title: breast cancer with BSC_LR395 [nanostring]

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)


title: BB-contralateral -8 days-rat 57

status: Public on Jul 01 2018

type: RNA

city: LA TRONCHE

first: Michèle

last: EL ATIFI

address: Chemin fortuné ferrini

country: France

institute: INSERM

description: SAMPLE 103

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.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: Normal brain

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: 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

tag: treatment

value: BB irradiation

tag: tissue

value: Normal brain tissue

tag: time

value: 8 days


title: FDR 49 v1

type: protein

city: La Jolla

first: Jan

middle: M

last: Hughes-Austin

state: CA

address: 9500 Gilman Drive

department: Orthopaedic Surgery

country: USA

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.
01-221-98

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

organism: Homo sapiens

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 50 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-229-02


title: breast cancer with BSC_LR394 [nanostring]

city: Lund

first: Martin

last: Sjöström

address: Scheelevägen 2

country: Sweden

institute: Lund University

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.

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

extract_protocol: Qiagen AllPrep kit with Qiacube automatization

tag: cohort

value: validation

tag: biobank center

tag: er (estrogen receptor status)

value: pos

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: follow-up time (years)


title: BB-contralateral -8 days-rat 54

description: SAMPLE 100

tag: strain

tag: treatment

tag: tissue

tag: time


title: 451Lu_singlecell_resistant_cell_91

type: SRA

city: Cold Spring Harbor

first: Molly

last: Hammell

state: New York

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

library_source: transcriptomic

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: cell line

value: Resistant - Cultured in 1uM PLX-4720


title: BB-contralateral -8 days-rat 55

description: SAMPLE 101


title: 451Lu_singlecell_resistant_cell_90


title: FDR 48 v2

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-221-04

tag: fdr visit number

tag: bmi

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

tag: categories of pack-years smoking

tag: adiponectin concentration

tag: natural log_adiponectin


title: 451Lu_singlecell_resistant_cell_89


title: BB-treated tumor-48 h-rat 52

description: SAMPLE 99

source_name: Cerebral tumor

value: Orthotopic brain tumor

tag: cell type

value: 9L rat cells (Glioblastoma)


title: BB-treated tumor-48 h-rat 51

description: SAMPLE 98


title: breast cancer with BSC_LR391 [nanostring]

tag: cohort

tag: biobank center

tag: ibtr (ipsilateral breast tumor recurrence)


title: breast cancer with BSC_LR389 [nanostring]

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)


title: 451Lu_singlecell_resistant_cell_88

tag: treatment


title: FDR 47 v2

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-209-01

tag: tissue

tag: age in years

tag: crp

tag: race (nhw = non-hispanic white)

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

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


title: 451Lu_singlecell_resistant_cell_87

tag: cell line


title: FDR 47 v1

tag: fdr visit number

tag: bmi

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

tag: categories of pack-years smoking

tag: adiponectin concentration


title: BB-treated tumor-48 h-rat 50

description: SAMPLE 96

tag: strain

tag: cell type

tag: time


title: BB-treated tumor-48 h-rat 53

description: SAMPLE 97


title: breast cancer with BSC_LR388 [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_LR387 [nanostring]


title: 451Lu_singlecell_resistant_cell_86

tag: treatment


title: breast cancer with BSC_LR392 [nanostring]


title: FDR 46 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-199-01

tag: tissue

tag: natural log_adiponectin

tag: age in years

tag: crp

tag: race (nhw = non-hispanic white)

value: Other

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

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


title: breast cancer with BSC_LR384 [nanostring]


title: FDR 46 v2

tag: fdr visit number

tag: bmi

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

tag: categories of pack-years smoking

tag: adiponectin concentration


title: breast cancer with BSC_LR383 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)

tag: rt (radiotherapy)


title: FDR 45 v2

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-198-01


title: breast cancer with BSC_LR382 [nanostring]

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: 451Lu_singlecell_resistant_cell_85

tag: cell line

tag: treatment


title: 451Lu_singlecell_resistant_cell_83


title: FDR 45 v1

tag: tissue

tag: natural log_adiponectin

tag: age in years

tag: crp

tag: race (nhw = non-hispanic white)


title: FDR 48 v1

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_2

value: Parental - no Treatment


title: 451Lu_singlecell_resistant_cell_84


title: breast cancer with BSC_LR381 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)


title: BB-treated tumor-6 h-rat 49

description: SAMPLE 92

tag: strain

tag: cell type

tag: time


title: 451Lu_singlecell_resistant_cell_82

tag: cell line

tag: treatment


title: FDR 44 v2

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-192-02

tag: tissue

tag: categories of pack-years smoking

tag: adiponectin concentration

tag: natural log_adiponectin


title: BB-contralateral -48 h-rat 50

description: SAMPLE 93


title: BB-contralateral -48 h-rat 51

description: SAMPLE 94


title: 451Lu_singlecell_resistant_cell_81


title: breast cancer with BSC_LR376 [nanostring]

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: BB-treated tumor-6 h-rat 48

description: SAMPLE 91


title: FDR 44 v1

tag: fdr visit number

tag: bmi

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

tag: age in years

tag: crp

tag: race (nhw = non-hispanic white)

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

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


title: 451Lu_singlecell_resistant_cell_80

tag: cell line

tag: treatment


title: BB-treated tumor-6 h-rat 47

description: SAMPLE 90

tag: strain

tag: tissue

tag: cell type

tag: time


title: breast cancer with BSC_LR374 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)


title: FDR 43 v3

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-192-01

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


title: BB-contralateral -48 h-rat 52

description: SAMPLE 95


title: breast cancer with BSC_LR372 [nanostring]

value: neg

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: BB-treated tumor-6 h-rat 46

description: SAMPLE 89

tag: strain

tag: treatment


title: FDR 43 v2

tag: tissue

tag: age in years

tag: crp

tag: race (nhw = non-hispanic white)

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

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


title: breast cancer with BSC_LR371 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)


title: BB-treated tumor-6 h-rat 45

description: SAMPLE 88

tag: cell type

tag: time


title: 451Lu_singlecell_resistant_cell_77

tag: cell line


title: breast cancer with BSC_LR370 [nanostring]

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: FDR 43 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


title: FDR 42 v2

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-189-01

tag: tissue

tag: age in years

tag: crp

tag: race (nhw = non-hispanic white)

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

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


title: breast cancer with BSC_LR369 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)


title: 451Lu_singlecell_resistant_cell_78

tag: cell line

tag: treatment


title: FDR 42 v1

tag: fdr visit number

tag: bmi

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


title: BB-contralateral -6 h-rat 49

description: SAMPLE 86

tag: strain

tag: time


title: 451Lu_singlecell_resistant_cell_76


title: breast cancer with BSC_LR368 [nanostring]

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: 451Lu_singlecell_resistant_cell_75


title: FDR 41 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-188-02

tag: tissue

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)


title: BB-contralateral -6 h-rat 48

description: SAMPLE 85


title: FDR 40 v3

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-184-01

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

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


title: 451Lu_singlecell_resistant_cell_74

tag: cell line

tag: treatment


title: BB-contralateral -6 h-rat 47

description: SAMPLE 84


title: breast cancer with BSC_LR367 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)


title: 451Lu_singlecell_resistant_cell_79


title: breast cancer with BSC_LR366 [nanostring]

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: FDR 40 v2

tag: fdr visit number

tag: tissue

tag: bmi

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

tag: categories of pack-years smoking


title: 451Lu_singlecell_resistant_cell_73


title: BB-treated tumor-6 h-rat 44

description: SAMPLE 87

tag: strain

tag: cell type

tag: time


title: 451Lu_singlecell_resistant_cell_72

tag: cell line


title: breast cancer with BSC_LR365 [nanostring]


title: BB-contralateral -6 h-rat 46

description: SAMPLE 83

tag: treatment


title: BB-contralateral -6 h-rat 45

description: SAMPLE 82


title: 451Lu_singlecell_resistant_cell_71


title: FDR 39 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-183-98

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)

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


title: 451Lu_singlecell_resistant_cell_70


title: FDR 38 v3

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-173-01

tag: fdr visit number


title: FDR 40 v1

tag: tissue


title: 451Lu_singlecell_resistant_cell_69


title: FDR 38 v2

tag: bmi


title: MRT-contralateral -15 days-rat 42

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

data_processing:
The data were normalized using RMA algorithm with the Affymetrix software Expression Console Suite.
Moreover, the probesets detection were flagged as Present (P) or Absent (A) using MAS5 processing.

