title: 5673

description: FFPE

tag: tissue

tag: institution

tag: group

value: survival analysis only

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause

value: A

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm

tag: _1=progress to metastatic disease in 5yrs


title: Sample 203_Single Dermal Fibroblast

status: Public on Jun 01 2020

type: SRA

city: Stanford

first: Alina

last: Isakova

state: CA

address: 318 Campus drive

department: Bioengineering

country: USA

institute: Stanford University

library_source: transcriptomic

data_processing:
Sequences from the NovaSeq were de-multiplexed using bcl2fastq version 2.19.0.316. Reads were trimmed from polyA tails using cutadapt v 1.18 with the following parameters: -m 18 -j 4 -a AAAAAAAAAA -a TTTTTTTTTT. Reads were then aligned to the human (GRCh38) or mouse genome (GRCm38) using STAR v2.7.0d 37 with the following parameters --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 18 --outFilterMatchNminOverLread 0 --outFilterScoreMinOverLread 0  --outMultimapperOrder Random. Reads mapping to multiple locations were assigned either to a location with the best mapping score or, in the case of equal multimapping score – to the genomic location randomly chosen as “primary”.
Genome_build: GRCm38, GRCh38
Supplementary_files_format_and_content: tab-delimited text files of count tables

molecule: total RNA

organism: Homo sapiens

source_name: Single Dermal Fibroblast

growth_protocol: HEK293T cells were cultured in complete DMEM high glucose medium (Gibco, ThermoFisher 11965092) supplemented with 5% Fetal Bovine Serum (ThermoFisher 16000044), 1mM Sodium Pyruvate (ThermoFisher 11360070) and 100 μg/mL Pencillin/Streptomycin (ThermoFisher 15070063). They were collected 2h after passaging and sorted in either 96-well plates with 3uL lysis buffer or 384-well paltes with 0.3 uL of lysis buffer in each well.    Human primary dermal fibroblasts were obtained from ATCC (ATCC® PCS-201-012™). Cells were cultured and passaged four times in Fibroblast Basal Medium (ATCC® PCS-201-030™) supplemented with 5ng/mL rh FGF β, 7.5mM L-glutamine, 50 ug/mL Ascorbic acid, 5ug/mL rh Insulin, and 1% Fetal Bovine Serum (Fibroblast Growth kit- low serum, ATCC® PCS-201-041™).  MCF7 cells (ATCC® HTB¬22™) were cultured in complete DMEM high glucose medium (Gibco, ThermoFisher 11965092) supplemented with 10% Fetal Bovine Serum (ThermoFisher 16000044), 1mM Sodium Pyruvate (ThermoFisher 11360070) and 100 μg/mL Pencillin/Streptomycin (ThermoFisher 15070063).  mESCs were maintained and differentiated as described previously35,36. Briefly, mESCs were grown in serum-free 2i+LIF medium (complete medium: DMEM/F12 glutaMAX (Gibco, ThermoFisher  10565018) , 1% N2 supplement (Gemini Bio), 2% B27 supplement (Gemini Bio), 0.05% BSA fraction V (ThermoFisher, 15260037), 1% MEM-non-essential amino acids (c  11140050), and 110 μM 2-mercaptoethanol (Pierce); supplemeted with MEK inhibitor PD0325901 (0.8 μM), GSK3β inhibitor CHIR99021 (3.3 μM) and 10ng/mL mouse LIF (Gibco, PMC9484) in tissue culture (TC) dishes pretreated with 7.5 μg/ml polyL-ornithine (Sigma) and 5 μg/ml laminine (BD). To induce spontaneous embryoid body formation cells were washed with PBS, dissociated with StemPro Accutase (Gibco, ThermoFisher cat# A1110501), transferred to serum-rich medium (complete medium: DMEM/F12 glutaMAX (Gibco) , 1% N2 supplement (Gemini Bio), 2% B27 supplement (Gemini Bio), 0.05% BSA fraction V, 1% MEM-non-essential amino acids, and 110 μM 2-mercaptoethanol; supplemented with 10% FBS (ThermoFisher 10439001) and diluted to 10^6 cells/mL. Each 10 uL of cell suspension were plated as a hanging drop in 10 cm2 TC dishes (15-20 drops per dish). 10uL of fresh serum-rich media was added to each drop on day 4 of the culture. Primed mESCs were collected 6h after hanging drop culture. Embryoid bodies were collected and dissociated at days 4, 8 and 12 of culture.

