title: breast cancer with BSC_LR161


title: breast cancer with BSC_LR163

status: Public on Jul 01 2018

type: RNA

city: Lund

first: Martin

last: Sjöström

address: Scheelevägen 2

country: Sweden

institute: Lund University

scan_protocol: Standard Illumina iScan N240 scanning protocol

data_processing:
The data was norm-exp background corrected and quantile normalized using the neqc function in the limma R package
Norm-exp background corrected with offset of 16, quantile normalized and log2 transformed

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: breast cancer operated with breast conserving surgery (BSC)

label_protocol: Illumina®Totalprep-96RNA Amplification kit 4397949 RevD, (Modification of Amplification kit v 2.2)

extract_protocol: Qiagen AllPrep protocol with Qiacube

tag: er (estrogen receptor status)

value: pos

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: breast cancer with BSC_LR158

value: neg


title: breast cancer with BSC_LR159


title: hbs1 rep2

type: SRA

city: Godollo

first: Daniel

last: Silhavy

state: US and Canada only

address: Szent-Gyorgyi 4

department: Agricultural Biotechnology Intsitute

country: Hungary

institute: National Agricultural Research and Innovation Cen.

description: Arabidopsis RNA-Seq experiment

library_source: transcriptomic

data_processing:
Read alignment (Hisat2 v2.1.0)
Transciprt assembly (StringTie v1.3.3b)
Differential Gene Expression (DESeq2 v1.18.1)
Genome_build: Solgenomics Niben v1.0.1, TAIR10
Supplementary_files_format_and_content: gtf files were generated using Stringtie v1.3.3b software including the assembled transcript structures and FPKM values.

organism: Arabidopsis thaliana

source_name: A. thaliana_hbs1

growth_protocol: Seeds of  Nicotiana benthamiana and Arabidopsis plants were germinated directly on Jiffy pellets (Jiffy-7 44mm; Jiffy International AS, Norway). Then seedlings were transferred to soil. N. benthamiana  plants were grown in a greenhouse. After VIGS-treatment N. benthamiana plants were kept in a growth chamber at 23°C under 14/10 h light/dark conditions. Arabidopsis seedlings were grown at growth chamber at 21°C under 16/8 h light/dark conditions.

extract_protocol:
Total RNA was extracted from 100 mg of leaf tissue (White and Kaper, 1989). Briefly, the homogenized plant materials were resuspended in 600 μL of extraction buffer (0.1 M glycine-NaOH, pH 9.0, 100 mM NaCl, 10 mM EDTA, 2% SDS, and 1% sodium lauroylsarcosine) and mixed with an equal volume of phenol. The aqueous phase was treated with equal volumes of phenol and chloroform, precipitated with ethanol, and resuspended in sterile water.
Libraries were prepared from total RNA samples with Illumina® Ribo-Zero™ rRNA Removal (Plant Leaf) and TruSeq™ v2 RNASeq Library Preparation Kits.

treatment_protocol: Virus-induced gene silencing (VIGS) was used to transiently silence Pelota. N. benthamiana plants were infected with Tobacco Rattle Virus VIGS vector containing a segment from the Pelota or from the PDS gene (called Pelota and control silenced plants, respectively).

tag: ecotype/stock

tag: genotype/variation

value: hbs1 mutant

tag: tissue

value: leaf


title: LIVER WT 6

city: Cincinnati

first: Jing

last: Chen

state: OH

address: 3333 Burnet Ave

country: USA

institute: CCHMC

data_processing:
Sequence reads were aligned to the genome by using the standard Illumina sequence analysis pipeline, which was analyzed by the Statistical Genomics and Systems Biology Core at the University of Cincinnati.
basecalling by Illumina Casava
alignment by TopHat
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file of raw count for each gene in each sample

organism: Mus musculus

source_name: LIVER

extract_protocol:
RNeasy Micro kit (Qiagen) was used for total RNA extraction. Each sample, together with Buffer RLT, were added to ceramic-beads (1.4-mm) in tubes and homogenized by using the Precellys homogenizer (Cayman Chemical Company; Ann Arbor, MI). RNA extraction was then performed, following manufacturer’s recommendations.
To prepare the RNA library for sequencing, we used TruSeq RNA Library Prep Kit (Illumina; San Diego, CA), according to manufacturer’s instructions. In brief, poly(A+) RNA was purified from total RNA and then fragmented before cDNA synthesis. Double-strand cDNA fragments were then end-repaired and TA-ligated to the sequencing adapter; the specific index was added to the library during the PCR amplification step. After 12 cycles of PCR enrichment, library quality was evaluated by a Bioanalyzer High Sensitivity chip and quantified by Kapa Library Quantification kit (Kapa Biosystem; Wilmington, MA), using the ABI 9700HT real-time PCR system (Thermo Fisher; Waltham, MA). Next, six individually indexed cDNA libraries were pooled in equal amounts for clustering in the cBot system (Illumina). Libraries were clustered onto a flow cell at concentration of 15 pM, using Illumina’s TruSeq SR Cluster Kit v3, and then sequenced for 50 cycles using TruSeq SBS kit on the Illumina HiSeq system. Each sample was expected to generate ~30 million reads.

value: LIVER

tag: developmental stage

tag: genotype


title: 6hr_A_2Gy_2

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

hyb_protocol: Labeled target was applied to Agilent miRNA mouse v19 arrays (Design ID#046065) and hybridized overnight.

scan_protocol: Slides were washed and scanned with an Agilent G2565 Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution.

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).

source_name: Whole Blood 6hr exp A 2Gy dose rep 2

label_protocol: Total RNA samples were dephosphorylated, denatured, and end-labeled according to Agilent's protocols.

extract_protocol: RNA was extracted and purified using Ribopure (Ambion) RNA isolation

treatment_protocol: whole body irradiation done with X-rays using the Small Animal Radiation Research Platform (SARRP Xstrahl Ltd.). Mice were placed in plastic containers and exposed to a single surface dose of 0-12 Gy with a dose rate of 1.05 Gy/min. Control mice (0 Gy) were placed in the same plastic container as the irradiated mice and sham irradiated. 3 animals/dose/time-point have been included in the study.

tag: strain

tag: age

value: Six to eight weeks

tag: gender

value: female

value: whole body


title: hbs1 rep1

description: Arabidopsis RNA-Seq experiment


title: 6hr_A_2Gy_1

source_name: Whole Blood 6hr exp A 2Gy dose rep 1


title: wt rep3

description: Arabidopsis RNA-Seq experiment

source_name: A. thaliana_WT

value: Columbia (col-0)

value: wild type


title: HEART MUT 5

source_name: HEART

value: HEART


title: wt rep2

description: Arabidopsis RNA-Seq experiment


title: CEREBELLUM MUT 4

source_name: CEREBELLUM

value: CEREBELLUM


title: 6hr_A_0Gy_1

source_name: Whole Blood 6hr exp A 0Gy dose rep 1


title: wt rep1

description: Arabidopsis RNA-Seq experiment


title: 6hr_A_0Gy_2

source_name: Whole Blood 6hr exp A 0Gy dose rep 2


title: 6hr_A_0Gy_3

source_name: Whole Blood 6hr exp A 0Gy dose rep 3


title: KIDNEY MUT 3

source_name: KIDNEY

value: KIDNEY


title: PLACENTA MUT 37

source_name: PLACENTA

value: PLACENTA


title: YOLK SAC MUT 36

source_name: YOLK SAC

value: YOLK SAC


title: PLACENTA WT 35


title: 24hr_B_0Gy_2

source_name: Whole Blood 24hr exp B 0Gy dose rep 2


title: breast cancer with BSC_LR155


title: YOLK SAC WT 34


title: breast cancer with BSC_LR146


title: breast cancer with BSC_LR156


title: breast cancer with BSC_LR153


title: breast cancer with BSC_LR154


title: PLACENTA WT 33


title: breast cancer with BSC_LR148


title: breast cancer with BSC_LR144


title: breast cancer with BSC_LR145


title: Luciferase knockdown and ERG Overexpression in RWPE-1 cells replicate 3

city: Bloomington

first: Peter

last: Hollenhorst

state: Indiana

address: 1001 E 3rd St

department: Medical Sciences

institute: Indiana University

description:
RWPE1_EMPTY_ERG_ERGshELF1.diff
ucscKnownGenes_geneid.gtf

data_processing:
Illumina Casava1.8.2 software used for basecalling
Reads were aligned to the Homo sapien genome (UCSC hg19) using TopHat2 (v2.0.7) running BowTie2 (v2.0.6) and Samtools (v.0.1.18) using a modified protocol from Trapnell et al., Nature Protocols,  2012. The parameters used were -G -p 8
Differential expression of aligned reads was produced using Cufflinks (v2.1.1) using a modified protocol from Trapnell et al., Nature Protocols,  2012. The three replicates for each condition were combined for the differential expression analysis. The parameters used were -b -p 8 -u -L
Genome_build: UCSC hg19
Supplementary_files_format_and_content: tab-delimited text files include for each combination of replicates: RPKM values, locus, status, log2(fold_change), test_stat, p-value, q-value, and significance

source_name: immortalized normal prostate cells

growth_protocol: RWPE1 cells were grown in Keratinocyte SFM media supplemented with bovine pitutiary extract, human recombinant epidermal growth factor, penicillin/streptomycin, and selection agents (puromycin/hygromycin)

extract_protocol:
Total RNA was isolated from RWPE-1 cells transduced with shRNA knockdown and retroviral overexpression vectors using the Rneasy mini kit (Qiagen) according to manufacturer's instruction
Sequencing libraries were generated using a modified Illumina Truseq sample preparation protocol.Total RNA was DNAase treated with TURBO DNase (Invitrogen). The DNase treated RNA was polyA selected with oligo(dT) beads (Invitrogen). A Superscript III Reverse Transcriptase First-Strand Synthesis (Invitrogen) system was used to generate cDNA from the polyA selected RNA with random hexamer primers (Invitrogen). After first strand synthesis a second strand was generated using E. coli DNA ligase (New England BioLabs) and E. coli DNA polymerase I (New England BioLabs). The double stranded cDNAs were sheared to ~150 nucleotides using a Diagenode BioRuptor and the size was confirmed by DNA gel electrophoresis. DNA end repair of the cDNA was performed using Klenow DNA polymerase (New England BioLabs), T4 DNA polymerase (New England BioLabs), and T4 DNA ligase (New England BioLabs) before the sample was subjected to QIAquick PCR purification (Qiagen). Adapters were ligated to DNA fragments using the T4 DNA ligase (New England BioLabs). The product was run on a 2% agarose gel and size selected between 200 and 300 nucleotides to then be purified by a Gel Extraction kit (Qiagen). Universal and indexing adapters were taken from the TruSeq sample preparation kit (Illumina).

