title: NiCl2_80ug_48H_3

tag: strain

tag: treatment

tag: time point

value: 48 Hour

tag: dose

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: C51_SC_3pr

status: Public on Jan 18 2024

type: SRA

city: Toronto

first: Diana

last: Nakib

state: ON

address: 101 College Street

country: Canada

institute: University of Toronto

description: 3pr scRNA-seq, 10x Genomics

library_source: transcriptomic single cell

data_processing:
Reads were QCed, mapped, and UMIs were quantilfied using cell-ranger (v3).
Viable cells were identified using EmptyDrops (v1.2.0), and ambient RNA was removed using SoupX (v1.2.2) with known markers
Feature selection, and dimensionality reduction was done with Seurat (v3)
Samples were integrated using Harmony (v1.0), and clustered using Seurat (v3)
Clusters were manually annotated.
Assembly: Genome_build: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of barcodes (raw feature matrix)
Supplementary files format and content: features.tsv.gz: list of gene IDs (raw feature matrix)
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange format (raw feature matrix)

molecule: cytoplasmic RNA

organism: Homo sapiens

source_name: Human liver

extract_protocol:
Samples were prepared as outlined by the 10x Genomics Single Cell 3′ v2 Reagent Kit user guide. Briefly, the samples were washed twice in PBS (Life Technologies) + 0.04% BSA (Sigma) and re-suspended in PBS + 0.04% BSA. Sample viability was assessed via Trypan Blue (Thermo Fisher) and using a haemocytometer (Thermo Fisher). Following counting, the appropriate volume for each sample was calculated for a target capture of 6000 cells. Samples below the required cell concentration as defined by the user guide (i.e., <400 cells/µl) were pelleted and re-suspended in a reduced volume and counted again using a haemocytometer prior to loading onto the 10x Genomics single-cell-A chip. After droplet generation, samples were transferred onto a pre-chilled 96-well plate (Eppendorf), heat-sealed and reverse transcription was performed using a Veriti 96-well thermal cycler (Thermo Fisher). After the reverse transcription, cDNA was recovered using Recovery Agent provided by 10x followed by a Silane DynaBead clean-up (Thermo Fisher) as outlined in the user guide. Purified cDNA was amplified for 12 cycles before being cleaned up using SPRIselect beads (Beckman). Samples were diluted 4:1 (elution buffer (Qiagen):cDNA) and run on a Bioanalyzer (Agilent Technologies) to determine cDNA concentration. cDNA libraries were prepared as outlined by the Single Cell 3′ Reagent Kits v2 user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration (as recommended by 10X Genomics).
The molarity of each library was calculated based on library size as measured using a bioanalyzer (Agilent Technologies) and qPCR amplification data (Kappa/Roche). Samples were pooled and normalized to 10 nM, then diluted to 2 nM using elution buffer (Qiagen) with 0.1% Tween20 (Sigma). Each 2 nM pool was denatured using 0.1 N NaOH at equal volumes for 5 min at room temperature. Library pools were further diluted to 20 pM using HT-1 (Illumina) before being diluted to a final loading concentration of 14 pM. 150 μl from the 14 pM pool was loaded into each well of an 8-well strip tube and loaded onto a cBot (Illumina) for cluster generation. Samples were sequenced on a HiSeq 2500 with the following run parameters: Read 1—26 cycles, read 2—98 cycles, index 1—8 cycles. A median sequencing depth of 60,000 reads/cell was targeted for each sample.

tag: tissue

value: Human liver


title: BPC415T

city: CLICHY

first: Camille

last: PIGNOLET

address: 100 Bd du Général Leclerc

department: CRI U1149

country: France

institute: INSERM

library_source: transcriptomic

data_processing:
Reads were aligned using STAR and gene expression counts obtained with FeatureCount
Assembly: hg38
Supplementary files format and content: tab_delimited text file includes raw counts for each Sample

molecule: polyA RNA

source_name: pancreatic adenocarcinoma

extract_protocol:
EUS-FNAB from primary tumors were performed prior to any treatment using 19 to 22 G FNA needles (Wilson Cook, Ireland; Boston Scientific, USA as previously described. The material for cytopathology was reclaimed by the use of a dedicated stylet and was instantly fixed in formalin. The remaining material was obtained by air blushing the FNA needle (so-called EUS-FNAB wash – EUS-FNAB-W) and immediately collected in 500 µl of RNAprotect cell reagent (Qiagen, Les Ulis, France). This procedure was previously validated in the coordinating center. EUS-FNA-W were centrifuged at 8 000 rpm Cell pellets were immediately frozen at – 80°C until nucleic acid extraction. Extraction of nucleic acids was centralized in a single platform of molecular biology at the IUCT Oncopole of Toulouse. DNA and mRNA  were extracted using AllPrep DNA/RNA/miRNA Universal kit (Qiagen, Les Ulis, France) according the manufacturer’s protocol
150 ng of total RNA was used to generate RNA-seq sequencing libraries using Lexogen Quantseq 3’ FWD kit and sequenced by the Institut du cerveau (Paris, France) iGenseq platform on a NovaSeq 6000 apparatus aiming for a minimum of 10 million reads.

tag: sample id

value: pancreatic adenocarcinoma

tag: historicpatient id

tag: normpatient id

tag: age

tag: Sex

value: M

tag: ecog

tag: clinicalcenter

value: CLB

tag: sizeprimary

tag: diseasestage

value: resectable

tag: pfsevent

tag: pfsdelay

tag: osevent

tag: osdelay

tag: firsttreatment

value: GEMCITABINE

tag: surgerytype

value: DPC

tag: surgerymargin


title: NiCl2_40ug_48H_3

type: RNA

city: Ottawa

first: Sabina

last: Halappanavar

address: 251 Sir Frederick Banting Driveway

institute: Health Canada

hyb_protocol: An equimolar amount of UMRR cRNA was mixed with each experimental cRNA and was hybridized to 8x60K Agilent SurePrint G3 Mouse Gene Expression v2 Microarray (Agilent Technologies, Inc., Santa Clara, USA) slides in a hybridization chamber for 17 h at 65°C rotating at 10 rpm.

scan_protocol: Microarray slides were washed according to manufacturer’s protocol and scanned on an Agilent G4900DA Microarray Scanner (Agilent Technologies, Inc., Santa Clara, USA). Data was retrieved using the Feature Extraction 11.0.1.1 software (Agilent). Data analysis is described below.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 11.0.1.1). Non background subtracted median signal intensities were LOWESS normalized using the maanova library in R. Probes with technical replicates were averaged using the median.

molecule: total RNA

organism: Mus musculus

source_name: Immortalized Lung Epithelial cells (FE1)

label_protocol: In brief, 200 ng of total RNA per cell pellet sample or Universal Mouse Reference RNA (UMRR; Agilent Technologies) were used to synthesise labelled cDNAs and cRNAs using the Linear Amplification Kit (Agilent Technologies). T7 RNA polymerase-transcribed cRNA from experimental samples were labelled with Cyanine-5 and UMRR was labelled with Cyanine-3.

growth_protocol: FE1 immortalized alveolar lung epithelial cells were cultured as described in Decan et al 2015, in Dulbecco’s Modified Eagle’s Medium Nutrient Mixture F-12HAM (DMEM F12HAM) supplemented with 2 % fetal bovine serum (FBS), 1 ng/mL epidermal growth factor (EGF), 1 U/mL penicillin G, and 1 µg/mL streptomycin and maintained at 37°C, with 5 % CO2.

extract_protocol: RNA extraction, quantification, and integrity analysis were conducted as in Boyadzhiev et al., 2021. Following exposure and collection of cell pellets, TRIzol reagent was used to isolate RNA in conjunction with Direct-zol RNA Miniprep Kit (Zymo Research Corp, Irvine, USA) according to manufacturer’s protocol . Total RNA concentration and purity was determined using a NanoDropOne spectrophotometer (Thermo Fisher Scientific Inc, Waltham, USA). RNA integrity and quality analysis was conducted using an Agilent 2100 Bioanalyzer system and an Agilent 4200 Tapestation System (Agilent Technologies, Inc., Santa Clara, USA). RNA samples with an RNA Integrity Number (RIN) of ≥6 were used for subsequent microarray experiments.

treatment_protocol: Cells were plated at a cell density of 130 000 cells/well in 6-well plates. Following overnight incubation, cells were exposed to 1.8 mL of 0 - 118 ug/mL metal oxide NPs, MPs, or metal chlorides. For all exposures, blank media exposed cells served as negative controls. Following 2, 24, and 48 h of exposure, cell supernatant was harvested, cells were washed with PBS, trypsinized and suspended in fresh cell culture media. An aliquot of cell suspension was used for Trypan Blue dye exclusion staining and the rest of the cells were pelleted by centrifugation (8000 rpm, 10 minutes, 4°C) and frozen at -80°C for microarray analysis. Two to four biological replicates were used for each condition.

tag: strain

value: MutaMouse

tag: treatment

value: Nickel Chloride

tag: time point

tag: dose

value: 40 ug/mL

tag: biological replicate

source_name: Universal Mouse Reference RNA

tag: sample type


title: BPC414T

tag: sample id

tag: tissue

tag: historicpatient id

tag: normpatient id

tag: age

tag: Sex

value: F

tag: ecog

value: meta

value: FOLFIRINOX;FOLFIRI


title: NiCl2_1.6ug_24H_1

value: 24 Hour

value: 1.6 ug/mL


title: C50_SC_3pr

description: 3pr scRNA-seq, 10x Genomics


title: NiCl2_1.6ug_2H_2

value: 2 Hour


title: BPC411T

tag: clinicalcenter

tag: sizeprimary

tag: diseasestage

value: locAdvanced

tag: pfsevent

tag: pfsdelay

tag: osevent

tag: osdelay


title: BPC409T

tag: firsttreatment


title: BPC410T

value: FOLFIRINOX;GEMCITABINE;NAB-PACLITAXEL


title: NiCl2_80ug_2H_1

tag: strain

tag: treatment

tag: time point

tag: dose

value: 80 ug/mL

tag: biological replicate

value: 11 mouse cell lines


title: C48_SC_3pr

description: 3pr scRNA-seq, 10x Genomics

tag: tissue

value: Human liver


title: BPC406T

tag: sample id

value: pancreatic adenocarcinoma

tag: historicpatient id

tag: normpatient id

tag: age

value: CLB


title: BPC408T

tag: Sex

tag: clinicalcenter

tag: sizeprimary

value: FOLFIRINOX;FOLFOX 4


title: BPC407T

tag: ecog

tag: diseasestage

tag: pfsevent

tag: pfsdelay

value: FOLFIRINOX;FOLFOX 4;FOLFOX


title: NiCl2_40ug_24H_1

tag: strain

value: MutaMouse

value: Nickel Chloride

tag: sample type


title: C49_SC_3pr

description: 3pr scRNA-seq, 10x Genomics


title: NiCl2_1.6ug_2H_1

tag: treatment

tag: time point


title: BPC405T

value: F

tag: osevent

tag: osdelay

tag: firsttreatment

value: FOLFIRINOX

tag: surgerytype

value: DPC

tag: surgerymargin


title: BPC417T

tag: sample id

tag: tissue

tag: historicpatient id

tag: normpatient id

tag: age

value: M

value: meta

value: FOLFIRINOX;FOLFIRI


title: C43_NPC_SC_3pr

description: 3pr scRNA-seq, 10x Genomics


title: NiCl2_40ug_2H_1

value: 2 Hour

tag: dose

value: 40 ug/mL

tag: biological replicate


title: BPC412T

tag: Sex

tag: ecog

tag: clinicalcenter

tag: sizeprimary

tag: diseasestage

value: locAdvanced

tag: pfsevent

tag: pfsdelay


title: BPC404T

tag: osevent

tag: osdelay

tag: firsttreatment


title: C46_SC_3pr

description: 3pr scRNA-seq, 10x Genomics


title: C51_flush_SC_3pr

description: 3pr scRNA-seq, 10x Genomics


title: ZnCl2_0ug_48H_3

tag: strain

tag: treatment

value: Zinc Chloride

tag: time point

value: 48 Hour

value: Media Control

tag: sample type

value: 11 mouse cell lines


title: BPC403T

tag: sample id

tag: tissue

value: pancreatic adenocarcinoma

tag: historicpatient id

tag: normpatient id

tag: age

value: CLB

value: resectable

tag: surgerytype

value: PC

tag: surgerymargin


title: BPC402T

tag: Sex

tag: ecog

tag: clinicalcenter

value: Clinique du Trocadero

tag: sizeprimary

tag: diseasestage

value: GEMCITABINE


title: BPC401T

value: F

tag: pfsevent

tag: pfsdelay

tag: osevent

tag: osdelay

tag: firsttreatment

value: FOLFIRINOX


title: ZnCl2_1.7ug_48H_2

tag: strain

value: MutaMouse

tag: treatment

tag: time point

tag: dose

value: 1.7 ug/mL

tag: biological replicate

tag: sample type


title: C42_NPC_SC_3pr

description: 3pr scRNA-seq, 10x Genomics

tag: tissue

value: Human liver


title: C41_NPC_SC_3pr

description: 3pr scRNA-seq, 10x Genomics


title: BPC400T

tag: sample id

tag: historicpatient id

tag: normpatient id

tag: age

tag: Sex


title: BPC399T

tag: ecog

tag: clinicalcenter

tag: sizeprimary

tag: diseasestage

tag: pfsevent

value: GEMCITABINE;OXALIPLATINE

tag: surgerytype

value: DPC

tag: surgerymargin


title: BPC398T

value: M

value: locAdvanced

tag: pfsdelay

tag: osevent

tag: osdelay


title: ZnCl2_0ug_48H_2

tag: strain

tag: treatment

value: Zinc Chloride

tag: time point

value: 48 Hour

tag: dose

value: Media Control

tag: biological replicate

tag: sample type


title: FPW1_TMZ_RT_biol_rep_2

city: Callaghan

first: Paul

last: Tooney

state: AUSTRALIA

address: University Drive

department: School of Biomedical Sciences and Pharmacy

country: Australia

institute: University of Newcastle, Australia

data_processing:
Mapping, quality control and quantification of reads were performed using the bcbioRNAseq pipeline.
Assembly: GRCh38/hg38
Supplementary files format and content: csv file of raw counts collated from all samples submitted (each column corresponds to one sample)
Supplementary files format and content: csv file of TPM counts collated from all samples submitted (each column corresponds to one sample)

growth_protocol: Cells were grown as adherent monolayers in Matrigel® (Corning®, USA)-coated tissue culture flasks in StemPro® NSC SFM (GibcoTM, USA) containing 100 U/mL penicillin and 100 µg/mL streptomycin (GibcoTM, USA), and incubated at 37 oC in 5% CO2/95% humified air.