extract_protocol:
Lysis plates were prepared by dispensing 0.3μL lysis buffer (4 U Recombinant RNase Inhibitor (RRI) (Takara Bio, 2313B), 0.12% TritonTM X-100 (Sigma, 93443-100ML), 1μM Smart-seq4 oligo-dT primer (5’-Biotin- /5BiosG/CATAGTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGT30VN-3’;IDT) (see Supplementary Table 3 for a full list of oligos used in the present study) into 384-well hard-shell PCR plates (Bio-Rad HSP3901) using Mantis liquid handler (Formulatrix). 96-well lysis plates were prepared with 3 μl lysis buffer. All plates were sealed with AlumaSeal CS Films (Sigma-Aldrich Z722634), spun down and snap-frozen on dry ice.   Cells were stained with calcein-AM and ethidium homodimer-1 (LIVE/DEAD® Viability/Cytotoxicity Kit, ThermoFisher L3224) and individual live cells were sorted in 384 well lysis plates using SONY sorter (SH800S) with 100um nozzle chip. Plates were spun down and stored at -80 degrees immediately after sorting.
Smart-seq-total

tag: cell line

value: primary cell

tag: day of differentiation


title: Sample 206_Single Dermal Fibroblast


title: Sample 204_Single Dermal Fibroblast


title: EORTC_Patient_70738

type: RNA

city: South San Francisco

first: Radia

last: Johnson

address: 1 DNA Way

country: United Kingdom

institute: Genentech

hyb_protocol: Per NanoString Total RNA Standard Protocol for formalin-fixed, paraffin-embedded (FFPE) samples.

data_processing:
Background correction was implemented using blank samples along with the global negative control probes. Sample-wise normalization was performed by transforming counts to the log2 scale and subtracting the sample-wise mean of housekeeping genes.
Water samples (used for the normalisation) and UHR control samples (used for cross-normalisation) using the NanoStringQCPro package on Bioconductor.

label: Nucleotide/fluorophore barcode

growth_protocol: Not applicable

extract_protocol: Not applicable

treatment_protocol: Not applicable

tag: age

tag: Sex

value: Male

tag: corticosteroids

value: On

tag: surgical status

tag: treatment

value: BEVACIZUMAB+LOMUSTINE

tag: phillips subtype

value: Proneural

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

value: Missing

tag: who category

tag: dataset

value: EORTC


title: Sample 201_Single Dermal Fibroblast

tag: cell line


title: Sample 202_Single Dermal Fibroblast

tag: day of differentiation


title: anoxic_1

city: Iowa City

first: Timothy

middle: E

last: Mattes

address: 4105 Seamans Center

institute: University of Iowa

data_processing:
Raw sequencing data was processed online with software available on the Galaxy server (usegalaxy.org). First, fastq data files were converted to fastqsanger format with the fastq groomer tool. The quality of transcriptomic sequence reads was assessed with FastQC.
Forward strand transcriptomic reads were then mapped to the T. autotrophicus strain EF1 genome sequence (Genbank accession no. CP010552) using HISAT2. This resulted in 6.97×105– 1.38×106 reads mapped to the EF1genome per treatment. Similarly, forward strand reads were also mapped to the internal mRNA standards, yielding 1.41×105 – 2.48×105 mRNA standard reads per treatment (9-22% of total reads).
HISAT2-generated BAM files for each treatment were loaded into ReadXplorer 2.2.3 where differential gene expression analyses were performed. First, a transcript count table was generated. The percent recovery of internal mRNA standards was used to estimate the absolute number of EF1 transcripts per treatment and subsequently normalized to the number of EF1 cells per RNA extraction to obtain absolute “transcript per cell” values
Differential gene expression analysis among the three different DO treatments was performed with the DeSeq2 algorithm. Genes that were differentially expressed at a statistically significant level (p<0.05) were considered for further analysis
Genome_build: T. autotrophicus strain EF1 genome sequence (Genbank accession no. CP010552)
Supplementary_files_format_and_content: excel files inlcude transcript counts, cell counts and transcript per cell values for each gene in the genome. DeSeq2 output provided in excel files.

organism: Candidatus Thioglobus autotrophicus

source_name: cells

growth_protocol: Filter-sterilized Puget Sound seawater (PS media; collected June 2017) was used as bacterial growth media with filter-sterilized thiosulfate (1 mM) added as the energy source. The PS media initially contained 13.5 ± 0.58 μM nitrate. No additional nitrate was added to the media. PS media (100 mL) was placed into acid-washed (10% HCl) and autoclaved 160 mL glass serum bottles and sealed with 20 mm blue butyl rubber stoppers and aluminum crimp caps (DWK Life Sciences, Millville, NJ). Sealed serum bottles were subsequently purged (7 minutes liquid, followed by 5 min headspace) with a mixture of nitrogen gas containing 1000 ppm carbon dioxide to remove dissolve oxygen (DO). Purged anoxic PS media bottles were prepared in triplicate.

extract_protocol:
When EF1 cell density reached approximately 1-3x106 cells/ml, bottles were sacrificed for RNA extraction. Cultures (~100 mL) were vacuum filtered onto 47 mm 0.2 μm IsoporeTM membrane filters (Millipore Inc., Billerica, MA, USA) under a nitrogen headspace to limit oxygen diffusion. Filters were placed into a 50 ml conical tube containing Trizol reagent (3 mL), 375 μL glass and zirconia bead mixture, and 12.5 μl (6.79×109 copies) internal mRNA standards. Bead-beating was performed for 5 minutes on a vortexer. After a 1 min centrifugation step at 3,220 xg, RNA was extracted from the supernatant with the Zymo Direct-zol RNA MiniPrep Plus kit (Zymo Research Corporation, Irvine, CA) according to the manufacturer’s protocol (including on-column DNase I treatment). To further minimize DNA contamination, RNA extracts were subjected to a separate DNase I treatment step with the TURBO DNA-freeTM kit (Thermofisher Scientific, Waltham, MA). RNA concentrations were estimated with the QubitTM fluorometer and HS RNA assay kit (Thermofisher Scientific,Waltham, MA)
rRNA was depleted from the extractions with the Ribozero rRNA removal kit for bacteria (Illumina, Inc.San Diego, CA). Libraries were prepared from the depleted RNA using the Illumina Truseq library prep kit v2, normalized and loaded at equal concentration on the Illumina MiSeq using V2 chemistry and then subjected to PE150 sequencing at the University of Washington