tag: cell line

value: Prostate

value: luciferase knockdown and ERG overexpression


title: ELF1 knockdown and ERG Overexpression in RWPE-1 cells replicate 2

value: ELF1 knockdown and ERG overexpression


title: ELF1 knockdown and ERG Overexpression in RWPE-1 cells replicate 3


title: ELF1 knockdown and ERG Overexpression in RWPE-1 cells replicate 1


title: breast cancer with BSC_LR141

value: neg


title: Group3_Library3

city: San Francisco

first: Roland

middle: S

last: Wu

state: CA

address: 555 Mission Bay Blvd South MC3122

department: CVRI

institute: UCSF

description: FACS sorted cardiomyocytes

data_processing:
Reads were filtered with sickle and scythe QC packages
Aligned to GRCz10.80 using Tophat2
Abundance estimated with Cufflinks
Genome_build: GRCz10
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each sample

organism: Danio rerio

source_name: Cardiomyocytes

growth_protocol: Embryos were raised in egg water

extract_protocol:
RNA extracted from FACS sorted cells
NuGen Ovation V2 RNA-Seq cDNA amplification and Ultralow Library DR library prep

treatment_protocol: Embryos were dissociated and FACS sorted for GFP

value: cardiomyocytes

value: 20 hpf


title: Group3_Library2

description: FACS sorted cardiomyocytes


title: Luciferase knockdown and ERG Overexpression in RWPE-1 cells replicate 2


title: YOLK SAC WT 32


title: Group2_Library3

description: FACS sorted cardiomyocytes


title: Group3_Library1

description: FACS sorted cardiomyocytes


title: PLACENTA MUT 31


title: Luciferase knockdown and ERG Overexpression in RWPE-1 cells replicate 1


title: Luciferase knockdown and Vector Overexpression in RWPE-1 cells replicate 3

value: luciferase knockdown and vector overexpression


title: breast cancer with BSC_LR137

source_name: breast cancer operated with breast conserving surgery (BSC)


title: YOLK SAC MUT 30


title: Group2_Library2

description: FACS sorted cardiomyocytes


title: breast cancer with BSC_LR138


title: LUNG MUT 2

source_name: LUNG

value: LUNG


title: Group2_Library1

description: FACS sorted cardiomyocytes


title: Luciferase knockdown and Vector Overexpression in RWPE-1 cells replicate 2


title: Group1_Library3

description: FACS sorted cardiomyocytes


title: PLACENTA WT 29


title: breast cancer with BSC_LR130

value: pos


title: breast cancer with BSC_LR135


title: YOLK SAC WT 27


title: Luciferase knockdown and Vector Overexpression in RWPE-1 cells replicate 1


title: PLACENTA MUT 28


title: Group1_Library2

description: FACS sorted cardiomyocytes


title: ELF1 ChIP PC3

description:
ChIP-seq
Blacklist_hg19.bed

library_source: genomic

data_processing:
Illumina Casava1.8.2 software used for basecalling
Reads were aligned to the Homo sapien genome (UCSC hg19) using Bowtie2 (v2.0.6)
If there was more than one replicate for a particular sample, the samtools merge function was used to combine the alignment files into one .bam file
Blacklist regions were removed from the alignment files using Bedtools (v2.20.1)
Peak calling was accomplished using the MACS platform (v1.4.2) with a with the homo sapiens genome size, p-value of 1e-5, a bandwidth of 210, and mfold of 5,30
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Binary alignment files (.bam) with blacklist regions removed and replicates merged. Also an excel file containing the called peaks from MACS with the parameters listed at the beginning of the file

molecule: genomic DNA

source_name: bone mets prostate adenocarcinoma

extract_protocol:
ChIP DNA was isolated as described in Hollenhorst et. al., Genes and Development, 2011
Sequencing libraries were created as described in Plotnik et.al. Nucleic Acids Research. 2014.

tag: chip antibody

value: ELF1 (sc-631, Santa Cruz Biotechnology)

tag: growth protocol

value: PC3 cells were maintained in F12K media with 10% FBS and 100 U/ml Penicillin/Streptomycin


title: Input PC3

description:
ChIP-seq
Blacklist_hg19.bed


title: Group1_Library1

description: FACS sorted cardiomyocytes

value: wild type


title: ELF1 ChIP RWPE-1

description:
ChIP-seq
Blacklist_hg19.bed

value: RWPE1 cells were grown in Keratinocyte SFM media supplemented with bovine pitutiary extract, human recombinant epidermal growth factor, and penicillin/streptomycin


title: YOLK SAC MUT 26


title: HEART WT 25

value: HEART


title: CEREBELLUM WT 24

value: CEREBELLUM


title: BEA2

city: Aarhus

first: Morten

middle: Muhlig

last: Nielsen

address: Palle Juul-Jensens Bouleward 99

department: Department of Molecular Medicine

country: Denmark

institute: Aarhus University

data_processing:
Bam files created using TopHat v2.
Expression counts estimated with HTSeq V2
GENCODE v19 was used as gene model.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tab delimited flat file, genes=rows, samples=cols, gene ID = GENCODE v19

source_name: BE-43547 sample 2

growth_protocol: PANC-1 cells were cultured in DMEM (Gibco, Cat#: 21969-035) supplemented with FBS (10%, Gibco, Cat#: A31698-02), Penicillin/Streptomycin (1%, Sigma-Aldrich, Cat#: P0781), and Ala-Gln (200 µM, Sigma-Aldrich, Cat#: G8541).

extract_protocol:
Total RNA was extracted using High Pure RNA Isolation Kit (Roche, Cat#: 11828665001) according to the manufacturers protocol.
Paired end, 76 bases, total RNA. Library preparation and sequencing on the Illumina NextSeq at Department of Molecular Medicine, Aarhus University Hospital, Denmark.

treatment_protocol: medium was exchanged for medium containing rakicidin A (42 nM), BE-43547A1 (41 nM) or DMSO (0.04%) in triplicates. The cells were placed under hypoxia for 12 hours after which total RNA was extracted.

value: Pancreas


title: BEA1

source_name: BE-43547 sample 1


title: BEA3

source_name: BE-43547 sample 3


title: breast cancer with BSC_LR136


title: breast cancer with BSC_LR123


title: KIDNEY WT 23

value: KIDNEY


title: LUNG WT 22


title: HEART MUT 20

source_name: HEART


title: DMSO1

source_name: DMSO control sample 1


title: breast cancer with BSC_LR129


title: DMSO2

source_name: DMSO control sample 2


title: breast cancer with BSC_LR127


title: breast cancer with BSC_LR128


title: breast cancer with BSC_LR124


title: breast cancer with BSC_LR126


title: RakA2

source_name: Rakicidin sample 2


title: RakA3

source_name: Rakicidin sample 3


title: LIVER MUT 1

source_name: LIVER

value: LIVER


title: breast cancer with BSC_LR122


title: KIDNEY MUT 18

source_name: KIDNEY


title: LUNG MUT 17


title: DMSO3

source_name: DMSO control sample 3


title: CEREBELLUM MUT 19

source_name: CEREBELLUM


title: A375_singlecell_resistant_cell_52

city: Cold Spring Harbor

first: Molly

last: Hammell

state: New York

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

data_processing:
Illumina NextSeq read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were quantified using kallisto v0.42.5 (RefSeq release 2016-5-25). Exclusions included a minimum raw count value of 1.0 in at least 95% of all samples. Raw read counts were normalized to RPM value and then were log2-transformed with an offset value of 1.0.
Genome_build: Reads was aligned to the transcriptome (hg19, GRCh37.72)
Supplementary_files_format_and_content: Tab-delimited text file includes estimated raw counts for each sample

source_name: Melanoma cell line

growth_protocol: Cells were cultured in Dulbecco's Modified Eagle Medium with 10% Fetal Bovine serum and 1% Pencillin-Streptavadin. Cells were grown to ~80% confluency in 10cm culture dishes and split every 2-3 days.

extract_protocol:
Single cell lysed in Clontech 10x Lysis buffer with Rnase Inhibitor
SMART-Seq v4 Ultra Low RNA Kit for the Fluidigm C1 System and Illumina Nextera XT Library Prep Kit used according to Fluidigm C1 manual

treatment_protocol: For treated cells, 1uM of drug was added to above mentioned media. Media with drug was prepared fresh every 10 days to ensue that the drug was active

tag: treatment

value: Resistant - Cultured in 1uM PLX-4720


title: 6hr_B_0Gy_1

source_name: Whole Blood 6hr exp B 0Gy dose rep 1

value: Six to eight weeks

value: female

value: whole body


title: HEART MUT 15


title: A375_singlecell_resistant_cell_51


title: RakA1

source_name: Rakicidin sample 1


title: breast cancer with BSC_LR117

source_name: breast cancer operated with breast conserving surgery (BSC)

tag: er (estrogen receptor status)


title: breast cancer with BSC_LR125

value: neg

tag: rt (radiotherapy)


title: A375_singlecell_resistant_cell_49


title: A375_singlecell_resistant_cell_48


title: A375_singlecell_resistant_cell_50


title: breast cancer with BSC_LR121

tag: lr (local recurrence)


title: LUNG MUT 12

source_name: LUNG


title: breast cancer with BSC_LR118

tag: ibtr (ipsilateral breast tumor recurrence)


title: LIVER MUT 11


title: breast cancer with BSC_LR115

tag: follow-up time (years)


title: KIDNEY MUT 13


title: breast cancer with BSC_LR119


title: breast cancer with BSC_LR116


title: breast cancer with BSC_LR113


title: breast cancer with BSC_LR112


title: A375_singlecell_resistant_cell_47


title: HEART WT 10


title: A375_singlecell_resistant_cell_46


title: breast cancer with BSC_LR111


title: A375_singlecell_resistant_cell_45


title: CEREBELLUM MUT 14


title: A375_singlecell_resistant_cell_44


title: breast cancer with BSC_LR108


title: breast cancer with BSC_LR110


title: A375_singlecell_resistant_cell_43


title: breast cancer with BSC_LR107


title: A375_singlecell_resistant_cell_39


title: A375_singlecell_resistant_cell_38


title: A375_singlecell_resistant_cell_37


title: breast cancer with BSC_LR104


title: breast cancer with BSC_LR103


title: breast cancer with BSC_LR106


title: A375_singlecell_resistant_cell_40


title: 58-10BUCYT_2

city: odense

first: mads

last: thomassen

address: soender boulevard 29

institute: odense university hospital

hyb_protocol: Labeled cRNA from the samples was hybridized with the labeled pooled reference cRNA according to Agilents protocol

scan_protocol: the arrays where scanned using the Agilent DNA Microarray Scanner with SureScan Technology

data_processing: Agilent Feature Extraction Software  was used for background subtraction. Array data pre-processing was performed using the R statistical package limma. Raw intensity data were background corrected using the “normexp” method, within-array normalized by the “loess” method, and between arrays normalized by the “quantile” method.

