytic leukemia 11 pre treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: not annotated


title: Affinity Mature 3F8 -- Anti-GD2 Antibody ch3F8_2

description: Chimeric mouse-human


title: CUTLL Geldanamycin rep 1

description: replicate 1


title: [3] Photo ox NQ, 5.5, Rep 2


title: CUTLL Prochlorperazine rep 1

description: replicate 1

value: Prochlorperazine 24h


title: [3] Photo ox NQ, 5.5, Rep 1


title: Chronic lymphocytic leukemia 11 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+

value: no TP53 disruption detected


title: 3F8 (HC:I56S) -- Anti-GD2 Antibody 3F8(HC-I56S)_7


title: Chronic lymphocytic leukemia 8 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: FCR


title: [3] NQ, Control, Rep 3

value: NQ


title: Chronic lymphocytic leukemia 9 pre treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells

value: IgHV unmutated


title: CUTLL Geldanamycin rep 2

description: replicate 2


title: CUTLL Vorinostat rep 2

description: replicate 2

value: Vorinostat 24h


title: CUTLL Vorinostat rep 1

description: replicate 1


title: [3] Photo ox NQ, 5.5, Rep 5


title: [3] Photo ox NQ, Control, Rep 3


title: CUTLL Vorinostat rep 3

description: replicate 3


title: 3F8 (HC:I56S) -- Anti-GD2 Antibody 3F8(HC-I56S)_5

value: IgG

value: IgM


title: 3F8 (HC:I56S) -- Anti-GD2 Antibody 3F8(HC-I56S)_4


title: Chronic lymphocytic leukemia 12 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: no ATM disruption detected


title: Chronic lymphocytic leukemia 8 pre treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: 3F8 (HC:I56S) -- Anti-GD2 Antibody 3F8(HC-I56S)_6


title: [3] NQ, Control, Rep 2

value: larvae


title: 3F8 (HC:I56S) -- Anti-GD2 Antibody 3F8(HC-I56S)_3


title: Chronic lymphocytic leukemia 17 pre treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: [3] Photo ox NQ, Control, Rep 2


title: 3F8 (HC:I56S) -- Anti-GD2 Antibody 3F8(HC-I56S)_2


title: Chronic lymphocytic leukemia 9 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: CUTLL Pyrvinium P rep 3

description: replicate 3

value: TALL Leukemia

value: Pyrvinium P 24h


title: 3F8 (HC:I56S) -- Anti-GD2 Antibody 3F8(HC-I56S)_1


title: Chronic lymphocytic leukemia 7 pre treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Affinity mature ch14.18 -- Anti-GD2 Antibody ch14.18_13

description:
ch14.18_13
Chimeric mouse-human


title: Affinity mature ch14.18 -- Anti-GD2 Antibody ch14.18_14

description:
ch14.18_14
Chimeric mouse-human


title: CUTLL Pyrvinium P rep 1

description: replicate 1


title: [3] NQ, 90.4, Rep 4


title: CUTLL Withaferin A rep 6

description: replicate 6

value: Withaferin A 24h


title: CUTLL Pyrvinium P rep 2

description: replicate 2


title: [3] NQ, 90.4, Rep 2


title: CUTLL Withaferin A rep 4

description: replicate 4


title: [3] NQ, Control, Rep 1


title: CUTLL Withaferin A rep 5

description: replicate 5


title: Chronic lymphocytic leukemia 6 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: IgHV mutated


title: Chronic lymphocytic leukemia 6 pre treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: not annotated


title: [3] NQ, 90.4, Rep 3


title: CUTLL Withaferin A rep 3

description: replicate 3


title: Chronic lymphocytic leukemia 10 pre treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 7 first treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 5 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: ATMmut

value: FC


title: CUTLL Withaferin A rep 1

description: replicate 1


title: Chronic lymphocytic leukemia 4 paired normal

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19-

value: no TP53 disruption detected


title: Affinity mature ch14.18 -- Anti-GD2 Antibody ch14.18_12

description:
ch14.18_12
Chimeric mouse-human


title: Affinity mature ch14.18 -- Anti-GD2 Antibody ch14.18_11

description:
ch14.18_11
Chimeric mouse-human


title: Affinity mature ch14.18 -- Anti-GD2 Antibody ch14.18_9

description:
ch14.18_9
Chimeric mouse-human


title: [3] NQ, 45.6, Rep 4

value: NQ


title: CUTLL Withaferin A rep 2

description: replicate 2


title: [3] NQ, 45.6, Rep 2


title: Affinity mature ch14.18 -- Anti-GD2 Antibody ch14.18_8

description:
ch14.18_8
Chimeric mouse-human


title: Chronic lymphocytic leukemia 5 pre treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells


title: CUTLL DMSO rep 6

description: replicate 6

value: DMSO 24h


title: Indian Hedgehog knockout colon 3

city: Amsterdam

first: Barbara

middle: Florien

last: Westendorp

state: Noord-Holland

address: Meibergdreef 69-71

department: Tytgat Institute for Liver and Intestinal Research

country: Netherlands

institute: Academic Medical Center

description:
Gene expression in the colon that were isolated 7 days after inactivation of the Hedgehog pathway
9257636071_G

hyb_protocol: Whole genome gene expression direct hybridisation of cRNA assay

scan_protocol: Standard Illumina differential expression on Illumina Bead Array Reader (BAR)

data_processing: Genome studio

organism: Mus musculus

source_name: Indian Hedgehog knockout colon

label_protocol: Illumina TotalPrep RNA amplification was used

extract_protocol: RNA from the colons was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Villin-CreERT2-Ihh+/+ and Villin-CreERT2-Ihhfl/fl mice were intraperitoneally injected with 1 mg tamoxifen for 5 consecutive days. At day 7 animals were sacificed and colons were isolated.

tag: strain background

value: Indian Hedgehog knockout

tag: injected with

value: 1 mg tamoxifen for 5 days

value: whole colon


title: Affinity mature ch14.18 -- Anti-GD2 Antibody ch14.18_10

description:
ch14.18_10
Chimeric mouse-human

value: IgG

value: IgM


title: Wildtype colon 4

description:
Gene expression in the colon that were isolated 7 days after inactivation of the Hedgehog pathway
9257636071_D

source_name: Wildtype colon

value: Wildtype


title: Affinity mature ch14.18 -- Anti-GD2 Antibody ch14.18_7

description:
ch14.18_7
Chimeric mouse-human


title: Chronic lymphocytic leukemia 3 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+

value: IgHV unmutated

value: no ATM disruption detected


title: Indian Hedgehog knockout colon 1

description:
Gene expression in the colon that were isolated 7 days after inactivation of the Hedgehog pathway
9257636071_E


title: CUTLL DMSO rep 5

description: replicate 5

value: TALL Leukemia


title: Indian Hedgehog knockout colon 2

description:
Gene expression in the colon that were isolated 7 days after inactivation of the Hedgehog pathway
9257636071_F


title: Indian Hedgehog knockout colon 4

description:
Gene expression in the colon that were isolated 7 days after inactivation of the Hedgehog pathway
9257636071_H


title: Chronic lymphocytic leukemia 4 pre treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: not annotated


title: CUTLL DMSO rep 4

description: replicate 4


title: [3] NQ, 45.6, Rep 1

value: larvae


title: [3] NQ, 5.5, Rep 4


title: [3] NQ, 90.4, Rep 1


title: Chronic lymphocytic leukemia 3 pre treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 3 paired normal