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

value: 15 days

value: MRT irradiation


title: 451Lu_singlecell_resistant_cell_68


title: FDR 38 v1

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


title: 451Lu_singlecell_resistant_cell_67


title: FDR 37 v3

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-167-01

tag: categories of pack-years smoking


title: 451Lu_singlecell_resistant_cell_66


title: FDR 37 v2


title: 451Lu_singlecell_resistant_cell_65


title: breast cancer with BSC_LR364 [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: MRT-contralateral -15 days-rat 40

tag: time

tag: treatment


title: FDR 37 v1

tag: adiponectin concentration

tag: natural log_adiponectin

tag: age in years

tag: crp

tag: race (nhw = non-hispanic white)


title: 451Lu_singlecell_resistant_cell_64

tag: cell line


title: MRT-contralateral -15 days-rat 43

tag: tissue


title: FDR 36 v4

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-163-01

tag: fdr visit number

tag: bmi

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

tag: categories of pack-years smoking

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

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


title: 451Lu_singlecell_resistant_cell_63


title: 451Lu_singlecell_resistant_cell_62


title: Wild Type N°4

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

institute: INRA

hyb_protocol: 600 ng of Cy3-cRNA was fragmented and hybridized on a sub-array. Hybridization was carried out for 17 hours at 65°C in a rotating hybridization oven prior to washing.

scan_protocol: Microarrays were scanned with an Agilent Scanner (Agilent DNA Microarray Scanner, Agilent Technologies, Massy, France) using the standard parameters for a gene expression 8x60K oligoarray (3µm and 20bits)

data_processing: Data were then obtained with the Agilent Feature Extraction software (10.7.3.1) according to the appropriate GE protocol (GE1_107_Sep09), scale normalized and log transformed using Genespring software (Agilent).

organism: Oryzias latipes

source_name: Wild Type

label_protocol: Labeling and hybridization steps were performed following the “One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling)”Agilent protocol. Briefly, for each sample, 150 ng of total RNA was amplified and labeled using Cy3-CTP. Yield (>0.825µg cRNA) and specific activity (> 6pmol of Cy3 per µg of cRNA) of Cy3-cRNA produced were checked with the Nanodrop.

extract_protocol: Total RNAs were extracted from adult medaka testes using the Tri-reagent (Sigma-Aldrich) according to the supplier’s recommendation. The total RNA yield was estimated using a Nanodrop ND-1000 spectrophotometer (Labtech, Palaiseau, France) and RNA integrity was checked with an Agilent Bioanalyzer (Agilent Technologies, Massy, France).

treatment_protocol: Transgenic fish were generated using the CRISPR/Cas 9 technology targeting intron #2 and exon #5 of the ol-bsf gene. This resulted in the excision of the whole fragment containing [intron#2 (79bp), exon #3 (123bp), intron#3 (258bp), exon#4 (122bp), intron#4 (119bp) and part of exon#5], creating a frame shift after exon 3 of the ol-bsf gene. This translates into a truncated non-functional OL-BSF protein.

tag: genotype/variation

value: wild type

tag: developmental stage

value: adult

value: testes


title: MRT- treated tumor-15 days-rat 42

tag: time

tag: cell type


title: breast cancer with BSC_LR363 [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: MRT- treated tumor-15 days-rat 43

tag: treatment

tag: tissue


title: BB-contralateral -6 h-rat 44

description: SAMPLE 81

tag: strain

value: Fisher

value: BB irradiation

value: Normal brain tissue


title: Wild Type N°3


title: MRT-contralateral -15 days-rat 41


title: FDR 36 v3

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


title: FDR 36 v2

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

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


title: breast cancer with BSC_LR362 [nanostring]

tag: cohort

value: validation

tag: biobank center

tag: er (estrogen receptor status)

value: pos

tag: rt (radiotherapy)

tag: lr (local recurrence)


title: breast cancer with BSC_LR359 [nanostring]

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: 451Lu_singlecell_resistant_cell_61

tag: cell line

tag: treatment

value: Resistant - Cultured in 1uM PLX-4720


title: 451Lu_singlecell_resistant_cell_60


title: MRT- treated tumor-15 days-rat 41

tag: time

tag: tissue

value: Orthotopic brain tumor

tag: cell type

value: 9L rat cells (Glioblastoma)


title: Wild Type N°1

tag: genotype/variation

tag: developmental stage


title: Transgenic fish N°4

source_name: Transgenic fish

value: ol-bsf gene mutation


title: MRT-contralateral -8 days-rat 35

value: 8 days


title: Wild Type N°2


title: MRT-contralateral -8 days-rat 37


title: Transgenic fish N°5


title: breast cancer with BSC_LR358 [nanostring]


title: MRT-contralateral -8 days-rat 34


title: 451Lu_singlecell_resistant_cell_59


title: MRT- treated tumor-15 days-rat 40

value: 15 days


title: MRT-contralateral -8 days-rat 38

value: MRT irradiation


title: 451Lu_singlecell_resistant_cell_58


title: 451Lu_singlecell_resistant_cell_57


title: FDR 36 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: crp

tag: race (nhw = non-hispanic white)


title: breast cancer with BSC_LR357 [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: FDR 35 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-162-01

tag: tissue

value: Other

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

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


title: breast cancer with BSC_LR356 [nanostring]


title: FDR 34 v3

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-154-99

tag: fdr visit number

tag: bmi

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


title: 451Lu_singlecell_resistant_cell_56

tag: cell line

tag: treatment


title: Transgenic fish N°2

tag: genotype/variation

tag: developmental stage

value: adult


title: FDR 33 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-154-98

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)


title: FDR 35 v3


title: FDR 35 v2


title: breast cancer with BSC_LR354 [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: FDR 32 v3

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-150-03

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)

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


title: breast cancer with BSC_LR353 [nanostring]

value: neg


title: breast cancer with BSC_LR349 [nanostring]


title: 451Lu_singlecell_resistant_cell_55

tag: cell line

tag: treatment


title: 451Lu_singlecell_resistant_cell_54


title: FDR 32 v2

tag: categories of pack-years smoking

tag: adiponectin concentration

tag: natural log_adiponectin

tag: age in years

tag: crp


title: FDR 32 v1

tag: race (nhw = non-hispanic white)


title: breast cancer with BSC_LR347 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)


title: Transgenic fish N°3

tag: genotype/variation

tag: developmental stage

tag: tissue

value: testes


title: FDR 31 v3

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-135-99

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: MRT-contralateral -8 days-rat 33

tag: time

tag: treatment


title: 451Lu_singlecell_resistant_cell_51

tag: cell line


title: breast cancer with BSC_LR346 [nanostring]

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: MRT-contralateral -8 days-rat 32


title: FDR 31 v2

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)


title: Untreated contralateral -8 days-rat 29

value: No irradiation

tag: tissue


title: Untreated contralateral -8 days-rat 30

value: Normal brain tissue


title: Untreated contralateral -8 days-rat 28


title: MRT- treated tumor-8 days-rat 37

tag: cell type


title: MRT- treated tumor-8 days-rat 38


title: breast cancer with BSC_LR345 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)


title: MRT- treated tumor-8 days-rat 36

tag: time

tag: treatment


title: 451Lu_singlecell_resistant_cell_50

tag: cell line


title: FDR 31 v1

tag: fdr visit number

value: serum

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: 451Lu_singlecell_resistant_cell_53


title: 451Lu_singlecell_resistant_cell_49


title: breast cancer with BSC_LR344 [nanostring]

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: MRT- treated tumor-8 days-rat 35

tag: tissue


title: 451Lu_singlecell_resistant_cell_52


title: breast cancer with BSC_LR348 [nanostring]


title: Untreated contralateral -8 days-rat 39


title: breast cancer with BSC_LR343 [nanostring]


title: 451Lu_singlecell_resistant_cell_48


title: 451Lu_singlecell_resistant_cell_47


title: FDR 29 v4

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-113-01

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)

value: NHW


title: breast cancer with BSC_LR341 [nanostring]

tag: cohort

value: validation

tag: biobank center

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)


title: FDR 29 v3

tag: fdr visit number

tag: bmi

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


title: 451Lu_singlecell_resistant_cell_46

tag: cell line

tag: treatment


title: FDR 29 v1

tag: tissue

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

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


title: breast cancer with BSC_LR340 [nanostring]

value: pos

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: 451Lu_singlecell_resistant_cell_44

value: Resistant - Cultured in 1uM PLX-4720


title: 451Lu_singlecell_resistant_cell_45


title: MRT- treated tumor-8 days-rat 32

tag: time

value: Orthotopic brain tumor

tag: cell type


title: FDR 28 v3

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-108-01

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)


title: MRT- treated tumor-8 days-rat 34

value: 9L rat cells (Glioblastoma)


title: FDR 28 v2

tag: fdr visit number

tag: bmi


title: FDR 30 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-134-02

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


title: 451Lu_singlecell_resistant_cell_42

tag: cell line

tag: treatment


title: breast cancer with BSC_LR336 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)


title: breast cancer with BSC_LR335 [nanostring]

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: FDR 28 v1

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: 451Lu_singlecell_resistant_cell_41


title: 451Lu_singlecell_resistant_cell_43


title: FDR 29 v2

tag: fdr visit number

tag: natural log_adiponectin

tag: age in years

tag: crp

tag: race (nhw = non-hispanic white)


title: breast cancer with BSC_LR338 [nanostring]

tag: cohort


title: breast cancer with BSC_LR339 [nanostring]

tag: biobank center


title: breast cancer with BSC_LR333 [nanostring]

tag: er (estrogen receptor status)


title: FDR 27 v1

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

tag: bmi

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


title: MRT- treated tumor-8 days-rat 33

tag: time

tag: treatment

tag: cell type


title: MRT-contralateral -48 h-rat 26

tag: tissue


title: Untreated tumor-8 days-rat 27


title: Untreated tumor-8 days-rat 28


title: 451Lu_singlecell_resistant_cell_40

tag: cell line


title: FDR 26 v4

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-099-01

tag: categories of pack-years smoking

tag: adiponectin concentration

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


title: breast cancer with BSC_LR330 [nanostring]