organism: Sus scrofa

source_name: BUCY treated pig

label_protocol: Agilent according to protocol

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

treatment_protocol: busulfan plus cyclophosphamide (BUCY) or doxorubicin (DOX) or control

value: small intestine

value: SPF piglets (Large White × Danish Landrace)

source_name: pool of all samples


title: A375_singlecell_resistant_cell_41


title: A375_singlecell_resistant_cell_36


title: 415DC

source_name: untreated pig (from DOX experiment)


title: 409DC


title: 414DC


title: A375_singlecell_resistant_cell_42


title: A375_singlecell_resistant_cell_35


title: 44-10BUCYC_2

source_name: untreated pig (from BUCY experiment)


title: 43-10BUCYC_2


title: breast cancer with BSC_LR102

value: pos


title: breast cancer with BSC_LR099


title: 412DT

source_name: DOX treated pig


title: breast cancer with BSC_LR098


title: breast cancer with BSC_LR097


title: breast cancer with BSC_LR101


title: breast cancer with BSC_LR100


title: 410DT


title: breast cancer with BSC_LR096


title: A375_singlecell_resistant_cell_34


title: A375_singlecell_resistant_cell_33


title: breast cancer with BSC_LR094


title: breast cancer with BSC_LR093


title: A375_singlecell_resistant_cell_32


title: A375_singlecell_resistant_cell_31


title: A375_singlecell_resistant_cell_30


title: A375_singlecell_resistant_cell_29


title: 39-10BUCYT_2


title: FDR 143 v1

type: protein

city: La Jolla

first: Jan

middle: M

last: Hughes-Austin

address: 9500 Gilman Drive

department: Orthopaedic Surgery

institute: University of California, San Diego

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
06-006-01

hyb_protocol: Spectrally-distinct polystyrene beads with magnetic cores were covalently coupled to capture antibodies by the manufacturer. The bead mix was added to a 96-well flat-bottom plate (1x concentration, 25 uL/well). The plate was washed twice with provided wash buffer using a Bio-Plex Pro II magnetic wash station (100 uL/well per wash). Serum was diluted 1:4 in provided universal sample diluent. Standard or diluted sample was added to the plate (25 uL/well), incubated at room temperature for one hour on a microtiter plate shaker, and removed by washing the plate three times on the wash station.

scan_protocol: Plates were analyzed using a Luminex 200 (Luminex Corporation, Austin, TX, USA) in combination with Bio-Plex Manager 5.0 software (Bio-Rad Laboratories, Hercules, CA, USA). Data were acquired with the following advanced settings: 125 beads per region, 50 uL sample size, and DD gate values of 5,000 to 25,000.

data_processing: Serum concentrations were interpolated from standard curves for each respective cytokine in Bio-Plex manager software. Data were log transformed [1+cytokine], then standardized by dividing the log transformed values by the standard deviation of the log transformed values. The formula = ln[1+cytokine] / SD. Where SD is the SD for the log transformed values of the cytokine. The file log_standardized_data.txt contains the values produced by the before-mentioned formula.

label: PE

molecule: protein

source_name: serum

label_protocol: Biotinylated detection antibodies were added (1x concentration, 25 uL/well), allowed to incubate at room temperature for 30 minutes, and removed by washing the plate three times. Streptavidin-PE was added (1x concentration, 50 uL/well), incubated at room temperature for 10 minutes, and promptly removed by washing the plate three times. Provided assay buffer was added to re-suspend the beads (90 uL/well) and the plate was placed on the shaker for 30 seconds before reading.

extract_protocol: Serum was isolated and provided by the central laboratory for the Studies of the Etiology of Rheumatoid Arthritis (SERA)

tag: fdr visit number

value: serum

tag: bmi

tag: current statin use (0=no/1=yes)

tag: categories of pack-years smoking

tag: adiponectin concentration

tag: natural log_adiponectin

tag: age in years

tag: crp

tag: race (nhw = non-hispanic white)

value: NHW

tag: high risk profile positive (0=no/1=yes)

tag: gender (0=female; 1=male)


title: FDR 142 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
06-001-99

tag: tissue

value: Other


title: breast cancer with BSC_LR092

tag: er (estrogen receptor status)


title: 406DT_2

tag: strain


title: breast cancer with BSC_LR091

tag: rt (radiotherapy)

tag: lr (local recurrence)


title: FDR 144 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
06-009-98


title: HCT116,NT

city: Hangzhou

first: Yanmei

last: Zhang

state: Zhejiang

address: Tianmushan Road No.182

department: Center for Molecular Medicine

country: China

institute: Zhejiang Academy of Medical Science

description: Gene expression data cells

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V,  Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US)

data_processing: Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings.

source_name: HCT116 cells silenced by negative siRNA

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3' IVT PLUS Reagent Kit (Cat#902416, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: HCT116 and Caco-2 colorectal cancer cells were cultured in DMEM high glucose medium supplied with 10% FBS and 5% CO2. Cells were plated on 6-well or 96-well plates for subsequent treatment.

extract_protocol: HCT116 and Caco-2 cells were silenced by siRNA of BORIS for 3 days and extracted for the RNA. Total RNA was extracted by TRIzol® (Thermo Fisher Scientific) and ethanol precipitation.

treatment_protocol: BORIS siRNA and Lipofectamine®RNAiMAX (Thermo Fisher Scientific, Waltham, MA, USA) was applied to silence the expression of BORIS.

tag: cell line

tag: sirna

value: negative


title: breast cancer with BSC_LR089

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: 404DC


title: HCT116,siBORIS

description: Gene expression data cells

source_name: HCT116 cells silenced by BORIS siRNA

value: BORIS


title: 408DT


title: 40-10BUCYT


title: 46-10BUCYT


title: 403DT


title: A375_singlecell_resistant_cell_28

tag: treatment


title: A375_singlecell_resistant_cell_27


title: Caco-2,NT

description: Gene expression data cells

source_name: Caco-2 cells silenced by negative siRNA


title: 64-10BUCYC


title: A375_singlecell_resistant_cell_26


title: 61-10BUCYC


title: breast cancer with BSC_LR087


title: breast cancer with BSC_LR084


title: 411DC


title: breast cancer with BSC_LR090


title: A375_singlecell_resistant_cell_25


title: 47-10BUCYC


title: FDR 139 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
05-081-04

tag: fdr visit number

tag: bmi

tag: current statin use (0=no/1=yes)

tag: categories of pack-years smoking

tag: adiponectin concentration


title: FDR 141 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
05-085-01

tag: natural log_adiponectin

tag: age in years

tag: crp

tag: race (nhw = non-hispanic white)

tag: high risk profile positive (0=no/1=yes)


title: Caco-2,siBORIS

description: Gene expression data cells

source_name: Caco-2 cells silenced by BORIS siRNA


title: breast cancer with BSC_LR085

tag: er (estrogen receptor status)

tag: rt (radiotherapy)


title: A375_singlecell_resistant_cell_24

tag: cell line


title: A375_singlecell_resistant_cell_23


title: FDR 140 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
05-084-01

tag: tissue

tag: gender (0=female; 1=male)


title: FDR 138 v2

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
05-058-02


title: FDR 137 v2

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
05-041-01


title: A375_singlecell_resistant_cell_22


title: A375_singlecell_resistant_cell_21


title: FDR 136 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
05-027-01


title: FDR 137 v1


title: A375_singlecell_resistant_cell_20


title: A375_singlecell_resistant_cell_19


title: FDR 134 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
05-024-01


title: 407DC

tag: strain


title: breast cancer with BSC_LR082

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: A375_singlecell_resistant_cell_18

tag: treatment


title: FDR 133 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
05-015-02

tag: fdr visit number

tag: bmi

tag: current statin use (0=no/1=yes)

tag: categories of pack-years smoking


title: breast cancer with BSC_LR081


title: A375_singlecell_resistant_cell_17


title: breast cancer with BSC_LR080


title: MYC T-ALL_26

type: genomic

city: Gent

first: Gloria

last: Milani

address: Pintelaan 185

country: Belgium

institute: Gent University

description: primary T-ALL sample from patient D08 vs. gender-matched control

hyb_protocol: Samples were hybridized on Agilent SurePrint G3 Human CGH 4x180K microarrays (G4449A, design ID: 022060) for 24h at 65 °C.

scan_protocol: The samples were scanned at 2 µm resolution using a DNA microarray scanner G2505B (Agilent Technologies).

data_processing: The scan images were analyzed using the feature extraction software 9.5.3.1 (Agilent Technologies).

source_name: primary T-ALL sample collected at diagnosis

label_protocol: 100 ng of genomic DNA was labeled with Cy3-dCTP (Perkin Elmer, NEL620001KT) using a Bioprime Array CGH Labeling System (Invitrogen, 10297-018). In parallel, Kreatech gender-matched controls were labeled with Cy5-dCTP.