treatment_protocol: One set of triplicate bottles was kept anoxic. A second set of bottles received 1 mL of filtered-sterilized air (approximate initial aqueous DO concentration = 3.8 μM), and a third set received 5 mL of filter-sterilized air (approximate initial aqueous DO concentration = 22 μM). All bottles were incubated without shaking at 13ºC during the experiments.

tag: strain

tag: dissolved oxygen (do) um


title: EORTC_Patient_70736

scan_protocol: Per NanoString Total RNA Standard Protocol for formalin-fixed, paraffin-embedded (FFPE) samples.

tag: age

tag: Sex

tag: corticosteroids

value: Off

value: Classical

value: Non-methylated


title: Sample 200_Single Dermal Fibroblast


title: Sample 199_Single Dermal Fibroblast


title: 15320

city: Burlington

first: Travis

last: Sullivan

state: MA

address: 41 Mall Rd.

institute: Lahey Hospital & Medical Center

description: FFPE

data_processing:
Non-normalized data are the Cq values computed by the Bio-Rad CFX themal cycler software, no adjustment to baseline backgrounds were made
Each microRNA of interest was normalized to the average of the insignificant control miRNA: miRs-28-5p, -125-5p, and -191-5p, selected from the screening array dataset using NormFinder©.  Prior to normalization each target value was scaled to the internal plate calibrator (IPC) by dividing the samples IPC by the grand average of all the IPCs and then multiplying the resulting value by the target Cq.  The global mean was calculated only using microRNA with a Cq<35 detected in all 20 samples.   2^-deltaCq, where deltaCq = (Cq_Target − Cq_global_mean).  All Cq values >37 were set to 40.
Fold change (delta delta Ct) values were not computed for this dataset
The file normalized_data.txt  reports normalized signal (against each samples global mean).

label: SYBR Green

source_name: clear cell renal cell carcinoma primary tumor

label_protocol: cDNA and RT-PCR were performed using miRCURY LNA custom miRnome PCR panel, currently provided by Qiagen formerly from Exiqon, following the manufacturer's recommendations. Catalog number 339317

extract_protocol: Total RNA was isolated using the Ambion RecoverAll Total Nucleic Acid Isolation Kit for FFPE following the manufacturer's recommendations

tag: tissue

tag: institution

value: LHMC

tag: group

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm

tag: _1=progress to metastatic disease in 5yrs

tag: grade


title: UCLA_S9917

data_processing:
Blanks were not available for the UCLA dataset, as a result background correction was implemented using global negative control probes. Sample-wise normalization was performed by transforming counts to the log2 scale and subtracting the sample-wise mean of housekeeping genes.
Water samples (used for the normalisation) using the NanoStringQCPro package on Bioconductor.

label_protocol: Per NanoString Total RNA Standard Protocol for formalin-fixed, paraffin-embedded (FFPE) samples.

value: Female

tag: surgical status

value: Total resection

tag: treatment

value: Control

tag: phillips subtype

tag: tcga subtype

tag: kps

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

value: Methylated


title: EORTC_Patient_70734

tag: age

tag: Sex

tag: corticosteroids

value: LOMUSTINE

value: Proliferative

tag: mmse

tag: rpa

tag: who category

tag: dataset


title: Sample 197_Single Dermal Fibroblast

tag: cell line

value: primary cell

tag: day of differentiation


title: 6427

description: FFPE

tag: tissue

value: clear cell renal cell carcinoma primary tumor

tag: institution

tag: group

value: validation and survival analyses

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause

value: A

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm

tag: _1=progress to metastatic disease in 5yrs

tag: grade


title: Sample 196_Single Dermal Fibroblast


title: 27559

description: FFPE

value: C


title: EORTC_Patient_70740

tag: age

tag: Sex

value: Male

tag: corticosteroids

value: On

tag: surgical status

tag: treatment

value: BEVACIZUMAB+LOMUSTINE

tag: phillips subtype

value: Proneural

tag: tcga subtype

tag: kps

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

value: Missing


title: 24564

description: FFPE

tag: tissue

tag: institution

value: LHMC

tag: group

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause


title: UCLA_S9760

value: Female

value: Partial resection

value: Mesenchymal

value: Non-methylated


title: EORTC_Patient_70732

value: Off

value: LOMUSTINE

tag: mmse

tag: rpa

tag: who category

tag: dataset

value: EORTC


title: 22208

description: FFPE

value: clear cell renal cell carcinoma primary tumor

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm

tag: _1=progress to metastatic disease in 5yrs

tag: grade


title: UCLA_S9791

tag: age

tag: Sex

tag: surgical status

value: Total resection

tag: treatment

value: Bevacizumab

tag: phillips subtype

tag: tcga subtype

tag: kps

tag: os (diagnosis)