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19-


title: [3] NQ, 45.6, Rep 3


title: Affinity mature ch14.18 -- Anti-GD2 Antibody ch14.18_6

description:
ch14.18_6
Chimeric mouse-human


title: Wildtype colon 3

description:
Gene expression in the colon that were isolated 7 days after inactivation of the Hedgehog pathway
9257636071_C


title: [3] NQ, 5.5, Rep 3


title: Chronic lymphocytic leukemia 4 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: no TP53 disruption detected

value: FC


title: Wildtype colon 2

description:
Gene expression in the colon that were isolated 7 days after inactivation of the Hedgehog pathway
9257636071_B


title: Affinity mature ch14.18 -- Anti-GD2 Antibody ch14.18_5

description:
ch14.18_5
Chimeric mouse-human


title: [3] NQ, 5.5, Rep 2

value: NQ


title: Affinity mature ch14.18 -- Anti-GD2 Antibody ch14.18_4

description:
ch14.18_4
Chimeric mouse-human


title: CUTLL DMSO rep 3

description: replicate 3

value: DMSO 24h


title: Affinity mature ch14.18 -- Anti-GD2 Antibody ch14.18_3

description:
ch14.18_3
Chimeric mouse-human


title: Affinity mature ch14.18 -- Anti-GD2 Antibody ch14.18_2

description:
ch14.18_2
Chimeric mouse-human


title: Wildtype colon 1

description:
Gene expression in the colon that were isolated 7 days after inactivation of the Hedgehog pathway
9257636071_A


title: Affinity mature ch14.18 -- Anti-GD2 Antibody ch14.18_1

description:
ch14.18_1
Chimeric mouse-human


title: CUTLL DMSO rep 2

description: replicate 2


title: Chronic lymphocytic leukemia 2 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: [3] Photo ox NQ, Control, Rep 1

value: Photo ox NQ


title: [3] NQ, 5.5, Rep 1


title: Chronic lymphocytic leukemia 2 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: IgHV mutated


title: Photo ox NQ, 90.4, Rep 3

hyb_protocol: All samples were hybridized to Agilent 8 x 60K, zebrafish microarrays (AMADID #36575).  Microarray hybridization experimental designs for UV-treated NQ exposures were completely randomized (using a random number generator).  Exposure concentrations were selected to represent both sublethal concentrations and concentrations beyond the threshold of lethality to facilitate identification of mechanisms of toxicity.  The UV-treated NQ experiment included the measured exposure concentrations: 5.5, 45.6 and 90.4 mg/L each including 4 replicates, in addition to 6 control (0 mg/L) exposure replicates.  Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) and with 37°C GE Wash buffer 2 (Agilent).

data_processing: Data were extracted from microarray images using Agilent Feature Extraction software (Agilent Technologies). Analysis of internal control spikes indicated that signal data was within the linear range of detection.  Microarray data were normalized to the 75th percentile within each array followed by median scaling among all exposures using GeneSpring Software version GX14.5 (Agilent Technologies).  GeneSpring was additionally used to conduct statistical analyses including gene set enrichment analysis (GSEA) and ANOVA-based differential transcript expression analyses.  For GSEA, the “50 hallmark gene sets” developed and curated by the Broad Institute (Liberzon et al 2015) were used to provide exploratory screening for biological processes affected by the UV-treated NQ exposures.  Algorithm parameters included a minimum of 15 matching genes within a gene set, a maximum number of 100 permutations and a false discovery rate q-value cut off ≤ 0.3.  In order to rank the importance of significant gene sets identified by GSEA, composite scores were developed using four criteria derived from the GSEA output where significant p-value (p = 0.05), significant q-value (p = 0.3), an enrichment score > |0.5|, and a normalized enrichment score > |1.5| each received scores of 0 or 1 depending if the criteria were met.  Additionally, ANOVA-based differential transcript expression was also conducted including one-way ANOVA to assess the effects of UV-treated NQ on transcript expression relative to controls.  In the one-way ANOVA test a p-value cutoff of 0.005 was utilized to identify significantly affected transcripts followed by post hoc pairwise tests comparing expression for each dose-level relative to controls by moderated t-test (p = 0.05) and a 1.5 fold change cut-off.

treatment_protocol: Zebrafish larvae were exposed to UV-treated NQ at 0, 5.5, 45.6, and 90.4 mg/L (initial measured concentrations prior to UV-treatment).  Danio rerio larvae were exposed in static nonrenewal acute 96-h bioassays.  Exposure chambers were 300-ml high-form lipless beakers with a test solution volume of 250 ml.  Eight larval fish per beaker were exposed the UV-treated NQ treatments each including at least 4 exposure replicates and 6 control exposure replicates.  Larval zebrafish were fed newly hatched Artemia nauplii two hours before the initiation of exposures and at the 48-h timepoint.  Surviving fish were enumerated daily and any fish found to be deceased were promptly removed from exposure chambers.

value: UV-treated NQ


title: Photo ox NQ, 90.4, Rep 2


title: CUTLL DMSO rep 1

description: replicate 1


title: Photo ox NQ, 45.6, Rep 5


title: Photo ox NQ, 45.6, Rep 4


title: Photo ox NQ, 90.4, Rep 1


title: Photo ox NQ, 90.4, Rep 4


title: Photo ox NQ, 45.6, Rep 2


title: Photo ox NQ, 5.5, Rep 5


title: Chronic lymphocytic leukemia 1 first treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: FCR


title: Photo ox NQ, 5.5, Rep 3


title: Photo ox NQ, 45.6, Rep 3


title: Photo ox NQ, 5.5, Rep 1


title: Photo ox NQ, 5.5, Rep 2


title: Photo ox NQ, 5.5, Rep 4


title: Photo ox NQ, Control, Rep 5


title: Photo ox NQ, Control, Rep 4


title: Photo ox NQ, Control, Rep 6


title: Chronic lymphocytic leukemia 1 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: NQ, Control, Rep 4

hyb_protocol: All samples were hybridized to Agilent 8 x 60K, zebrafish microarrays (AMADID #36575).  Microarray hybridization experimental designs for NQ exposures were completely randomized (using a random number generator).  Exposure concentrations were selected to represent both sublethal concentrations and concentrations beyond the threshold of lethality to facilitate identification of mechanisms of toxicity.  The NQ experiment included the measured exposure concentrations: 5.5, 45.6 and 90.4 mg/L each including 4 replicates, in addition to 6 control (0 mg/L) exposure replicates.  Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) and with 37°C GE Wash buffer 2 (Agilent).