extract_protocol: DNA was extracted from T-ALL patient samples using the AllPrep DNA/RNA Mini Kit (Qiagen) according to the manufacturer’s instructions.

tag: age

tag: gender

value: Male

value: primary pediatric T-ALL sample

source_name: gender-matched control DNA

value: gender-matched control


title: breast cancer with BSC_LR079


title: FDR 135 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
05-026-98

tag: adiponectin concentration

tag: natural log_adiponectin

tag: age in years

tag: crp

tag: race (nhw = non-hispanic white)

tag: high risk profile positive (0=no/1=yes)


title: breast cancer with BSC_LR076

tag: er (estrogen receptor status)

tag: rt (radiotherapy)


title: breast cancer with BSC_LR074

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)


title: 42-10BUCYT_2

tag: tissue

tag: strain


title: MYC T-ALL_23

description: primary T-ALL sample from patient D04 vs. gender-matched control

value: Female


title: 405DT


title: breast cancer with BSC_LR078

tag: follow-up time (years)


title: breast cancer with BSC_LR086


title: FDR 132 v2

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
05-015-01

tag: fdr visit number

tag: bmi

tag: current statin use (0=no/1=yes)

tag: gender (0=female; 1=male)


title: breast cancer with BSC_LR066


title: MYC T-ALL_22

description: primary T-ALL sample from patient D03 vs. gender-matched control

tag: age

tag: gender


title: breast cancer with BSC_LR070


title: MYC T-ALL_25

description: primary T-ALL sample from patient D06 vs. gender-matched control


title: MYC T-ALL_21

description: primary T-ALL sample from patient C31 vs. gender-matched control


title: MYC T-ALL_20

description: primary T-ALL sample from patient C30 vs. gender-matched control


title: FDR 132 v1

tag: categories of pack-years smoking

tag: adiponectin concentration

tag: natural log_adiponectin

tag: age in years


title: MYC T-ALL_19

description: primary T-ALL sample from patient C28 vs. gender-matched control


title: A375_singlecell_resistant_cell_15

source_name: Melanoma cell line

tag: cell line

tag: treatment

value: Resistant - Cultured in 1uM PLX-4720


title: breast cancer with BSC_LR064

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)


title: FDR 131 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
05-013-01

tag: tissue

tag: crp

tag: race (nhw = non-hispanic white)

tag: high risk profile positive (0=no/1=yes)


title: MYC T-ALL_18

description: primary T-ALL sample from patient C24 vs. gender-matched control


title: A375_singlecell_resistant_cell_13


title: A375_singlecell_resistant_cell_14


title: A375_singlecell_resistant_cell_12


title: FDR 131 v2

tag: fdr visit number

tag: bmi

tag: current statin use (0=no/1=yes)


title: breast cancer with BSC_LR061

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: FDR 130 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
05-011-01

tag: categories of pack-years smoking

tag: adiponectin concentration

tag: gender (0=female; 1=male)


title: breast cancer with BSC_LR058


title: breast cancer with BSC_LR060


title: A375_singlecell_resistant_cell_11

tag: cell line


title: breast cancer with BSC_LR057


title: MYC T-ALL_15

description: primary T-ALL sample from patient C20 vs. gender-matched control

tag: age

tag: gender


title: A375_singlecell_resistant_cell_16

tag: treatment


title: MYC T-ALL_16

description: primary T-ALL sample from patient C21 vs. gender-matched control


title: MYC T-ALL_17

description: primary T-ALL sample from patient C23 vs. gender-matched control


title: FDR 129 v2

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
05-005-02

tag: natural log_adiponectin

tag: age in years


title: A375_singlecell_resistant_cell_9


title: FDR 130 v2

tag: tissue

tag: crp


title: FDR 128 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
04-075-98

tag: race (nhw = non-hispanic white)

tag: high risk profile positive (0=no/1=yes)


title: A375_singlecell_resistant_cell_8


title: FDR 129 v1

tag: fdr visit number

tag: bmi


title: FDR 127 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
04-071-02

tag: current statin use (0=no/1=yes)


title: A375_singlecell_resistant_cell_10


title: A375_singlecell_resistant_cell_7


title: A375_singlecell_resistant_cell_6


title: FDR 126 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
04-068-03


title: breast cancer with BSC_LR055

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: breast cancer with BSC_LR044


title: A375_singlecell_resistant_cell_5

tag: cell line


title: FDR 124 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
04-059-01

tag: categories of pack-years smoking

tag: adiponectin concentration

tag: gender (0=female; 1=male)


title: MYC T-ALL_13

description: primary T-ALL sample from patient C18 vs. gender-matched control

tag: age

tag: gender


title: MYC T-ALL_14

description: primary T-ALL sample from patient C19 vs. gender-matched control

tag: tissue


title: breast cancer with BSC_LR040


title: MYC T-ALL_12

description: primary T-ALL sample from patient C17 vs. gender-matched control


title: FDR 123 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
04-052-01

tag: natural log_adiponectin

tag: age in years

tag: crp

tag: race (nhw = non-hispanic white)


title: breast cancer with BSC_LR054


title: breast cancer with BSC_LR043


title: A375_singlecell_resistant_cell_3

tag: treatment


title: MYC T-ALL_8

description: primary T-ALL sample from patient C12 vs. gender-matched control


title: breast cancer with BSC_LR039

tag: er (estrogen receptor status)


title: MYC T-ALL_9

description: primary T-ALL sample from patient C14 vs. gender-matched control


title: MYC T-ALL_7

description: primary T-ALL sample from patient C11 vs. gender-matched control


title: FDR 122 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
04-051-01

tag: fdr visit number

tag: bmi

tag: current statin use (0=no/1=yes)

tag: high risk profile positive (0=no/1=yes)


title: MYC T-ALL_10

description: primary T-ALL sample from patient C15 vs. gender-matched control


title: MYC T-ALL_11

description: primary T-ALL sample from patient C16 vs. gender-matched control


title: FDR 121 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
04-044-01


title: A375_singlecell_resistant_cell_1

tag: cell line


title: FDR 120 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
04-041-99

tag: categories of pack-years smoking


title: A375_singlecell_resistant_cell_4


title: MYC T-ALL_6

description: primary T-ALL sample from patient C10 vs. gender-matched control


title: FDR 119 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
04-039-03

tag: adiponectin concentration


title: breast cancer with BSC_LR037

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: breast cancer with BSC_LR033


title: A375_singlecell_parental_cell_78

value: Parental - no Treatment


title: A375_singlecell_parental_cell_77


title: MYC T-ALL_5

description: primary T-ALL sample from patient C09 vs. gender-matched control

tag: age

tag: gender

tag: tissue


title: FDR 118 v2

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
04-038-01

tag: natural log_adiponectin

tag: age in years

tag: crp

tag: race (nhw = non-hispanic white)

tag: gender (0=female; 1=male)


title: MYC T-ALL_4

description: primary T-ALL sample from patient C06 vs. gender-matched control


title: A375_singlecell_parental_cell_76

tag: treatment


title: FDR 118 v1

tag: fdr visit number

tag: bmi

tag: current statin use (0=no/1=yes)

tag: high risk profile positive (0=no/1=yes)


title: A375_singlecell_parental_cell_75

tag: cell line


title: breast cancer with BSC_LR032

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)


title: breast cancer with BSC_LR031

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: breast cancer with BSC_LR018


title: breast cancer with BSC_LR029


title: breast cancer with BSC_LR030


title: breast cancer with BSC_LR038


title: A375_singlecell_resistant_cell_2


title: MYC T-ALL_3

description: primary T-ALL sample from patient C03 vs. gender-matched control

tag: age

tag: gender

tag: tissue


title: breast cancer with BSC_LR023


title: Triple Negative Breast Tumor with decreased SPARC Expression Replicate 2

city: São Paulo

first: Ana Carolina

last: Pavanelli

state: SP

address: Dr. Arnaldo 251

department: Radiologia e Oncologia

country: Brazil

institute: ICESP

description: Biological replicate 2 of 2. Triple Negative Breast Tumor,  decreased SPARC Expression

hyb_protocol: 825ng of labeled cRNAs were hybridized with the Human GE 4X44K V2 slides for 17 hours at 65°C. The slides were washed with the GE Wash Buffer 1 and GE Wash Buffer 2 (Agilent), following manufacturer´s instructions.

scan_protocol: Scanned on an Agilent G2600D scanner using the GE2_107_Sep09 protocol.

data_processing: The data quantification and the quality control were performed using the Agilent Feature Extration (v 11.5.1.1) Software.

source_name: Triple Negative Breast Tumor Sample with SPARC Negative expression

label_protocol: 162 ng of total RNA (human reference RNA and samples) were primed with 0.8 µl of T7 promoter primer (Agilent) at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of AffinityScript RNA Block Mix (Agilent), and 1 mM of dNTP mix (Agilent). Human RNA reference was labled with Cy3 and samples were labled with  Cy5 at 40°C for 2 h in the presence of T7 RNA polymerase blend (Agilent). The cRNAs were purified using the Qiagen RNeasy mini kit according manufacturer instructions and quantified using NanoDrop (ND-1000).

extract_protocol:
Sample characteristics: Primary breast tumor samples were obtained  at the Department of Pathology, Hospital AC Camargo, São Paulo, Brazil as decribed in Nagai et al., 2011 (Breast Cancer Res Treat (2011) 126:1–14)
Total RNA extracted using guanidinium thiocyanate-phenol-chloroform method  according Chomczynsky and Sacchi (1987).