title: EORTC_Patient_70730

tag: corticosteroids

tag: mmse

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

value: Methylated


title: Sample 195_Single Dermal Fibroblast

tag: cell line

value: primary cell

tag: day of differentiation


title: UCLA_S9713

value: Control


title: 3075

description: FFPE

tag: tissue

tag: institution

tag: group

value: validation and survival analyses

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause

value: A

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm


title: Sample 194_Single Dermal Fibroblast


title: EORTC_Patient_70724

tag: age

tag: Sex

value: Male

tag: surgical status

tag: treatment

value: BEVACIZUMAB+LOMUSTINE

tag: phillips subtype

value: Unclassified

tag: tcga subtype

value: Classical

tag: rpa

tag: who category

tag: dataset


title: EORTC_Patient_70728

value: Female

tag: corticosteroids

value: On

value: Proliferative

tag: kps

tag: mmse

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status


title: EORTC_Patient_70722

value: Off

value: Mesenchymal

value: Non-methylated


title: UCLA_S9698

value: Partial resection


title: Sample 198_Single Dermal Fibroblast

tag: cell line

tag: day of differentiation


title: Sample 193_Single Dermal Fibroblast


title: UCLA_S9672

tag: age

value: Total resection

value: Bevacizumab


title: EORTC_Patient_70718

tag: Sex

value: Methylated

value: EORTC


title: Sample 192_Single Dermal Fibroblast

value: primary cell


title: 5087

description: FFPE

tag: tissue

value: clear cell renal cell carcinoma primary tumor

tag: institution

value: LHMC

tag: group

value: survival analysis only

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause

value: C

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm

tag: _1=progress to metastatic disease in 5yrs

tag: grade


title: 17148

description: FFPE


title: 18841

description: FFPE

value: validation and survival analyses


title: EORTC_Patient_70714

value: Male

tag: corticosteroids

tag: surgical status

tag: treatment

value: BEVACIZUMAB+LOMUSTINE

tag: phillips subtype

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: who category

tag: dataset


title: UCLA_S9670

tag: age

tag: Sex

value: Classical

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status


title: Sample 191_Single Dermal Fibroblast

tag: cell line

tag: day of differentiation


title: 3660

description: FFPE

tag: tissue

tag: institution

tag: group

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm

tag: _1=progress to metastatic disease in 5yrs

tag: grade


title: UCLA_S9653

tag: surgical status

tag: treatment

tag: phillips subtype

tag: tcga subtype

tag: kps

tag: os (diagnosis)


title: EORTC_Patient_70712

tag: age

tag: Sex

value: Female

tag: corticosteroids

value: On

value: LOMUSTINE

value: Proneural

tag: mmse

tag: rpa

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

tag: who category

tag: dataset


title: Sample 190_Single Dermal Fibroblast

tag: cell line

tag: day of differentiation


title: UCLA_S9489

tag: surgical status

value: Total resection

value: Mesenchymal


title: 28286

description: FFPE

tag: tissue

tag: institution

tag: group

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm

tag: _1=progress to metastatic disease in 5yrs

tag: grade


title: EORTC_Patient_70682

tag: age

tag: Sex

tag: corticosteroids

value: Off

tag: treatment

tag: phillips subtype

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

value: Methylated


title: Sample 189_Single Dermal Fibroblast

tag: cell line

value: primary cell

tag: day of differentiation


title: EORTC_Patient_70678

tag: surgical status

tag: mgmt status

tag: who category

tag: dataset

value: EORTC


title: 12313

description: FFPE

tag: tissue

value: clear cell renal cell carcinoma primary tumor

tag: institution

value: LHMC

tag: group

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm

tag: _1=progress to metastatic disease in 5yrs

tag: grade


title: UCLA_S9456

tag: age

tag: Sex

value: Partial resection

tag: treatment

value: Control

tag: phillips subtype

tag: tcga subtype

tag: kps

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)