data_processing: Data were extracted from microarray images using Agilent Feature Extraction software (Agilent Technologies). Analysis of internal control spikes indicated that signal data was within the linear range of detection.  Microarray data were normalized to the 75th percentile within each array followed by median scaling among all exposures using GeneSpring Software version GX14.5 (Agilent Technologies).  GeneSpring was additionally used to conduct statistical analyses including gene set enrichment analysis (GSEA) and ANOVA-based differential transcript expression analyses.  For GSEA, the “50 hallmark gene sets” developed and curated by the Broad Institute (Liberzon et al 2015) were used to provide exploratory screening for biological process affected by the NQ exposures.  Algorithm parameters included a minimum of 15 matching genes within a gene set, a maximum number of 100 permutations and a false discovery rate q-value cut off ≤ 0.3.  In order to rank the importance of significant gene sets identified by GSEA, composite scores were developed using four criteria derived from the GSEA output where significant p-value (p = 0.05), significant q-value (p = 0.3), an enrichment score > |0.5|, and a normalized enrichment score > |1.5| each received scores of 0 or 1 depending if the criteria were met.  Additionally, ANOVA-based differential transcript expression was conducted where one-way ANOVA was used to assess the effects of NQ exposure on transcript expression relative to controls.  In the one-way ANOVA test a p-value cutoff of 0.005 was utilized to identify significantly affected transcripts followed by post hoc pairwise tests comparing expression for each dose-level relative to controls by moderated t-test (p = 0.05) and a 1.5 fold change cut-off.

growth_protocol: Exposure chambers were 300-ml high-form lipless beakers with a test solution volume of 250 ml.  Eight larval fish per beaker were exposed in the parent or UV-treated NQ treatments each including 4 exposure replicates and 6 control replicates.  Larval zebrafish were fed newly hatched Artemia nauplii two hours before the initiation of exposures and at the 48-h timepoint.

treatment_protocol: Zebrafish larvae were exposed to NQ at 0, 5.5, 45.6, and 90.4 mg/L (measured concentrations).  Danio rerio larvae were exposed in static nonrenewal acute 96-h bioassays.  Exposure chambers were 300-ml high-form lipless beakers with a test solution volume of 250 ml.  Eight larval fish per beaker were exposed in the parent NQ treatments each including 4 exposure replicates and 6 control replicates.  Larval zebrafish were fed newly hatched Artemia nauplii two hours before the initiation of exposures and at the 48-h timepoint.  Surviving fish were enumerated daily and any fish found to be deceased were promptly removed from exposure chambers.


title: Chronic lymphocytic leukemia 2 pre treatment

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells


title: Photo ox NQ, Control, Rep 1


title: Chronic lymphocytic leukemia 1 pre treatment

description: Hybridized to GenomeWide SNP 6.0 array


title: NQ, Control, Rep 3


title: NQ, Control, Rep 5


title: Photo ox NQ, Control, Rep 2


title: NQ, 90.4, Rep 4


title: Photo ox NQ, Control, Rep 3


title: NQ, Control, Rep 2


title: NQ, Control, Rep 6


title: Photo ox NQ, 45.6, Rep 1


title: NQ, 90.4, Rep 2


title: NQ, 5.5, Rep 3


title: NQ, 45.6, Rep 2


title: NQ, 5.5, Rep 4


title: NQ, 45.6, Rep 3


title: NQ, 90.4, Rep 1


title: NQ, 5.5, Rep 1


title: NQ, 45.6, Rep 1


title: NQ, 90.4, Rep 3


title: NQ, 45.6, Rep 4


title: NQ, 5.5, Rep 2


title: transgenes_d12_2

status: Public on Aug 24 2017

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

country: Sweden

institute: BMC

description: transduced, exposed to N2B27 medium, 12 days of dox

hyb_protocol: Samples were hybridised to the Affymetrix HG-U133_Plus_2 array accroding to Affymetrix protocols

scan_protocol: Scanning was performed according to Affymetrix protocols

data_processing: Signal intensities were rma normalized using the R Affy package

source_name: Human Fetal Lung Fibroblasts (hFL1)

label_protocol: Not provided

growth_protocol: hFL fibroblasts were obtained from ATCC (ATCC- CCL- 153)

extract_protocol: 160000 - 300000 cells were sorted directly into FACS buffer. Cells were pelletized (500g, 5min) and resuspended in RLT buffer (Qiagen) containing 2-β-Mercaptoethanol (Invitrogen) and the RNA extraction was performed with an RNA micro kit, according to manufacturer’s instructions (Qiagen).

treatment_protocol: GFP expressing cells were isolated at different days of transgene expression (=different days of conversion/ days of exposure to chemicals) using FACSAria III (BD Biosciences) and the average purity of sorted cells in all experiments was 95%

value: Human Fetal Lung Fibroblasts (hFL1)

value: hFL1,  P14, d7.1,  AiGBM, N2B27 + dox-delay _Gr1_Repl3

tag: timepoint

tag: groupname


title: transgenes_d7_2

description: transduced, exposed to N2B27 medium, 7 days of dox

value: hFL1,  P14, d12.1,  AiGBM, N2B27 + dox-delay _Gr1_Repl3


title: transgenes_d7

value: hFL1,  P14, d12.1,  AiGBM, N2B27 + dox-delay _Gr1_Repl1


title: dualSMADi_d12

description: transduced, exposed to N2B27 medium + dualSMADi, 12 days of dox

value: hFL1,  P14, d7.1,  AiGBM, N2B27 + dox-delay_dualSMADi_Gr2_Repl1


title: transgenes_d7_1

value: hFL1,  P14, d12.1,  AiGBM, N2B27 + dox-delay _Gr1_Repl2


title: transgenes_d12_1

value: hFL1,  P14, d7.1,  AiGBM, N2B27 + dox-delay _Gr1_Repl2


title: FK_d7_1

description: transduced, exposed to N2B27 medium + Forskolin, 7 days of dox

value: hFL1,  P14, d12.2,  AiGBM, N2B27 + dox-delay_FK_Gr3_Repl2


title: FK_d12_1

description: transduced, exposed to N2B27 medium + Forskolin, 12 days of dox

value: hFL1,  P14, d7.2,  AiGBM, N2B27 + dox-delay_FK_Gr3_Repl2


title: transgenes_d12

value: hFL1,  P14, d7.1,  AiGBM, N2B27 + dox-delay _Gr1_Repl1


title: FK_d12

value: hFL1,  P14, d7.2,  AiGBM, N2B27 + dox-delay_FK_Gr3_Repl1


title: dualSMADi_d7_2

description: transduced, exposed to N2B27 medium + dualSMADi, 7 days of dox

value: hFL1,  P14, d12.1,  AiGBM, N2B27 + dox-delay_dualSMADi_Gr2_Repl3


title: dualSMADi_d12_1

value: hFL1,  P14, d7.1,  AiGBM, N2B27 + dox-delay_dualSMADi_Gr2_Repl2


title: FK_d12_2

value: hFL1,  P14, d7.2,  AiGBM, N2B27 + dox-delay_FK_Gr3_Repl3


title: dualSMADi_d12_2

value: hFL1,  P14, d7.1,  AiGBM, N2B27 + dox-delay_dualSMADi_Gr2_Repl3


title: FK_d7_2

value: hFL1,  P14, d12.2,  AiGBM, N2B27 + dox-delay_FK_Gr3_Repl3


title: dualSMADi_d7_1

value: hFL1,  P14, d12.1,  AiGBM, N2B27 + dox-delay_dualSMADi_Gr2_Repl2


title: dualSMADi_d7

value: Human Fetal Lung Fibroblasts (hFL1)