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: 451Lu_singlecell_resistant_cell_38


title: MRT-contralateral -48 h-rat 25


title: breast cancer with BSC_LR329 [nanostring]

tag: cohort


title: FDR 26 v3

tag: fdr visit number

tag: natural log_adiponectin

tag: age in years

tag: crp

tag: race (nhw = non-hispanic white)

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


title: Untreated tumor-8 days-rat 30

tag: time

tag: treatment

tag: cell type


title: Untreated tumor-8 days-rat 29

tag: tissue


title: FDR 26 v2

tag: bmi

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

tag: categories of pack-years smoking

tag: adiponectin concentration


title: MRT-contralateral -48 h-rat 23


title: MRT-contralateral -48 h-rat 21


title: FDR 26 v1

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


title: FDR 25 v2

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-098-01


title: 451Lu_singlecell_resistant_cell_37

tag: cell line


title: breast cancer with BSC_LR328 [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: MRT-contralateral -48 h-rat 20

tag: time


title: breast cancer with BSC_LR332 [nanostring]


title: MRT-contralateral -48 h-rat 22

tag: treatment


title: MRT-contralateral -48 h-rat 19


title: 451Lu_singlecell_resistant_cell_36


title: FDR 25 v1

tag: fdr visit number

tag: natural log_adiponectin

tag: age in years

tag: crp

tag: race (nhw = non-hispanic white)

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


title: breast cancer with BSC_LR323 [nanostring]


title: 451Lu_singlecell_resistant_cell_35


title: 451Lu_singlecell_resistant_cell_39


title: breast cancer with BSC_LR322 [nanostring]


title: 451Lu_singlecell_resistant_cell_34


title: breast cancer with BSC_LR321 [nanostring]


title: FDR 24 v3

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-096-01

tag: tissue

tag: bmi

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

tag: categories of pack-years smoking

tag: adiponectin concentration

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


title: 451Lu_singlecell_resistant_cell_33

tag: cell line


title: FDR 23 v5

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-081-01


title: Untreated contralateral -48 h-rat 18


title: breast cancer with BSC_LR317 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)


title: breast cancer with BSC_LR320 [nanostring]

tag: follow-up time (years)


title: Untreated contralateral -48 h-rat 16

tag: time

tag: treatment


title: 451Lu_singlecell_resistant_cell_32


title: Untreated contralateral -48 h-rat 15


title: FDR 23 v4

tag: fdr visit number

tag: natural log_adiponectin

tag: age in years

tag: crp

tag: race (nhw = non-hispanic white)

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


title: FDR 23 v3

tag: tissue

tag: bmi

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

tag: categories of pack-years smoking

tag: adiponectin concentration

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


title: breast cancer with BSC_LR313 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)


title: 451Lu_singlecell_resistant_cell_29

tag: cell line

tag: treatment


title: breast cancer with BSC_LR312 [nanostring]

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: 451Lu_singlecell_resistant_cell_30


title: 451Lu_singlecell_resistant_cell_31


title: breast cancer with BSC_LR311 [nanostring]


title: FDR 23 v1

tag: fdr visit number

tag: natural log_adiponectin

tag: age in years

tag: crp

tag: race (nhw = non-hispanic white)


title: breast cancer with BSC_LR310 [nanostring]


title: FDR 22 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-076-99

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: Untreated contralateral -48 h-rat 17

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

tag: time


title: 451Lu_singlecell_resistant_cell_27


title: 451Lu_singlecell_resistant_cell_28


title: FDR 21 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-076-98

tag: adiponectin concentration

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


title: breast cancer with BSC_LR308 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)


title: 451Lu_singlecell_resistant_cell_26

tag: cell line

tag: treatment


title: breast cancer with BSC_LR307 [nanostring]

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: breast cancer with BSC_LR309 [nanostring]


title: FDR 23 v2

tag: fdr visit number

tag: tissue

tag: natural log_adiponectin

tag: age in years

tag: crp

tag: race (nhw = non-hispanic white)


title: 451Lu_singlecell_resistant_cell_25


title: breast cancer with BSC_LR306 [nanostring]


title: FDR 20 v3

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

tag: bmi

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

tag: categories of pack-years smoking

tag: adiponectin concentration

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


title: 451Lu_singlecell_resistant_cell_24


title: MRT- treated tumor-48 h-rat 26

tag: time

tag: cell type


title: 451Lu_singlecell_resistant_cell_23

tag: cell line


title: 451Lu_singlecell_resistant_cell_22

tag: treatment


title: MRT- treated tumor-48 h-rat 25


title: MRT- treated tumor-48 h-rat 23


title: MRT- treated tumor-48 h-rat 24


title: MRT- treated tumor-48 h-rat 21


title: breast cancer with BSC_LR305 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)


title: breast cancer with BSC_LR304 [nanostring]

tag: follow-up time (years)


title: FDR 19 v2

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-068-98

tag: fdr visit number

tag: tissue

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: MRT- treated tumor-48 h-rat 22

tag: time

tag: cell type


title: 451Lu_singlecell_resistant_cell_21

tag: cell line

tag: treatment


title: FDR 19 v3

tag: bmi

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

tag: categories of pack-years smoking

tag: adiponectin concentration

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


title: FDR 20 v1


title: breast cancer with BSC_LR303 [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: MRT- treated tumor-48 h-rat 19

tag: tissue


title: Untreated tumor-48 h-rat 17

tag: time


title: MRT- treated tumor-48 h-rat 20

tag: cell type


title: Untreated tumor-48 h-rat 18


title: FDR 20 v2

tag: fdr visit number

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: FDR 19 v1

tag: bmi

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

tag: categories of pack-years smoking

tag: adiponectin concentration

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


title: FDR 18 v3

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-068-01


title: 451Lu_singlecell_resistant_cell_20

tag: cell line

tag: treatment


title: Untreated tumor-48 h-rat 16


title: 451Lu_singlecell_resistant_cell_19


title: breast cancer with BSC_LR301 [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_LR302 [nanostring]


title: breast cancer with BSC_LR300 [nanostring]


title: 451Lu_singlecell_resistant_cell_18


title: FDR 18 v2

tag: fdr visit number

tag: tissue

tag: natural log_adiponectin

tag: age in years

tag: crp


title: Untreated tumor-48 h-rat 15

tag: time

tag: cell type


title: MRT-contralateral-6 h-rat 14


title: 451Lu_singlecell_resistant_cell_16


title: 451Lu_singlecell_resistant_cell_17


title: FDR 18 v1

tag: bmi

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

tag: categories of pack-years smoking

tag: adiponectin concentration

tag: race (nhw = non-hispanic white)

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

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


title: breast cancer with BSC_LR299 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)


title: FDR 17 v3

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-061-98

tag: fdr visit number

tag: tissue

tag: natural log_adiponectin


title: FDR 17 v4

tag: age in years

tag: crp


title: breast cancer with BSC_LR298 [nanostring]

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: FDR 17 v2

tag: bmi

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

tag: categories of pack-years smoking


title: breast cancer with BSC_LR297 [nanostring]


title: MRT-contralateral-6 h-rat 11

tag: time

tag: treatment


title: 451Lu_singlecell_resistant_cell_15

tag: cell line


title: MRT-contralateral-6 h-rat 13


title: MRT-contralateral-6 h-rat 12


title: breast cancer with BSC_LR296 [nanostring]

tag: cohort

tag: biobank center


title: MRT-contralateral -6 h-rat 10


title: MRT-contralateral -6 h-rat 8


title: 451Lu_singlecell_resistant_cell_14


title: FDR 17 v1

tag: adiponectin concentration

tag: race (nhw = non-hispanic white)

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

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


title: 451Lu_singlecell_resistant_cell_13


title: FDR 16 v4

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-060-01

tag: fdr visit number

tag: tissue

tag: natural log_adiponectin


title: 451Lu_singlecell_resistant_cell_12


title: FDR 16 v3

tag: age in years

tag: crp


title: 451Lu_singlecell_resistant_cell_11


title: breast cancer with BSC_LR293 [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: FDR 16 v2

tag: bmi

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

tag: categories of pack-years smoking


title: MRT-contralateral -6 h-rat 7

tag: time

tag: treatment


title: 451Lu_singlecell_resistant_cell_10

tag: cell line


title: breast cancer with BSC_LR290 [nanostring]

tag: cohort

tag: biobank center


title: 451Lu_singlecell_resistant_cell_9


title: FDR 16 v1

tag: fdr visit number

tag: tissue

tag: adiponectin concentration

tag: race (nhw = non-hispanic white)

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

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


title: FDR 15 v2

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-056-01

tag: natural log_adiponectin

tag: age in years

tag: crp


title: 451Lu_singlecell_resistant_cell_8


title: breast cancer with BSC_LR286 [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: FDR 15 v1

tag: bmi

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

tag: categories of pack-years smoking


title: breast cancer with BSC_LR283 [nanostring]

tag: cohort

tag: biobank center


title: breast cancer with BSC_LR295 [nanostring]


title: MRT-contralateral -6 h-rat 9

tag: time

tag: treatment

tag: tissue


title: breast cancer with BSC_LR282 [nanostring]


title: Untreated contralateral -6 h-rat 5


title: FDR 14 v4

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-055-01

tag: fdr visit number

tag: adiponectin concentration

tag: race (nhw = non-hispanic white)

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

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


title: breast cancer with BSC_LR280 [nanostring]

tag: er (estrogen receptor status)

tag: rt (radiotherapy)


title: Untreated contralateral -6 h-rat 4


title: breast cancer with BSC_LR287 [nanostring]