title: UCLA_S9897

tag: surgical status

tag: mgmt status


title: Sample 188_Single Dermal Fibroblast

tag: cell line

tag: day of differentiation


title: UCLA_S9420

value: Male

value: Bevacizumab

value: Proliferative


title: Sample 187_Single Dermal Fibroblast


title: EORTC_Patient_70676

value: Female

tag: corticosteroids

value: BEVACIZUMAB+LOMUSTINE

value: Classical

tag: mmse

tag: rpa

tag: who category

tag: dataset


title: 37965

description: FFPE

tag: tissue

tag: institution

value: PSU

tag: group

value: survival analysis only

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause

value: C

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm

tag: _1=progress to metastatic disease in 5yrs

tag: grade


title: EORTC_Patient_70670

tag: age

tag: Sex

value: On

tag: surgical status

tag: treatment

tag: phillips subtype

value: Mesenchymal

tag: tcga subtype

value: Proneural

tag: kps

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status


title: UCLA_S9321


title: Sample 186_Single Dermal Fibroblast

tag: cell line

value: primary cell

tag: day of differentiation


title: UCLA_S9357


title: 4140

description: FFPE

tag: tissue

value: clear cell renal cell carcinoma primary tumor

tag: institution

tag: group

value: validation and survival analyses

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause

tag: time_months to last fu or death


title: EORTC_Patient_70666

tag: age

tag: Sex

tag: corticosteroids

value: Off

tag: mmse

tag: rpa

value: Non-methylated

tag: who category

tag: dataset

value: EORTC


title: UCLA_S9269

value: Male

tag: surgical status

value: Total resection

tag: treatment

value: Bevacizumab

tag: phillips subtype

tag: tcga subtype

tag: kps

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)


title: EORTC_Patient_70660

value: LOMUSTINE

tag: mgmt status


title: EORTC_Patient_70662

value: Female


title: 36037

description: FFPE

tag: tissue

tag: institution

value: PSU

tag: group

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause

tag: Stage

tag: tumor size_cm

tag: _1=progress to metastatic disease in 5yrs

tag: grade


title: 20406

description: FFPE

value: survival analysis only

tag: time_months to last fu or death


title: UCLA_S9200

tag: age

tag: Sex

tag: surgical status

tag: treatment

value: Control

value: Proliferative


title: 8607

description: FFPE

value: LHMC

value: O


title: 2424

description: FFPE

value: C


title: UCLA_S9152

value: Biopsy

tag: phillips subtype

tag: tcga subtype

value: Classical

tag: kps

tag: os (diagnosis)


title: Sample 184_Single Dermal Fibroblast

tag: cell line

value: primary cell

tag: day of differentiation


title: Sample 183_Single Dermal Fibroblast


title: 20720

description: FFPE

tag: tissue

value: clear cell renal cell carcinoma primary tumor

tag: institution

tag: group

value: validation and survival analyses

tag: obese_1 is bmi>=30

value: A


title: EORTC_Patient_70658

tag: corticosteroids

value: Off

value: BEVACIZUMAB+LOMUSTINE

value: Unclassified

tag: mmse

tag: rpa

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

value: Methylated

tag: who category

tag: dataset

value: EORTC


title: Sample 182_Single Dermal Fibroblast


title: 5015

description: FFPE

value: PSU

tag: death_a=alive, c=died of ccrcc, o=death from other cause

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm

tag: _1=progress to metastatic disease in 5yrs

tag: grade


title: UCLA_S9086

tag: age

tag: Sex

value: Male

tag: surgical status

value: Total resection

tag: treatment

value: Bevacizumab

tag: phillips subtype

value: Mesenchymal

tag: tcga subtype

tag: kps

tag: os (diagnosis)


title: EORTC_Patient_70656

tag: corticosteroids

value: On

tag: mmse

tag: rpa

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

value: Non-methylated


title: Sample 181_Single Dermal Fibroblast

tag: cell line

tag: day of differentiation


title: UCLA_S9068

value: Control

value: Proneural


title: EORTC_Patient_70602

value: Proliferative

value: Classical

tag: who category

tag: dataset


title: Sample 185_Single Dermal Fibroblast

value: primary cell


title: UCLA_S9067

tag: age

value: Partial resection


title: 22061

description: FFPE

tag: tissue

value: clear cell renal cell carcinoma primary tumor

tag: institution

tag: group

value: validation and survival analyses

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause

value: A

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm

tag: _1=progress to metastatic disease in 5yrs

tag: grade


title: Sample 179_Single Dermal Fibroblast


title: Sample 180_Single Dermal Fibroblast


title: EORTC_Patient_70654

tag: Sex

tag: corticosteroids

tag: surgical status

tag: treatment

value: BEVACIZUMAB+LOMUSTINE

tag: phillips subtype

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

value: Methylated

value: EORTC


title: 16559

description: FFPE

tag: tissue

tag: institution

value: PSU

tag: group

value: survival analysis only

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause


title: UCLA_S9066

tag: age

value: Male

value: Total resection

value: Bevacizumab

tag: mgmt status


title: EORTC_Patient_70592

tag: Sex

tag: corticosteroids

value: On

value: Mesenchymal

value: Non-methylated

tag: who category

tag: dataset


title: UCLA_S8915

tag: surgical status

tag: treatment

tag: phillips subtype

value: Proneural

tag: tcga subtype


title: 565

description: FFPE

value: LHMC

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm

tag: _1=progress to metastatic disease in 5yrs

tag: grade


title: EORTC_Patient_70590

value: Female

value: Proliferative

value: Classical

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)