value: Primary breast tumor sample

tag: molecular classification

value: Triple Negative

source_name: Agilent's Universal Human Reference RNA

tag: content

value: total RNA from 10 human cell lines


title: breast cancer with BSC_LR016

source_name: breast cancer operated with breast conserving surgery (BSC)

value: neg


title: Triple Negative Breast Tumor with increased SPARC Expression Replicate 1

description: Biological replicate 1 of 2. Triple Negative Breast Tumor,  increased SPARC Expression

source_name: Triple Negative Breast Tumor Sample with SPARC Positive expression


title: MYC T-ALL_2

description: primary T-ALL sample from patient C02 vs. gender-matched control


title: FDR 117 v3

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
04-026-01

tag: categories of pack-years smoking

tag: adiponectin concentration

tag: natural log_adiponectin

tag: age in years

tag: crp

tag: race (nhw = non-hispanic white)

tag: gender (0=female; 1=male)


title: MYC T-ALL_1

description: primary T-ALL sample from patient C01 vs. gender-matched control


title: A375_singlecell_parental_cell_74

tag: cell line

tag: treatment


title: FDR 117 v1

tag: fdr visit number

tag: bmi

tag: current statin use (0=no/1=yes)

tag: high risk profile positive (0=no/1=yes)


title: FDR 117 v2


title: A375_singlecell_parental_cell_73


title: FDR 116 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
04-008-98


title: A375_singlecell_parental_cell_72


title: FDR 115 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
04-005-01


title: A375_singlecell_parental_cell_69


title: FDR 114 v2

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
04-002-03


title: FDR 114 v1


title: A375_singlecell_parental_cell_68


title: FDR 113 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-273-98


title: breast cancer with BSC_LR015

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: Triple Negative Breast Tumor with decreased SPARC Expression Replicate 1

description: Biological replicate 1 of 2. Triple Negative Breast Tumor,  decreased SPARC Expression

tag: tissue

tag: molecular classification

tag: content


title: A375_singlecell_parental_cell_67


title: mock-treated cells, biological rep3

city: Rome

first: domenico

last: raimondo

address: Viale Regina Elena 324

department: Molecular Medicine

country: Italy

institute: Sapienza University of Rome

description: mock-treated cells, biological rep1, sample 39

hyb_protocol: Affymetrix standard Protocol

scan_protocol: Affymetrix standard Protocol

data_processing: Data were analyzed using GCOS, dChip®, Partek GS® and R (Bioconductor).

source_name: human bone marrow stromal cells (hBMSCs) (derived from bone marrow aspirates)

label_protocol: Affymetrix standard Protocol

growth_protocol: Cells were cultured in α-MEM, 2mM L-glutamine, 20% FBS, 100U/ml penicillin, 100µg/ml streptomycin (Invitrogen, Carlsbad, CA), 10-8M dexamethasone and 10-4M L-ascorbic acid.  293T cells (ATCC CRL-11268) were maintained in DMEM (Invitrogen), 10% FBS, 100U/ml penicillin and 100µg/ml streptomycin.

extract_protocol: Total cellular RNA was isolated from cell populations using an RNeasy RNA isolation kit (Qiagen) following manufacturer’s recommendations

treatment_protocol: The LV-vector integrated copy number was calculated by Q-PCR as described and was established as ~1 copy of integrated lentiviral sequence per transduced cell. hBMSCs were transduced with LV-GSαR201C and LV-ctr or mock treated.

value: human bone marrow

tag: cell type

value: Human bone marrow stromal cells (hBMSCs)

tag: genotype/variation

value: mock-treated

tag: donor id


title: R201C mutation containing cells, biological rep3

description: R201C mutation containing cells, biological rep1, sample 39

value: R201C mutation


title: breast cancer with BSC_LR012


title: FDR 112 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-267-98

value: serum

tag: categories of pack-years smoking

tag: adiponectin concentration

tag: natural log_adiponectin

tag: age in years

tag: crp

tag: race (nhw = non-hispanic white)

value: NHW

tag: gender (0=female; 1=male)


title: breast cancer with BSC_LR010

tag: er (estrogen receptor status)

value: pos

tag: rt (radiotherapy)


title: breast cancer with BSC_LR014

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)


title: A375_singlecell_parental_cell_66

tag: cell line

tag: treatment


title: A375_singlecell_parental_cell_70


title: A375_singlecell_parental_cell_71


title: R201C mutation containing cells, , biological rep2

description: R201C mutation containing cells, biological rep1, sample 36

tag: tissue


title: FDR 111 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-247-01

tag: fdr visit number

tag: bmi

tag: current statin use (0=no/1=yes)

tag: high risk profile positive (0=no/1=yes)


title: breast cancer with BSC_LR007

tag: follow-up time (years)


title: breast cancer with BSC_LR009


title: Triple Negative Breast Tumor with increased SPARC Expression Replicate 2

description: Biological replicate 2 of 2. Triple Negative Breast Tumor,  increased SPARC Expression

tag: molecular classification

tag: content


title: control cells, biological rep3

description: cells transduced with the LV-control vector, sample 39

tag: cell type

tag: genotype/variation

value: LV-control

tag: donor id


title: breast cancer with BSC_LR011

tag: er (estrogen receptor status)


title: A375_singlecell_parental_cell_65


title: mock-treated cells , biological rep2

description: mock-treated cells, biological rep1, sample 36


title: FDR 110 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-245-01

tag: categories of pack-years smoking

tag: adiponectin concentration

tag: natural log_adiponectin

tag: age in years

tag: crp

tag: race (nhw = non-hispanic white)

tag: gender (0=female; 1=male)


title: A375_singlecell_parental_cell_64

tag: cell line

tag: treatment


title: FDR 109 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-230-01

tag: fdr visit number

tag: tissue

tag: bmi

tag: current statin use (0=no/1=yes)

tag: high risk profile positive (0=no/1=yes)


title: breast cancer with BSC_LR005

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: A375_singlecell_parental_cell_63


title: FDR 108 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-222-01

tag: categories of pack-years smoking

tag: adiponectin concentration


title: A375_singlecell_parental_cell_62


title: FDR 107 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-221-02

tag: natural log_adiponectin

tag: age in years


title: A375_singlecell_parental_cell_61


title: control cells, biological rep2

description: cells transduced with the LV-control vector, sample 36

tag: cell type

tag: genotype/variation

tag: donor id


title: A375_singlecell_parental_cell_60

tag: cell line

tag: treatment


title: mock-treated cells, biological rep1

description: mock-treated cells, biological rep1, sample 29

tag: tissue


title: A375_singlecell_parental_cell_59


title: FDR 105 v2

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-187-01

tag: fdr visit number

tag: bmi

tag: crp

tag: race (nhw = non-hispanic white)

tag: gender (0=female; 1=male)


title: breast cancer with BSC_LR002

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)


title: FDR 105 v1

tag: current statin use (0=no/1=yes)

tag: categories of pack-years smoking

tag: adiponectin concentration

tag: natural log_adiponectin

tag: high risk profile positive (0=no/1=yes)


description: R201C mutation containing cells, biological rep1, sample 29

tag: cell type

tag: genotype/variation

tag: donor id


title: breast cancer with BSC_LR003

tag: follow-up time (years)


title: FDR 104 v2

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-183-01

tag: fdr visit number

tag: tissue

tag: bmi

tag: age in years

value: Other


title: breast cancer with BSC_LR001

tag: er (estrogen receptor status)


title: A375_singlecell_parental_cell_58

tag: cell line

tag: treatment


title: control cells, biological rep1

description: cells transduced with the LV-control vector, sample 29


title: FDR 106 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-211-01

tag: crp

tag: race (nhw = non-hispanic white)

tag: gender (0=female; 1=male)


title: FDR 125 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
04-066-98

tag: current statin use (0=no/1=yes)

tag: categories of pack-years smoking

tag: adiponectin concentration


title: A375_singlecell_parental_cell_57


title: T4hSub_2

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

description: Intercalary meristem at the 10~12 weeks stem in 4h Submergence, non-transgenic, biological replicate 2

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

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

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

organism: Oryza sativa

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

growth_protocol: Seeds (Oriza sativa L. indica cultivar Pin Gaew 56) were geminated in darkness in petri dishes on moist filter paper at 30℃ for 72 h. Seedling were transplanted in plastic pots and grown in greenhouse. Twenty-cm-long stem sections containing the uppermost internode were excised from 10- to 12-week-old plants.

extract_protocol: Total RNAs were extracted using MiniBEST Plant RNA Extraction kit (TAKARA, Japan).

treatment_protocol: Deepwater rice stem sections were pre-incubated for 4 h and then further incubated complete submergence or air in continuous light for 24 h. Twenty stem sections were placed in an upright position in a 200-ml glass beaker which was then filled with glass beads to prevent the submerged sections from floating up. Each beaker containing the sections was lowered to the bottom of a plastic cylinder, filled to the 50-cm deep with distilled water. Stem sections were incubated under complete submergence or in air for 3 different times (0, 1 and 4 h).

tag: cultivar

value: cv. Pin Gaew 56 (PG56)

tag: stress

value: Submergence

tag: time

value: intercalary meristem


title: FDR 104 v1

tag: natural log_adiponectin

tag: high risk profile positive (0=no/1=yes)


title: T4hSub_1

description: Intercalary meristem at the 10~12 weeks stem in 4h Submergence, non-transgenic, biological replicate 1

tag: tissue


title: A375_singlecell_parental_cell_56

value: Parental - no Treatment


title: breast cancer with BSC_LR526 [nanostring]

hyb_protocol: Hybridization Protocol for nCounter XT CodeSet Gene Expression assays (version: APRIL 2016 MAN-10023-09)

scan_protocol: Nanostring Digital Analyzer with RLF file: Sjostrom_1_C4440. FOV: 555

data_processing:
Summarization of RCC files with nSolver, no further processing for the raw data (included in the sample data table)
The 'final_nano_data (SUPPLEMENTAL FILE).csv' contains the final filtered, processed data as described below;
Quality filtering of the probes was applied based on negative control probes. Probes expressed above the negative controls (geometric mean) in less than 80% the samples were removed from further analysis. This affected 7/248 probes (AKNA, KCNMB2, OR8G2, hcg2023290, GCSH, PRAME and MYOG1). Samples were then normalized based on the positive control probes and a normalization factor calculated as the average geometric mean of positive controls divided by the sample specific geometric mean of positive controls. As a quality filter for technical problems, samples with positive normalization factors <0.3 or >3 were removed, excluding four samples (three from the discovery set and one from the validation set). The data was further normalized based on housekeeping genes and the seven most stable housekeeping genes from analysis with the NormqPCR package were used (MRPL19, PUM1, SF3A1, PSMC4, HPRT1, ACTB, PGK1). A normalization factor was calculated as the average geometric mean of the seven housekeeping genes divided with the geometric mean of the seven housekeeping genes of each sample. As a quality filter for sample problems, samples with normalization factors <0.1 or >10 were excluded (25 samples were excluded, one from the discovery cohort and 24 from the validation cohort). Finally, log2 transformation was performed. For the final analysis, 168 samples were used from the discovery cohort and 139 from the validation cohort.