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)


title: FDR 14 v3

tag: bmi

tag: natural log_adiponectin

tag: age in years

tag: crp


title: Untreated contralateral -6 h-rat 3


title: Untreated contralateral -6 h-rat 2


title: MRT-contralateral -6 h-rat 6


title: Untreated contralateral -6 h-rat 1


title: FDR 14 v2

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

tag: categories of pack-years smoking


title: 451Lu_singlecell_resistant_cell_5

tag: cell line

tag: treatment


title: breast cancer with BSC_LR279 [nanostring]

tag: cohort

tag: biobank center

tag: follow-up time (years)


title: 451Lu_singlecell_resistant_cell_6


title: breast cancer with BSC_LR277 [nanostring]


title: 451Lu_singlecell_resistant_cell_4


title: 451Lu_singlecell_resistant_cell_7


title: FDR 14 v1

tag: fdr visit number

tag: tissue

tag: adiponectin concentration

tag: race (nhw = non-hispanic white)

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


title: MRT- treated tumor-6 h-rat 14

tag: time

tag: cell type


title: FDR 13 v2

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-051-98

tag: bmi

tag: natural log_adiponectin

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


title: 451Lu_singlecell_resistant_cell_3


title: MRT- treated tumor-6 h-rat 12


title: 451Lu_singlecell_resistant_cell_2


title: breast cancer with BSC_LR275 [nanostring]

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)


title: FDR 13 v1

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

tag: categories of pack-years smoking

tag: age in years

tag: crp


title: breast cancer with BSC_LR274 [nanostring]

tag: cohort

tag: biobank center

tag: follow-up time (years)


title: MRT- treated tumor-6 h-rat 11

tag: treatment

tag: tissue


title: 451Lu_singlecell_resistant_cell_1

tag: cell line


title: MRT- treated tumor-6 h-rat 10

tag: time

tag: cell type


title: MRT- treated tumor-6 h-rat 13


title: breast cancer with BSC_LR271 [nanostring]


title: MRT- treated tumor-6 h-rat 9


title: FDR 12 v3

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-048-01

tag: fdr visit number

tag: bmi

tag: adiponectin concentration

tag: natural log_adiponectin

tag: race (nhw = non-hispanic white)

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

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


title: 451Lu_singlecell_parental_cell_83

value: Parental - no Treatment


title: MRT- treated tumor-6 h-rat 8


title: 451Lu_singlecell_parental_cell_84


title: breast cancer with BSC_LR276 [nanostring]

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)


title: FDR 12 v4

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

tag: categories of pack-years smoking

tag: age in years

tag: crp


title: FDR 12 v2

tag: tissue


title: breast cancer with BSC_LR268 [nanostring]

tag: cohort

tag: biobank center

tag: follow-up time (years)


title: 451Lu_singlecell_parental_cell_81

tag: cell line

tag: treatment


title: FDR 12 v1

tag: fdr visit number

tag: bmi

tag: adiponectin concentration

tag: natural log_adiponectin

tag: race (nhw = non-hispanic white)


title: 451Lu_singlecell_parental_cell_80


title: breast cancer with BSC_LR267 [nanostring]

value: training

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)


title: breast cancer with BSC_LR270 [nanostring]

tag: ibtr (ipsilateral breast tumor recurrence)


title: MRT- treated tumor-6h-rat 6

tag: time

tag: cell type


title: breast cancer with BSC_LR266 [nanostring]


title: FDR 11 v2

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-046-01

tag: tissue

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

tag: categories of pack-years smoking

tag: age in years

tag: crp

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

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


title: breast cancer with BSC_LR265 [nanostring]

tag: cohort

tag: biobank center

tag: follow-up time (years)


title: MRT- treated tumor-6 h-rat 7

tag: treatment


title: FDR 11 v1

tag: fdr visit number

tag: bmi

tag: adiponectin concentration

tag: natural log_adiponectin

tag: race (nhw = non-hispanic white)


title: breast cancer with BSC_LR254 [nanostring]

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)


title: FDR 10 v4

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-043-01

tag: tissue

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

tag: categories of pack-years smoking

tag: age in years


title: Untreated tumor-6 h-rat 5

tag: time

tag: cell type


title: Untreated tumor-6 h-rat 3


title: 451Lu_singlecell_parental_cell_82

tag: cell line


title: 451Lu_singlecell_parental_cell_78

tag: treatment


title: FDR 11 v3

tag: fdr visit number

tag: crp

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

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


title: breast cancer with BSC_LR253 [nanostring]

tag: cohort

tag: biobank center

tag: follow-up time (years)


title: FDR 10 v3

tag: bmi

tag: adiponectin concentration

tag: natural log_adiponectin

tag: race (nhw = non-hispanic white)


title: 451Lu_singlecell_parental_cell_76


title: 451Lu_singlecell_parental_cell_77


title: Untreated tumor-6 h-rat 4

tag: tissue


title: FDR 10 v2

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

tag: categories of pack-years smoking

tag: age in years


title: 451Lu_singlecell_parental_cell_79

tag: cell line


title: 451Lu_singlecell_parental_cell_75

tag: treatment


title: Untreated tumor-6 h-rat 1

tag: time

tag: cell type


title: breast cancer with BSC_LR251 [nanostring]

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)


title: Untreated tumor-6 h-rat 2


title: breast cancer with BSC_LR252 [nanostring]

tag: cohort

tag: biobank center

tag: follow-up time (years)


title: FDR 10 v1

tag: fdr visit number

tag: bmi

tag: adiponectin concentration

tag: natural log_adiponectin

tag: crp

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

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


title: breast cancer with BSC_LR250 [nanostring]


title: 451Lu_singlecell_parental_cell_74

tag: cell line

tag: treatment


title: 451Lu_singlecell_parental_cell_73


title: breast cancer with BSC_LR249 [nanostring]


title: breast cancer with BSC_LR248 [nanostring]


title: 451Lu_singlecell_parental_cell_71


title: FDR 8 v2

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-017-02

tag: tissue

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

tag: categories of pack-years smoking

tag: age in years

tag: race (nhw = non-hispanic white)


title: FDR 8 v3


title: breast cancer with BSC_LR246 [nanostring]

tag: cohort

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)


title: FDR 9 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-020-01

tag: fdr visit number

tag: bmi

tag: adiponectin concentration


title: breast cancer with BSC_LR247 [nanostring]

tag: biobank center

tag: follow-up time (years)


title: 4538 F 139

city: Bar Harbor

first: Jason

middle: A

last: Bubier

state: ME

address: 600 Main St

institute: The Jackson Laboratory

hyb_protocol: The resulting cRNA was column purified, quantitated, and diluted to 150 ng/µl in RNase free water. The sample was then applied to a BeadChip (Illumina MouseWG-6 v2 BeadChip) and hybridized overnight at 58ºC to allow the cRNA to anneal to the oligonucleotides corresponding to their specific gene. The BeadChips were then washed, blocked with E1, and fluorescently labeled with streptavidin-Cy3

scan_protocol: BeadChips were dried by spinning 300 rpm for 4 min in a benchtop centrifuge and imaged using the Illumina BeadArray Reader

data_processing: Image data obtained from the BeadArray Reader was analyzed using BeadStudio version 3.0.19 with Gene Expression module 3.0.14. Rank invariant normalization was used with no background subtraction. We filtered the probes that targeted polymorphic sequence due to the bias introduced by microarray probe-target variation in genetic studies and the high density of mouse polymorphisms in the CC. The probes on the Ilumina Mouse WG-6v2.0 Bead Chip were tested by comparing the sequenced genomes from Sanger Wellcome Trust (https://www.sanger.ac.uk/) 78 to determine if they contained a SNP between the strains. 8,972 probes were removed due to SNPs in one of the eight strains and 36,308 probes remained for subsequent QTL mapping and genetic correlation analysis.

organism: Mus musculus

source_name: cecal tissue

label_protocol: All assay methods conformed to the exact protocol listed in the Whole-Genome Gene Expression Assay Manual. Diluted RNA (11 µl, ~500ng) was converted to biotinylated cRNA using the Illumina TotalPrep RNA Amplification Kit (Ambion). First, single-stranded cDNA was synthesized from the total RNA using the T7 Oligo(dT) primer, then converted to double-stranded cDNA using the combination of DNA polymerase and RNase H. Second, the cDNA was transcribed to biotinylated cRNA using the T7 enzyme and biotin-labled NTP’s.

extract_protocol: Each dissected cecum was filled with a solution of 1.5mM KCL/96 mM NaCl/27mM NaCitrate/8mM KH2PO4/5.6 mM Na2HPO4, pH7.3. were incubated at 37°C after which the intestines were rinsed and filled with Phosphate-buffered saline/1.5 mM EDTA/0.5 mM dithiothreitol. They were incubated at 37°C in a conical centrifuge tube. After an incubation time of 15 minutes, the tube was centrifuged at 900 x g. The resulting pellet was rinsed 3x in Phosphate-buffered saline (centrifuged at 900 x g for 5 minutes after each rinse). The resulting cell pellet was suspended in Trizol (Invitrogen) and RNA was purified by column chromatography as specified by the manufacturer’s protocol. Purified total RNA was fluorescently labeled with riboGreen (Invitrogen) and quantitated using a Spectamax Gemini XPS spectrofluorometer (Molecular Devices). RNA was then prepared for assay by diluting to 50 ng/µl in RNase free water and transferring to a clean 1.5 ml assay tube.