title: EORTC_Patient_70586

tag: age

tag: Sex

tag: corticosteroids

value: LOMUSTINE

value: Unclassified

tag: mgmt status


title: Sample 177_Single Dermal Fibroblast

tag: cell line

value: primary cell

tag: day of differentiation


title: Sample 178_Single Dermal Fibroblast


title: Sample 176_Single Dermal Fibroblast


title: 8540

description: FFPE

tag: tissue

value: clear cell renal cell carcinoma primary tumor

tag: institution

tag: group

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause

value: A


title: 28034

description: FFPE

value: validation and survival analyses

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm

tag: _1=progress to metastatic disease in 5yrs

tag: grade


title: Sample 175_Single Dermal Fibroblast


title: 2778

description: FFPE


title: EORTC_Patient_70584

value: Male

value: Off

tag: surgical status

tag: treatment

tag: phillips subtype

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

value: Methylated

tag: who category

tag: dataset

value: EORTC


title: UCLA_S7962

tag: age

tag: Sex

value: Total resection

value: Bevacizumab

value: Mesenchymal

tag: mgmt status


title: UCLA_S7916

value: Biopsy

value: Control

value: Proneural


title: 33281

description: FFPE

tag: tissue

tag: institution

value: PSU

tag: group

value: survival analysis only

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm


title: UCLA_S7781

tag: surgical status

tag: treatment

tag: phillips subtype

value: Proliferative

tag: tcga subtype

value: Classical

tag: kps


title: Sample 173_Single Dermal Fibroblast

tag: cell line

value: primary cell

tag: day of differentiation


title: 23639_screen

description: FFPE

data_processing:
Non-normalized data are the Cq values computed by the Bio-Rad CFX themal cycler software, no adjustment to baseline backgrounds were made
Each microRNA of interest was normalized to the global mean within each sample.  Prior to normalization each target value was scaled to the internal plate calibrator (IPC) by dividing the samples IPC by the grand average of all the IPCs and then multiplying the resulting value by the target Cq.  The global mean was calculated only using microRNA with a Cq<35 detected in all 20 samples.   2^-deltaCq, where deltaCq = (Cq_Target − Cq_global_mean).  All Cq values >37 were set to 40.
Fold change (delta delta Ct) values were not computed for this dataset
The file normalized_data.txt reports normalized signal (against each samples global mean).

label_protocol: cDNA and RT-PCR were performed using miRCURY LNA miRnome PCR panels I&II, currently provided by Qiagen formerly from Exiqon, following the manufacturer's recommendations. Catalog number 339322.

value: clear cell renal cell carcinoma primary tumor

value: LHMC

value: screen analysis

value: A

tag: _1=progress to metastatic disease in 5yrs

tag: grade


title: EORTC_Patient_70306

tag: age

tag: Sex

value: Female

tag: corticosteroids

value: Off

value: BEVACIZUMAB+LOMUSTINE

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

value: Methylated

tag: who category

tag: dataset


title: Sample 174_Single Dermal Fibroblast


title: 22846

description: FFPE

tag: tissue

tag: institution

tag: group

value: validation and survival analyses

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm


title: 29231_screen

description: FFPE

tag: _1=progress to metastatic disease in 5yrs

tag: grade


title: UCLA_S8888

tag: age

tag: Sex

value: Male

tag: surgical status

value: Partial resection

tag: treatment

value: Bevacizumab

tag: phillips subtype

tag: tcga subtype

tag: kps


title: EORTC_Patient_70286

tag: corticosteroids

value: On

value: LOMUSTINE

value: Mesenchymal

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

tag: who category

tag: dataset

value: EORTC


title: UCLA_S7697

value: Proneural


title: Sample 171_Single Dermal Fibroblast

tag: cell line

value: primary cell

tag: day of differentiation


title: 39163_screen

description: FFPE

tag: tissue

value: clear cell renal cell carcinoma primary tumor

tag: institution

value: PSU

tag: group

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm

tag: _1=progress to metastatic disease in 5yrs

tag: grade


title: EORTC_Patient_70284

tag: age

tag: Sex

tag: corticosteroids

tag: surgical status

tag: treatment

tag: phillips subtype

value: Proliferative

tag: tcga subtype

value: Classical

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

value: Non-methylated


title: Sample 172_Single Dermal Fibroblast

tag: cell line

tag: day of differentiation


title: 1414_screen

description: FFPE

tag: tissue

tag: institution

value: LHMC

tag: group

value: screen analysis

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause

value: A

tag: time_months to last fu or death

tag: Stage


title: UCLA_S7625

tag: age

tag: Sex

value: Male

tag: surgical status

value: Total resection

value: Control

value: Unclassified

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status


title: 6093_screen

description: FFPE

tag: tumor size_cm

tag: _1=progress to metastatic disease in 5yrs

tag: grade


title: EORTC_Patient_70282

value: Female

tag: corticosteroids

value: On

tag: treatment

value: LOMUSTINE

tag: phillips subtype

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

value: Methylated

tag: who category

tag: dataset


title: EORTC_Patient_70280

tag: age

tag: Sex

value: Off

value: BEVACIZUMAB+LOMUSTINE

value: Mesenchymal

value: EORTC


title: EORTC_Patient_70278

tag: surgical status

value: Proliferative

value: Classical

tag: os cnsr (event = 1, censor = 0)