extract_protocol:
Cell lines were detached using StemPro® Accutase® solution (GibcoTM, USA) and RNA was extracted using the AllPrep DNA/RNA/Protein Mini Kit (Qiagen, USA).
At least 1μg total RNA was used for library synthesis. RNA libraries were prepared for sequencing using standard Illumina protocols by the Australian Genome Research Facility (AGRF), Australia.

treatment_protocol: Glioblastoma cell lines (n=12) were seeded at 2 x 10^6 cells/flask in Matrigel-coated T75 flasks overnight and treated with DMSO (untreated control), TMZ (35μM) + RT (2Gy) or M4344 (1μM) + TMZ (35μM) + RT (2Gy). Cells were harvested 4 days (96hr) after treatment.

tag: cell line

tag: cell type

value: Glioblastoma cell line

value: TMZ+RT


title: BPC396T

tag: sample id

tag: tissue

value: pancreatic adenocarcinoma

tag: historicpatient id

tag: normpatient id

tag: age

tag: Sex

tag: ecog

tag: clinicalcenter

value: borderline

tag: firsttreatment


title: BPC397T

value: Clinique du Trocadero

tag: sizeprimary

tag: diseasestage

value: resectable

tag: pfsevent

tag: pfsdelay

tag: osevent

tag: osdelay

tag: surgerytype


title: FPW1_TMZ_RT_biol_rep_1

tag: cell line

tag: cell type

tag: treatment


title: BPC395T

tag: sample id

tag: tissue

tag: historicpatient id

value: F


title: BPC394T

tag: normpatient id

tag: age

tag: Sex


title: ZnCl2_5.1ug_48H_2

tag: strain

value: MutaMouse

tag: time point

tag: dose

value: 5.1 ug/mL

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: FPW1_M4344_TMZ_RT_biol_rep_2


title: FPW1_M4344_TMZ_RT_biol_rep_1


title: ZnCl2_1.7ug_48H_1

value: 1.7 ug/mL


title: BPC393T

tag: ecog

tag: clinicalcenter

tag: sizeprimary

tag: diseasestage

value: meta

tag: pfsevent

tag: pfsdelay

tag: osevent


title: BPC390T

tag: sample id

tag: tissue

tag: osdelay

tag: firsttreatment

value: GEMCITABINE

tag: surgerytype

value: DPC

tag: surgerymargin


title: BPC392T

tag: historicpatient id

tag: normpatient id

tag: age

tag: Sex

value: M


title: BPC391T

tag: ecog

value: PC


title: ZnCl2_8.5ug_48H_1

tag: strain

tag: treatment

value: Zinc Chloride

tag: time point

value: 48 Hour

tag: dose

value: 8.5 ug/mL

tag: biological replicate

tag: sample type


title: BPC389T

tag: sample id

value: pancreatic adenocarcinoma

tag: clinicalcenter

tag: sizeprimary

tag: diseasestage

value: locAdvanced

tag: pfsevent

tag: pfsdelay

tag: osevent

value: FOLFIRINOX


title: BPC388T

tag: tissue

tag: historicpatient id

tag: normpatient id

value: Clinique du Trocadero

value: resectable

tag: osdelay

tag: firsttreatment

tag: surgerytype

tag: surgerymargin


title: ZnCl2_5.1ug_2H_3

tag: strain

value: MutaMouse

tag: treatment

tag: time point

value: 2 Hour

tag: dose


title: BPC387T

tag: sample id

tag: age

tag: Sex

value: F

tag: ecog

tag: clinicalcenter


title: BPC386T

tag: sizeprimary

tag: diseasestage

tag: pfsevent

tag: pfsdelay

tag: osevent

value: GEMOX


title: FPW1_DMSO_biol_rep_1

tag: cell line

tag: cell type

value: Glioblastoma cell line

value: DMSO control


title: ZnCl2_1.7ug_2H_3

value: 1.7 ug/mL

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: ZnCl2_5.1ug_48H_1

tag: strain

tag: treatment

value: 5.1 ug/mL


title: SJH1_TMZ_RT_biol_rep_2

value: TMZ+RT


title: BPC384T

tag: tissue

tag: historicpatient id

tag: normpatient id

value: M

tag: osdelay


title: BPC383T

tag: sample id

tag: age

tag: Sex

tag: ecog

value: meta

tag: firsttreatment

value: FOLFIRINOX;XELODA;FOLFIRI


title: ZnCl2_0ug_48H_1

value: Zinc Chloride

tag: time point

value: 48 Hour

tag: dose

value: Media Control


title: SJH1_TMZ_RT_biol_rep_1

tag: cell line


title: BPC381T

value: pancreatic adenocarcinoma

tag: clinicalcenter

value: Clinique du Trocadero

tag: sizeprimary

tag: diseasestage

value: resectable

tag: pfsevent

tag: pfsdelay

tag: osevent

value: FOLFIRINOX

tag: surgerytype

value: DPC


title: ZnCl2_8.5ug_2H_3

tag: strain

value: MutaMouse

tag: treatment

value: 2 Hour

value: 8.5 ug/mL

tag: biological replicate

tag: sample type


title: SJH1_M4344_TMZ_RT_biol_rep_2

tag: cell type

value: Glioblastoma cell line


title: BPC379T

tag: sample id

tag: tissue

tag: historicpatient id

tag: normpatient id

tag: age

tag: Sex

value: F

tag: ecog

tag: osdelay

value: GEMCITABINE

tag: surgerymargin


title: BPC380T

value: M

tag: clinicalcenter

tag: sizeprimary

tag: diseasestage

tag: pfsevent

tag: pfsdelay

tag: firsttreatment


title: BPC376T

value: CHU de Nice

value: meta

tag: osevent


title: FPW1_DMSO_biol_rep_2

tag: cell line

tag: cell type

tag: treatment

value: DMSO control


title: BPC378T

tag: sample id

tag: tissue

tag: historicpatient id

value: locAdvanced

value: FOLFIRINOX;XELODA


title: ZnCl2_1.7ug_24H_3

tag: strain

value: Zinc Chloride

tag: time point

value: 24 Hour

tag: dose

value: 1.7 ug/mL

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: BPC374T

value: pancreatic adenocarcinoma

tag: normpatient id

tag: age

tag: Sex

tag: ecog

tag: clinicalcenter

tag: sizeprimary

tag: osdelay

value: FOLFOX


title: BPC372T

tag: diseasestage

tag: pfsevent

tag: pfsdelay

tag: osevent


title: SJH1_M4344_TMZ_RT_biol_rep_1

tag: cell line

tag: cell type

tag: treatment


title: SJH1_DMSO_biol_rep_1


title: ZnCl2_8.5ug_48H_2

tag: strain

value: MutaMouse

tag: time point

value: 48 Hour

tag: dose


title: ZnCl2_0ug_2H_3

value: 2 Hour

value: Media Control

tag: biological replicate

tag: sample type


title: BPC371T

tag: sample id

tag: tissue

tag: historicpatient id

tag: normpatient id

tag: age

tag: Sex

tag: firsttreatment

value: GEMCITABINE


title: ZnCl2_5.1ug_24H_3

value: 5.1 ug/mL


title: BPC366T

value: M

tag: ecog

tag: clinicalcenter

value: ICM

tag: sizeprimary

tag: diseasestage

tag: pfsevent

tag: pfsdelay

tag: osdelay


title: BPC369T

value: CHU de Nice

tag: osevent

value: FOLFIRINOX


title: SB2b_TMZ_RT_biol_rep_1

tag: cell line

tag: cell type

value: Glioblastoma cell line

tag: treatment

value: TMZ+RT


title: BPC364T

tag: sample id

tag: tissue

value: borderline


title: ZnCl2_8.5ug_24H_3

tag: strain

value: Zinc Chloride

tag: time point

value: 24 Hour

tag: dose

value: 8.5 ug/mL

tag: biological replicate

tag: sample type


title: SB2b_M4344_TMZ_RT_biol_rep_2


title: SB2b_TMZ_RT_biol_rep_2


title: SJH1_DMSO_biol_rep_2

value: DMSO control


title: SB2b_M4344_TMZ_RT_biol_rep_1


title: BPC363T

value: pancreatic adenocarcinoma

tag: historicpatient id

tag: normpatient id

tag: age

tag: Sex

value: F

tag: ecog

tag: clinicalcenter

value: locAdvanced

tag: firsttreatment


title: BPC365T

tag: sizeprimary

tag: diseasestage

tag: pfsevent

tag: pfsdelay

tag: osevent

tag: osdelay

value: FOLFOX


title: BPC357T

tag: sample id

tag: tissue

value: FOLFOX;FOLFIRINOX


title: BPC359T


title: BPC361T

value: FOLFIRINOX;XELODA


title: BPC358T

value: M


title: BPC367T

value: meta


title: BPC360T

value: ICM

value: TAXANE;GEMCITABINE;PEGPH20/PLACEBO ESSAI CLINIQUE;PEGPH20/PLACEBO;ABRAXANE;PEGPH20/PLACEBO ( ESSAI )