tag: gender

value: F

tag: animal id


title: 451Lu_singlecell_parental_cell_69

tag: cell line

tag: treatment


title: FDR 8 v1

tag: tissue

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

tag: categories of pack-years smoking

tag: natural log_adiponectin

tag: crp

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

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


title: 5515 F 133


title: 451Lu_singlecell_parental_cell_68


title: 821 F 44


title: FDR 9 v2

tag: age in years

tag: race (nhw = non-hispanic white)


title: 1401 F 135


title: 1519 F 141


title: 1549 M 61

value: M


title: 1401 M 145


title: breast cancer with BSC_LR244 [nanostring]

tag: cohort

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)


title: 451Lu_singlecell_parental_cell_70


title: breast cancer with BSC_LR243 [nanostring]

tag: biobank center

tag: follow-up time (years)


title: 451Lu_singlecell_parental_cell_67

tag: cell line

tag: treatment


title: 451Lu_singlecell_parental_cell_72


title: 451Lu_singlecell_parental_cell_66


title: FDR 7 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-011-02

tag: fdr visit number

tag: tissue

tag: bmi

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

tag: adiponectin concentration


title: FDR 7 v4

tag: categories of pack-years smoking

tag: natural log_adiponectin

tag: crp

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

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


title: FDR 6 v3

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

tag: age in years

tag: race (nhw = non-hispanic white)


title: breast cancer with BSC_LR242 [nanostring]

tag: cohort

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)


title: FDR 7 v3

tag: fdr visit number


title: breast cancer with BSC_LR245 [nanostring]

tag: biobank center

tag: follow-up time (years)


title: 451Lu_singlecell_parental_cell_65

tag: cell line

tag: treatment


title: breast cancer with BSC_LR241 [nanostring]


title: 912 M 51

tag: gender

tag: animal id


title: 79 F 54


title: 1459 F 49


title: 1200 F 134


title: 538 M 140


title: FDR 6 v2

tag: tissue

tag: bmi

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

tag: categories of pack-years smoking

tag: adiponectin concentration

tag: natural log_adiponectin

tag: crp


title: FDR 6 v1

tag: age in years

tag: race (nhw = non-hispanic white)

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

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


title: 451Lu_singlecell_parental_cell_64


title: FDR 5 v4

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

tag: fdr visit number


title: 451Lu_singlecell_parental_cell_63


title: breast cancer with BSC_LR239 [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_LR236 [nanostring]


title: 451Lu_singlecell_parental_cell_61

tag: cell line

tag: treatment


title: FDR 5 v3

tag: tissue

tag: bmi

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

tag: categories of pack-years smoking

tag: adiponectin concentration


title: FDR 5 v2

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: 451Lu_singlecell_parental_cell_60


title: breast cancer with BSC_LR234 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)


title: FDR 5 v1

tag: fdr visit number

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


title: breast cancer with BSC_LR233 [nanostring]

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: 451Lu_singlecell_parental_cell_59

tag: cell line

tag: treatment


title: breast cancer with BSC_LR232 [nanostring]


title: breast cancer with BSC_LR237 [nanostring]


title: FDR 4 v4

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-004-02

tag: tissue

tag: bmi

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

tag: categories of pack-years smoking

tag: adiponectin concentration


title: 451Lu_singlecell_parental_cell_62


title: 451Lu_singlecell_parental_cell_58


title: FDR 4 v3

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: 451Lu_singlecell_parental_cell_57


title: 923 F 49

tag: gender

tag: animal id


title: 749 G 58

value: G


title: 754 F 47


title: 92 M 54


title: 451Lu_singlecell_parental_cell_56


title: breast cancer with BSC_LR228 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)


title: breast cancer with BSC_LR231 [nanostring]

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: 618 M 144


title: FDR 2 v3

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
00852-1

tag: fdr visit number

tag: tissue

tag: bmi

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

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


title: 451Lu_singlecell_parental_cell_55

tag: cell line

tag: treatment


title: FDR 4 v1

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


title: 451Lu_singlecell_parental_cell_54


title: 72 F 44

tag: gender

tag: animal id


title: breast cancer with BSC_LR226 [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: 699 M 60


title: FDR 3 v1

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
01-002-02

tag: fdr visit number

tag: tissue

tag: bmi

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

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


title: breast cancer with BSC_LR227 [nanostring]


title: 451Lu_singlecell_parental_cell_53

tag: cell line

tag: treatment


title: breast cancer with BSC_LR225 [nanostring]


title: 652 F 142


title: FDR 2 v2

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


title: 690 F 42

tag: gender

tag: animal id


title: FDR 2 v1


title: breast cancer with BSC_LR230 [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: 451Lu_singlecell_parental_cell_51

tag: cell line

tag: treatment


title: 618 F 142


title: breast cancer with BSC_LR219 [nanostring]


title: 451Lu_singlecell_parental_cell_52


title: FDR 1 v3

description:
Bead-based multiplex immunoassay. Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.
00305-2

tag: fdr visit number

tag: tissue

tag: bmi

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

tag: categories of pack-years smoking

tag: adiponectin concentration

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


title: 5513 M 141

tag: gender

tag: animal id


title: 5549 F 131


title: FDR 1 v4

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_LR218 [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: 451Lu_singlecell_parental_cell_50

tag: cell line

tag: treatment


title: 5232 F 124


title: breast cancer with BSC_LR217 [nanostring]


title: FDR 1 v2

tag: fdr visit number

tag: tissue

tag: bmi

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

tag: categories of pack-years smoking

tag: adiponectin concentration

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


title: 4093 M 13.3

tag: gender

tag: animal id


title: FDR 1 v1

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: 451Lu_singlecell_parental_cell_49


title: breast cancer with BSC_LR216 [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: 381 F 51


title: 451Lu_singlecell_parental_cell_48

tag: cell line

tag: treatment


title: breast cancer with BSC_LR215 [nanostring]


title: 451Lu_singlecell_parental_cell_47


title: 451Lu_singlecell_parental_cell_46


title: 451Lu_singlecell_parental_cell_45


title: 3581 F 53


title: breast cancer with BSC_LR208 [nanostring]


title: breast cancer with BSC_LR207 [nanostring]


title: 451Lu_singlecell_parental_cell_43


title: breast cancer with BSC_LR204 [nanostring]


title: 451Lu_singlecell_parental_cell_42


title: breast cancer with BSC_LR211 [nanostring]


title: REPOC-99

city: BARCELONA

first: Guillaume

last: Noell

address: C/Casanova 143

country: Spain

institute: CIBER Enfermedades Respiratorias, Grupo 10, IDIBAPS-Fundació Privada Clínic de Barcelona

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: RNA samples with integrity numbers (RIN) ≥ 7 (Agilent technologies, Germany), where analyzed with the Affymetrix GeneChip® Human Genome U219 Array Plate at the IDIBAPS genomics platform. Microarray results were RMA normalized and probes in the lowest quartile of variability were removed. Remaining probes were then collapsed to gene Symbols

source_name: fresh lung tissue

label_protocol: total RNA was isolated with PureLink RNA-MiniKit (Life Technologies, US), quantified by Nanodrop (Thermo Scientific, Germany).

extract_protocol: It was then incubated at 37ºC for 30 minutes and mechanically digested with GentleMACS M-dissociator tubes (Miltenyi Biotech, Germany). The cellular suspension was filtered (serially with 100μm, 70 μm and 40 μm filters, BD, US) and a final haemolysis step was performed.

treatment_protocol: Fresh lung tissue from 53 individuals was washed with PBS, enzymatically digested with 0.5mg/ml Collagenase P and 0.1 mg/ml DNase I (Roche, Germany),

tag: batch

tag: group

value: FS

tag: Sex

value: male

tag: age

tag: smoking

value: no

tag: copd

value: yes

tag: pack years

tag: bmi

tag: dlco

tag: tissue

value: lung

tag: lung t cells

tag: lung macrophages

tag: lung monocytes


title: REPOC-97

value: CS


title: breast cancer with BSC_LR202 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)


title: breast cancer with BSC_LR210 [nanostring]

tag: follow-up time (years)


title: 451Lu_singlecell_parental_cell_44

tag: cell line

tag: treatment


title: 1605 F 136

tag: gender

tag: animal id


title: 451Lu_singlecell_parental_cell_40


title: 2075 F 51


title: 3515 F 43


title: REPOC-92

tag: batch

tag: group

tag: Sex

value: female

tag: age

tag: smoking

tag: copd

tag: pack years

tag: bmi


title: 3515 M 46


title: breast cancer with BSC_LR201 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)


title: REPOC-93

tag: dlco

tag: tissue

tag: lung t cells

tag: lung macrophages

tag: lung monocytes


title: 780 M 51

tag: gender

tag: animal id


title: 134 F 57


title: breast cancer with BSC_LR206 [nanostring]

value: neg

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: REPOC-91

tag: batch

tag: group

tag: Sex

tag: age

tag: smoking

tag: copd


title: REPOC-96

tag: pack years

tag: bmi

tag: dlco


title: 1288 F 141


title: 125 M 69


title: breast cancer with BSC_LR200 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)

value: pos


title: 3080 M 50

tag: gender

tag: animal id


title: REPOC-89

tag: tissue

tag: lung t cells

tag: lung macrophages

tag: lung monocytes


title: 5181 F 143


title: 451Lu_singlecell_parental_cell_39

tag: cell line

tag: treatment


title: 451Lu_singlecell_parental_cell_41


title: REPOC-90

tag: batch

tag: group

tag: Sex

tag: age


title: breast cancer with BSC_LR199 [nanostring]