title: UCLA_S7590

value: Bevacizumab

value: Proneural

tag: mgmt status


title: EORTC_Patient_70304


title: UCLA_S7238


title: Sample 168_Single Dermal Fibroblast

tag: cell line

value: primary cell

tag: day of differentiation


title: 28331_screen

description: FFPE

tag: tissue

value: clear cell renal cell carcinoma primary tumor

tag: institution

value: PSU

tag: group

value: screen analysis

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause

value: A

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm

tag: _1=progress to metastatic disease in 5yrs

tag: grade


title: Sample 169_Single Dermal Fibroblast


title: 7438_screen

description: FFPE

value: LHMC


title: EORTC_Patient_70274

tag: age

value: Male

tag: corticosteroids

value: On

tag: treatment

tag: phillips subtype

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

value: Non-methylated

tag: who category

tag: dataset


title: UCLA_S7405

tag: Sex

tag: surgical status

value: Biopsy

value: Control

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status


title: 21628_screen

description: FFPE

tag: tissue

tag: institution

tag: group

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm

tag: _1=progress to metastatic disease in 5yrs


title: EORTC_Patient_70272

tag: age

value: Female

tag: corticosteroids

tag: treatment

value: LOMUSTINE

tag: phillips subtype

value: Mesenchymal

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

value: Methylated


title: Sample 170_Single Dermal Fibroblast

tag: cell line

tag: day of differentiation


title: EORTC_Patient_70270

tag: Sex

tag: surgical status

value: BEVACIZUMAB+LOMUSTINE

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

tag: who category

tag: dataset

value: EORTC


title: Sample 166_Single Dermal Fibroblast

value: primary cell


title: UCLA_S7237

tag: age

value: Partial resection

value: Bevacizumab


title: UCLA_S7157

value: Total resection

value: Proliferative

value: Classical


title: UCLA_S7680


title: Sample 165_Single Dermal Fibroblast


title: UCLA_S7040


title: Sample 164_Single Dermal Fibroblast


title: UCLA_S6922

value: Male


title: EORTC_Patient_70256

tag: corticosteroids

value: Off

value: Unclassified


title: Sample 163_Single Dermal Fibroblast


title: Sample 167_Single Dermal Fibroblast


title: Sample 162_Single Dermal Fibroblast


title: 5087_screen

description: FFPE

tag: tissue

value: clear cell renal cell carcinoma primary tumor

tag: institution

value: LHMC

tag: group

value: screen analysis

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause

value: C

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm

tag: _1=progress to metastatic disease in 5yrs

tag: grade


title: EORTC_Patient_70254

tag: Sex

tag: surgical status

tag: treatment

value: LOMUSTINE

tag: phillips subtype

value: Mesenchymal

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

value: Missing


title: EORTC_Patient_70252

tag: age

tag: corticosteroids

value: On

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

tag: who category

tag: dataset

value: EORTC


title: 17148_screen

description: FFPE

tag: tissue

tag: institution

tag: group

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm

tag: _1=progress to metastatic disease in 5yrs


title: UCLA_S6896

tag: Sex

value: Female

tag: surgical status

tag: treatment

value: Control

tag: phillips subtype

tag: tcga subtype

tag: kps


title: Sample 161_Single Dermal Fibroblast

tag: cell line

value: primary cell

tag: day of differentiation


title: UCLA_S6717

tag: age

value: Total resection

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status


title: UCLA_S6816


title: 5673_screen

description: FFPE

tag: tissue

tag: institution

tag: group

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause

value: A

tag: grade


title: EORTC_Patient_70250

tag: Sex

value: Male

tag: corticosteroids

tag: surgical status

value: Proneural

value: Classical

tag: mmse

tag: rpa

value: Methylated

tag: who category

tag: dataset


title: EORTC_Patient_70248

tag: age

value: Off

tag: treatment

value: BEVACIZUMAB+LOMUSTINE

tag: phillips subtype

value: Proliferative

tag: tcga subtype

tag: kps

value: Non-methylated


title: 15320_screen

description: FFPE

tag: tissue

value: clear cell renal cell carcinoma primary tumor

tag: institution

value: LHMC

value: screen analysis

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm

tag: _1=progress to metastatic disease in 5yrs


title: Sample 158_Single Dermal Fibroblast

tag: cell line

tag: day of differentiation


title: EORTC_Patient_70246

tag: Sex

tag: corticosteroids

tag: surgical status

value: LOMUSTINE

value: Mesenchymal

tag: mmse

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

value: EORTC


title: 36037_screen

description: FFPE

value: PSU

tag: group

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause

value: C

tag: grade


title: Sample 160_Single Dermal Fibroblast

value: primary cell


title: Sample 157_Single Dermal Fibroblast


title: 28286_screen

description: FFPE

tag: tissue

tag: institution

tag: time_months to last fu or death


title: UCLA_S6825

tag: age

value: Female

value: Partial resection

tag: treatment

value: Bevacizumab

tag: phillips subtype