value: hFL1,  P14, d12.1,  AiGBM, N2B27 + dox-delay_dualSMADi_Gr2_Repl1


title: NQ, Control, Rep 1

tag: tissue

value: larvae

value: NQ


title: FK_d7

value: hFL1,  P14, d12.2,  AiGBM, N2B27 + dox-delay_FK_Gr3_Repl1


title: C6_d12_2

description: transduced, exposed to N2B27 medium + 6 compounds, 12 days of dox

value: hFL1,  P14, d7.2,  AiGBM, N2B27 + dox-delay_6C_Gr9_Repl3


title: C6_d7_1

description: transduced, exposed to N2B27 medium + 6 compounds, 7 days of dox

value: hFL1,  P14, d12.2,  AiGBM, N2B27 + dox-delay_6C_Gr9_Repl2


title: C6_d7_2

value: hFL1,  P14, d12.2,  AiGBM, N2B27 + dox-delay_6C_Gr9_Repl3


title: RNA-seq in MSCs infected with shGFP and control vector (rep5b)

city: Boston

first: Sowmya

last: Iyer

state: MA

department: Pathology

institute: Massachusetts General Hospital

data_processing:
Reads were aligned to hg19 using STAR. Mapped reads were filtered to exclude PCR duplicates and reads mapping to known ribosomal RNA coordinates, obtained from rmsk table in the UCSC database
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression was calculated using featureCounts. Only primary alignments with mapping quality of 10 or more were counted.

extract_protocol:
Total RNA was isolated using NucleoSpin RNA (Clontech).  1 μg of total RNA was treated with Ribogold zero to remove ribosomal RNA. Remaining RNA was used to construct Illumina sequencing libraries with random primers according to manufacturer instructions using the Truseq Stranded RNA LT Kit.
RNA samples were used to generate Illumina sequencing libraries following standard protocols.

tag: source type

value: primary tissue


title: RNA-seq in MSCs infected with shGFP and EWS-FLI1 (rep5b)


title: transgenes_d2_2

description: transduced, exposed to MEF medium + dox

tag: cell type

value: hFL1,  P14, d2,  AiGBM, N2B27 + dox-delay_Gr1_Repl3


title: fibroblasts_d0_1

description: untransduced Fibroblasts, MEF medium

tag: treatment

value: hFL1,  P14, untransduced_Repl2


title: transgenes_d2

description: transduced, exposed to MEF medium + dox

value: hFL1,  P14, d2,  AiGBM, N2B27 + dox-delay_Gr1_Repl1


title: fibroblasts_d0

description: untransduced Fibroblasts, MEF medium

value: hFL1,  P14, untransduced_Repl1


title: fibroblasts_d0_2

description: untransduced Fibroblasts, MEF medium

value: hFL1,  P14, untransduced_Repl3


title: RNA-seq in MSCs infected with shGFP and control vector (rep5)


title: C6_d12

value: hFL1,  P14, d7.2,  AiGBM, N2B27 + dox-delay_6C_Gr9_Repl1


title: RNA-seq in MSCs infected with shBRG1 and EWS-FLI1 (rep5b)


title: RNA-seq in MSCs infected with shBRG1 and EWS-FLI1 (rep5)


title: transgenes_d2_1

description: transduced, exposed to MEF medium + dox

value: hFL1,  P14, d2,  AiGBM, N2B27 + dox-delay_Gr1_Repl2


title: C6_d12_1

value: hFL1,  P14, d7.2,  AiGBM, N2B27 + dox-delay_6C_Gr9_Repl2


title: RNA-seq in MSCs infected with control (rep4)


title: RNA-seq in MSCs infected with BAF47FLI1 (rep4b)


title: RNA-seq in MSCs infected with SYGQ2-FLI1 (rep3)


title: RNA-seq in MSCs infected with control (rep3)


title: RNA-seq in MSCs infected with SYGQ2-FLI1 (rep2b)


title: RNA-seq in MSCs infected with control (rep4b)


title: RNA-seq in MSCs infected with shGFP and EWS-FLI1 (rep5)


title: RNA-seq in MSCs infected with EWS(YS37)-FLI1 (rep2b)


title: RNA-seq in MSCs infected with control (rep2b)


title: RNA-seq in MSCs infected with EWSFLI1 (rep2b)


title: RNA-seq in MSCs infected with EWS(YS37)-FLI1 (rep2)


title: RNA-seq in MSCs infected with control (rep2)


title: RNA-seq in MSCs infected with EWSFLI1 (rep2)


title: RNA-seq in MSCs infected with wild-type FLI1 (rep1b)


title: RNA-seq in MSCs infected with BAF47FLI1 (rep4)


title: RNA-seq in MSCs infected with EWSFLI1 (rep1b)


title: RNA-seq in MSCs infected with wild-type FLI1 (rep1)


title: RNA-seq in MSCs infected with EWSFLI1 (rep1)


title: RNA-seq in MSCs infected with control (rep1)


title: H3K27ac ChIP-seq in MSC4 infected with BAF47FLI1

library_source: genomic

data_processing:
Reads were aligned to hg19 using bwa (Li and Durbin, 2009). Aligned reads were then filtered to exclude PCR duplicates.
Genome_build: hg19
Supplementary_files_format_and_content: Aligned reads were extended to 200 bp to approximate fragment sizes. Density maps were generated by counting the number of fragments overlapping each position using igvtools, and normalized to 10 million reads.

extract_protocol:
Chromatin from formaldehyde-fixed cells (2-5 x 10^6 cells per epitope) was fragmented to a size range of 200 - 700 bases with a Branson 250 Sonifier. Solubilized chromatin was immunoprecipitated with the indicated antibodies and Protein G-Dynabeads (Life Technologies). Immunoprecipitated DNA was extracted with AMP Pure beads(Beckman Coulter) after crosslink reversal, RNAse A and Proteinase K treatment.
ChIP DNA samples were used to generate Illumina sequencing libraries following standard protocols.