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: 451Lu_singlecell_parental_cell_38


title: REPOC-88

value: S

tag: smoking

tag: copd

tag: pack years

tag: bmi

tag: dlco


title: breast cancer with BSC_LR198 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)


title: 451Lu_singlecell_parental_cell_37

tag: cell line

tag: treatment


title: 451Lu_singlecell_parental_cell_36


title: REPOC-86

tag: batch

tag: group

value: NS

tag: tissue

tag: lung t cells

tag: lung macrophages

tag: lung monocytes


title: 2595 M 41

tag: gender

tag: animal id


title: breast cancer with BSC_LR196 [nanostring]

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: 451Lu_singlecell_parental_cell_35


title: 451Lu_singlecell_parental_cell_34


title: breast cancer with BSC_LR195 [nanostring]

tag: cohort


title: breast cancer with BSC_LR194 [nanostring]

tag: biobank center


title: 451Lu_singlecell_parental_cell_33


title: REPOC-84

tag: Sex

tag: age

tag: smoking

tag: copd

tag: pack years

tag: bmi

tag: dlco


title: breast cancer with BSC_LR193 [nanostring]

tag: er (estrogen receptor status)


title: 451Lu_singlecell_parental_cell_32

tag: cell line

tag: treatment


title: REPOC-79

tag: batch

tag: group

tag: tissue

tag: lung t cells

tag: lung macrophages

tag: lung monocytes


title: REPOC-78


title: 5049 F 128

tag: gender

tag: animal id


title: breast cancer with BSC_LR192 [nanostring]

tag: cohort

tag: biobank center

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: 680 F 45


title: 451Lu_singlecell_parental_cell_31


title: REPOC-83

tag: Sex

tag: age

tag: smoking

tag: copd

tag: pack years

tag: bmi

tag: dlco


title: 2075 M 53


title: breast cancer with BSC_LR190 [nanostring]

tag: er (estrogen receptor status)


title: REPOC-77

tag: batch

tag: group

tag: tissue

tag: lung t cells

tag: lung macrophages

tag: lung monocytes


title: 3011 F 55

tag: gender

tag: animal id


title: 3564 F 57


title: 3168 M 68


title: REPOC-72


title: breast cancer with BSC_LR188 [nanostring]

tag: cohort

tag: biobank center

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: 176 M 48


title: 451Lu_singlecell_parental_cell_29

tag: cell line

tag: treatment


title: 451Lu_singlecell_parental_cell_30


title: 1141 F 137


title: breast cancer with BSC_LR187 [nanostring]

tag: er (estrogen receptor status)


title: breast cancer with BSC_LR186 [nanostring]


title: 451Lu_singlecell_parental_cell_28


title: 451Lu_singlecell_parental_cell_27


title: breast cancer with BSC_LR185 [nanostring]


title: REPOC-71

tag: batch

tag: Sex

tag: age

tag: smoking

tag: copd

tag: pack years

tag: bmi

tag: dlco


title: breast cancer with BSC_LR183 [nanostring]

tag: cohort


title: REPOC-73

tag: group

tag: tissue

tag: lung t cells

tag: lung macrophages

tag: lung monocytes


title: 451Lu_singlecell_parental_cell_26

tag: cell line


title: breast cancer with BSC_LR181 [nanostring]

tag: biobank center

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: 451Lu_singlecell_parental_cell_25

tag: treatment


title: 451Lu_singlecell_parental_cell_24


title: REPOC-66

tag: batch

tag: Sex

tag: age

tag: smoking

tag: copd


title: breast cancer with BSC_LR180 [nanostring]

tag: cohort

tag: er (estrogen receptor status)


title: REPOC-63

tag: group

tag: pack years

tag: bmi

tag: dlco

tag: tissue

tag: lung t cells


title: 3513 F 52

tag: gender

tag: animal id


title: REPOC-69

tag: lung macrophages

tag: lung monocytes


title: 692 F 152


title: REPOC-61

tag: batch


title: 451Lu_singlecell_parental_cell_23

tag: cell line

tag: treatment


title: 232 M 146


title: 220 F 47


title: REPOC-58

tag: Sex

tag: age

tag: smoking


title: REPOC-67

tag: copd


title: breast cancer with BSC_LR178 [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: 125 F 67

tag: gender

tag: animal id


title: REPOC-57

tag: group

tag: pack years

tag: bmi

tag: dlco

tag: tissue

tag: lung t cells

tag: lung macrophages

tag: lung monocytes


title: 3087 M 48


title: 1485 F 137


title: breast cancer with BSC_LR176 [nanostring]

tag: cohort


title: 451Lu_singlecell_parental_cell_21

tag: cell line

tag: treatment


title: 555 F 48


title: 451Lu_singlecell_parental_cell_22


title: breast cancer with BSC_LR175 [nanostring]

tag: biobank center

tag: er (estrogen receptor status)

tag: rt (radiotherapy)


title: REPOC-56

tag: batch

tag: Sex

tag: age

tag: smoking

tag: copd


title: 4445 M 131

tag: gender

tag: animal id


title: 451Lu_singlecell_parental_cell_20


title: 2558 F 48


title: breast cancer with BSC_LR173 [nanostring]

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: REPOC-55

tag: group

tag: pack years

tag: bmi

tag: dlco

tag: tissue

tag: lung t cells

tag: lung macrophages

tag: lung monocytes


title: 451Lu_singlecell_parental_cell_17

tag: cell line

tag: treatment


title: 451Lu_singlecell_parental_cell_19


title: 451Lu_singlecell_parental_cell_18


title: breast cancer with BSC_LR172 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)

tag: rt (radiotherapy)


title: breast cancer with BSC_LR170 [nanostring]

tag: lr (local recurrence)


title: REPOC-52

tag: batch

tag: Sex

tag: age

tag: smoking

tag: copd


title: breast cancer with BSC_LR169 [nanostring]

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: 220 M 48

tag: gender

tag: animal id


title: REPOC-49

tag: group

tag: pack years

tag: bmi

tag: dlco

tag: tissue

tag: lung t cells

tag: lung macrophages

tag: lung monocytes


title: 1258 F 131


title: breast cancer with BSC_LR174 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)

tag: rt (radiotherapy)

tag: lr (local recurrence)


title: 451Lu_singlecell_parental_cell_16

tag: cell line

tag: treatment


title: 3232 F 52

tag: gender


title: REPOC-50

tag: batch

tag: Sex

tag: age

tag: smoking

tag: copd


title: REPOC-46

tag: group

tag: pack years

tag: bmi

tag: dlco

tag: tissue


title: REPOC-48

tag: lung t cells

tag: lung macrophages

tag: lung monocytes


title: breast cancer with BSC_LR168 [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: 5154 F 143

tag: gender

tag: animal id


title: 5168 M 133


title: breast cancer with BSC_LR167 [nanostring]


title: 451Lu_singlecell_parental_cell_14

tag: cell line

tag: treatment


title: 451Lu_singlecell_parental_cell_15


title: breast cancer with BSC_LR165 [nanostring]


title: breast cancer with BSC_LR166 [nanostring]


title: 451Lu_singlecell_parental_cell_12


title: REPOC-45

tag: batch

tag: group

tag: Sex

tag: age

tag: smoking

tag: copd

tag: pack years

tag: bmi


title: breast cancer with BSC_LR163 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)


title: 451Lu_singlecell_parental_cell_11


title: breast cancer with BSC_LR164 [nanostring]

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)


title: 451Lu_singlecell_parental_cell_9


title: REPOC-44

tag: dlco

tag: tissue

tag: lung t cells

tag: lung macrophages

tag: lung monocytes


title: 451Lu_singlecell_parental_cell_10

tag: cell line

tag: treatment


title: breast cancer with BSC_LR161 [nanostring]

tag: follow-up time (years)


title: REPOC-43

tag: batch

tag: group

tag: Sex

tag: age

tag: smoking

tag: copd


title: breast cancer with BSC_LR162 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)

tag: rt (radiotherapy)


title: 2533 F 45

tag: gender

tag: animal id


title: 451Lu_singlecell_parental_cell_13


title: REPOC-42

tag: pack years

tag: bmi

tag: dlco

tag: tissue

tag: lung t cells

tag: lung macrophages


title: 41 M 68


title: REPOC-39

tag: batch

tag: group

tag: lung monocytes


title: 667 F 55


title: REPOC-37

tag: Sex

tag: age

tag: smoking


title: REPOC-40

tag: copd


title: 4410 F 162


title: 4533 F 126


title: 5415 F 119


title: 451Lu_singlecell_parental_cell_7

tag: cell line

tag: treatment


title: breast cancer with BSC_LR160 [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: 5049 M 129

tag: gender

tag: animal id


title: 451Lu_singlecell_parental_cell_4


title: breast cancer with BSC_LR159 [nanostring]


title: breast cancer with BSC_LR158 [nanostring]


title: REPOC-36

tag: batch

tag: group

tag: bmi

tag: dlco

tag: tissue

tag: lung t cells

tag: lung macrophages


title: 451Lu_singlecell_parental_cell_5

tag: cell line

tag: treatment


title: 451Lu_singlecell_parental_cell_8


title: breast cancer with BSC_LR155 [nanostring]