title: SB2b_DMSO_biol_rep_2

tag: cell line

tag: cell type

value: Glioblastoma cell line

tag: treatment


title: BPC355T

tag: historicpatient id

tag: normpatient id

value: Hopital Nord Marseille

value: FOLFIRINOX


title: BPC356T

tag: age

tag: Sex


title: ZnCl2_0ug_24H_3

tag: strain

value: MutaMouse

value: Zinc Chloride

tag: time point

tag: dose

value: Media Control

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: BPC353T

value: pancreatic adenocarcinoma

tag: ecog

tag: clinicalcenter

value: Hopital Mermoz

tag: sizeprimary

tag: diseasestage

value: borderline

tag: pfsevent

tag: pfsdelay


title: ZnCl2_1.7ug_2H_2

value: 2 Hour

value: 1.7 ug/mL


title: BPC362T

tag: sample id

tag: tissue

value: F

tag: osevent

tag: osdelay

tag: firsttreatment


title: BPC352T

tag: historicpatient id

tag: normpatient id

tag: age

tag: Sex

value: locAdvanced

value: FOLFIRINOX;FOLFIRI


title: SB2b_DMSO_biol_rep_1

tag: cell line

tag: cell type

tag: treatment

value: DMSO control


title: ZnCl2_0ug_2H_2

tag: strain

tag: time point

tag: dose

tag: biological replicate

tag: sample type


title: ZnCl2_5.1ug_2H_2

value: 5.1 ug/mL


title: JK2_TMZ_RT_biol_rep_2

value: Glioblastoma cell line

value: TMZ+RT


title: ZnCl2_1.7ug_48H_3

value: 48 Hour


title: ZnCl2_8.5ug_2H_2

value: MutaMouse

value: 8.5 ug/mL


title: BPC351T

tag: sample id

tag: ecog

tag: clinicalcenter

tag: sizeprimary

tag: diseasestage

value: meta

tag: pfsevent

tag: pfsdelay

value: FOLFIRINOX


title: BPC354T

tag: tissue

value: pancreatic adenocarcinoma

tag: historicpatient id

tag: normpatient id

tag: age

value: M

value: resectable

tag: osevent

tag: osdelay

tag: firsttreatment

value: GEMCITABINE


title: JK2_TMZ_RT_biol_rep_1

tag: cell line

tag: cell type

tag: treatment


title: JK2_M4344_TMZ_RT_biol_rep_2


title: ZnCl2_8.5ug_48H_3

tag: strain

value: Zinc Chloride

tag: time point

tag: dose

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: ZnCl2_5.1ug_24H_1

value: 24 Hour


title: ZnCl2_8.5ug_24H_1


title: BPC349T

tag: sample id

tag: Sex

value: F

tag: clinicalcenter

value: Hopital Mermoz

tag: sizeprimary

tag: diseasestage

value: locAdvanced

tag: pfsevent


title: JK2_M4344_TMZ_RT_biol_rep_1

value: Glioblastoma cell line


title: BPC350T

tag: tissue

tag: historicpatient id

tag: normpatient id

tag: age

tag: pfsdelay

tag: osevent


title: BPC348T

tag: ecog

tag: osdelay

tag: firsttreatment


title: JK2_DMSO_biol_rep_1

tag: cell line

tag: cell type

tag: treatment

value: DMSO control


title: JK2_DMSO_biol_rep_2


title: BPC347T

tag: sample id

tag: Sex


title: ZnCl2_1.7ug_24H_1

tag: strain

tag: time point

tag: dose

value: 1.7 ug/mL

tag: biological replicate

tag: sample type


title: BPC345T

tag: tissue

tag: historicpatient id

tag: normpatient id

tag: clinicalcenter

tag: sizeprimary

tag: diseasestage

tag: pfsevent


title: BPC343T

tag: age

tag: ecog

tag: pfsdelay

tag: osevent

tag: osdelay

tag: firsttreatment

tag: surgerytype

value: DPC

tag: surgerymargin


title: RKI1_TMZ_RT_biol_rep_2

tag: cell line

tag: cell type

tag: treatment

value: TMZ+RT


title: BPC344T

tag: sample id

tag: tissue

tag: historicpatient id

tag: Sex

value: borderline

value: FOLFIRINOX;NIVOLUMAB;IPILIMUMAB


title: BPC341T

value: pancreatic adenocarcinoma

tag: normpatient id

tag: clinicalcenter

tag: sizeprimary

tag: diseasestage


title: RKI1_TMZ_RT_biol_rep_1


title: BPC339T

tag: age

value: M

tag: ecog

tag: pfsevent

tag: pfsdelay


title: RKI1_M4344_TMZ_RT_biol_rep_2


title: BPC338T

tag: osevent

tag: osdelay


title: BPC336T

value: meta


title: RKI1_M4344_TMZ_RT_biol_rep_1

tag: cell line


title: BPC335T

tag: firsttreatment

value: GEMCITABINE


title: ZnCl2_0ug_2H_1

tag: strain

value: MutaMouse

tag: treatment

value: Zinc Chloride

tag: time point

value: 2 Hour

tag: dose

value: Media Control

tag: biological replicate

tag: sample type


title: ZnCl2_5.1ug_2H_1

value: 5.1 ug/mL

value: 11 mouse cell lines


title: ZnCl2_8.5ug_24H_2

value: 24 Hour

value: 8.5 ug/mL


title: RKI1_DMSO_biol_rep_2

tag: cell type

value: Glioblastoma cell line

value: DMSO control


title: BPC334T

tag: sample id

tag: tissue

tag: historicpatient id

tag: normpatient id

tag: Sex

tag: clinicalcenter

value: Hopital Mermoz

tag: sizeprimary

tag: surgerytype

value: DPC

tag: surgerymargin


title: ZnCl2_1.7ug_24H_2

value: 1.7 ug/mL


title: ZnCl2_0ug_24H_1


title: ZnCl2_0ug_24H_2


title: BPC333T

value: pancreatic adenocarcinoma

tag: age

tag: ecog

tag: diseasestage

tag: pfsevent

tag: pfsdelay

tag: osevent

tag: osdelay

tag: firsttreatment


title: BPC332T

tag: sample id

value: M

value: locAdvanced

value: FOLFIRINOX


title: BPC340T

tag: tissue

value: F


title: ZnCl2_5.1ug_48H_3

tag: strain

value: MutaMouse

tag: treatment

value: Zinc Chloride

tag: time point

value: 48 Hour

tag: dose

tag: biological replicate

tag: sample type


title: BPC342T

tag: historicpatient id

tag: normpatient id

tag: Sex

tag: clinicalcenter

tag: sizeprimary

value: meta


title: BPC346T

tag: age

tag: ecog

tag: diseasestage

tag: pfsevent

tag: pfsdelay

value: GEMCITABINE


title: RKI1_DMSO_biol_rep_1

tag: cell line

tag: cell type


title: BPC331T

tag: sample id

tag: tissue

value: borderline

tag: osevent

tag: osdelay


title: PB1_TMZ_RT_biol_rep_2

tag: treatment

value: TMZ+RT


title: ZnCl2_8.5ug_2H_1

tag: strain

tag: time point

value: 2 Hour

tag: dose

value: 8.5 ug/mL

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: PB1_TMZ_RT_biol_rep_1

value: Glioblastoma cell line


title: BPC330T

tag: historicpatient id

tag: normpatient id

tag: age

tag: Sex

tag: clinicalcenter

value: Hopital Mermoz

tag: sizeprimary

tag: firsttreatment


title: BPC329T

tag: sample id

value: pancreatic adenocarcinoma

tag: ecog

tag: diseasestage

tag: pfsevent

tag: pfsdelay


title: BPC328T

tag: tissue

value: resectable

tag: osevent

tag: osdelay


title: BPC326T

value: locAdvanced


title: BPC325T

value: M


title: BPC324T

value: F

tag: surgerytype

value: PC

tag: surgerymargin


title: PB1_M4344_TMZ_RT_biol_rep_1

tag: cell line

tag: cell type

tag: treatment


title: ZnCl2_1.7ug_2H_1

tag: strain

value: MutaMouse

value: Zinc Chloride

tag: time point

tag: dose

value: 1.7 ug/mL

tag: biological replicate

tag: sample type


title: TiO2_MP_100ug_48H_2

value: TiO2 Microparticle

value: 48 Hour

value: 100 ug/mL


title: ZnCl2_5.1ug_24H_2

value: 24 Hour

value: 5.1 ug/mL


title: BPC323T

tag: sample id

tag: historicpatient id

tag: normpatient id

tag: age

tag: Sex

tag: ecog

tag: clinicalcenter

tag: sizeprimary

value: meta

tag: firsttreatment

value: FOLFIRINOX;GEMBRAX


title: PB1_M4344_TMZ_RT_biol_rep_2

tag: cell line

value: Glioblastoma cell line


title: BPC322T

tag: tissue

value: pancreatic adenocarcinoma

value: Hopital Mermoz

tag: diseasestage

tag: pfsevent

tag: pfsdelay

tag: osevent

tag: osdelay

value: GEMCITABINE

tag: surgerytype

value: DPC

tag: surgerymargin


title: PB1_DMSO_biol_rep_2

tag: cell type

tag: treatment

value: DMSO control


title: BPC321T

tag: sample id

tag: historicpatient id

tag: normpatient id

tag: age

value: M

value: locAdvanced


title: PB1_DMSO_biol_rep_1


title: TiO2_MP_0ug_48H_2

tag: strain

value: MutaMouse

tag: time point

tag: dose

value: Media Control

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: BPC320T

tag: tissue

tag: Sex

value: F

tag: ecog

tag: clinicalcenter

tag: sizeprimary

tag: diseasestage

tag: pfsevent


title: HW1_TMZ_RT_biol_rep_2

tag: cell line

tag: cell type

tag: treatment

value: TMZ+RT


title: BPC319T

tag: sample id

tag: historicpatient id

tag: normpatient id

tag: pfsdelay

tag: osevent

tag: osdelay

tag: firsttreatment

value: FOLFIRINOX


title: BPC327T

tag: tissue

tag: age


title: BPC318T

tag: Sex

tag: ecog


title: TiO2_MP_50ug_24H_1

tag: strain

value: TiO2 Microparticle

tag: time point

value: 24 Hour

tag: dose

value: 50 ug/mL

tag: biological replicate

tag: sample type


title: BPC316T

tag: clinicalcenter

tag: sizeprimary

tag: diseasestage

value: borderline

tag: pfsevent


title: HW1_TMZ_RT_biol_rep_1

tag: cell line

tag: cell type

value: Glioblastoma cell line

tag: treatment


title: BPC315T

tag: sample id

value: pancreatic adenocarcinoma

tag: historicpatient id

tag: normpatient id

value: Hopital Mermoz

tag: pfsdelay

tag: osevent

tag: osdelay

tag: firsttreatment

value: ABRAXANE;GEMCITABINE


title: HW1_M4344_TMZ_RT_biol_rep_2


title: TiO2_MP_100ug_24H_1

tag: strain

tag: time point

tag: dose

value: 100 ug/mL


title: TiO2_MP_50ug_48H_2

value: 48 Hour

tag: biological replicate

tag: sample type


title: TiO2_MP_0ug_2H_2

value: 2 Hour


title: BPC313T

tag: tissue

tag: age

tag: Sex

value: M

tag: ecog

tag: clinicalcenter

tag: sizeprimary

tag: diseasestage

value: meta

value: GEMCITABINE


title: HW1_M4344_TMZ_RT_biol_rep_1

tag: cell line

tag: cell type

tag: treatment


title: BPC312T

tag: sample id

tag: historicpatient id

tag: normpatient id

value: F

value: locAdvanced

tag: pfsevent

tag: pfsdelay

tag: osevent

tag: osdelay

value: FOLFIRINOX;FOLFIRI;LV5FU2 SIMPLIFIE


title: HW1_DMSO_biol_rep_2

value: DMSO control


title: TiO2_MP_0ug_48H_1

tag: strain

value: MutaMouse

value: TiO2 Microparticle

tag: time point

tag: dose

value: Media Control

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: BPC311T

tag: tissue

value: pancreatic adenocarcinoma

tag: age

tag: Sex

tag: ecog

tag: clinicalcenter

tag: sizeprimary


title: TiO2_MP_25ug_48H_1

tag: treatment

value: 25 ug/mL


title: BPC309T

tag: sample id

tag: historicpatient id

tag: normpatient id

value: Hopital Mermoz

tag: diseasestage

tag: firsttreatment

value: FOLFIRINOX;FOLFIRI


title: MMK1_TMZ_RT_biol_rep_2

tag: cell line

tag: cell type

value: Glioblastoma cell line

value: TMZ+RT


title: BPC308T

tag: pfsevent

tag: pfsdelay

tag: osevent

tag: osdelay

value: FOLFOX


title: TiO2_MP_25ug_2H_3

tag: strain

tag: time point

value: 2 Hour

tag: dose

tag: biological replicate

tag: sample type


title: BPC310T

tag: tissue

tag: age

tag: Sex

value: M

tag: ecog

tag: clinicalcenter

tag: sizeprimary

value: meta

value: GEMCITABINE


title: BPC307T

tag: sample id

tag: historicpatient id

tag: normpatient id

tag: diseasestage

tag: firsttreatment


title: HW1_DMSO_biol_rep_1

tag: cell line

tag: cell type

tag: treatment


title: BPC305T

value: F

value: borderline

tag: pfsevent

tag: pfsdelay

tag: osevent

tag: osdelay

value: FOLFIRINOX

tag: surgerytype

value: PC

tag: surgerymargin


title: BPC304T

tag: tissue

tag: age

tag: Sex

tag: ecog

value: DPC


title: BPC306T

tag: sample id

tag: historicpatient id

tag: clinicalcenter

tag: sizeprimary

value: locAdvanced


title: BPC314T

value: pancreatic adenocarcinoma

tag: normpatient id

tag: diseasestage

tag: firsttreatment


title: BPC302T

tag: pfsevent


title: TiO2_MP_100ug_2H_3

tag: strain

value: MutaMouse

tag: treatment

value: TiO2 Microparticle

tag: time point

tag: dose

value: 100 ug/mL

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: BPC303T

tag: tissue

tag: age

value: Hopital Mermoz

tag: pfsdelay

tag: osevent

tag: osdelay


title: BPC301T

tag: sample id

tag: historicpatient id

tag: Sex

tag: ecog

tag: clinicalcenter


title: TiO2_MP_50ug_2H_3

value: 50 ug/mL


title: BPC300T

tag: normpatient id

tag: sizeprimary

tag: diseasestage

tag: pfsevent

tag: firsttreatment


title: TiO2_MP_100ug_48H_1

tag: strain

tag: treatment

tag: time point

value: 48 Hour

tag: dose

tag: biological replicate


title: MMK1_M4344_TMZ_RT_biol_rep_1

tag: cell line

tag: cell type

value: Glioblastoma cell line


title: BPC299T

tag: sample id

tag: tissue

tag: age

value: M

tag: pfsdelay

tag: osevent

tag: osdelay

value: FOLFIRINOX;FOLFIRI


title: BPC298T

tag: historicpatient id

tag: normpatient id

tag: Sex

value: F

tag: ecog

tag: clinicalcenter

tag: sizeprimary

value: GEMCITABINE


title: MMK1_DMSO_biol_rep_2

tag: treatment

value: DMSO control


title: TiO2_MP_0ug_2H_3

tag: strain

tag: time point

value: 2 Hour

tag: dose

value: Media Control

tag: sample type


title: TiO2_MP_50ug_2H_2

tag: biological replicate


title: MMK1_TMZ_RT_biol_rep_1

tag: cell line

tag: cell type

value: TMZ+RT


title: MMK1_DMSO_biol_rep_1


title: BPC295T

tag: sample id

tag: tissue

value: pancreatic adenocarcinoma

tag: age

tag: diseasestage

value: resectable

tag: pfsevent

tag: pfsdelay

tag: firsttreatment

tag: surgerytype

value: DPC

tag: surgerymargin


title: BPC292T

tag: historicpatient id

tag: normpatient id

tag: Sex

tag: ecog

tag: clinicalcenter

tag: sizeprimary

tag: osevent

tag: osdelay


title: BPC294T

tag: sample id

value: locAdvanced

value: GEMBRAX


title: BAH1_TMZ_RT_biol_rep_2

tag: cell line

tag: cell type

tag: treatment


title: MMK1_M4344_TMZ_RT_biol_rep_2


title: BPC296T

tag: tissue

tag: age

value: Hopital Mermoz

tag: diseasestage

tag: pfsevent

value: FOLFIRINOX;XELODA


title: BPC293T

tag: pfsdelay

tag: firsttreatment

tag: surgerytype

tag: surgerymargin


title: BAH1_TMZ_RT_biol_rep_1


title: BPC291T

tag: historicpatient id

tag: normpatient id

tag: Sex

tag: ecog

value: borderline

value: PC


title: BPC290T

tag: clinicalcenter

tag: sizeprimary

tag: osevent

tag: osdelay


title: TiO2_MP_50ug_48H_1

tag: strain

value: MutaMouse

tag: treatment

value: TiO2 Microparticle

tag: time point

value: 48 Hour

tag: dose

value: 50 ug/mL

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: TiO2_MP_100ug_24H_3

value: 24 Hour

value: 100 ug/mL


title: TiO2_MP_25ug_2H_2

value: 2 Hour

value: 25 ug/mL


title: TiO2_MP_50ug_24H_3


title: TiO2_MP_100ug_2H_2


title: TiO2_MP_25ug_24H_3


title: BPC297T

tag: sample id

tag: tissue

value: pancreatic adenocarcinoma

tag: age

value: F

tag: diseasestage

value: resectable

tag: pfsevent

tag: pfsdelay

tag: firsttreatment

value: GEMCITABINE


title: BPC288T

tag: historicpatient id

tag: normpatient id

tag: Sex

tag: ecog

tag: clinicalcenter

value: Hopital Mermoz

value: FOLFIRINOX

tag: surgerytype

value: DPC

tag: surgerymargin


title: BAH1_M4344_TMZ_RT_biol_rep_2

tag: cell line

tag: cell type

value: Glioblastoma cell line

tag: treatment


title: BPC286T

tag: sample id

value: Toulouse

tag: sizeprimary

value: borderline

tag: osevent

tag: osdelay


title: BPC289T

tag: tissue

tag: age

tag: diseasestage

tag: pfsevent


title: BAH1_DMSO_biol_rep_2

value: DMSO control


title: BPC285T

tag: historicpatient id

tag: normpatient id

tag: pfsdelay

tag: firsttreatment

value: FOLFIRINOX;FOLFOX


title: BPC284T

tag: Sex

value: M

tag: ecog

tag: clinicalcenter

value: locAdvanced

value: CYL 02;GEMCITABINE


title: BPC282T

value: FOLFIRINOX;XELODA


title: BPC280T

value: meta


title: BPC283T

value: pancreatic adenocarcinoma

tag: surgerytype

value: PC

tag: surgerymargin


title: BPC281T

tag: sample id

value: F

value: resectable


title: MN1_TMZ_RT_biol_rep_2

tag: cell line

tag: cell type

tag: treatment

value: TMZ+RT


title: BPC279T

tag: tissue

tag: sizeprimary

tag: osevent

tag: osdelay

value: FOLFIRINOX


title: BPC278T

tag: historicpatient id

tag: age

tag: diseasestage

tag: pfsevent

value: GEMCITABINE


title: MN1_M4344_TMZ_RT_biol_rep_2

value: Glioblastoma cell line


title: TiO2_MP_0ug_48H_3

tag: strain

value: MutaMouse

value: TiO2 Microparticle

tag: time point

value: 48 Hour

tag: dose

value: Media Control

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: BAH1_M4344_TMZ_RT_biol_rep_1