extract_protocol: Qiagen AllPrep kit with Qiacube automatization

tag: cohort

value: validation

tag: biobank center

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: FDR 103 v2

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-180-01

tag: fdr visit number

tag: bmi

tag: age in years

tag: crp

tag: race (nhw = non-hispanic white)


title: T4hSub_3

description: Intercalary meristem at the 10~12 weeks stem in 4h Submergence, non-transgenic, biological replicate 3

tag: cultivar


title: T1hSub_3

description: Intercalary meristem at the 10~12 weeks stem in 1h Submergence, non-transgenic, biological replicate 3

tag: stress


title: A375_singlecell_parental_cell_55

tag: cell line

tag: treatment


title: FDR 103 v1

tag: current statin use (0=no/1=yes)

tag: categories of pack-years smoking

tag: adiponectin concentration

tag: natural log_adiponectin

tag: high risk profile positive (0=no/1=yes)

tag: gender (0=female; 1=male)


title: A375_singlecell_parental_cell_54


title: A375_singlecell_parental_cell_53


title: FDR 102 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-177-01

tag: tissue


title: breast cancer with BSC_LR521 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: breast cancer with BSC_LR523 [nanostring]


title: Glio6 at 3% O2, biological replicat 2

city: LA TRONCHE

first: Michèle

last: EL ATIFI

address: Chemin fortuné ferrini

country: France

institute: INSERM

description: primary culture from human glioblastoma (Platet and al.,2007)

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 hr at 45°C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were normalized with Expression console Suite (RMA) using Affymetrix default analysis settings.

source_name: Glio6 at 3% O2, biological replicat 2

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix protocol from 200 ng of total RNA using the GeneChip®  3’IVT Express Kit

growth_protocol: U87 and Glio6 were cultured in the presence of fœtal calf serum (10%), at 3% of oxygene in an hypoxic workstation

extract_protocol: Total RNA were extracted from cells with the MirVana isolation kit.

value: brain


title: T1hSub_2

description: Intercalary meristem at the 10~12 weeks stem in 1h Submergence, non-transgenic, biological replicate 2

tag: cultivar

tag: stress

tag: time


title: T1hAir_2

description: Intercalary meristem at the 10~12 weeks stem in 1h Air, non-transgenic, biological replicate 2

value: Air


title: U87 at 3% O2, biological replicat 2

source_name: U87 at 3% O2, biological replicat 2

tag: cell line


title: U87 at 3% O2, biological replicat 3

source_name: U87 at 3% O2, biological replicat 3


title: Glio6 at 3% O2, biological replicat 3

source_name: Glio6 at 3% O2, biological replicat 3


title: Glio6 at 3% O2, biological replicat 1

source_name: Glio6 at 3% O2, biological replicat 1


title: U87 at 3% O2, biological replicat 1

source_name: U87 at 3% O2, biological replicat 1


title: FDR 101 v2

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-169-01

source_name: serum

tag: fdr visit number

tag: bmi

tag: current statin use (0=no/1=yes)

tag: categories of pack-years smoking

tag: age in years

tag: crp

tag: race (nhw = non-hispanic white)


title: A375_singlecell_parental_cell_52

tag: treatment


title: T1hAir_1

description: Intercalary meristem at the 10~12 weeks stem in 1h Air, non-transgenic, biological replicate 1

tag: tissue


title: T0h_2

description: Intercalary meristem at the 10~12 weeks stem in 0h Air, non-transgenic, biological replicate 2


title: breast cancer with BSC_LR520 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)

value: neg

tag: rt (radiotherapy)


title: Isg20(D94G) rep2

city: Pittsburgh

first: William

last: Klimstra

state: PA

address: 3501 Fifth Ave, 9052 BST3

department: Microbiology and Molecular Genetics

institute: University of Pittsburgh

description: rRNA-depleted

data_processing:
Pre-trimmed, sequenced reads (Axeq Technologies, Macrogen Corp.) were mapped to UCSC mm9 genome using TopHat v2.0.12 with Bowtie2 v2.2.3 and Samtools v0.1.19 with parameters --library-type=fr-secondstrand
Mapped reads were assembled with Cufflinks v2.2.1
Final Transcriptome assembly was generated by Cuffmerge in Cufflinks v2.2.1
Mapped reads were quantified as Fragments Per Kilobase of transcript per Million mapped reads (FPKM) by Cuffquant in Cufflinks v2.2.1
Differential gene expression was determined on quantified reads by Cuffdiff in Cufflinks v2.2.1
Genome_build: mm9
Supplementary_files_format_and_content: Cufflinks output containing tracking information for genes and isoforms, plus assembled transcripts
Supplementary_files_format_and_content: Cuffquant output containing transcript abundances
Supplementary_files_format_and_content: Cufmerge output containing final merged assemblies
Supplementary_files_format_and_content: Cuffdiff output containing differential expression output plus run information for CummeRbund analysis

source_name: Isg20(D94G) tet-off MEF

growth_protocol: MEFs were expanded on T-75 culture flasks in DMEM with 10% heat-inactivated tet-approved FBS, 200 mM L-glutamine, 10,000 units/mL penicillin, 10 mg/mL streptomycin, 100 ug/mL G-418 sulfate, 100 ug/mL hygromycin sulfate, and 2 ug/mL doxycycline hyclate. MEFs were trypsinized and washed for induction.

extract_protocol:
RNA was phenol/chloroform extracted from MEFs in trizol reagent and depleted of rRNA with RiboMinus Eukaryotic Kit v2 (Life Technologies #A15020) according to manufacturer's protocol
Libraries were prepared according to the provided protocol for NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB#E7420S/L) with NEBNext Multiplex Oligos for Illumina (Index Primer Set 1) (NEB#E7335S/L)

treatment_protocol: MEFs were washed 3 times in sterile DPBS with Mg and induced in doxycycline free cell culture media for 72 hours on 150mm culture dishes, with 1 media change 24 hours after induction initiation

value: Mouse embryonic fibroblasts (MEFs)

tag: overexpressed target

value: murine Isg20(D94G)

tag: induction time

value: 72 hr

value: MEF/3T3 Tet-off (Clontech #631139)

tag: overexpression vector


title: breast cancer with BSC_LR524 [nanostring]

city: Lund

first: Martin

last: Sjöström

address: Scheelevägen 2

institute: Lund University

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: FDR 101 v1

tag: fdr visit number

value: serum

tag: bmi

tag: current statin use (0=no/1=yes)

tag: adiponectin concentration

tag: natural log_adiponectin

tag: high risk profile positive (0=no/1=yes)

tag: gender (0=female; 1=male)


title: Isg20(D94G) rep1

description: rRNA-depleted

tag: tissue

tag: cell line


title: A375_singlecell_parental_cell_51

tag: treatment


title: breast cancer with BSC_LR518 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)

tag: rt (radiotherapy)


title: T1hSub_1

description: Intercalary meristem at the 10~12 weeks stem in 1h Submergence, non-transgenic, biological replicate 1

tag: cultivar

tag: stress

tag: time


title: breast cancer with BSC_LR516 [nanostring]

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: U87 at 3% O2, biological replicat 4

source_name: U87 at 3% O2, biological replicat 4


title: A375_singlecell_parental_cell_50


title: FDR 100 v2

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-165-04

tag: fdr visit number

tag: bmi

tag: current statin use (0=no/1=yes)

tag: categories of pack-years smoking

tag: adiponectin concentration

tag: age in years

tag: crp

tag: race (nhw = non-hispanic white)

value: NHW


title: T0h_1

description: Intercalary meristem at the 10~12 weeks stem in 0h Air, non-transgenic, biological replicate 1

tag: tissue


title: Isg20 rep1

description: rRNA-depleted

source_name: Isg20 tet-off MEF

tag: overexpressed target

value: murine Isg20

tag: induction time

tag: cell line

tag: overexpression vector


title: FDR 100 v1

tag: natural log_adiponectin

tag: high risk profile positive (0=no/1=yes)

tag: gender (0=female; 1=male)


title: A375_singlecell_parental_cell_49

tag: treatment


title: eGFP control rep1

description: rRNA-depleted

source_name: eGFP tet-off MEF

value: eGFP


title: FDR 98 v2

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-161-01

tag: fdr visit number


title: eGFP control rep2

description: rRNA-depleted


title: A375_singlecell_parental_cell_47

source_name: Melanoma cell line


title: FDR 98 v1

tag: bmi


title: A375_singlecell_parental_cell_46


title: A375_singlecell_parental_cell_48


title: breast cancer with BSC_LR514 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: Isg20 rep2

description: rRNA-depleted

tag: tissue

tag: overexpressed target


title: A375_singlecell_parental_cell_45

tag: cell line


title: breast cancer with BSC_LR513 [nanostring]


title: A375_singlecell_parental_cell_44


title: FDR 97 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-156-01

tag: current statin use (0=no/1=yes)

tag: categories of pack-years smoking

tag: adiponectin concentration

tag: age in years

tag: crp

tag: race (nhw = non-hispanic white)

value: Other


title: FDR 96 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-154-98

tag: fdr visit number

tag: bmi

tag: natural log_adiponectin

tag: high risk profile positive (0=no/1=yes)

tag: gender (0=female; 1=male)


title: breast cancer with BSC_LR512 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)

value: pos

tag: rt (radiotherapy)

tag: lr (local recurrence)


title: breast cancer with BSC_LR511 [nanostring]

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: breast cancer with BSC_LR508 [nanostring]


title: breast cancer with BSC_LR510 [nanostring]


title: A375_singlecell_parental_cell_43

tag: cell line

tag: treatment


title: A375_singlecell_parental_cell_42


title: A375_singlecell_parental_cell_41


title: breast cancer with BSC_LR505 [nanostring]


title: FDR 94 v2

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-151-01

tag: tissue

tag: current statin use (0=no/1=yes)

tag: categories of pack-years smoking

tag: adiponectin concentration

tag: age in years


title: FDR 95 v2

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-151-02

tag: fdr visit number

tag: bmi

tag: natural log_adiponectin

tag: crp

tag: race (nhw = non-hispanic white)


title: breast cancer with BSC_LR504 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)


title: A375_singlecell_parental_cell_40


title: FDR 97 v2

tag: high risk profile positive (0=no/1=yes)

tag: gender (0=female; 1=male)


title: FDR 99 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-161-02


title: A375_singlecell_parental_cell_39

tag: cell line


title: A375_singlecell_parental_cell_38

tag: treatment


title: FDR 93 v2

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-149-99

tag: tissue


title: FDR 94 v1

tag: current statin use (0=no/1=yes)


title: breast cancer with BSC_LR503 [nanostring]