tag: cohort

tag: biobank center


title: REPOC-34

tag: Sex

tag: age

tag: smoking

tag: copd

tag: pack years

tag: lung monocytes


title: REPOC-38

tag: batch


title: REPOC-33

tag: group


title: 4001 M 131

tag: gender

tag: animal id


title: 451Lu_singlecell_parental_cell_6


title: 451Lu_singlecell_parental_cell_3


title: REPOC-32

tag: bmi

tag: dlco

tag: tissue


title: 691 M 49


title: breast cancer with BSC_LR156 [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: 451Lu_singlecell_parental_cell_2

tag: cell line

tag: treatment


title: 5612 F 120


title: 739 M 138


title: 695 F 58


title: 451Lu_singlecell_parental_cell_1


title: REPOC-31

tag: Sex

tag: age

tag: smoking

tag: copd

tag: lung t cells

tag: lung macrophages


title: breast cancer with BSC_LR154 [nanostring]

tag: cohort

tag: biobank center


title: 2041 M 51

tag: gender

tag: animal id


title: breast cancer with BSC_LR148 [nanostring]

tag: er (estrogen receptor status)


title: REPOC-29

tag: batch

tag: group

tag: pack years

tag: bmi

tag: dlco

tag: tissue

tag: lung monocytes


title: breast cancer with BSC_LR146 [nanostring]

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: 1200 M 136


title: breast cancer with BSC_LR145 [nanostring]


title: breast cancer with BSC_LR144 [nanostring]


title: breast cancer with BSC_LR141 [nanostring]


title: breast cancer with BSC_LR153 [nanostring]


title: 3370 F 50


title: breast cancer with BSC_LR137 [nanostring]


title: REPOC-21

tag: Sex

tag: age

tag: smoking

tag: copd

tag: lung t cells

tag: lung macrophages


title: REPOC-25

tag: batch


title: REPOC-20

tag: group


title: breast cancer with BSC_LR136 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)


title: 380 M 53

tag: gender

tag: animal id


title: 695 M 59


title: breast cancer with BSC_LR135 [nanostring]

tag: rt (radiotherapy)


title: REPOC-22

tag: bmi

tag: dlco

tag: tissue

tag: lung monocytes


title: REPOC-28

tag: Sex

tag: age

tag: pack years


title: REPOC-27

tag: smoking

tag: copd

tag: lung t cells


title: 5156 F 129


title: 79 M 55


title: 4533 M 127


title: REPOC-100

tag: batch

tag: group

tag: lung macrophages


title: breast cancer with BSC_LR129 [nanostring]

tag: cohort

tag: biobank center

tag: er (estrogen receptor status)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: pair 28, diagnosis Schiz, replicate 2

city: Pittsburgh

first: David

last: Lewis

state: PA

address: 3811 O'Hara St

department: Psychiatry and Neuroscience

institute: University of Pittsburgh

hyb_protocol: CDNA was synthesized and amplified using the Ovation Pico WTA System.

scan_protocol: Loaded on an Affymetrix GeneChip® U219.

data_processing: Expression intensities were extracted from Affymetrix Expression Console and normalized using Robust Multi-array Average Express.

label: Encore Biotin module (Nugen)

source_name: pair 28_diagnosis Schiz

label_protocol: Labeled using the Encore Biotin module (Nugen).

growth_protocol: Brain specimens were obtained during autopsies conducted at the Allegheny County Office of the Medical Examiner (Pittsburgh, PA) after consent was obtained from the next-of-kin.

extract_protocol: For each sample, RNA was extracted using the QIAGEN® RNeasy Plus Micro kit (QIAGEN, Valencia).

treatment_protocol: An independent committee of experienced research clinicians made consensus DSM-IV diagnoses for each subject using information obtained from medical records and structured diagnostic interviews conducted with the decedent’s family members.

tag: pair id

value: pair 28

tag: dsm-iv diagnoses

value: Undifferentiated schizophrenia; ADR

tag: subject group

value: schizophrenia

tag: tissue

value: dorsolateral prefrontal cortex (DLPFC)

tag: cell type

value: parvalbumin (PV) neurons


title: 3080 F 49

tag: gender

value: F

tag: animal id


title: pair 28, diagnosis Schiz, replicate 1


title: 5180 F 141


title: 5019 F 151


title: breast cancer with BSC_LR138 [nanostring]

value: training

tag: rt (radiotherapy)


title: breast cancer with BSC_LR127 [nanostring]


title: pair 27, diagnosis Schiz, replicate 2

source_name: pair 27_diagnosis Schiz

value: pair 27

value: Undifferentiated schizophrenia; AAC


title: breast cancer with BSC_LR126 [nanostring]


title: breast cancer with BSC_LR124 [nanostring]


title: breast cancer with BSC_LR128 [nanostring]


title: breast cancer with BSC_LR130 [nanostring]


title: breast cancer with BSC_LR125 [nanostring]


title: breast cancer with BSC_LR123 [nanostring]


title: 1485 M 141

value: M


title: pair 27, diagnosis Schiz, replicate 1


title: 491 F 137


title: pair 26, diagnosis Schiz, replicate 1

source_name: pair 26_diagnosis Schiz

value: pair 26


title: 4285 M 138


title: breast cancer with BSC_LR122 [nanostring]


title: 2417 M 52


title: pair 24, diagnosis Schiz, replicate 1

source_name: pair 24_diagnosis Schiz

value: pair 24

value: Schizoaffective disorder


title: breast cancer with BSC_LR121 [nanostring]

value: neg


title: pair 24, diagnosis Schiz, replicate 2


title: pair 25, diagnosis Schiz, replicate 2

source_name: pair 25_diagnosis Schiz

value: pair 25

value: Undifferentiated schizophrenia; AAR; OAR


title: 2020 M 49


title: pair 25, diagnosis Schiz, replicate 1


title: 205 F  39


title: 1635 M 142


title: pair 23, diagnosis Schiz, replicate 1

source_name: pair 23_diagnosis Schiz

value: pair 23

value: Disorganized schizophrenia; ADR


title: 810 M 53


title: breast cancer with BSC_LR119 [nanostring]


title: pair 22, diagnosis Schiz, replicate 1

source_name: pair 22_diagnosis Schiz

value: pair 22


title: breast cancer with BSC_LR118 [nanostring]

value: pos


title: 1605 M 137


title: pair 23, diagnosis Schiz, replicate 2

value: schizophrenia

value: dorsolateral prefrontal cortex (DLPFC)


title: 72 M 47


title: pair 22, diagnosis Schiz, replicate 2

value: parvalbumin (PV) neurons


title: 5513 F 140

value: F


title: pair 21, diagnosis Schiz, replicate 2

source_name: pair 21_diagnosis Schiz

value: pair 21

value: Disorganized schizophrenia; OAR


title: 363 M 47

value: M


title: breast cancer with BSC_LR115 [nanostring]

value: training


title: pair 36, diagnosis Schiz, replicate 1

source_name: pair 36_diagnosis Schiz

value: pair 36

value: Schizoaffective disorder; ODC


title: breast cancer with BSC_LR116 [nanostring]


title: breast cancer with BSC_LR117 [nanostring]


title: breast cancer with BSC_LR112 [nanostring]


title: breast cancer with BSC_LR113 [nanostring]


title: 3612 F 55


title: 5019 M 152


title: breast cancer with BSC_LR110 [nanostring]


title: 2558 M 50


title: pair 21, diagnosis Schiz, replicate 1


title: 381 M 53


title: breast cancer with BSC_LR108 [nanostring]


title: pair 36, diagnosis Schiz, replicate 2


title: 380 F 49


title: pair 35, diagnosis Schiz, replicate 2

source_name: pair 35_diagnosis Schiz

value: pair 35

value: Undifferentiated schizophrenia


title: 491 M 139


title: pair 34, diagnosis Schiz, replicate 2

source_name: pair 34_diagnosis Schiz

value: pair 34


title: breast cancer with BSC_LR107 [nanostring]