title: BPC287T

tag: sample id

tag: normpatient id

tag: Sex

tag: ecog

tag: clinicalcenter

value: Hopital Mermoz

value: borderline

tag: pfsdelay

tag: firsttreatment


title: TiO2_MP_0ug_24H_1

tag: treatment

value: 24 Hour


title: MN1_M4344_TMZ_RT_biol_rep_1

tag: cell line

tag: cell type


title: BPC275T

tag: tissue

tag: historicpatient id

tag: age

value: M

value: Toulouse

tag: osevent

tag: osdelay


title: TiO2_MP_25ug_48H_3

tag: strain

tag: time point

tag: dose

value: 25 ug/mL

tag: biological replicate


title: TiO2_MP_50ug_48H_3

value: 50 ug/mL

tag: sample type


title: TiO2_MP_0ug_24H_3


title: MN1_TMZ_RT_biol_rep_1


title: BPC272T

tag: sample id

value: pancreatic adenocarcinoma

tag: normpatient id

tag: Sex

value: F

tag: ecog

tag: sizeprimary

tag: diseasestage

value: locAdvanced

tag: pfsevent

value: FOLFIRINOX;XELODA


title: BPC273T

tag: tissue

tag: clinicalcenter

tag: pfsdelay

tag: firsttreatment

value: GEMCITABINE


title: MN1_DMSO_biol_rep_1

tag: cell line

tag: cell type

value: Glioblastoma cell line

tag: treatment

value: DMSO control


title: MN1_DMSO_biol_rep_2


title: BAH1_DMSO_biol_rep_1


title: BPC271T

tag: historicpatient id

tag: age

tag: osevent

tag: osdelay


title: BPC277T

tag: sample id

tag: normpatient id

value: meta


title: TiO2_MP_25ug_24H_1

tag: strain

value: MutaMouse

value: TiO2 Microparticle

tag: time point

tag: dose

tag: biological replicate

tag: sample type


title: BPC270T

tag: tissue

tag: Sex

tag: clinicalcenter

tag: sizeprimary

tag: diseasestage

value: resectable

tag: pfsevent

value: FOLFIRINOX

tag: surgerytype

value: PC

tag: surgerymargin


title: WK1_TMZ_RT_biol_rep_2

tag: cell line

tag: cell type

tag: treatment

value: TMZ+RT


title: BPC269T

tag: sample id

tag: historicpatient id

tag: normpatient id

tag: age

value: M

value: Toulouse

tag: pfsdelay

tag: osevent

tag: osdelay


title: TiO2_MP_25ug_2H_1

tag: strain

tag: time point

value: 2 Hour

tag: dose

value: 25 ug/mL

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: BPC268T

tag: tissue

value: pancreatic adenocarcinoma

tag: Sex

value: F

tag: ecog

tag: clinicalcenter

tag: sizeprimary

tag: diseasestage

value: locAdvanced

tag: pfsevent

tag: firsttreatment


title: TiO2_MP_100ug_24H_2

tag: treatment

value: 24 Hour

value: 100 ug/mL


title: BPC274T

tag: sample id

tag: historicpatient id

tag: normpatient id

tag: age

value: meta

tag: pfsdelay

value: FOLFOX;XELODA


title: WK1_TMZ_RT_biol_rep_1

tag: cell line

tag: cell type

value: Glioblastoma cell line


title: BPC267T

tag: osevent

tag: osdelay

value: GEMCITABINE


title: BPC266T

tag: tissue

tag: Sex

value: borderline

value: CYL 02;GEMCITABINE


title: WK1_M4344_TMZ_RT_biol_rep_2


title: BPC265T

tag: ecog

tag: clinicalcenter


title: BPC264T

tag: sizeprimary

tag: diseasestage


title: TiO2_MP_25ug_24H_2

tag: strain

value: MutaMouse

value: TiO2 Microparticle

tag: time point

tag: dose

tag: biological replicate

tag: sample type


title: TiO2_MP_0ug_24H_2

tag: treatment

value: Media Control


title: WK1_M4344_TMZ_RT_biol_rep_1


title: BPC263T

tag: sample id

tag: historicpatient id

tag: normpatient id

tag: age

value: Toulouse

tag: pfsevent

tag: pfsdelay

tag: firsttreatment


title: BPC262T

tag: tissue

tag: Sex

tag: ecog

tag: osevent

tag: osdelay

value: FOLFIRINOX


title: WK1_DMSO_biol_rep_2

tag: cell line

tag: cell type

value: DMSO control


title: BPC261T

value: pancreatic adenocarcinoma

value: M

tag: clinicalcenter

tag: sizeprimary

tag: diseasestage

value: resectable


title: BPC260T

tag: sample id

value: F

value: locAdvanced


title: BPC259T

tag: historicpatient id

value: GEMCITABINE;XELODA

tag: surgerytype

value: DPC

tag: surgerymargin


title: WK1_DMSO_biol_rep_1

value: Glioblastoma cell line

tag: treatment


title: TiO2_MP_100ug_2H_1

tag: strain

tag: time point

value: 2 Hour

tag: dose

value: 100 ug/mL

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: RN1_TMZ_RT_biol_rep_2

value: TMZ+RT


title: BPC258T

tag: tissue

tag: normpatient id

tag: age

tag: Sex

tag: ecog

tag: pfsevent

tag: pfsdelay

tag: osevent


title: TiO2_MP_50ug_2H_1

value: MutaMouse

value: TiO2 Microparticle

value: 50 ug/mL


title: BPC257T

tag: sample id

tag: historicpatient id

tag: clinicalcenter

value: Toulouse

tag: sizeprimary

tag: diseasestage

value: meta

tag: osdelay

tag: firsttreatment

value: FOLFIRINOX


title: BPC256T

value: pancreatic adenocarcinoma

value: GEMCITABINE


title: RN1_TMZ_RT_biol_rep_1

tag: cell line

tag: cell type

tag: treatment


title: BPC255T

tag: tissue

tag: normpatient id

value: M

value: borderline

tag: surgerytype


title: TiO2_MP_50ug_24H_2

tag: strain

tag: time point

value: 24 Hour

tag: dose

tag: biological replicate

tag: sample type


title: Al2O3_MP_50ug_2H_1

value: Al2O3 Microparticle


title: RN1_M4344_TMZ_RT_biol_rep_2

value: Glioblastoma cell line


title: BPC252T

tag: sample id

tag: historicpatient id

tag: age

tag: Sex

tag: ecog

value: locAdvanced

tag: pfsevent

tag: pfsdelay

tag: osevent


title: BPC251T

value: F

tag: clinicalcenter

tag: sizeprimary

tag: diseasestage

tag: osdelay

tag: firsttreatment

value: GEMCITABINE;ABRAXANE


title: RN1_M4344_TMZ_RT_biol_rep_1

tag: cell line

tag: cell type

tag: treatment


title: BPC317T

tag: tissue

tag: normpatient id

value: Hopital Mermoz

tag: surgerytype

value: DPC

tag: surgerymargin


title: Al2O3_MP_10ug_48H_2

tag: strain

value: MutaMouse

tag: time point

value: 48 Hour

tag: dose

value: 10 ug/mL

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: BPC250T

tag: sample id

tag: historicpatient id

tag: age

tag: Sex

tag: ecog

tag: clinicalcenter

value: Toulouse

tag: pfsevent

tag: pfsdelay

tag: osevent


title: BPC249T

tag: tissue

value: pancreatic adenocarcinoma

tag: normpatient id

tag: sizeprimary

tag: diseasestage

value: meta

tag: osdelay

tag: firsttreatment

value: FOLFIRINOX


title: Al2O3_MP_50ug_48H_2

tag: strain

tag: treatment

tag: time point

tag: dose

value: 50 ug/mL

tag: biological replicate


title: RN1_DMSO_biol_rep_2

tag: cell line

tag: cell type

value: DMSO control


title: BPC248T

tag: sample id

tag: historicpatient id

tag: age

tag: Sex

value: M

tag: ecog

tag: clinicalcenter

value: borderline


title: TiO2_MP_0ug_2H_1

value: TiO2 Microparticle

value: 2 Hour

value: Media Control

tag: sample type


title: BPC247T

tag: tissue

tag: normpatient id

value: F

tag: sizeprimary

tag: diseasestage

value: resectable

tag: pfsevent

tag: pfsdelay

tag: osevent

value: GEMCITABINE;XELODA

tag: surgerytype

tag: surgerymargin


title: BPC246T

value: locAdvanced

tag: osdelay

tag: firsttreatment

value: GEMCITABINE


title: BPC245T

tag: sample id

tag: historicpatient id


title: RN1_DMSO_biol_rep_1

tag: cell line

tag: cell type

value: Glioblastoma cell line

tag: treatment


title: Al2O3_MP_25ug_48H_2

tag: strain

value: MutaMouse

value: Al2O3 Microparticle

tag: time point

value: 48 Hour

tag: dose

value: 25 ug/mL

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: BPC254T

tag: tissue

value: pancreatic adenocarcinoma

tag: normpatient id

tag: age

tag: Sex

tag: ecog

tag: clinicalcenter

value: Toulouse

tag: sizeprimary

tag: diseasestage

value: meta

tag: pfsevent

value: FOLFIRINOX


title: BPC253T

tag: sample id

tag: historicpatient id

value: M

tag: pfsdelay

tag: osevent

tag: osdelay

tag: firsttreatment


title: Al2O3_MP_0ug_2H_3

tag: strain

tag: treatment

tag: time point

value: 2 Hour

tag: dose

value: Media Control

tag: biological replicate


title: BPC244T

tag: tissue

tag: normpatient id

tag: age

tag: Sex

value: resectable

tag: surgerytype

value: DPC

tag: surgerymargin


title: arid1b, adult, rep14

city: Worcester

first: Summer

last: Thyme

state: MA

address: 364 Plantation St

country: USA

institute: UMass Chan Medical School

data_processing:
Single-end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner (2.7.3a-GCC-6.4.0-2.28). https://www.umassmed.edu/lawson-lab/reagents/zebrafish-transcriptome/
The raw counts files from STAR, in this record, were normalized using the rlog method in DESeq2 for subsequent published analysis.
Assembly: GRCz11
Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.

organism: Danio rerio

source_name: single dissected adult brain, male

extract_protocol:
RNA was extracted using the MicroElute Total RNA Kit (Omega Bio-Tek R6834-02), with a 15-min incubation with Dnase I.
Libraries were constructed using an in-house protocol based on SMART-Seq2, followed by Nextera XT Library Preparation (FC-131-1096).