tag: chip antibody

value: H3K27ac (Active Motif #39133)


title: H3K27ac ChIP-seq in MSC3 infected with SYGQ2-FLI1


title: FLI1 ChIP-seq in MSC4 infected with BAF47FLI1

value: FLI1 (ABCAM #ab15289)


title: H3K27ac ChIP-seq in MSC4 infected with control


title: INPUT library in MSC4 infected with BAF47FLI1


title: FLI1 ChIP-seq in MSC3 infected with SYGQ2-FLI1


title: INPUT library in MSC4 infected with control


title: H3K27ac ChIP-seq in MSC3 infected with EWSFLI1


title: BAF155 ChIP-seq in MSC3 infected with SYGQ2-FLI1

value: BAF155 (generated in-house epitope=aa924-1004; C-terminus)


title: FLI1 ChIP-seq in MSC3 infected with control


title: FLI1 ChIP-seq in MSC2 infected with EWS(YS37)-FLI1


title: FLI1 ChIP-seq in MSC2 infected with EWSFLI1


title: FLI1 ChIP-seq in MSC3 infected with EWSFLI1


title: H3K27ac ChIP-seq in MSC2 infected with EWSFLI1


title: H3K27ac ChIP-seq in MSC2 infected with EWS(YS37)-FLI1


title: BAF155 ChIP-seq in MSC3 infected with control


title: BAF155 ChIP-seq in MSC3 infected with EWSFLI1


title: H3K27ac ChIP-seq in MSC3 infected with control


title: BAF155 ChIP-seq in MSC2 infected with EWS(YS37)-FLI1


title: H3K27ac ChIP-seq in MSC2 infected with control


title: FLI1 ChIP-seq in MSC2 infected with control


title: FLI1 ChIP-seq in MSC4 infected with control


title: BAF155 ChIP-seq in MSC2 infected with control


title: H3K27ac ChIP-seq in MSC1 infected with wild-type FLI1


title: INPUT library in MSC1 infected with wild-type FLI1


title: BAF155 ChIP-seq in MSC1 infected with wild-type FLI1


title: FLI1 ChIP-seq in MSC1 infected with wild-type FLI1


title: BAF155 ChIP-seq in MSC2 infected with EWSFLI1


title: INPUT library in MSC1 infected with EWSFLI1


title: H3K27ac ChIP-seq in MSC1 infected with control


title: INPUT library in MSC1 infected with control


title: FLI1 ChIP-seq in MSC1 infected with control


title: BAF155 ChIP-seq in MSC1 infected with control


title: BAF155 ChIP-seq in MSC1 infected with EWSFLI1


title: FLI1 ChIP-seq in MSC1 infected with EWSFLI1


title: ATAC-seq in MSCs infected with BAF47FLI1 (rep4)

data_processing:
Reads were aligned to hg19 using bwa. Reads that aligned in the proper orientation and on the same chromosome were then filtered to exclude PCR duplicates. Signal densities were calculated over a sliding 150 bp window at 20 bp steps and normalized to 10M reads in each experiment
Genome_build: hg19

extract_protocol:
5x10^4 cells for each condition were first incubated in hypotonic buffer then resuspended in lysis buffer, centrifugated and resuspended in Transposase reaction mix for additional 30 min at 37C, following manufacturer recommendations (Nextera DNA sample Prep Kit, Illumina).
DNA was purified and adaptor sequences were added to the fragmented DNA by PCR to construct Illumina sequencing libraries. Purified PCR products were sequenced using the Illumina Nextseq device.


title: ATAC-seq in MSCs infected with control (rep1)


title: ATAC-seq in MSCs infected with control (rep3)


title: ATAC-seq in MSCs infected with BAF47FLI1 (rep1)


title: ATAC-seq in MSCs infected with control (rep2)


title: ATAC-seq in MSCs infected with EWSFLI1 (rep2)


title: ATAC-seq in MSCs infected with EWSFLI1 (rep4)


title: ATAC-seq in MSCs infected with EWSFLI1 (rep1)


title: ATAC-seq in MSCs infected with EWS(YS37)-FLI1 (rep2)


title: ATAC-seq in MSCs infected with wild-type FLI1 (rep1)


title: ATAC-seq in MSCs infected with control (rep4)


title: H3K27ac ChIP-seq in MSC1 infected with EWSFLI1


title: C6_d7

value: Human Fetal Lung Fibroblasts (hFL1)

value: hFL1,  P14, d12.2,  AiGBM, N2B27 + dox-delay_6C_Gr9_Repl1


title: ATAC-seq in MSCs infected with SYGQ2-FLI1 (rep3)


title: ATAC-seq in MSCs infected with EWSFLI1 (rep3)


title: IEC Active CD 3

city: Umeå

first: Marie-Louise

last: Hammarström

address: Peter Lestadius väg

department: Clinical Microbiology

institute: Umeå universitet

description:
Active CD
SAMPLE 7

data_processing: Background was first subtracted from the data and then normalized using Beadstudios cubic spline algorithm.

source_name: Human small intestinal

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: Total RNA was extracted from IECs by using the Qiagen RNeasy Mini Kit according to the manufacturer's instructions and dissolved in RNase-free water containing Promega rRNasin ribonuclease inhibitor. Quality control was performed with Agilent 2100 Bioanalyser and NanoDrop.

value: intestinal epithelial cells


title: IEL Active CD 2

description:
Active CD 2
SAMPLE 5

extract_protocol: Total RNA was extracted from IELs by using the Qiagen RNeasy Mini Kit according to the manufacturer's instructions and dissolved in RNase-free water containing Promega rRNasin ribonuclease inhibitor. Quality control was performed with Agilent 2100 Bioanalyser and NanoDrop.

value: intraepithelial lymphocytes


title: IEC Active CD 1

description:
Active CD
SAMPLE 5


title: IEL Active CD 5

description:
Active CD 5
SAMPLE 8


title: IEL Active CD 1

description:
Active CD 1
SAMPLE 4


title: IEL Active CD 3

description:
Active CD 3
SAMPLE 6


title: IEC Clinical Control 4

description:
Clinical control 4
SAMPLE 4


title: IEL Clinical Control 1

description:
Clinical control 1
SAMPLE 1


title: IEL Clinical Control 2

description:
Clinical control 2
SAMPLE 2


title: IEC Active CD 4

description:
Active CD
SAMPLE 8


title: IEC Clinical Control 3

description:
Clinical control 3
SAMPLE 3


title: IEC Active CD 2

description:
Active CD
SAMPLE 6


title: IEL Clinical Control 3

description:
Clinical control 3
SAMPLE 3


title: IEC Clinical Control 1

description:
Clinical control 1
SAMPLE 1


title: IEL Active CD 4

description:
Active CD 4
SAMPLE 7


title: IEC Clinical Control 2

description:
Clinical control 2
SAMPLE 2


title: Pericycle-Rhizobium-24hr-Rep3

status: Public on Aug 23 2017

city: Coventry

first: Miriam

last: Gifford

address: Gibbet Hill Road

department: School of Life Sciences

institute: University of Warwick

description: NimbleGen gene expression array data for custom-design array based on the TAIR10 release of the Arabidopsis thaliana genome

hyb_protocol: Following fragmentation, 4 ug of cRNA was hybridized for 16 hr at 42oC on a NimbleGen.