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: breast cancer with BSC_LR501 [nanostring]


title: FDR 95 v1

tag: fdr visit number

tag: bmi

tag: categories of pack-years smoking

tag: adiponectin concentration

tag: age in years


title: breast cancer with BSC_LR498 [nanostring]

tag: cohort

tag: biobank center


title: FDR 92 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-147-01

tag: natural log_adiponectin

tag: crp

tag: race (nhw = non-hispanic white)

tag: high risk profile positive (0=no/1=yes)


title: breast cancer with BSC_LR491 [nanostring]

tag: er (estrogen receptor status)


title: A375_singlecell_parental_cell_35

tag: cell line

tag: treatment


title: FDR 95 v3

tag: tissue

tag: current statin use (0=no/1=yes)

tag: gender (0=female; 1=male)


title: breast cancer with BSC_LR506 [nanostring]

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: breast cancer with BSC_LR489 [nanostring]


title: FDR 91 v3

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-146-98

tag: fdr visit number

tag: bmi

tag: categories of pack-years smoking

tag: adiponectin concentration

tag: age in years


title: FDR 91 v2

tag: natural log_adiponectin

tag: crp

tag: race (nhw = non-hispanic white)


title: breast cancer with BSC_LR484 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)


title: A375_singlecell_parental_cell_33

tag: cell line

tag: treatment


title: breast cancer with BSC_LR482 [nanostring]

tag: rt (radiotherapy)


title: FDR 91 v1

tag: tissue

tag: current statin use (0=no/1=yes)

tag: high risk profile positive (0=no/1=yes)

tag: gender (0=female; 1=male)


title: FDR 93 v1

tag: fdr visit number

tag: bmi


title: A375_singlecell_parental_cell_36


title: FDR 90 v2

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-134-98

tag: categories of pack-years smoking

tag: adiponectin concentration


title: A375_singlecell_parental_cell_31


title: breast cancer with BSC_LR479 [nanostring]

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: breast cancer with BSC_LR480 [nanostring]

tag: cohort


title: breast cancer with BSC_LR476 [nanostring]

tag: biobank center


title: A375_singlecell_parental_cell_30


title: A375_singlecell_parental_cell_37


title: A375_singlecell_parental_cell_29


title: A375_singlecell_parental_cell_34


title: FDR 89 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-128-01

tag: natural log_adiponectin

tag: age in years

tag: crp

tag: race (nhw = non-hispanic white)


title: FDR 88 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-123-01

tag: tissue


title: breast cancer with BSC_LR474 [nanostring]

tag: er (estrogen receptor status)

tag: rt (radiotherapy)


title: A375_singlecell_parental_cell_32

tag: cell line

tag: treatment


title: FDR 88 v2

tag: fdr visit number

tag: bmi

tag: current statin use (0=no/1=yes)

tag: high risk profile positive (0=no/1=yes)

tag: gender (0=female; 1=male)


title: A375_singlecell_parental_cell_27


title: A375_singlecell_parental_cell_28


title: FDR 87 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-114-98

tag: categories of pack-years smoking

tag: adiponectin concentration


title: A375_singlecell_parental_cell_26


title: breast cancer with BSC_LR469 [nanostring]

tag: cohort

tag: biobank center

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: FDR 86 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-104-01

tag: tissue

tag: natural log_adiponectin

tag: age in years

tag: crp

tag: race (nhw = non-hispanic white)


title: breast cancer with BSC_LR468 [nanostring]

tag: er (estrogen receptor status)

tag: rt (radiotherapy)


title: FDR 85 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-101-03

tag: fdr visit number

tag: bmi

tag: current statin use (0=no/1=yes)


title: FDR 90 v1

tag: categories of pack-years smoking

tag: high risk profile positive (0=no/1=yes)

tag: gender (0=female; 1=male)


title: A375_singlecell_parental_cell_24

tag: cell line

tag: treatment


title: breast cancer with BSC_LR467 [nanostring]

tag: cohort

tag: biobank center

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)


title: FDR 84 v2

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-101-01

tag: tissue

tag: adiponectin concentration

tag: natural log_adiponectin

tag: age in years


title: breast cancer with BSC_LR473 [nanostring]

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: follow-up time (years)


title: A375_singlecell_parental_cell_23


title: FDR 84 v1

tag: fdr visit number

tag: bmi

tag: current statin use (0=no/1=yes)

tag: crp

tag: race (nhw = non-hispanic white)


title: breast cancer with BSC_LR475 [nanostring]


title: FDR 83 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-088-98

tag: categories of pack-years smoking

tag: high risk profile positive (0=no/1=yes)

tag: gender (0=female; 1=male)


title: breast cancer with BSC_LR466 [nanostring]

tag: cohort

tag: biobank center

tag: lr (local recurrence)


title: FDR 82 v2

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-078-05

tag: tissue

tag: adiponectin concentration


title: FDR 81 v2

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-077-01

tag: natural log_adiponectin

tag: age in years


title: FDR 82 v1


title: A375_singlecell_parental_cell_18

tag: cell line

tag: treatment


title: breast cancer with BSC_LR455 [nanostring]

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: breast cancer with BSC_LR450 [nanostring]


title: breast cancer with BSC_LR465 [nanostring]


title: breast cancer with BSC_LR447 [nanostring]


title: A375_singlecell_parental_cell_19


title: FDR 81 v1

tag: fdr visit number

tag: bmi

tag: current statin use (0=no/1=yes)

tag: crp

tag: race (nhw = non-hispanic white)


title: A375_singlecell_parental_cell_25


title: A375_singlecell_parental_cell_17


title: breast cancer with BSC_LR445 [nanostring]

tag: cohort

tag: biobank center


title: A375_singlecell_parental_cell_16


title: A375_singlecell_parental_cell_22


title: FDR 78 v2

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-054-01

tag: tissue

tag: categories of pack-years smoking

tag: high risk profile positive (0=no/1=yes)

tag: gender (0=female; 1=male)


title: breast cancer with BSC_LR441 [nanostring]

tag: lr (local recurrence)


title: FDR 77 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-052-01

tag: adiponectin concentration

tag: natural log_adiponectin

tag: age in years


title: A375_singlecell_parental_cell_21

tag: cell line

tag: treatment


title: A375_singlecell_parental_cell_14


title: A375_singlecell_parental_cell_15


title: breast cancer with BSC_LR439 [nanostring]

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: FDR 76 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-051-98

tag: fdr visit number

tag: bmi

tag: current statin use (0=no/1=yes)

tag: crp

tag: race (nhw = non-hispanic white)


title: breast cancer with BSC_LR440 [nanostring]

tag: cohort

tag: biobank center


title: breast cancer with BSC_LR448 [nanostring]

tag: lr (local recurrence)


title: A375_singlecell_parental_cell_20


title: FDR 75 v2

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-048-02

tag: tissue

tag: categories of pack-years smoking

tag: adiponectin concentration

tag: high risk profile positive (0=no/1=yes)

tag: gender (0=female; 1=male)


title: A375_singlecell_parental_cell_13

tag: cell line

tag: treatment


title: breast cancer with BSC_LR438 [nanostring]

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: ibtr (ipsilateral breast tumor recurrence)


title: A375_singlecell_parental_cell_11


title: FDR 74 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-031-01

tag: fdr visit number

tag: bmi

tag: natural log_adiponectin

tag: age in years


title: A375_singlecell_parental_cell_10


title: breast cancer with BSC_LR437 [nanostring]

tag: cohort

tag: follow-up time (years)


title: breast cancer with BSC_LR436 [nanostring]

tag: biobank center

tag: lr (local recurrence)


title: FDR 73 v3

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-024-02

tag: tissue

tag: current statin use (0=no/1=yes)

tag: categories of pack-years smoking

tag: crp

tag: race (nhw = non-hispanic white)


title: FDR 80 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-074-01

tag: adiponectin concentration

tag: high risk profile positive (0=no/1=yes)

tag: gender (0=female; 1=male)


title: A375_singlecell_parental_cell_9

tag: cell line

tag: treatment


title: breast cancer with BSC_LR435 [nanostring]

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: ibtr (ipsilateral breast tumor recurrence)


title: FDR 79 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-058-98

tag: fdr visit number

tag: bmi

tag: natural log_adiponectin

tag: age in years


title: breast cancer with BSC_LR443 [nanostring]

tag: cohort

tag: biobank center

tag: lr (local recurrence)

tag: follow-up time (years)


title: FDR 73 v2

tag: tissue

tag: current statin use (0=no/1=yes)

tag: categories of pack-years smoking

tag: crp

tag: race (nhw = non-hispanic white)


title: breast cancer with BSC_LR434 [nanostring]


title: A375_singlecell_parental_cell_8

tag: cell line

tag: treatment


title: FDR 72 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-014-01

tag: adiponectin concentration

tag: high risk profile positive (0=no/1=yes)

tag: gender (0=female; 1=male)


title: FDR 73 v1

tag: fdr visit number

tag: bmi


title: A375_singlecell_parental_cell_12


title: A375_singlecell_parental_cell_7


title: breast cancer with BSC_LR433 [nanostring]