value: single dissected adult brain, male

tag: genotype

value: arid1b homozygote


title: Al2O3_MP_10ug_48H_1

value: 10 ug/mL

tag: sample type


title: BPC242T

tag: sample id

tag: historicpatient id

value: F

tag: clinicalcenter

tag: sizeprimary

tag: diseasestage

value: locAdvanced

tag: pfsevent

tag: pfsdelay

value: GEMCITABINE


title: arid1b, adult, rep15


title: BPC243T

tag: osevent

tag: osdelay

tag: firsttreatment

value: PC


title: BPC241T

tag: tissue

tag: normpatient id

value: borderline

value: FOLFIRINOX;XELODA


title: Al2O3_MP_0ug_48H_2

tag: strain

value: MutaMouse

tag: treatment

value: Al2O3 Microparticle

tag: time point

value: 48 Hour

tag: dose

tag: biological replicate

value: 11 mouse cell lines


title: BPC236T

tag: sample id

value: pancreatic adenocarcinoma

tag: age

tag: Sex

tag: ecog

value: Toulouse

value: meta


title: BPC237T

tag: historicpatient id

value: M

tag: clinicalcenter

tag: sizeprimary

tag: diseasestage

value: resectable

tag: surgerytype

tag: surgerymargin


title: arid1b, adult, rep10

tag: tissue

value: single dissected adult brain, male

tag: genotype

value: arid1b heterozygote


title: BPC234T

tag: normpatient id

tag: pfsevent

tag: pfsdelay

tag: osevent

tag: osdelay

tag: firsttreatment

value: FOLFOX


title: BPC240T

tag: sample id

tag: age

value: locAdvanced

value: FOLFIRINOX


title: BPC233T

tag: Sex

value: F


title: BPC235T

tag: historicpatient id

value: GEMCITABINE


title: arid1b, adult, rep9


title: BPC232T

tag: clinicalcenter

value: DPC


title: arid1b, adult, rep8


title: arid1b, adult, rep12

value: arid1b homozygote


title: BPC229T

tag: sizeprimary


title: Al2O3_MP_25ug_48H_1

tag: strain

value: MutaMouse

tag: treatment

value: Al2O3 Microparticle

tag: time point

tag: dose

value: 25 ug/mL

tag: biological replicate

tag: sample type


title: arid1b, adult, rep7

source_name: single dissected adult brain, female

tag: tissue

value: single dissected adult brain, female

tag: genotype


title: Al2O3_MP_25ug_2H_3

value: 2 Hour

value: 11 mouse cell lines


title: Al2O3_MP_50ug_48H_1

value: 48 Hour

value: 50 ug/mL


title: Al2O3_MP_10ug_2H_3

value: 10 ug/mL


title: Al2O3_MP_0ug_48H_1

value: Media Control


title: Al2O3_MP_50ug_2H_2


title: BPC228T

value: pancreatic adenocarcinoma

tag: normpatient id

tag: ecog

value: Toulouse

tag: diseasestage

tag: pfsevent

tag: pfsdelay

tag: osevent


title: arid1b, adult, rep6


title: BPC227T

tag: sample id

tag: historicpatient id

tag: age

tag: Sex

value: M

value: resectable

tag: osdelay


title: BPC226T

tag: clinicalcenter

tag: sizeprimary

value: meta

tag: firsttreatment

value: FOLFIRINOX


title: BPC231T

value: locAdvanced

value: FOLFOX


title: arid1b, adult, rep5

value: arid1b homozygote


title: BPC225T

value: GEMCITABINE

tag: surgerytype

value: PC

tag: surgerymargin


title: BPC224T

tag: tissue


title: Al2O3_MP_0ug_24H_3

tag: strain

value: MutaMouse

tag: treatment

value: Al2O3 Microparticle

tag: time point

value: 24 Hour

tag: dose

tag: biological replicate

tag: sample type


title: arid1b, adult, rep4

value: single dissected adult brain, female

tag: genotype

value: arid1b heterozygote


title: Al2O3_MP_10ug_24H_3

value: 10 ug/mL

value: 11 mouse cell lines


title: arid1b, adult, rep3


title: Al2O3_MP_25ug_24H_3

value: 25 ug/mL


title: BPC220T

tag: sample id

value: pancreatic adenocarcinoma

tag: historicpatient id

tag: normpatient id

value: M

tag: ecog

value: Toulouse

tag: diseasestage

tag: pfsevent

tag: pfsdelay

tag: osevent


title: BPC218T

tag: age

tag: Sex

tag: clinicalcenter

tag: sizeprimary

value: resectable

tag: osdelay

tag: firsttreatment

tag: surgerytype

tag: surgerymargin


title: arid1b, adult, rep2

tag: tissue

tag: genotype


title: arid1b, adult, rep1


title: BPC217T

tag: sample id

tag: historicpatient id

value: borderline

value: FOLFIRINOX

value: DPC


title: Al2O3_MP_50ug_24H_3

tag: strain

tag: treatment

tag: time point

tag: dose

value: 50 ug/mL

tag: biological replicate

tag: sample type


title: BPC216T

tag: normpatient id

tag: age

tag: Sex

value: F

value: CLB

tag: diseasestage

value: meta

tag: pfsevent

tag: pfsdelay

tag: osevent


title: BPC223T

tag: tissue

tag: ecog

tag: clinicalcenter

tag: sizeprimary

tag: osdelay

tag: firsttreatment


title: BPC215T

tag: sample id

tag: historicpatient id

value: Clinique du Trocadero

value: locAdvanced


title: BPC213T


title: kmt5b, 6 dpf, rep11

source_name: head with eyes, 2-5 heads combined

value: head with eyes, 2-5 heads combined

tag: genotype

value: kmt5b wild types


title: Al2O3_MP_10ug_2H_2

tag: strain

value: MutaMouse

tag: treatment

value: Al2O3 Microparticle

tag: time point

value: 2 Hour

tag: dose

value: 10 ug/mL

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: BPC222T

value: pancreatic adenocarcinoma

tag: normpatient id

tag: age

tag: Sex

value: Toulouse

tag: diseasestage

value: resectable

tag: pfsevent

tag: pfsdelay

value: GEMCITABINE

tag: surgerytype

tag: surgerymargin


title: kmt5b, 6 dpf, rep10

tag: tissue


title: Al2O3_MP_0ug_2H_2

value: Media Control


title: BPC210T

tag: sample id

tag: historicpatient id

value: M

tag: ecog

tag: clinicalcenter

tag: sizeprimary

value: borderline

tag: osevent

tag: osdelay


title: kmt5b, 6 dpf, rep9

tag: genotype


title: BPC209T

tag: normpatient id

value: F

tag: firsttreatment

value: FOLFIRINOX

value: DPC


title: Al2O3_MP_10ug_48H_3

tag: strain

tag: treatment

tag: time point

value: 48 Hour

tag: dose

tag: biological replicate

tag: sample type


title: BPC208T

tag: tissue

tag: age

tag: Sex

value: Clinique du Trocadero

tag: diseasestage

value: meta

tag: pfsevent

tag: pfsdelay

value: ABRAXANE;GEMCITABINE


title: kmt5b, 6 dpf, rep8

value: head with eyes, 2-5 heads combined

value: kmt5b homozygotes


title: Al2O3_MP_25ug_48H_3

value: MutaMouse

value: Al2O3 Microparticle

value: 25 ug/mL

value: 11 mouse cell lines


title: BPC207T

tag: sample id

value: pancreatic adenocarcinoma

tag: historicpatient id

tag: ecog

tag: clinicalcenter

tag: sizeprimary

value: locAdvanced


title: Al2O3_MP_0ug_24H_1

tag: strain

value: 24 Hour

value: Media Control


title: kmt5b, 6 dpf, rep7

tag: genotype


title: BPC205T

tag: normpatient id

value: M

tag: osevent

tag: osdelay

tag: firsttreatment


title: arid1b, adult, rep13

tag: tissue

value: single dissected adult brain, male

value: arid1b homozygote


title: BPC204T

tag: age

value: borderline

tag: surgerytype

value: DPC

tag: surgerymargin


title: BPC203T

tag: Sex

value: Clinique du Trocadero

tag: diseasestage

tag: pfsevent


title: BPC238T

tag: sample id

tag: historicpatient id

value: Toulouse

tag: pfsdelay


title: Al2O3_MP_50ug_48H_3

tag: treatment

tag: time point

value: 48 Hour

tag: dose

value: 50 ug/mL

tag: biological replicate

tag: sample type


title: Al2O3_MP_25ug_24H_1

tag: strain

value: MutaMouse


title: Al2O3_MP_50ug_24H_1

value: Al2O3 Microparticle


title: BPC206T

tag: normpatient id

value: F

tag: ecog

tag: clinicalcenter

tag: sizeprimary

value: meta

tag: osevent

tag: osdelay

tag: firsttreatment

value: FOLFIRINOX


title: kmt5b, 6 dpf, rep5

tag: tissue

value: head with eyes, 2-5 heads combined

tag: genotype

value: kmt5b homozygotes


title: BPC202T

tag: sample id

value: pancreatic adenocarcinoma

tag: historicpatient id

tag: age

tag: Sex

tag: diseasestage

value: locAdvanced

tag: pfsevent

value: FOLFIRINOX;FOLFIRI;IRINOTECAN


title: kmt5b, 6 dpf, rep4

value: kmt5b heterozygotes


title: Al2O3_MP_10ug_24H_1

tag: treatment

tag: time point

value: 24 Hour

tag: dose

value: 10 ug/mL

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: BPC200T

tag: normpatient id

value: M

tag: ecog

tag: clinicalcenter

value: Clinique du Trocadero

tag: sizeprimary

value: resectable

tag: pfsdelay

value: XELODA;FOLFIRINOX;FOLFIRI


title: BPC201T

tag: tissue

value: borderline

tag: osevent

tag: osdelay


title: BPC198T

tag: sample id

tag: historicpatient id

tag: age

tag: firsttreatment


title: BPC197T

tag: Sex

tag: diseasestage

tag: pfsevent


title: BPC196T


title: BPC195T


title: Al2O3_MP_0ug_24H_2

tag: strain

value: MutaMouse

tag: treatment

value: Al2O3 Microparticle

tag: time point

tag: dose

value: Media Control

tag: biological replicate


title: kmt5b, 6 dpf, rep2

value: head with eyes, 2-5 heads combined

tag: genotype


title: BPC194T

tag: normpatient id

value: F

tag: ecog

tag: clinicalcenter

tag: sizeprimary

tag: pfsdelay


title: BPC199T

tag: sample id

tag: tissue

value: pancreatic adenocarcinoma

tag: historicpatient id

tag: osevent

tag: osdelay

value: GEMCITABINE


title: BPC193T

tag: age

tag: Sex

tag: diseasestage

tag: pfsevent


title: Al2O3_MP_0ug_48H_3

tag: strain

tag: treatment

tag: time point

value: 48 Hour

tag: dose

tag: sample type


title: kmt5b, 6 dpf, rep1

tag: genotype

value: kmt5b heterozygotes


title: hdlbpa, 6 dpf, rep10

value: hdlbpa wild types


title: BPC192T

tag: normpatient id

tag: ecog

tag: clinicalcenter

tag: sizeprimary

value: locAdvanced

tag: firsttreatment

value: FOLFIRINOX


title: BPC191T

tag: sample id

tag: tissue

tag: historicpatient id

tag: pfsdelay

tag: osevent

tag: surgerytype

value: DPC

tag: surgerymargin


title: kmt5b, 6 dpf, rep3


title: BPC190T

tag: age

tag: Sex

value: M

value: Clinique du Trocadero

tag: diseasestage

tag: pfsevent

tag: osdelay

value: GEMCITABINE;XELODA

value: PC


title: Al2O3_MP_25ug_24H_2

tag: strain

value: MutaMouse

tag: treatment

tag: time point

value: 24 Hour

tag: dose

value: 25 ug/mL

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: hdlbpa, 6 dpf, rep9

tag: tissue

value: head with eyes, 2-5 heads combined

tag: genotype


title: Al2O3_MP_10ug_2H_1

value: Al2O3 Microparticle

value: 2 Hour

value: 10 ug/mL


title: BPC189T

tag: sample id

value: pancreatic adenocarcinoma

tag: historicpatient id

tag: normpatient id

value: F

tag: ecog

tag: clinicalcenter

tag: sizeprimary

tag: pfsdelay

tag: firsttreatment


title: Al2O3_MP_50ug_2H_3

value: 50 ug/mL


title: Al2O3_MP_50ug_24H_2


title: BPC188T

tag: age

tag: Sex

tag: diseasestage

value: borderline

tag: pfsevent

tag: osevent

tag: osdelay

value: FOLFIRINOX;XELODA

tag: surgerytype

tag: surgerymargin


title: hdlbpa, 6 dpf, rep8

tag: tissue

tag: genotype

value: hdlbpa wild types


title: BPC187T

tag: sample id

tag: historicpatient id

value: M

value: Clinique du Trocadero

value: locAdvanced

value: FOLFIRINOX


title: BPC186T

tag: normpatient id

tag: ecog


title: arid1b, adult, rep11

value: single dissected adult brain, male

value: arid1b heterozygote


title: Al2O3_MP_25ug_2H_1

tag: strain

value: MutaMouse

tag: treatment

tag: time point

tag: dose

value: 25 ug/mL

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: hdlbpa, 6 dpf, rep7

value: head with eyes, 2-5 heads combined


title: Al2O3_MP_0ug_2H_1

value: Al2O3 Microparticle

value: 2 Hour

value: Media Control


title: hdlbpa, 6 dpf, rep6

value: hdlbpa homozygotes


title: BPC183T

value: pancreatic adenocarcinoma

tag: age

tag: Sex

value: F

tag: clinicalcenter

tag: sizeprimary

tag: diseasestage

value: borderline

tag: pfsevent

tag: pfsdelay

tag: firsttreatment


title: BPC184T

tag: sample id

tag: tissue

tag: historicpatient id

tag: osevent

tag: osdelay


title: BPC181T

tag: normpatient id

tag: ecog


title: BPC182T

value: ABRAXANE;GEMCITABINE


title: BPC214T

value: M

value: Clinique du Trocadero


title: BPC180T


title: BPC179T

value: CARBOPLATINE


title: BPC178T

value: locAdvanced


title: hdlbpa, 6 dpf, rep3

tag: genotype


title: hdlbpa, 6 dpf, rep4


title: BPC177T

value: FOLFIRINOX

tag: surgerytype

value: DPC

tag: surgerymargin


title: hdlbpa, 6 dpf, rep2

value: hdlbpa heterozygotes


title: BPC176T

tag: age

tag: Sex

value: meta


title: hdlbpa, 6 dpf, rep5

value: head with eyes, 2-5 heads combined


title: BPC174T

tag: clinicalcenter

tag: sizeprimary


title: BPC175T

tag: diseasestage

tag: pfsevent


title: hdlbpa, 6 dpf, rep1


title: NiO_MP_0ug_48H_2

tag: strain

value: MutaMouse

tag: treatment

value: NiO Microparticle

tag: time point

value: 48 Hour

tag: dose

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: Al2O3_MP_10ug_24H_2

value: Al2O3 Microparticle

value: 24 Hour

value: 10 ug/mL


title: NiO_MP_25ug_2H_1

value: 2 Hour

value: 25 ug/mL


title: NiO_MP_0ug_24H_2

value: Media Control


title: BPC230T

tag: sample id

tag: tissue

value: pancreatic adenocarcinoma

tag: historicpatient id

tag: normpatient id

value: M

value: Toulouse

tag: pfsdelay

tag: osevent

tag: osdelay

tag: firsttreatment


title: deaf1, 2 dpf, rep13

tag: genotype

value: deaf1 23d46i wild types


title: Al2O3_MP_25ug_2H_2


title: NiO_MP_25ug_48H_2


title: NiO_MP_25ug_48H_1


title: NiO_MP_10ug_48H_2


title: NiO_MP_50ug_48H_2

value: 50 ug/mL


title: deaf1, 2 dpf, rep12


title: BPC169T

tag: age

tag: Sex

tag: ecog

tag: clinicalcenter

value: Clinique du Trocadero

tag: sizeprimary

tag: diseasestage

value: resectable

value: FOLFIRINOX;FOLFIRI

tag: surgerytype

value: DPC

tag: surgerymargin


title: BPC172T

tag: sample id

value: borderline

tag: pfsevent


title: BPC168T

tag: tissue

tag: historicpatient id

value: locAdvanced


title: BPC170T

tag: normpatient id

value: meta

tag: pfsdelay


title: BPC173T

value: F

tag: osevent

tag: osdelay


title: deaf1, 2 dpf, rep11

value: head with eyes, 2-5 heads combined

tag: genotype


title: BPC165T

tag: age

tag: firsttreatment


title: BPC166T

tag: Sex

tag: ecog


title: BPC164T

tag: clinicalcenter

tag: sizeprimary


title: deaf1, 2 dpf, rep10


title: kmt5b, 6 dpf, rep6

value: kmt5b homozygotes


title: BPC171T

tag: diseasestage

value: XELODA;GEMCITABINE


title: deaf1, 2 dpf, rep8

value: deaf1 23d46i homozygotes


title: BPC162T

value: pancreatic adenocarcinoma

value: FOLFIRINOX


title: NiO_MP_0ug_48H_1

tag: strain

value: MutaMouse

tag: treatment

value: NiO Microparticle

tag: time point

value: 48 Hour

tag: dose

value: Media Control

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: deaf1, 2 dpf, rep9

tag: tissue

value: deaf1 23d46i wild types


title: NiO_MP_10ug_48H_1

value: 10 ug/mL


title: BPC167T

tag: sample id

tag: historicpatient id

tag: normpatient id

value: M

value: Clinique du Trocadero

tag: pfsevent

tag: pfsdelay

tag: osevent


title: BPC158T

tag: age

tag: Sex

value: locAdvanced