scan_protocol: Slides were scanned using an MS 200 microarray scanner and associated NimbleGen software using only the 480 nm laser with gain calculated using the autogain feature of NimbleScan, based on a representative region of the slide (an area covering around half an array found to have average intensity based on a prescan at lower resolution), as per manufacturer’s instructions. Grids were aligned automatically to each microarray image and manually veriﬁed, ensuring reference spots in each corner and in the centre of the array were aligned to the grid and the alignment score minimised.

data_processing: Data were obtained using NimbleScan and normalised by robust multichip averaging (RMA) (quantile normalisation, taking into account outlier probes per gene) and summarised to gene level by median polish.

source_name: 12 day old Arabidopsis Col0 root pericycle cells,

label_protocol: RNA samples were amplified using Ovation Pico WTA System V2 kit (NuGEN Technologies Inc., San Carlos, CA, USA) as per the manufacturer’s ‘quick’ protocol. Post-ampliﬁcation puriﬁcation of cDNA was performed using the QIAquick PCR Puriﬁcation Kit (Qiagen) as manufacturer’s guidelines. RNA was labelled with the Cy3 dye according to NimbleGen protocols.

growth_protocol: Plants were grown for 9 days in long day (16hr light/8hr dark) 22 oC conditions in a Sanyo growth chamber (MLR251).  Plants were grown vertically on plates on basal MS containing no nitrogen, supplemented with 0.1mM KNO3 and 30mM sucrose.

extract_protocol: FACS samples were collected in RLT lysis buffer (Qiagen) with 1 % (v:v) β-mercaptoethanol, then total RNA extracted using the Qiagen plant RNeasy kit.

treatment_protocol: At dawn on the 9th day plants were either transferred to 5mM KNO3-containing plates (High N), treated with a 0.8 OD600 of Sinorhizobium meliloti culture (rhizobium treatment), or moved to fresh 0.1mM KNO3 (Low N) plates. Whole roots were harvested then prototplast generation and Fluorescence-Activated Cell Sorting (FACS) used to isolate pericycle or cortical cells (following methods in Gifford et al 2008 PNAS).

value: root

value: pericycle cells


title: Pericycle-Rhizobium-48hr-Rep2


title: Pericycle-Rhizobium-24hr-Rep4


title: Pericycle-Rhizobium-48hr-Rep1


title: Pericycle-Rhizobium-48hr-Rep3


title: Pericycle-Rhizobium-36hr-Rep1


title: Pericycle-Rhizobium-24hr-Rep1


title: Pericycle-Rhizobium-24hr-Rep2


title: Pericycle-Rhizobium-20hr-Rep1


title: Pericycle-Rhizobium-16hr-Rep3


title: Pericycle-Rhizobium-20hr-Rep3


title: Pericycle-Rhizobium-20hr-Rep2


title: Pericycle-Rhizobium-36hr-Rep2


title: Pericycle-Rhizobium-16hr-Rep2


title: Pericycle-Rhizobium-10hr-Rep1


title: Pericycle-Rhizobium-10hr-Rep2


title: Pericycle-Rhizobium-6hr-Rep3


title: Pericycle-Rhizobium-10hr-Rep3


title: Pericycle-Rhizobium-12hr-Rep3


title: Pericycle-Rhizobium-8hr-Rep2


title: Pericycle-Rhizobium-16hr-Rep1


title: Pericycle-Rhizobium-6hr-Rep2


title: Pericycle-Rhizobium-12hr-Rep2


title: Pericycle-Rhizobium-12hr-Rep1


title: Pericycle-Rhizobium-14hr-Rep1


title: Pericycle-Rhizobium-2hr-Rep4


title: Pericycle-Rhizobium-4hr-Rep4


title: Pericycle-Rhizobium-12hr-Rep4


title: Pericycle-Rhizobium-2hr-Rep3


title: Pericycle-Rhizobium-6hr-Rep1


title: Pericycle-Rhizobium-14hr-Rep2


title: Pericycle-Rhizobium-8hr-Rep1


title: Pericycle-Rhizobium-1hr-Rep4


title: Pericycle-Rhizobium-1hr-Rep3


title: Pericycle-Rhizobium-2hr-Rep1


title: Pericycle-Rhizobium-10hr-Rep4


title: Pericycle-Rhizobium-4hr-Rep3


title: Pericycle-Rhizobium-4hr-Rep1


title: RNA-seq in MSCs infected with control (rep1b)