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: ibtr (ipsilateral breast tumor recurrence)


title: A375_singlecell_parental_cell_6


title: A375_singlecell_parental_cell_5


title: breast cancer with BSC_LR431 [nanostring]

tag: cohort

tag: biobank center

tag: lr (local recurrence)


title: FDR 71 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-011-01

tag: tissue

tag: current statin use (0=no/1=yes)

tag: natural log_adiponectin

tag: age in years


title: FDR 70 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
03-002-01

tag: categories of pack-years smoking

tag: crp

tag: race (nhw = non-hispanic white)


title: FDR 69 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
02-912-02

tag: adiponectin concentration

tag: high risk profile positive (0=no/1=yes)


title: breast cancer with BSC_LR429 [nanostring]

tag: follow-up time (years)


title: FDR 68 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
02-758-02

tag: fdr visit number

tag: bmi

tag: gender (0=female; 1=male)


title: A375_singlecell_parental_cell_3

tag: cell line

tag: treatment


title: A375_singlecell_parental_cell_4


title: FDR 67 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
02-740-01


title: breast cancer with BSC_LR426 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: ibtr (ipsilateral breast tumor recurrence)


title: breast cancer with BSC_LR427 [nanostring]

tag: lr (local recurrence)


title: breast cancer with BSC_LR428 [nanostring]


title: A375_singlecell_parental_cell_1


title: FDR 66 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
02-513-02

tag: tissue

tag: current statin use (0=no/1=yes)

tag: categories of pack-years smoking

tag: natural log_adiponectin

tag: age in years


title: 451Lu_singlecell_resistant_cell_113

value: Resistant - Cultured in 1uM PLX-4720


title: breast cancer with BSC_LR425 [nanostring]

tag: follow-up time (years)


title: FDR 65 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
02-475-98

tag: fdr visit number

tag: adiponectin concentration

tag: crp

tag: race (nhw = non-hispanic white)

tag: high risk profile positive (0=no/1=yes)


title: 451Lu_singlecell_resistant_cell_112

tag: cell line

tag: treatment


title: breast cancer with BSC_LR424 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)


title: breast cancer with BSC_LR515 [nanostring]

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)


title: 451Lu_singlecell_resistant_cell_111


title: breast cancer with BSC_LR423 [nanostring]


title: 451Lu_singlecell_resistant_cell_110


title: 451Lu_singlecell_resistant_cell_109


title: FDR 61 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-301-02

tag: tissue

tag: bmi

tag: current statin use (0=no/1=yes)

tag: categories of pack-years smoking

tag: gender (0=female; 1=male)


title: 451Lu_singlecell_resistant_cell_108


title: breast cancer with BSC_LR421 [nanostring]

tag: follow-up time (years)


title: FDR 62 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
02-226-98

tag: fdr visit number

tag: adiponectin concentration

tag: natural log_adiponectin

tag: age in years

tag: crp


title: FDR 63 v2

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
02-230-01

tag: race (nhw = non-hispanic white)

tag: high risk profile positive (0=no/1=yes)


title: breast cancer with BSC_LR419 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)


title: FDR 60 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-291-02


title: breast cancer with BSC_LR420 [nanostring]

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)


title: FDR 59 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-284-02

tag: tissue

tag: bmi

tag: current statin use (0=no/1=yes)


title: breast cancer with BSC_LR418 [nanostring]

tag: follow-up time (years)


title: 451Lu_singlecell_resistant_cell_106

tag: cell line

tag: treatment


title: 451Lu_singlecell_resistant_cell_107


title: 451Lu_singlecell_resistant_cell_105


title: FDR 64 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
02-346-01

tag: fdr visit number

tag: categories of pack-years smoking

tag: adiponectin concentration

tag: natural log_adiponectin

tag: gender (0=female; 1=male)


title: breast cancer with BSC_LR416 [nanostring]

tag: cohort


title: breast cancer with BSC_LR413 [nanostring]

tag: biobank center


title: FDR 58 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-283-01

tag: age in years

tag: crp

tag: race (nhw = non-hispanic white)

tag: high risk profile positive (0=no/1=yes)


title: breast cancer with BSC_LR412 [nanostring]

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)


title: 451Lu_singlecell_resistant_cell_104

tag: cell line


title: FDR 57 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-279-01

tag: tissue

tag: bmi

tag: current statin use (0=no/1=yes)


title: 451Lu_singlecell_resistant_cell_103

tag: treatment


title: breast cancer with BSC_LR411 [nanostring]

tag: follow-up time (years)


title: breast cancer with BSC_LR422 [nanostring]


title: FDR 56 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-262-01

tag: fdr visit number

tag: categories of pack-years smoking

tag: adiponectin concentration

tag: natural log_adiponectin

tag: gender (0=female; 1=male)


title: breast cancer with BSC_LR410 [nanostring]

tag: cohort

tag: biobank center


title: 451Lu_singlecell_resistant_cell_102


title: FDR 55 v2

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-243-01

tag: age in years

tag: crp

tag: race (nhw = non-hispanic white)

tag: high risk profile positive (0=no/1=yes)


title: 451Lu_singlecell_resistant_cell_101

tag: cell line


title: FDR 55 v1

tag: tissue


title: BB-treated tumor-15 days-rat 60

description: SAMPLE 114

hyb_protocol: After fragmentation, biotinylated cRNA were hybridized for 16h at 45 °C on GeneChip® Rat 230_ 2 . Then arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000.

data_processing: The data were normalized using RMA algorithm with the Affymetrix software Expression Console Suite.

organism: Rattus norvegicus

source_name: Cerebral tumor

growth_protocol: Rat glioblastoma cells 9L were cultured in complete medium (DMEM/Fetal bovin serum 10%/Penicillin and Streptavidin 1%) at 37°C in a humidified 5% CO2 incubator.

extract_protocol: 6 hours, 48 hours, 8 days or 15 days after treatment (MRT, BB or no treatment), brain tumors or contralateral regions, were resected and total RNA were extracted with the MirVana TM isolation kit (AppliedBiosystems)

treatment_protocol: Brain tumors were developed in Fisher rats by injection of 100.000 9L cells into the right caudate nucleus. 10 days after tumor implantation,  rats were treated with MRT radiation (90 KeV, Microbeam dose : 400 Gy, valley dose : 18 Gy, dose rate 62 Gy.mA-1.s-1) or with BB irradiation (17,4 Gy).

tag: strain

value: Fisher

value: BB irradiation

value: Orthotopic brain tumor

tag: cell type

value: 9L rat cells (Glioblastoma)

tag: time

value: 15 days


title: BB-treated tumor-15 days-rat 61

description: SAMPLE 115

tag: treatment


title: 451Lu_singlecell_resistant_cell_100


title: breast cancer with BSC_LR408 [nanostring]

value: validation

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: FDR 54 v2

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-242-03

tag: fdr visit number

tag: bmi

tag: current statin use (0=no/1=yes)

tag: categories of pack-years smoking

tag: adiponectin concentration

tag: natural log_adiponectin

tag: gender (0=female; 1=male)


title: BB-treated tumor-15 days-rat 58

description: SAMPLE 112

tag: tissue


title: 451Lu_singlecell_resistant_cell_99

tag: cell line


title: breast cancer with BSC_LR407 [nanostring]

tag: cohort

tag: biobank center


title: BB-contralateral -15 days-rat 61

description: SAMPLE 111

source_name: Normal brain

tag: strain

tag: treatment

value: Normal brain tissue

tag: time


title: FDR 57 v2

tag: age in years

tag: crp

tag: race (nhw = non-hispanic white)

tag: high risk profile positive (0=no/1=yes)


title: BB-contralateral -15 days-rat 60

description: SAMPLE 110


title: FDR 54 v1

tag: fdr visit number

tag: bmi


title: breast cancer with BSC_LR402 [nanostring]

source_name: breast cancer operated with breast conserving surgery (BSC)

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: 451Lu_singlecell_resistant_cell_98

tag: cell line


title: BB-treated tumor-15 days-rat 59

description: SAMPLE 113

tag: tissue

tag: cell type


title: FDR 53 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-242-01

tag: current statin use (0=no/1=yes)

tag: categories of pack-years smoking

tag: adiponectin concentration

tag: natural log_adiponectin

tag: gender (0=female; 1=male)


title: breast cancer with BSC_LR409 [nanostring]

tag: cohort

tag: biobank center


title: BB-contralateral -15 days-rat 59

description: SAMPLE 109

tag: strain

tag: treatment

tag: time


title: FDR 52 v2

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-232-99

tag: fdr visit number

tag: bmi

tag: age in years

tag: crp

tag: race (nhw = non-hispanic white)

tag: high risk profile positive (0=no/1=yes)


title: BB-contralateral -15 days-rat 58

description: SAMPLE 108

tag: tissue


title: BB-treated tumor-8 days-rat 57

description: SAMPLE 107

tag: cell type

value: 8 days


title: breast cancer with BSC_LR401 [nanostring]

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: BB-treated tumor-8 days-rat 56

description: SAMPLE 106


title: 451Lu_singlecell_resistant_cell_97

tag: cell line


title: 451Lu_singlecell_resistant_cell_96


title: FDR 52 v1

tag: current statin use (0=no/1=yes)

tag: categories of pack-years smoking

tag: adiponectin concentration

tag: natural log_adiponectin

tag: gender (0=female; 1=male)


title: FDR 51 v3

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-232-98

tag: fdr visit number

tag: bmi

tag: age in years


title: 451Lu_singlecell_resistant_cell_95

tag: treatment


title: breast cancer with BSC_LR399 [nanostring]

tag: cohort

tag: biobank center


title: BB-treated tumor-8 days-rat 54

description: SAMPLE 104

tag: strain

tag: tissue

tag: cell type

tag: time


title: 451Lu_singlecell_resistant_cell_94


title: FDR 51 v2

tag: crp

tag: race (nhw = non-hispanic white)

tag: high risk profile positive (0=no/1=yes)


title: 451Lu_singlecell_resistant_cell_93

tag: cell line


title: BB-treated tumor-8 days-rat 55

description: SAMPLE 105


title: breast cancer with BSC_LR396 [nanostring]

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: breast cancer with BSC_LR397 [nanostring]


title: FDR 51 v1

tag: fdr visit number

tag: bmi

tag: current statin use (0=no/1=yes)

tag: categories of pack-years smoking

tag: adiponectin concentration

tag: natural log_adiponectin

tag: age in years

tag: gender (0=female; 1=male)


title: 451Lu_singlecell_resistant_cell_92

tag: treatment


title: BB-contralateral -8 days-rat 56

description: SAMPLE 102

tag: strain

tag: tissue

tag: time


title: breast cancer with BSC_LR400 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)