tag: osdelay

tag: firsttreatment

value: GEMCITABINE;ABRAXANE


title: BPC160T

tag: ecog

tag: clinicalcenter

tag: sizeprimary

tag: diseasestage

value: resectable

value: GEMCITABINE


title: BPC239T

value: Toulouse


title: BPC161T

value: F

value: FOLFIRINOX;XELODA;FOLFIRI


title: NiO_MP_0ug_2H_3

tag: strain

tag: treatment

tag: time point

value: 2 Hour

tag: dose

tag: biological replicate


title: deaf1, 2 dpf, rep7

tag: tissue

value: head with eyes, 2-5 heads combined

tag: genotype

value: deaf1 23d46i homozygotes


title: BPC276T

tag: sample id

value: pancreatic adenocarcinoma

tag: historicpatient id

tag: normpatient id

value: meta

tag: pfsevent

tag: pfsdelay

value: FOLFIRINOX


title: BPC157T

tag: age

tag: Sex

tag: osevent

tag: osdelay

tag: firsttreatment


title: BPC159T

tag: ecog

tag: clinicalcenter

tag: sizeprimary

tag: diseasestage


title: BPC155T


title: BPC163T


title: deaf1, 2 dpf, rep5


title: BPC154T


title: NiO_MP_50ug_2H_3

tag: strain

value: MutaMouse

tag: treatment

value: NiO Microparticle

tag: time point

tag: dose

value: 50 ug/mL

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: deaf1, 2 dpf, rep6

tag: tissue

tag: genotype


title: deaf1, 2 dpf, rep4


title: deaf1, 2 dpf, rep3

value: deaf1 23d46i heterozygotes


title: BPC153T

tag: sample id

tag: historicpatient id

tag: normpatient id

tag: age

value: Clinique du Trocadero

tag: pfsevent

tag: pfsdelay

value: ABRAXANE;GEMCITABINE


title: BPC150T

tag: Sex

tag: ecog

tag: clinicalcenter

value: borderline


title: deaf1, 2 dpf, rep2


title: BPC149T

value: M

tag: sizeprimary

tag: diseasestage

value: locAdvanced

tag: osevent

tag: osdelay

tag: firsttreatment

value: GEMCITABINE;XELODA


title: BPC151T

value: F

value: resectable


title: BPC148T


title: deaf1, 2 dpf, rep1

value: head with eyes, 2-5 heads combined


title: NiO_MP_10ug_2H_3

tag: strain

tag: treatment

tag: time point

value: 2 Hour

tag: dose

value: 10 ug/mL

tag: biological replicate

tag: sample type


title: BPC147T

tag: sample id

tag: tissue

value: pancreatic adenocarcinoma

tag: historicpatient id

tag: normpatient id

tag: age

value: FOLFIRINOX

tag: surgerytype

value: DPC

tag: surgerymargin


title: NiO_MP_0ug_24H_3

value: MutaMouse

value: NiO Microparticle

value: 24 Hour

value: Media Control


title: BPC146T

tag: Sex

tag: ecog

tag: clinicalcenter

value: Clinique du Trocadero

tag: sizeprimary

tag: diseasestage

value: meta

tag: pfsevent

tag: pfsdelay


title: NiO_MP_25ug_2H_3

tag: strain

tag: treatment

tag: time point

tag: dose

value: 25 ug/mL

value: 11 mouse cell lines


title: NiO_MP_50ug_48H_1

value: 48 Hour

value: 50 ug/mL

tag: biological replicate

tag: sample type


title: BPC152T

tag: sample id

tag: tissue

tag: historicpatient id

tag: normpatient id

value: M

tag: osevent

tag: osdelay


title: BPC145T

tag: age

tag: Sex

tag: ecog

tag: clinicalcenter

value: borderline

tag: firsttreatment

tag: surgerytype

tag: surgerymargin


title: NiO_MP_10ug_2H_2

tag: strain

tag: treatment

tag: time point

value: 2 Hour


title: NiO_MP_50ug_2H_2

tag: dose

tag: biological replicate

tag: sample type


title: TiO2_MP_100ug_48H_3

value: TiO2 Microparticle

value: 100 ug/mL


title: NiO_MP_25ug_24H_3


title: BPC143T

tag: sample id

tag: tissue

value: pancreatic adenocarcinoma

tag: historicpatient id

tag: sizeprimary

tag: diseasestage

tag: pfsevent

tag: pfsdelay


title: BPC144T

tag: normpatient id

tag: age

tag: Sex

value: F

tag: ecog

tag: clinicalcenter

tag: osevent

tag: osdelay


title: deaf1-c207y, 2 dpf, rep12

value: head with eyes, 2-5 heads combined

tag: genotype

value: deaf1 c207y wild types


title: BPC141T

value: resectable


title: BPC212T


title: deaf1-c207y, 2 dpf, rep11


title: BPC140T

value: locAdvanced

tag: firsttreatment

value: FOLFIRINOX


title: BPC139T

value: Clinique du Trocadero

value: FOLFIRINOX;FOLFIRI;OXALIPLATINE;XELODA


title: deaf1-c207y, 2 dpf, rep10


title: deaf1-c207y, 2 dpf, rep13


title: BPC211T

value: GEMCITABINE


title: BPC137T

value: meta


title: NiO_MP_10ug_24H_3

tag: strain

value: MutaMouse

tag: treatment

value: NiO Microparticle

tag: time point

value: 24 Hour

tag: dose

value: 10 ug/mL

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: NiO_MP_0ug_2H_2

value: 2 Hour

value: Media Control


title: NiO_MP_50ug_24H_3

value: 50 ug/mL


title: BPC136T

tag: sample id

tag: tissue

value: pancreatic adenocarcinoma

tag: historicpatient id

value: F

tag: sizeprimary

tag: diseasestage

tag: pfsevent


title: BPC135T

tag: normpatient id

tag: age

tag: Sex

value: M

tag: ecog

tag: clinicalcenter

tag: pfsdelay


title: deaf1-c207y, 2 dpf, rep8

value: head with eyes, 2-5 heads combined

tag: genotype

value: deaf1 c207y homozygotes


title: deaf1-c207y, 2 dpf, rep7


title: NiO_MP_0ug_48H_3

tag: strain

tag: treatment

tag: time point

value: 48 Hour


title: BPC142T

value: Clinique du Trocadero

value: locAdvanced

tag: osevent

tag: osdelay

tag: firsttreatment


title: BPC133T

tag: sample id

tag: tissue

tag: historicpatient id

value: meta

value: GEMCITABINE


title: NiO_MP_0ug_24H_1

value: MutaMouse

value: NiO Microparticle

tag: dose

tag: biological replicate

tag: sample type


title: deaf1-c207y, 2 dpf, rep6


title: BPC132T

tag: normpatient id

tag: age

tag: Sex

tag: sizeprimary

tag: diseasestage

tag: pfsevent

value: FOLFIRINOX


title: NiO_MP_25ug_2H_2

tag: strain

tag: treatment

value: 25 ug/mL

value: 11 mouse cell lines


title: NiO_MP_10ug_48H_3

tag: time point

value: 10 ug/mL


title: BPC131T

tag: ecog

tag: clinicalcenter

value: borderline

tag: pfsdelay

tag: osevent

tag: osdelay


title: deaf1-c207y, 2 dpf, rep5

tag: tissue

tag: genotype

value: deaf1 c207y heterozygotes


title: deaf1-c207y, 2 dpf, rep9

value: deaf1 c207y wild types


title: NiO_MP_25ug_24H_1

value: 24 Hour

tag: dose

tag: biological replicate

tag: sample type


title: BPC134T

tag: sample id

value: pancreatic adenocarcinoma

tag: historicpatient id

tag: normpatient id

tag: age

tag: Sex

value: M

value: resectable

tag: firsttreatment

value: GEMOX


title: BPC127T

value: Clinique du Trocadero

tag: diseasestage

value: locAdvanced

tag: pfsevent


title: BPC126T

value: F

tag: ecog

tag: clinicalcenter

tag: sizeprimary

value: XELODA


title: BPC128T

value: meta

tag: pfsdelay

tag: osevent

tag: osdelay


title: NiO_MP_50ug_24H_1

tag: strain

value: MutaMouse

tag: treatment

value: NiO Microparticle

tag: time point

tag: dose

value: 50 ug/mL


title: BPC125T

tag: sample id

tag: tissue

tag: historicpatient id

value: FOLFIRINOX;FOLFIRI


title: deaf1-c207y, 2 dpf, rep4

value: head with eyes, 2-5 heads combined

tag: genotype


title: deaf1-c207y, 2 dpf, rep2

value: deaf1 c207y heterozygotes


title: BPC124T

tag: normpatient id

tag: age

tag: Sex

value: borderline

tag: firsttreatment

value: GEMCITABINE


title: deaf1-c207y, 2 dpf, rep3


title: BPC123T

value: pancreatic adenocarcinoma

tag: ecog

tag: clinicalcenter

tag: diseasestage

tag: pfsevent


title: NiO_MP_10ug_24H_1

value: 24 Hour

value: 10 ug/mL

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: BPC122T

value: M

value: Clinique du Trocadero

tag: sizeprimary

value: resectable

tag: pfsdelay

tag: osevent

tag: osdelay

value: FOLFIRINOX

tag: surgerytype

value: DPC

tag: surgerymargin


title: BPC130T

tag: sample id

tag: tissue

tag: historicpatient id

value: F

value: PC


title: NiO_MP_25ug_48H_3

tag: strain

value: MutaMouse

tag: treatment

value: NiO Microparticle

tag: time point

value: 48 Hour

tag: dose

value: 25 ug/mL


title: deaf1-c207y, 2 dpf, rep1

value: head with eyes, 2-5 heads combined

tag: genotype

value: deaf1 c207y heterozygotes


title: BPC121T

value: pancreatic adenocarcinoma

tag: normpatient id

tag: age

tag: Sex

tag: ecog

tag: clinicalcenter

tag: diseasestage

value: locAdvanced

tag: pfsevent

tag: firsttreatment


title: NiO_MP_0ug_2H_1

value: 2 Hour

value: Media Control

tag: biological replicate

tag: sample type


title: BPC129T

tag: sample id

tag: tissue

value: M

tag: pfsdelay

tag: osevent

tag: osdelay

tag: surgerytype

tag: surgerymargin


title: NiO_MP_50ug_2H_1

tag: strain

tag: treatment

tag: time point

tag: dose

value: 50 ug/mL

value: 11 mouse cell lines


title: deaf1, 6 dpf, rep14

tag: genotype

value: deaf1 23d46i wild types


title: BPC120T

tag: historicpatient id

tag: normpatient id

tag: age

tag: Sex

tag: ecog

tag: clinicalcenter

value: Clinique du Trocadero

tag: sizeprimary

tag: diseasestage

value: resectable

value: FOLFIRINOX;FOLFIRI

value: DPC


title: BPC119T

tag: sample id

tag: tissue

value: F

value: meta

tag: pfsevent

tag: pfsdelay

tag: osevent

tag: firsttreatment

value: FOLFIRINOX;TAXANE;GEMCITABINE


title: BPC118T

value: borderline

tag: osdelay

value: FOLFIRINOX;XELODA

tag: surgerytype

tag: surgerymargin


title: deaf1, 6 dpf, rep13

value: head with eyes, 2-5 heads combined

tag: genotype


title: NiO_MP_50ug_24H_2

tag: strain

value: MutaMouse

tag: treatment

value: NiO Microparticle

tag: time point

value: 24 Hour

tag: dose

tag: biological replicate

tag: sample type


title: BPC117T

value: pancreatic adenocarcinoma

tag: historicpatient id

tag: normpatient id

tag: age

tag: Sex

value: M

tag: ecog

tag: clinicalcenter

tag: sizeprimary

tag: diseasestage

value: locAdvanced


title: NiO_MP_25ug_24H_2

value: 25 ug/mL

value: 11 mouse cell lines


title: BPC116T

tag: sample id

tag: tissue

value: Clinique du Trocadero

tag: pfsevent

tag: pfsdelay

tag: osevent

tag: osdelay

tag: firsttreatment

value: GEMCITABINE


title: deaf1, 6 dpf, rep12

tag: genotype

value: deaf1 23d46i wild types


title: BPC114T

value: resectable

tag: surgerytype

value: DPC

tag: surgerymargin


title: BPC113T

tag: historicpatient id

tag: normpatient id

value: PC


title: deaf1, 6 dpf, rep11


title: BPC112T

tag: age

tag: Sex

value: F


title: BPC111T

tag: ecog

tag: clinicalcenter

value: ABRAXANE;GEMCITABINE


title: deaf1, 6 dpf, rep10

value: head with eyes, 2-5 heads combined

value: deaf1 23d46i homozygotes


title: BPC109T

tag: sizeprimary

tag: diseasestage


title: NiO_MP_10ug_24H_2

tag: strain

value: MutaMouse

tag: treatment

value: NiO Microparticle

tag: time point

tag: dose

value: 10 ug/mL

tag: biological replicate

tag: sample type


title: BPC110T

tag: sample id

tag: tissue

value: pancreatic adenocarcinoma

tag: pfsevent

tag: pfsdelay

tag: osevent

tag: osdelay

tag: firsttreatment


title: deaf1, 6 dpf, rep9

tag: genotype


title: ZnO_MP_0ug_48H_1

value: ZnO Microparticle

value: 48 Hour

value: Media Control


title: BPC107T

tag: historicpatient id

tag: normpatient id

tag: age

tag: Sex

value: M

tag: ecog

tag: clinicalcenter

value: Clinique du Trocadero

value: borderline


title: BPC108T

tag: sizeprimary

tag: diseasestage

value: locAdvanced


title: deaf1, 6 dpf, rep8


title: BPC106T

value: OXALIPLATINE;FOLFIRINOX


title: BPC105T

value: meta

value: FOLFIRINOX


title: ZnO_MP_5ug_48H_2

tag: strain

tag: treatment

tag: time point

tag: dose

value: 5 ug/mL

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: BPC104T

tag: sample id

tag: tissue

tag: pfsevent

tag: pfsdelay

tag: osevent

tag: osdelay


title: deaf1, 6 dpf, rep7

value: head with eyes, 2-5 heads combined

tag: genotype

value: deaf1 23d46i homozygotes


title: BPC115T

tag: historicpatient id

tag: normpatient id

tag: age

tag: Sex

value: F

tag: ecog


title: BPC103T

tag: clinicalcenter

tag: sizeprimary

tag: diseasestage

tag: firsttreatment

value: GEMCITABINE


title: deaf1, 6 dpf, rep6


title: ZnO_MP_0.5ug_48H_2

tag: strain

value: MutaMouse

tag: treatment

tag: time point

tag: dose

value: 0.5 ug/mL

tag: biological replicate

tag: sample type


title: NiO_MP_10ug_2H_1

value: NiO Microparticle

value: 2 Hour

value: 10 ug/mL


title: ZnO_MP_0.5ug_2H_3

value: ZnO Microparticle


title: BPC102T

tag: sample id

tag: tissue

value: pancreatic adenocarcinoma

value: M

value: Clinique du Trocadero

tag: pfsevent

tag: pfsdelay

tag: osevent

tag: osdelay

value: FOLFIRINOX;OXALIPLATINE


title: BPC185T

tag: historicpatient id

tag: normpatient id

tag: age

tag: Sex

tag: ecog

value: locAdvanced

value: OXALIPLATINE;FOLFIRINOX


title: BPC101T

tag: clinicalcenter

tag: diseasestage

value: resectable


title: ZnO_MP_0.5ug_48H_1

tag: strain

tag: treatment

tag: time point

value: 48 Hour

value: 11 mouse cell lines


title: BPC100T

value: meta

tag: firsttreatment


title: deaf1, 6 dpf, rep4

value: head with eyes, 2-5 heads combined

tag: genotype

value: deaf1 23d46i heterozygotes


title: BPC098T

tag: sample id

tag: tissue

tag: sizeprimary


title: BPC099T

tag: pfsevent

tag: pfsdelay

tag: osevent

value: FOLFIRINOX


title: BPC097T

tag: historicpatient id

tag: normpatient id

tag: osdelay


title: ZnO_MP_0ug_48H_2

value: MutaMouse

tag: dose

value: Media Control

tag: biological replicate

tag: sample type


title: ZnO_MP_5ug_48H_1

tag: strain

value: 5 ug/mL


title: BPC095T

tag: age

tag: Sex

value: F

tag: ecog

tag: clinicalcenter

tag: diseasestage

value: FOLFIRINOX;FOLFIRI


title: deaf1, 6 dpf, rep2

tag: tissue

tag: genotype


title: ZnO_MP_0ug_2H_3

tag: treatment

value: ZnO Microparticle

tag: time point

value: 2 Hour


title: BPC093T

tag: sample id

value: pancreatic adenocarcinoma

value: M

value: Clinique du Trocadero

tag: sizeprimary

tag: pfsevent

tag: pfsdelay

tag: osevent


title: deaf1, 6 dpf, rep1


title: ZnO_MP_1ug_48H_2

tag: dose

value: 1 ug/mL

tag: biological replicate


title: BPC091T

tag: historicpatient id

tag: normpatient id

value: resectable

tag: osdelay


title: BPC092T

tag: age

tag: Sex

tag: ecog

tag: surgerytype

value: PC

tag: surgerymargin


title: D4, replicate 1, scRNAseq

city: Jinan

first: Lin

last: Zhang

state: Shandong

address: No.9-7 Jiangshuiquan Road

department: Clinical Medical Research Center for Women and Children Diseases

country: China

institute: Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University

description: 10× Genomics

data_processing:
Sequencing data were demultiplexed and converted to FASTQ format using bcl2fastq (v2.20). Cell Ranger (v6.1.1) was then used for sample demultiplexing, barcode processing, and 3' gene counting of single cells against the Ensembl mRatBN7.2 (rat) reference genomes.
Assembly: rn6
Supplementary files format and content: Tab-separated values files and matrix files