value: primary tissue


title: Pericycle-Rhizobium-4hr-Rep2


title: Pericycle-Nitrogen-48hr-Rep3


title: Pericycle-Rhizobium-1hr-Rep2


title: Pericycle-Rhizobium-2hr-Rep2


title: Pericycle-Nitrogen-24hr-Rep2


title: Pericycle-Rhizobium-1hr-Rep1


title: Pericycle-Nitrogen-36hr-Rep3


title: Pericycle-Nitrogen-20hr-Rep1


title: Pericycle-Nitrogen-24hr-Rep1


title: Pericycle-Nitrogen-36hr-Rep1


title: Pericycle-Nitrogen-14hr-Rep4


title: Pericycle-Nitrogen-16hr-Rep3


title: Pericycle-Nitrogen-20hr-Rep3


title: Pericycle-Nitrogen-48hr-Rep2


title: Pericycle-Nitrogen-36hr-Rep2


title: Pericycle-Nitrogen-12hr-Rep2


title: Pericycle-Nitrogen-12hr-Rep1


title: Pericycle-Nitrogen-14hr-Rep3


title: Pericycle-Nitrogen-48hr-Rep1


title: Pericycle-Nitrogen-10hr-Rep1


title: Pericycle-Nitrogen-16hr-Rep2


title: Pericycle-Nitrogen-14hr-Rep2


title: Pericycle-Nitrogen-16hr-Rep1


title: Pericycle-Nitrogen-20hr-Rep2


title: Pericycle-Nitrogen-24hr-Rep3


title: Pericycle-Nitrogen-8hr-Rep3


title: Pericycle-Nitrogen-6hr-Rep3


title: Pericycle-Nitrogen-8hr-Rep2


title: Pericycle-Nitrogen-10hr-Rep3


title: Pericycle-Nitrogen-2hr-Rep2


title: Pericycle-Nitrogen-14hr-Rep1


title: Pericycle-Nitrogen-6hr-Rep2


title: Pericycle-Nitrogen-4hr-Rep1


title: Pericycle-Standard-48hr-Rep3


title: Pericycle-Nitrogen-1hr-Rep1


title: Pericycle-Nitrogen-10hr-Rep2


title: Pericycle-Nitrogen-6hr-Rep4


title: Pericycle-Nitrogen-4hr-Rep3


title: Pericycle-Standard-48hr-Rep1


title: Pericycle-Nitrogen-6hr-Rep1


title: Pericycle-Standard-36hr-Rep3


title: Pericycle-Nitrogen-2hr-Rep3


title: Pericycle-Nitrogen-8hr-Rep1


title: Pericycle-Nitrogen-2hr-Rep1


title: Pericycle-Nitrogen-1hr-Rep2


title: Pericycle-Nitrogen-4hr-Rep2


title: Pericycle-Nitrogen-2hr-Rep4


title: Pericycle-Nitrogen-1hr-Rep3


title: Pericycle-Standard-48hr-Rep2


title: Pericycle-Standard-36hr-Rep2


title: Pericycle-Standard-20hr-Rep2


title: Pericycle-Standard-4hr-Rep3


title: Pericycle-Standard-20hr-Rep1


title: Pericycle-Standard-24hr-Rep3


title: Pericycle-Standard-12hr-Rep2


title: Pericycle-Standard-10hr-Rep2


title: Pericycle-Standard-8hr-Rep1


title: Pericycle-Standard-8hr-Rep2


title: Pericycle-Standard-10hr-Rep3


title: Pericycle-Standard-12hr-Rep3


title: Pericycle-Standard-14hr-Rep3


title: Pericycle-Standard-36hr-Rep1


title: Pericycle-Standard-16hr-Rep1


title: Pericycle-Standard-24hr-Rep1


title: Pericycle-Standard-10hr-Rep1


title: Pericycle-Standard-6hr-Rep1


title: Pericycle-Standard-16hr-Rep2


title: Pericycle-Standard-14hr-Rep1


title: Pericycle-Standard-16hr-Rep3


title: Pericycle-Standard-14hr-Rep2


title: Pericycle-Standard-6hr-Rep3


title: Pericycle-Standard-4hr-Rep2


title: Pericycle-Standard-24hr-Rep2


title: Pericycle-Standard-8hr-Rep3


title: Pericycle-Standard-12hr-Rep1


title: Pericycle-Standard-6hr-Rep2


title: Pericycle-Standard-4hr-Rep1


title: Pericycle-Standard-2hr-Rep3


title: Pericycle-Standard-2hr-Rep2


title: Pericycle-Standard-2hr-Rep1


title: Pericycle-0hr-Rep5


title: Cortex-Rhizobium-20hr-Rep2

source_name: 12 day old Arabidopsis Col0 root cortex cells,

value: cortex cells


title: Cortex-Rhizobium-48hr-Rep1


title: Cortex-Rhizobium-24hr-Rep3


title: Cortex-Rhizobium-48hr-Rep3


title: Cortex-Rhizobium-48hr-Rep2


title: Cortex-Rhizobium-36hr-Rep2


title: Cortex-Rhizobium-16hr-Rep1


title: Pericycle-0hr-Rep2


title: Cortex-Rhizobium-36hr-Rep3


title: Cortex-Rhizobium-14hr-Rep2


title: Pericycle-Standard-1hr-Rep2


title: Pericycle-0hr-Rep3


title: Pericycle-Standard-1hr-Rep1


title: Cortex-Rhizobium-20hr-Rep3


title: Cortex-Rhizobium-16hr-Rep3


title: Pericycle-Standard-1hr-Rep3


title: Pericycle-0hr-Rep4


title: Cortex-Rhizobium-12hr-Rep2


title: Cortex-Rhizobium-24hr-Rep1


title: Cortex-Rhizobium-16hr-Rep2


title: Cortex-Rhizobium-12hr-Rep3


title: Pericycle-0hr-Rep1


title: Cortex-Rhizobium-14hr-Rep3


title: Cortex-Rhizobium-20hr-Rep1


title: Cortex-Rhizobium-24hr-Rep2


title: Cortex-Rhizobium-36hr-Rep1


title: Cortex-Rhizobium-14hr-Rep1


title: Cortex-Rhizobium-12hr-Rep1


title: Cortex-Rhizobium-10hr-Rep2


title: Cortex-Rhizobium-10hr-Rep3


title: Cortex-Rhizobium-8hr-Rep2


title: Cortex-Rhizobium-2hr-Rep1


title: Cortex-Rhizobium-4hr-Rep2


title: Cortex-Rhizobium-6hr-Rep2


title: Cortex-Rhizobium-6hr-Rep1


title: Cortex-Rhizobium-4hr-Rep1


title: Cortex-Rhizobium-4hr-Rep3


title: Cortex-Rhizobium-2hr-Rep2


title: Cortex-Nitrogen-48hr-Rep2


title: Cortex-Nitrogen-36hr-Rep3


title: Cortex-Nitrogen-48hr-Rep3


title: Cortex-Rhizobium-10hr-Rep1


title: Cortex-Rhizobium-1hr-Rep3


title: Cortex-Rhizobium-2hr-Rep3


title: Cortex-Nitrogen-48hr-Rep1


title: Cortex-Rhizobium-1hr-Rep1


title: Cortex-Rhizobium-1hr-Rep2


title: Cortex-Rhizobium-8hr-Rep3


title: Cortex-Nitrogen-20hr-Rep2


title: Cortex-Nitrogen-16hr-Rep2


title: Cortex-Rhizobium-8hr-Rep1


title: Cortex-Nitrogen-36hr-Rep2


title: Cortex-Nitrogen-36hr-Rep1


title: Cortex-Nitrogen-16hr-Rep3


title: Cortex-Nitrogen-24hr-Rep2


title: Cortex-Nitrogen-24hr-Rep1


title: Cortex-Nitrogen-24hr-Rep3


title: Cortex-Nitrogen-20hr-Rep1


title: Cortex-Nitrogen-14hr-Rep2


title: Cortex-Nitrogen-10hr-Rep3


title: Cortex-Nitrogen-12hr-Rep2


title: Cortex-Nitrogen-4hr-Rep1


title: Cortex-Nitrogen-6hr-Rep1


title: Cortex-Standard-48hr-Rep2


title: Cortex-Nitrogen-1hr-Rep3


title: Cortex-Nitrogen-10hr-Rep1


title: Cortex-Nitrogen-1hr-Rep2


title: Cortex-Nitrogen-1hr-Rep1


title: Cortex-Nitrogen-14hr-Rep1


title: Cortex-Nitrogen-16hr-Rep1


title: Cortex-Nitrogen-2hr-Rep1


title: Cortex-Nitrogen-6hr-Rep2


title: Cortex-Nitrogen-2hr-Rep2


title: Cortex-Nitrogen-10hr-Rep2


title: Cortex-Nitrogen-8hr-Rep2


title: Cortex-Nitrogen-12hr-Rep1


title: Cortex-Nitrogen-4hr-Rep2


title: Cortex-Nitrogen-8hr-Rep1


title: Cortex-Standard-48hr-Rep3


title: Cortex-Standard-24hr-Rep3


title: Cortex-Standard-36hr-Rep2


title: Cortex-Standard-24hr-Rep1


title: Cortex-Standard-24hr-Rep2


title: Cortex-Standard-20hr-Rep3


title: Cortex-Standard-36hr-Rep1


title: Cortex-Standard-48hr-Rep1


title: Cortex-Standard-20hr-Rep1


title: Cortex-Standard-20hr-Rep2


title: Cortex-Standard-16hr-Rep1


title: Cortex-Standard-16hr-Rep2