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


title: pair 35, diagnosis Schiz, replicate 1


title: breast cancer with BSC_LR111 [nanostring]


title: pair 34, diagnosis Schiz, replicate 1


title: pair 33, diagnosis Schiz, replicate 1

source_name: pair 33_diagnosis Schiz

value: pair 33

value: Schizoaffective disorder


title: breast cancer with BSC_LR106 [nanostring]

value: neg


title: 190 F 49


title: 2227 M 42


title: 291 M 135


title: 2020 F 46


title: breast cancer with BSC_LR103 [nanostring]

value: pos


title: pair 32, diagnosis Schiz, replicate 1

source_name: pair 32_diagnosis Schiz

value: pair 32

value: Schizoaffective disorder; AAR

value: schizophrenia


title: breast cancer with BSC_LR102 [nanostring]


title: breast cancer with BSC_LR104 [nanostring]


title: pair 32, diagnosis Schiz, replicate 2

value: dorsolateral prefrontal cortex (DLPFC)

value: parvalbumin (PV) neurons


title: breast cancer with BSC_LR100 [nanostring]


title: breast cancer with BSC_LR099 [nanostring]


title: breast cancer with BSC_LR098 [nanostring]


title: breast cancer with BSC_LR096 [nanostring]


title: breast cancer with BSC_LR097 [nanostring]


title: pair 33, diagnosis Schiz, replicate 2


title: 1119 M 136


title: pair 31, diagnosis Schiz, replicate 2

source_name: pair 31_diagnosis Schiz

value: pair 31

value: Paranoid schizophrenia


title: 2533 M 49

source_name: cecal tissue

value: M


title: 792 M 56


title: 2041 F 50

value: F


title: pair 31, diagnosis Schiz, replicate 1


title: pair 30, diagnosis Schiz, replicate 2

source_name: pair 30_diagnosis Schiz

value: pair 30

value: Disorganized schizophrenia


title: 1515 M 146


title: breast cancer with BSC_LR101 [nanostring]

value: training


title: pair 29, diagnosis Schiz, replicate 1

source_name: pair 29_diagnosis Schiz

value: pair 29

value: Paranoid schizophrenia; AAC; OAC


title: pair 9, diagnosis Schiz, replicate 1

source_name: pair 9_diagnosis Schiz

value: pair 9

value: Schizoaffective disorder; ODC


title: 5154 M 144


title: pair 20, diagnosis Schiz, replicate 1

source_name: pair 20_diagnosis Schiz

value: pair 20

value: Schizoaffective disorder


title: pair 20, diagnosis Schiz, replicate 2


title: 5168 F 132


title: 5389 F 145


title: pair 9, diagnosis Schiz, replicate 2


title: pair 29, diagnosis Schiz, replicate 2


title: breast cancer with BSC_LR093 [nanostring]

value: pos


title: 5076 M 137


title: pair 8, diagnosis Schiz, replicate 1

source_name: pair 8_diagnosis Schiz

value: pair 8

value: Chronic paranoid schizophrenia; ADC

value: schizophrenia


title: breast cancer with BSC_LR091 [nanostring]


title: 5232 M 133


title: breast cancer with BSC_LR090 [nanostring]


title: breast cancer with BSC_LR092 [nanostring]

value: neg


title: breast cancer with BSC_LR094 [nanostring]


title: pair 8, diagnosis Schiz, replicate 2

value: dorsolateral prefrontal cortex (DLPFC)

value: parvalbumin (PV) neurons


title: breast cancer with BSC_LR089 [nanostring]


title: breast cancer with BSC_LR087 [nanostring]


title: 3118 F 47

value: F


title: breast cancer with BSC_LR085 [nanostring]


title: 680 M 46

value: M


title: breast cancer with BSC_LR086 [nanostring]


title: 5415 M 121


title: pair 7, diagnosis Schiz, replicate 2

source_name: pair 7_diagnosis Schiz

value: pair 7

value: Chronic paranoid schizophrenia


title: 190 M 52


title: breast cancer with BSC_LR084 [nanostring]

value: training


title: 4001 F 130


title: pair 5, diagnosis Schiz, replicate 1

source_name: pair 5_diagnosis Schiz

value: pair 5

value: Chronic undifferentiated schizophrenia; AAR


title: pair 4, diagnosis Schiz, replicate 2

source_name: pair 4_diagnosis Schiz

value: pair 4

value: Chronic paranoid schizophrenia; ADC; OAC


title: 555 M 50


title: pair 5, diagnosis Schiz, replicate 2


title: 2662 M 41


title: 3370 M 52


title: breast cancer with BSC_LR082 [nanostring]


title: breast cancer with BSC_LR081 [nanostring]


title: pair 6, diagnosis Schiz, replicate 1

source_name: pair 6_diagnosis Schiz

value: pair 6

value: Chronic disorganized schizophrenia; AAC


title: pair 6, diagnosis Schiz, replicate 2


title: pair 4, diagnosis Schiz, replicate 1


title: breast cancer with BSC_LR080 [nanostring]

value: pos


title: breast cancer with BSC_LR079 [nanostring]


title: pair 7, diagnosis Schiz, replicate 1


title: 5076 F 136


title: 5067 M 135


title: pair 3, diagnosis Schiz, replicate 2

source_name: pair 3_diagnosis Schiz

value: pair 3


title: 1114 M 52


title: breast cancer with BSC_LR076 [nanostring]


title: 4285 F 137


title: pair 3, diagnosis Schiz, replicate 1

value: schizophrenia


title: breast cancer with BSC_LR070 [nanostring]

value: neg


title: breast cancer with BSC_LR066 [nanostring]


title: pair 2, diagnosis Schiz, replicate 2

source_name: pair 2_diagnosis Schiz

value: pair 2

value: Schizoaffective disorder

value: dorsolateral prefrontal cortex (DLPFC)


title: pair 2, diagnosis Schiz, replicate 1

value: parvalbumin (PV) neurons


title: breast cancer with BSC_LR078 [nanostring]


title: pair 19, diagnosis Schiz, replicate 2

source_name: pair 19_diagnosis Schiz

value: pair 19

value: Disorganized schizophrenia


title: pair 19, diagnosis Schiz, replicate 1


title: 5180 M 143

value: M


title: breast cancer with BSC_LR064 [nanostring]

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

value: training


title: 3078 M 47


title: 1234 F 140

value: F


title: pair 18, diagnosis Schiz, replicate 2

source_name: pair 18_diagnosis Schiz

value: pair 18

value: Disorganized schizophrenia; ADR; OAR


title: pair 18, diagnosis Schiz, replicate 1


title: pair 17, diagnosis Schiz, replicate 1

source_name: pair 17_diagnosis Schiz

value: pair 17

value: Schizoaffective disorder; ADC; ODR


title: breast cancer with BSC_LR061 [nanostring]

value: pos


title: 5370 F 140


title: breast cancer with BSC_LR074 [nanostring]


title: breast cancer with BSC_LR060 [nanostring]


title: pair 17, diagnosis Schiz, replicate 2


title: breast cancer with BSC_LR058 [nanostring]


title: breast cancer with BSC_LR057 [nanostring]


title: 2662 F 39


title: breast cancer with BSC_LR044 [nanostring]


title: breast cancer with BSC_LR043 [nanostring]


title: 5546 F 142


title: breast cancer with BSC_LR055 [nanostring]


title: 176 F 46


title: 4410 M 167


title: pair 16, diagnosis Schiz, replicate 1

source_name: pair 16_diagnosis Schiz

value: pair 16

value: Schizoaffective disorder; ADR


title: 1114 F 51

source_name: cecal tissue


title: 5067 F 131


title: breast cancer with BSC_LR040 [nanostring]

value: neg


title: pair 16, diagnosis Schiz, replicate 2

value: schizophrenia


title: pair 15, diagnosis Schiz, replicate 2

source_name: pair 15_diagnosis Schiz

value: pair 15

value: Chronic undifferentiated schizophrenia; ODR; OAR


title: breast cancer with BSC_LR039 [nanostring]


title: 3564 M 58


title: 3041 M 51


title: pair 14, diagnosis Schiz, replicate 2

source_name: pair 14_diagnosis Schiz

value: pair 14

value: Schizoaffective disorder; ADC

value: dorsolateral prefrontal cortex (DLPFC)

value: parvalbumin (PV) neurons


title: pair 14, diagnosis Schiz, replicate 1


title: 896 M 57

value: M


title: 1234 M 142


title: 1639 M 136


title: breast cancer with BSC_LR038 [nanostring]

value: training


title: pair 13, diagnosis Schiz, replicate 1

source_name: pair 13_diagnosis Schiz

value: pair 13

value: Chronic undifferentiated schizophrenia


title: 3513 M 54


title: pair 12, diagnosis Schiz, replicate 2

source_name: pair 12_diagnosis Schiz

value: pair 12


title: pair 12, diagnosis Schiz, replicate 1


title: pair 13, diagnosis Schiz, replicate 2


title: 3078 F 42

value: F


title: breast cancer with BSC_LR037 [nanostring]

value: pos


title: breast cancer with BSC_LR031 [nanostring]


title: breast cancer with BSC_LR033 [nanostring]


title: pair 11, diagnosis Schiz, replicate 1

source_name: pair 11_diagnosis Schiz

value: pair 11

value: Disorganized schizophrenia; ADC


title: breast cancer with BSC_LR032 [nanostring]


title: pair 15, diagnosis Schiz, replicate 1


title: breast cancer with BSC_LR030 [nanostring]

value: neg


title: pair 11, diagnosis Schiz, replicate 2

value: schizophrenia


title: breast cancer with BSC_LR029 [nanostring]


title: 1258 M 132


title: pair 10, diagnosis Schiz, replicate 2

source_name: pair 10_diagnosis Schiz

value: pair 10

value: Schizoaffective disorder; ADC; OAR


title: breast cancer with BSC_LR023 [nanostring]


title: 3548 M 58


title: 4445 F 129


title: pair 10, diagnosis Schiz, replicate 1


title: breast cancer with BSC_LR018 [nanostring]


title: 41 F 64


title: 2459 M 51


title: pair 28, diagnosis Control, replicate 1

source_name: pair 28_diagnosis Control

value: pair 28

value: Unaffected Comparison

value: Control


title: pair 1, diagnosis Schiz, replicate 1

source_name: pair 1_diagnosis Schiz

value: pair 1

value: dorsolateral prefrontal cortex (DLPFC)

value: parvalbumin (PV) neurons


title: 1639 F 134


title: pair 28, diagnosis Control, replicate 2


title: breast cancer with BSC_LR015 [nanostring]

value: training


title: 3612 M 57

value: M


title: 3041 F 45