organism: Rattus norvegicus

source_name: Lung

growth_protocol: SPF

extract_protocol:
Fresh rat lung tissues were obtained from rats exposed or unexposed to gas explosions. The tissues were immediately transferred into sterile, RNase-free culture dishes containing calcium- and magnesium-free PBS (CMF-PBS) on ice. They were then dissected into ~0.5 mm2 pieces, rinsed in CMF-PBS to remove blood and fat, and dissociated into single-cell suspensions using 0.35% collagenase IV, 5.2 mg/ml papain, and 120 U/ml DNase I in a 37°C shaking water bath (100 rpm, 20 min). Digestion was stopped with CMF-PBS + 10% FBS, followed by 5-10 pipetting passes through a Pasteur pipette. The cell suspension was filtered through stacked 70-30 μm pore cell strainers and centrifuged (300g, 5 min, 4°C). The pellet was resuspended in PBS + 0.04% BSA and treated with red blood cell lysis buffer (130-094-183, 10X) for 2-10 min at room temperature or on ice. After washing via centrifugation (300g, 5 min, room temperature), dead cells were removed using Dead Cell Removal MicroBeads (130-090-101). The cells were washed twice more with PBS + 0.04% BSA via centrifugation (300g, 3 min, 4°C) before final resuspension in the same buffer. Cell viability exceeding 85% was confirmed by trypan blue exclusion. Cells were counted on a hemocytometer or with a Countess II Automated Cell Counter and resuspended to 700-1,200 cells/μl.
Single-cell suspensions were loaded onto the 10x Chromium Controller to capture no less than 5,000 single cells per the manufacturer's instructions (10X Genomics Chromium Single-Cell 3' kit v3). Subsequent cDNA amplification and library construction steps followed the standard protocol. Libraries were sequenced by LC-Bio Technology Co. Ltd. (Hangzhou, China) on an Illumina NovaSeq 6000 system (150 bp paired-end multiplexed run) to a minimum depth of 20,000 reads per cell.

treatment_protocol: Gas explosion

tag: tissue

value: Lung

tag: treatment

value: Explosion


title: deaf1, 6 dpf, rep5

value: head with eyes, 2-5 heads combined

tag: genotype

value: deaf1 23d46i heterozygotes


title: BPC090T

tag: sample id

tag: clinicalcenter

tag: sizeprimary

tag: diseasestage

value: locAdvanced


title: BPC089T

tag: pfsevent

tag: pfsdelay

tag: osevent


title: ZnO_MP_5ug_2H_3

tag: strain

value: MutaMouse

tag: time point

tag: dose

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: C3, replicate 1, scRNAseq

description: 10× Genomics

value: Control


title: deaf1, 6 dpf, rep3


title: deaf1-t238p, 2 dpf, rep13

value: deaf1 t238p wild types


title: BPC088T

tag: historicpatient id

tag: normpatient id

tag: age

tag: Sex

tag: ecog

tag: osdelay

tag: firsttreatment

value: FOLFIRINOX


title: BPC096T

tag: sample id

tag: tissue

tag: clinicalcenter

tag: sizeprimary


title: BPC087T

tag: diseasestage

tag: pfsevent

tag: pfsdelay

tag: osevent


title: BPC085T

value: F

value: borderline

value: GEMCITABINE

tag: surgerytype

tag: surgerymargin


title: BPC094T

value: pancreatic adenocarcinoma

tag: historicpatient id

value: M

value: Clinique du Trocadero


title: deaf1-t238p, 2 dpf, rep12

tag: genotype


title: BPC084T

tag: normpatient id

tag: age

value: meta


title: ZnO_MP_5ug_24H_3

tag: strain

tag: treatment

value: ZnO Microparticle

tag: time point

value: 24 Hour

tag: dose

value: 5 ug/mL

tag: biological replicate

tag: sample type


title: ZnO_MP_1ug_2H_3

value: 2 Hour

value: 1 ug/mL


title: ZnO_MP_1ug_2H_2

value: MutaMouse


title: BPC083T

tag: sample id

tag: tissue

tag: Sex

tag: ecog

tag: clinicalcenter

tag: sizeprimary

tag: osdelay

tag: firsttreatment

value: DPC


title: deaf1-t238p, 2 dpf, rep11

value: head with eyes, 2-5 heads combined

tag: genotype


title: BPC081T

tag: historicpatient id

tag: normpatient id

tag: diseasestage

value: locAdvanced

tag: pfsevent

tag: pfsdelay

tag: osevent


title: ZnO_MP_0ug_2H_2

tag: strain

tag: treatment

tag: time point

tag: dose

value: Media Control

tag: biological replicate

value: 11 mouse cell lines


title: BPC079T

tag: sample id

tag: tissue

tag: age

tag: Sex

tag: ecog

value: CHU de Nice


title: ZnO_MP_1ug_48H_1

value: 48 Hour

tag: sample type


title: ZnO_MP_0.5ug_24H_3

value: 0.5 ug/mL


title: BPC078T

value: pancreatic adenocarcinoma

tag: historicpatient id

value: M

tag: clinicalcenter

value: Hopital Mermoz

tag: sizeprimary

tag: osdelay

tag: firsttreatment

value: GEMCITABINE


title: deaf1-t238p, 2 dpf, rep10

tag: genotype

value: deaf1 t238p wild types


title: BPC077T

tag: normpatient id

value: F

tag: diseasestage

value: meta

tag: pfsevent

tag: pfsdelay

tag: osevent


title: deaf1-t238p, 2 dpf, rep9

value: deaf1 t238p homozygotes


title: ZnO_MP_1ug_24H_3

tag: strain

value: MutaMouse

tag: treatment

value: ZnO Microparticle

tag: time point

value: 24 Hour

tag: dose

value: 1 ug/mL

tag: biological replicate


title: BPC076T

tag: sample id

tag: tissue

tag: age

tag: Sex

tag: ecog

value: locAdvanced


title: BPC071T

tag: historicpatient id

tag: clinicalcenter

value: Clinique du Trocadero

tag: sizeprimary

tag: osdelay

tag: firsttreatment


title: BPC074T

tag: normpatient id

value: Toulouse

tag: diseasestage

tag: pfsevent

tag: pfsdelay


title: BPC060T

value: CHU Lille

tag: osevent

value: FOLFIRINOX;XELODA


title: BPC059T

value: pancreatic adenocarcinoma

value: FOLFOX


title: deaf1-t238p, 2 dpf, rep8

value: head with eyes, 2-5 heads combined

tag: genotype


title: BPC058T

value: M

value: FOLFIRINOX


title: deaf1-t238p, 2 dpf, rep6


title: BPC057T


title: ZnO_MP_0.5ug_2H_2

tag: strain

tag: treatment

tag: time point

value: 2 Hour

tag: dose

value: 0.5 ug/mL

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: BPC056T

tag: sample id

tag: tissue

tag: historicpatient id

tag: age

tag: Sex

value: F

tag: ecog

value: ABRAXANE;GEMCITABINE


title: deaf1-t238p, 2 dpf, rep5

value: deaf1 t238p heterozygotes


title: BPC054T

tag: normpatient id

tag: clinicalcenter

tag: sizeprimary

tag: diseasestage

tag: osdelay

tag: firsttreatment


title: ZnO_MP_0ug_24H_3

tag: strain

value: MutaMouse

tag: treatment

value: ZnO Microparticle

value: 24 Hour

value: Media Control


title: deaf1-t238p, 2 dpf, rep7

tag: genotype

value: deaf1 t238p homozygotes


title: deaf1-t238p, 2 dpf, rep4


title: BPC055T

value: Clinique du Trocadero

value: locAdvanced

tag: pfsevent

tag: pfsdelay

tag: osevent


title: BPC052T

tag: sample id

tag: tissue

value: pancreatic adenocarcinoma

value: ICM

value: meta


title: ZnO_MP_5ug_2H_2

tag: time point

tag: dose

value: 5 ug/mL

tag: biological replicate

tag: sample type


title: ZnO_MP_1ug_24H_1

value: 1 ug/mL


title: deaf1-t238p, 2 dpf, rep3

value: head with eyes, 2-5 heads combined


title: BPC050T

tag: historicpatient id

tag: normpatient id

tag: age

tag: Sex

tag: clinicalcenter

value: Hopital Mermoz

value: GEMCITABINE


title: ZnO_MP_1ug_48H_3

tag: strain

value: 48 Hour

value: 11 mouse cell lines


title: BPC049T

value: M

tag: ecog

tag: sizeprimary

tag: diseasestage

tag: osdelay

tag: firsttreatment


title: deaf1-t238p, 2 dpf, rep2

tag: genotype

value: deaf1 t238p heterozygotes


title: BPC048T

tag: sample id

tag: tissue

tag: pfsevent

tag: pfsdelay

tag: osevent

value: FOLFIRINOX


title: ZnO_MP_0.5ug_48H_3

value: MutaMouse

tag: treatment

value: ZnO Microparticle

tag: time point

tag: dose

value: 0.5 ug/mL

tag: biological replicate

tag: sample type


title: BPC047T

tag: historicpatient id

tag: normpatient id

tag: age

tag: Sex

value: F

tag: clinicalcenter


title: ZnO_MP_5ug_24H_1

tag: strain

value: 24 Hour


title: BPC046T

value: pancreatic adenocarcinoma

tag: ecog

tag: sizeprimary

tag: diseasestage

tag: osdelay

tag: firsttreatment


title: deaf1-t238p, 2 dpf, rep1

tag: tissue

tag: genotype


title: U2932_shZNF587-417v1_D6_RNA_Rep2_2

city: Lausanne

first: Filipe

last: Martins

address: Station 19

country: Switzerland

institute: Epfl

description:
OCI_Ly7_U2932_D6_RNA.tab
OCI_Ly7_U2932_D6_RNA_TEs.tab

data_processing:
RNA-seq reads were mapped to the hg19 using hisat v2.1.0
Mapped reads were filtered for uniquely mapping reads (MAPQ > 10)
Read counts on genes and repetitive sequence integrants was performed with featureCounts v2
Assembly: hg19
Supplementary files format and content: OCI_Ly7_U2932_D6_RNA.tab: coma-separated table containing raw read counts on genes
Supplementary files format and content: OCI_Ly7_U2932_D6_RNA_TEs.tab: coma-separated table containing raw read counts on TEs

growth_protocol: U2932 = RPMI 1640 + 10% FCS + 1% Pen-Strep / OCI-Ly7 = IMDM + 20% FCS + 1% Pen-Strep

extract_protocol:
Total RNA extraction was performed using the NucleoSpin RNA plus kit (Machery-Nagel) according to the manufacturer’s recommendations. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using the Illumina Truseq Stranded mRNA kit.