title: Cortex-Standard-14hr-Rep2


title: Cortex-Standard-16hr-Rep3


title: Cortex-Standard-12hr-Rep3


title: Cortex-Standard-4hr-Rep3


title: Cortex-Standard-14hr-Rep1


title: Cortex-Standard-8hr-Rep1


title: Cortex-Standard-8hr-Rep3


title: Cortex-Standard-6hr-Rep1


title: Cortex-Standard-8hr-Rep2


title: Cortex-Standard-10hr-Rep3


title: Cortex-Standard-2hr-Rep2


title: Cortex-Standard-6hr-Rep2


title: Cortex-Standard-10hr-Rep1


title: Cortex-Standard-6hr-Rep3


title: Cortex-Standard-12hr-Rep2


title: Cortex-Standard-4hr-Rep1


title: Cortex-Standard-12hr-Rep1


title: Cortex-Standard-2hr-Rep3


title: Cortex-Standard-2hr-Rep1


title: Cortex-Standard-1hr-Rep2


title: Cortex-Standard-1hr-Rep1


title: Bbifidum PRL2010 and B adolescentis 22L supplemented to mice vs only Bbifidum PRL2010 supplemented to mice

city: Parma

first: Marco

last: Ventura

address: Viale delle Scienze 11/A

department: Dept. Life Sciences

country: Italy

institute: University of Parma

description: Sample name: PRL_22L_vs PRL

hyb_protocol: Labelled cDNA was hybridized using the Agilent Gene Transcription hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Transcription Analysis v4.0 manual (G4140-90050). Following hybridization, microarrays were washed in accordance with Agilent's standard procedures.

scan_protocol: Scanning was performed on InnoScan 700 (Innopsys) scanner.

data_processing: Signal intensities for each spot and data extraction were carried out using Mapix 5.5 software (Innopsys, Carbonne, France). The normalization of data was performed using Linear Normalization Correction Method by Agilent Feature Extraction 10.10 software. Data processing was performed using Limma package for R software.

organism:
Bifidobacterium adolescentis
Bifidobacterium bifidum PRL2010

source_name: B.bifidum PRL2010 was supplemented to BALB/c mice. B. adolescentis 22L was supplemented to BALB/c mice.

label_protocol: Reverse transcription and amplification of 500 ng of total RNA was performed with ImProm-IITM Reverse Transcriptase (Promega, Madison, USA) according to the manufacturer’s instructions. Five µg of cDNA was then labeled with ULS Labeling kit with Cy5 or Cy3 (Kreatech, The Netherlands).

growth_protocol:
B.bifidum PRL2010 was supplemented to five 3 months old female BALB/c mice. Bacterial colonization will be established by five consecutive daily administrations whereby each animal received 20 µl of 10E9 cells using a micropipette tip placed immediately behind the incisors.
B. adolescentis 22L was supplemented to five 3 months old female BALB/c mice. Bacterial colonization will be established by five consecutive daily administrations whereby each animal received 20 µl of 10E9 cells using a micropipette tip placed immediately behind the incisors.

extract_protocol: Total RNA was isolated using a previously described method (Turroni et al., 2013, PNAS). Briefly, tissue materials were resuspended in 1 ml of QUIAZOL (Qiagen, UK) and placed in a tube containing 0.8 g of glass beads (diameter, 106 μm; Sigma). The cells were lysed by shaking the mix on a BioSpec homogenizer at 4°C for 2 min (maximum setting). The mixture was then centrifuged at 12,000 rpm for 15 min, and the upper phase containing the RNA-containing sample was recovered. The RNA sample was further purified by phenol extraction and ethanol precipitation according to an established method (Sambrook et al., 1989). The quality of the RNA was checked by analysing the integrity of rRNA molecules by Experion (BioRad).

tag: strain

value: 22L (Bifidobacterium adolescentis 22L)

organism: Bifidobacterium bifidum PRL2010


title: Bbifidum PRL2010 and B breve 12L supplemented to mice vs only Bbifidum PRL2010 supplemented to mice

description: Sample name: PRL_12L_vs PRL

organism:
Bifidobacterium bifidum PRL2010
Bifidobacterium breve 12L

source_name: B.bifidum PRL2010 was supplemented to BALB/c mice. B.breve 12L was supplemented to BALB/c mice.

growth_protocol:
B.bifidum PRL2010 was supplemented to five 3 months old female BALB/c mice. Bacterial colonization will be established by five consecutive daily administrations whereby each animal received 20 µl of 10E9 cells using a micropipette tip placed immediately behind the incisors.
B.breve 12L was supplemented to five 3 months old female BALB/c mice. Bacterial colonization will be established by five consecutive daily administrations whereby each animal received 20 µl of 10E9 cells using a micropipette tip placed immediately behind the incisors.


title: Bbifidum PRL2010 supplemented to mice vs Bbifidum PRL2010 growth in mice food

description: Sample name: PRL_mono

source_name: B.bifidum PRL2010 supplemented to mice.

growth_protocol: Five animals of 3 months old female BALB/c mice were orally inoculated with B. breve PRL2010. Bacterial colonization will be established by five consecutive daily administrations whereby each animal received 20 µl of 10E9 cells using a micropipette tip placed immediately behind the incisors.

source_name: B.bifidum PRL2010 growth in mice food.

growth_protocol: B. bifidum PRL2010 was grown anaerobically in mice food medium supplemented with 0.05% (w/v) L-cysteine hydrochloride and incubated at 37°C.


title: all 4 bifidobacteria species supplemented to mice vs only Bbifidum PRL2010 supplemented to mice

description: Sample name: ALL_PRL

organism:
Bifidobacterium adolescentis
Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088
Bifidobacterium bifidum PRL2010
Bifidobacterium breve 12L

growth_protocol: All 4 bifidobacterial species were supplemented to mice. Five animals of 3 months old female BALB/c mice were orally inoculated with all 4 bifidobacterial species. Bacterial colonization will be established by five consecutive daily administrations whereby each animal received 20 µl of 10E9 cells using a micropipette tip placed immediately behind the incisors.

source_name: B.bifidum PRL2010 was supplemented to BALB/c mice.

growth_protocol: Five animals of 3 months old female BALB/c mice were orally inoculated with B. bifidum PRL2010. Bacterial colonization will be established by five consecutive daily administrations whereby each animal received 20 µl of 10E9 cells using a micropipette tip placed immediately behind the incisors.