treatment_protocol: Lentiviral transduction

tag: cell line

tag: cell type

value: Diffuse large B cell lymphoma

value: ZNF587,ZNF417 knockdown

tag: treatment

value: Lentiviral transduction

tag: time

value: Day 6


title: BPC045T

tag: sample id

tag: historicpatient id

value: Hopital Mermoz

value: locAdvanced

tag: pfsevent

tag: pfsdelay

tag: osevent


title: ZnO_MP_5ug_48H_3

tag: strain

tag: time point

value: 48 Hour

tag: dose

value: 5 ug/mL

tag: biological replicate

tag: sample type


title: BPC043T

tag: normpatient id

tag: age

tag: Sex

tag: ecog

tag: clinicalcenter

tag: sizeprimary

tag: diseasestage

tag: osdelay

tag: firsttreatment


title: BPC042T

tag: sample id

tag: tissue

tag: historicpatient id

value: M

tag: pfsevent


title: U2932_shZNF587-417v1_D6_RNA_Rep2_1

tag: cell line

tag: cell type

tag: genotype

tag: treatment

tag: time


title: BPC051T

tag: normpatient id

tag: age

value: meta

tag: pfsdelay

tag: osevent

value: FOLFIRINOX;FOLFIRI;FOLFIRI 3


title: U2932_shZNF587-417v1_D6_RNA_Rep1_2


title: BPC041T

tag: Sex

tag: ecog

tag: clinicalcenter

tag: sizeprimary


title: BPC040T

tag: sample id

tag: diseasestage

tag: osdelay

tag: firsttreatment

value: FOLFIRINOX


title: BPC039T

tag: tissue

tag: historicpatient id

value: borderline

tag: pfsevent

tag: surgerytype

value: DPC

tag: surgerymargin


title: ZnO_MP_0.5ug_24H_1

tag: strain

value: MutaMouse

tag: treatment

value: ZnO Microparticle

tag: time point

tag: dose

value: 0.5 ug/mL

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: ZnO_MP_0ug_48H_3

value: Media Control


title: BPC038T

value: pancreatic adenocarcinoma

tag: normpatient id

tag: age

tag: Sex

value: F

tag: ecog

tag: clinicalcenter

tag: pfsdelay

tag: osevent

value: FOLFIRINOX;FOLFIRI;XELODA


title: ZnO_MP_0ug_24H_1

value: 24 Hour


title: U2932_shZNF587-417v1_D6_RNA_Rep1_1

tag: cell line

tag: cell type

value: Diffuse large B cell lymphoma

tag: genotype

value: ZNF587,ZNF417 knockdown

value: Lentiviral transduction

tag: time

value: Day 6


title: BPC037T

tag: sample id

tag: tissue

tag: historicpatient id

value: M

value: Hopital Mermoz

tag: sizeprimary

tag: diseasestage

value: locAdvanced

tag: pfsevent

tag: osdelay

tag: firsttreatment

value: GEMCITABINE


title: BPC138T

tag: normpatient id

tag: age

tag: Sex

value: Clinique du Trocadero

value: borderline


title: BPC036T

tag: ecog

tag: clinicalcenter

value: meta

tag: pfsdelay


title: ZnO_MP_0.5ug_2H_1

tag: strain

value: MutaMouse

tag: treatment

value: ZnO Microparticle

tag: time point

value: 2 Hour

tag: dose

value: 0.5 ug/mL

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: BPC034T

tag: sample id

tag: tissue

value: pancreatic adenocarcinoma

tag: historicpatient id

tag: sizeprimary

tag: osevent


title: BPC035T

tag: normpatient id

value: F

tag: diseasestage

tag: pfsevent

tag: osdelay


title: BPC030T

tag: age

tag: Sex

tag: ecog

tag: clinicalcenter


title: ZnO_MP_1ug_2H_1

tag: strain

tag: treatment

tag: time point

value: 1 ug/mL


title: U2932_Control_shRNA_D6_RNA_Rep2_1

tag: cell line

tag: cell type

value: Diffuse large B cell lymphoma

tag: genotype

value: Control

value: Lentiviral transduction

tag: time


title: BPC033T

tag: sample id

tag: tissue

tag: historicpatient id

value: Hopital Mermoz

tag: sizeprimary

tag: pfsdelay

tag: firsttreatment

value: FOLFIRINOX


title: U2932_Control_shRNA_D6_RNA_Rep1_2

value: Day 6


title: BPC029T

tag: normpatient id

tag: age

value: M

value: Toulouse

tag: diseasestage

value: locAdvanced

tag: pfsevent

tag: osevent

tag: osdelay

value: GEMCITABINE


title: ZnO_MP_5ug_24H_2

tag: strain

value: MutaMouse

tag: treatment

value: ZnO Microparticle

tag: time point

value: 24 Hour

tag: dose

value: 5 ug/mL

tag: biological replicate

tag: sample type


title: BPC028T

tag: sample id

tag: tissue

value: pancreatic adenocarcinoma

tag: Sex

tag: ecog

tag: clinicalcenter

value: GEMCITABINE;CYL 02


title: BPC027T

tag: historicpatient id

tag: normpatient id

value: F

tag: sizeprimary

tag: pfsdelay

tag: firsttreatment

value: GEMCITABINE;CYL 02 (THERGAP 2)


title: U2932_Control_shRNA_D6_RNA_Rep1_1

tag: cell line

tag: cell type

value: Diffuse large B cell lymphoma

tag: genotype

value: Control

tag: time


title: BPC025T

tag: age

tag: diseasestage

value: meta

tag: pfsevent

tag: osevent

tag: osdelay


title: OCI_Ly7_shZNF587-417v1_D6_RNA_Rep2_2

value: ZNF587,ZNF417 knockdown

tag: treatment

value: Lentiviral transduction


title: BPC026T

tag: sample id

tag: tissue

tag: Sex

value: M

tag: ecog

value: FOLFIRINOX


title: ZnO_MP_1ug_24H_2

tag: strain

tag: time point

tag: dose

value: 1 ug/mL

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: ZnO_MP_0.5ug_24H_2

value: MutaMouse

value: 0.5 ug/mL


title: BPC024T

tag: historicpatient id

tag: normpatient id

tag: clinicalcenter

value: Toulouse

tag: sizeprimary

value: borderline

tag: pfsdelay

tag: firsttreatment

value: GEMCITABINE


title: ZnO_MP_0ug_2H_1

value: ZnO Microparticle

value: 2 Hour

value: Media Control


title: BPC023T

value: pancreatic adenocarcinoma

tag: age

value: F

tag: diseasestage

value: locAdvanced

tag: pfsevent

tag: osevent

tag: osdelay


title: OCI_Ly7_shZNF587-417v1_D6_RNA_Rep2_1

tag: cell line

tag: cell type

value: Diffuse large B cell lymphoma

tag: genotype

value: ZNF587,ZNF417 knockdown

tag: treatment

tag: time

value: Day 6


title: U2932_Control_shRNA_D6_RNA_Rep2_2

value: Control

value: Lentiviral transduction


title: BPC022T

tag: sample id

tag: tissue

tag: Sex

value: M

value: FOLFIRINOX


title: BPC021T

tag: historicpatient id

tag: normpatient id

tag: clinicalcenter

value: meta


title: ZnO_MP_5ug_2H_1

tag: strain

value: MutaMouse

tag: time point

tag: dose

value: 5 ug/mL

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: OCI_Ly7_shZNF587-417v1_D6_RNA_Rep1_2


title: OCI_Ly7_shZNF587-417v1_D6_RNA_Rep1_1


title: BPC020T

tag: age

value: Toulouse

tag: sizeprimary

tag: diseasestage

value: borderline

tag: pfsevent

tag: pfsdelay

tag: osevent

tag: osdelay

tag: firsttreatment

value: GEMCITABINE


title: ZnO_MP_0ug_24H_2

tag: treatment

value: ZnO Microparticle

value: 24 Hour

value: Media Control


title: BPC019T

tag: sample id

tag: tissue

value: pancreatic adenocarcinoma

tag: historicpatient id

tag: Sex

value: F


title: BPC017T

tag: normpatient id

tag: clinicalcenter

value: locAdvanced


title: BPC018T

tag: ecog


title: OCI_Ly7_Control_shRNA_D6_RNA_Rep2_2

tag: cell line

tag: cell type

value: Diffuse large B cell lymphoma

tag: genotype

value: Control

tag: time

value: Day 6


title: TiO2_NP_25ug_24H_3

tag: strain

value: TiO2 Nanoparticle

tag: time point

tag: dose

value: 25 ug/mL

tag: biological replicate

tag: sample type


title: OCI_Ly7_Control_shRNA_D6_RNA_Rep2_1

tag: treatment

value: Lentiviral transduction


title: BPC013T

tag: sample id

tag: age

value: M

value: Clinique du Trocadero

tag: diseasestage

value: meta

tag: pfsevent

tag: pfsdelay

tag: osevent

tag: osdelay

tag: firsttreatment


title: BPC016T

tag: tissue

tag: historicpatient id

tag: normpatient id

tag: Sex

tag: ecog

tag: clinicalcenter

value: Toulouse

tag: sizeprimary


title: OCI_Ly7_Control_shRNA_D6_RNA_Rep1_2

tag: cell line

tag: cell type

tag: genotype

tag: time


title: BPC012T

tag: sample id

tag: age

tag: diseasestage

value: ABRAXANE;GEMCITABINE


title: BPC009T

tag: pfsevent

tag: pfsdelay

tag: osevent

value: GEMCITABINE


title: BPC010T

tag: tissue

tag: osdelay


title: BPC008T

tag: historicpatient id

tag: normpatient id


title: BPC011T

tag: Sex

tag: ecog

tag: firsttreatment


title: BPC007T

tag: clinicalcenter

tag: sizeprimary


title: U2932_shZNF587-417v1_72H_RNA_Rep3

description:
U2932_72H_RNA.tab
U2932_72H_RNA_TEs.tab

data_processing:
RNA-seq reads were mapped to the hg19 using hisat v2.1.0
Mapped reads were filtered for uniquely mapping reads (MAPQ > 10)
Read counts on genes and repetitive sequence integrants was performed with featureCounts v2
Assembly: hg19
Supplementary files format and content: U2932_72H_RNA.tab: coma-separated table containing raw read counts on genes
Supplementary files format and content: U2932_72H_RNA_TEs.tab: coma-separated table containing raw read counts on TEs

growth_protocol: RPMI 1640 + 10% FCS + 1% Pen-Strep

tag: cell line

tag: cell type

tag: genotype

value: ZNF587,ZNF417 knockdown

tag: treatment


title: TiO2_NP_0ug_24H_2

tag: strain

value: MutaMouse

tag: time point

value: 24 Hour

tag: dose

value: Media Control

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: TiO2_NP_0ug_48H_3

value: 48 Hour


title: OCI_Ly7_Control_shRNA_D6_RNA_Rep1_1

value: Diffuse large B cell lymphoma

value: Control

tag: time


title: TiO2_NP_100ug_48H_3

value: TiO2 Nanoparticle

value: 100 ug/mL


title: U2932_shZNF587-417v1_72H_RNA_Rep1

description:
U2932_72H_RNA.tab
U2932_72H_RNA_TEs.tab

value: Lentiviral transduction


title: TiO2_NP_50ug_48H_3

value: 50 ug/mL


title: TiO2_NP_25ug_48H_2

value: 25 ug/mL


title: BPC005T

tag: sample id

tag: tissue

value: pancreatic adenocarcinoma

tag: historicpatient id

tag: age

value: F

value: Clinique du Trocadero

tag: diseasestage

value: meta

tag: pfsevent

tag: pfsdelay

tag: osevent

tag: osdelay


title: BPC002T

tag: normpatient id

tag: Sex

value: M

tag: ecog

tag: clinicalcenter

tag: sizeprimary

value: locAdvanced

tag: firsttreatment

value: FOLFIRINOX


title: U2932_shZNF587-417v1_72H_RNA_Rep2

description:
U2932_72H_RNA.tab
U2932_72H_RNA_TEs.tab

tag: cell line

tag: cell type

tag: genotype

value: ZNF587,ZNF417 knockdown

tag: treatment


title: U2932_Control_shRNA_72H_RNA_Rep3

description:
U2932_72H_RNA.tab
U2932_72H_RNA_TEs.tab

tag: time


title: BPC156T

tag: sample id

tag: tissue

tag: historicpatient id

tag: age


title: TiO2_NP_0ug_2H_3

tag: strain

value: MutaMouse

tag: time point

value: 2 Hour

tag: dose

value: Media Control

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: BPC003T

tag: normpatient id

tag: Sex

tag: ecog

tag: clinicalcenter

tag: diseasestage

tag: pfsevent

tag: pfsdelay

tag: osevent

tag: osdelay


title: U2932_Control_shRNA_72H_RNA_Rep2

description:
U2932_72H_RNA.tab
U2932_72H_RNA_TEs.tab

tag: cell line

tag: cell type

value: Diffuse large B cell lymphoma

tag: genotype

value: Control

tag: treatment

tag: time


title: BPC006T

tag: sample id

tag: tissue

tag: historicpatient id

tag: age

tag: sizeprimary

tag: firsttreatment


title: U2932_Control_shRNA_72H_RNA_Rep1

description:
U2932_72H_RNA.tab
U2932_72H_RNA_TEs.tab

value: Lentiviral transduction


title: Sample 1, Day 14, replicate 3

city: Los Angeles

first: Asha

last: Kar

state: CA

address: 695 Charles E. Young Drive South

department: Human Genetics

institute: University of California Los Angeles

data_processing:
We aligned the reads to the GRCh38 genome with GENCODE v39 annotations using STAR v.2.7.10a, using the two-pass method to account for novel splice junctions (Kar et. al, Genome Medicine 2024).
We filtered the aligned reads to exclude reads mapped to the mitochondrial genome or multiple transcripts (Kar et. al, Genome Medicine 2024).
We used featureCounts v2.0.3 to perform read summarization at the gene level (Kar et. al, Genome Medicine 2024).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes the raw counts for each Sample

source_name: cryopreserved human subcutaneous primary white preadipocytes (Zen-Bio catalog # SP-F-2, lot L120116E).

growth_protocol: Cryopreserved human subcutaneous primary white preadipocytes (Zen-Bio catalog # SP-F-2, lot L120116E) were seeded into PromoCell Pad growth medium (PromoCell C-27410) with 1% Gibco Penicillin-Streptomycin (ThermoFisher 15140122) and cultured according to PromoCell Pad culturing protocols. Cells were maintained in a monolayer culture at 37C and 5% CO2. Cells were propagated for the full experiment and not cultured beyond 5 passages (Kar et. al, Genome Medicine 2024).

extract_protocol:
For the RNA collection, cells were washed with PBS once and then lysed with TriZOL (Invitrogen 15596026), and RNA was purified using Direct-Zol RNA Mini-Prep (Zymo Research R2061) (Kar et. al, Genome Medicine 2024).
Libraries were prepared using the Illumina TruSeq Stranded mRNA kit (Kar et. al, Genome Medicine 2024).

treatment_protocol: To induce adipogenesis, cells were plated at confluency into 12-well plates for both RNA-seq (4 isogenic biological replicates per time point and assay) and the following day, adipogenesis was initiated using preadipocyte differentiation medium (PromoCell C-27436). The 1d and 2d timepoints were collected before any further media changes. For all other differentiation timepoints, 72 hours after the preadipocyte differentiation medium was added, it was replaced with adipocyte nutrition medium (PromoCell C-27438), following PromoCell ASPC differentiation protocols (Kar et. al, Genome Medicine 2024).

value: subcutaneous adipose tissue

value: primary white preadipocyte

value: Day 14


title: Sample 1, Day 14, replicate 2


title: Sample 1, Day 14, replicate 1


title: Sample 1, Day 7, replicate 4

value: Day 7


title: BPC004T

value: pancreatic adenocarcinoma

tag: normpatient id

tag: Sex

value: F

tag: ecog

tag: clinicalcenter

value: Clinique du Trocadero


title: TiO2_NP_25ug_2H_2

tag: strain

value: TiO2 Nanoparticle

tag: time point

tag: dose

value: 25 ug/mL

tag: biological replicate

tag: sample type


title: TiO2_NP_50ug_2H_3

tag: treatment

value: 50 ug/mL


title: Pancreatic organoids (passage 3)

city: Rotterdam

first: Kalyan

last: Dulla

address: Postbus 2040

country: Netherlands

institute: Erasmus MC

data_processing:
CLC genomic workbench version 21.0 (Qiagen)
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork default parameters
Trimmed sequence reads were mapped to Sus scrofa genome data set assemble 11.1.103 (NCBI) using CLC genomic benchwork default parameters
Read count extraction was performed using CLC genomic benchwork
Assembly: Sus scrofa genome data set assemble 11.1.103 (NCBI)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Sus scrofa

source_name: Organoids

growth_protocol: Organoids were embedded in extracellular matrix and maintained in medium containing the growth factors Wnt3a, Noggin, R-Spondin 1, FGF10 and EGF (Driehuis et al. 2020. STAR Protoc. 1, 100192).

extract_protocol:
RNA (>5 µg) was extracted using the NucleoSpin RNA kit (Macherey-Nagel).
BGI library construction protocol and sequencing on DNBseq platform

tag: cell line

value: Organoids

tag: cell type

value: Endodermal; epithelial

tag: genotype

value: WT

tag: passages

tag: time


title: Sample 1, Day 14, replicate 4

tag: tissue


title: Sample 1, Day 7, replicate 3


title: Sample 1, Day 7, replicate 2