tag: tcga subtype

tag: kps


title: EORTC_Patient_70240

tag: Sex

value: Male

tag: corticosteroids

tag: surgical status

value: Proneural

tag: rpa

tag: who category

tag: dataset


title: Sample 159_Single Dermal Fibroblast

tag: cell line

tag: day of differentiation


title: UCLA_S6621

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status


title: EORTC_Patient_70244

value: Off

value: BEVACIZUMAB+LOMUSTINE

value: Classical

tag: mmse


title: 37965_screen

description: FFPE

tag: tissue

value: clear cell renal cell carcinoma primary tumor

tag: institution

tag: group

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm

tag: _1=progress to metastatic disease in 5yrs

tag: grade


title: EORTC_Patient_70238

tag: age

tag: Sex

tag: corticosteroids

value: On

tag: surgical status

tag: treatment

tag: phillips subtype

value: Proliferative

tag: tcga subtype

tag: kps

tag: rpa

value: Non-methylated

tag: who category

tag: dataset


title: EORTC_Patient_70242

value: Mesenchymal

tag: mmse

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status


title: UCLA_S6610

value: Control


title: 20406_screen

description: FFPE

tag: tissue

tag: institution

value: PSU

tag: group

value: screen analysis

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm

tag: _1=progress to metastatic disease in 5yrs


title: Sample 155_Single Dermal Fibroblast

tag: cell line

value: primary cell

tag: day of differentiation


title: 8540_screen

description: FFPE

value: LHMC

value: A

tag: grade


title: 8607_screen

description: FFPE

value: O


title: UCLA_S6413

tag: age

tag: Sex

value: Male

tag: surgical status

value: Biopsy

tag: treatment

tag: phillips subtype

tag: tcga subtype

tag: kps

value: Methylated


title: UCLA_S6439

value: Total resection

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status


title: UCLA_S6445

value: Partial resection

value: Bevacizumab

value: Proneural


title: 33281_screen

description: FFPE

tag: tissue

value: clear cell renal cell carcinoma primary tumor

tag: institution

tag: group

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause

tag: time_months to last fu or death


title: UCLA_S6308


title: UCLA_S6341

value: Proliferative

value: Classical

value: Non-methylated


title: 16559_screen

description: FFPE

value: PSU

tag: Stage

tag: tumor size_cm

tag: _1=progress to metastatic disease in 5yrs

tag: grade


title: 3424

description: FFPE

value: validation and survival analyses


title: EORTC_Patient_70228

tag: age

tag: Sex

value: Female

tag: corticosteroids

value: Off

tag: surgical status

tag: treatment

value: LOMUSTINE

tag: mmse

tag: rpa

tag: who category

tag: dataset

value: EORTC


title: Sample 153_Single Dermal Fibroblast

tag: cell line

value: primary cell

tag: day of differentiation


title: EORTC_Patient_70226

value: On

tag: phillips subtype

tag: tcga subtype

tag: kps

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status


title: UCLA_S6257

tag: age

value: Male

value: Mesenchymal


title: Sample 151_Single Dermal Fibroblast


title: EORTC_Patient_70232

tag: Sex

value: BEVACIZUMAB+LOMUSTINE

value: Missing


title: EORTC_Patient_70224

tag: corticosteroids


title: Sample 152_Single Dermal Fibroblast


title: 41302

description: FFPE

tag: tissue

tag: institution

tag: group

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause

value: A

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm

tag: _1=progress to metastatic disease in 5yrs

tag: grade


title: EORTC_Patient_70234

tag: surgical status

tag: treatment

tag: phillips subtype

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

value: Methylated

tag: who category

tag: dataset


title: 39163

description: FFPE

tag: tissue

value: clear cell renal cell carcinoma primary tumor

tag: institution

tag: group

value: survival analysis only


title: EORTC_Patient_70222

tag: age

tag: Sex

tag: corticosteroids

value: Unclassified

value: Classical

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

value: Non-methylated


title: Sample 154_Single Dermal Fibroblast

tag: cell line

tag: day of differentiation


title: EORTC_Patient_70218

tag: surgical status

tag: treatment

tag: phillips subtype

tag: tcga subtype


title: Sample 149_Single Dermal Fibroblast


title: Sample 156_Single Dermal Fibroblast


title: UCLA_S6227

value: Female

value: Partial resection

value: Bevacizumab

value: Proneural

tag: kps


title: 754

description: FFPE

value: LHMC

value: validation and survival analyses

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm

tag: _1=progress to metastatic disease in 5yrs

tag: grade


title: UCLA_S6096

tag: age

tag: Sex

value: Total resection

tag: os (diagnosis)


title: EORTC_Patient_70216

tag: corticosteroids

value: On

value: LOMUSTINE

value: Mesenchymal

tag: mmse

tag: rpa

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

tag: who category

tag: dataset

value: EORTC


title: 1414

description: FFPE

tag: tissue

tag: institution

tag: group

tag: obese_1 is bmi>=30

value: A


title: UCLA_S6181

value: Male

tag: surgical status

tag: treatment

value: Control

tag: phillips subtype

tag: tcga subtype

tag: kps


title: EORTC_Patient_70230

tag: age

tag: Sex

value: Off

value: BEVACIZUMAB+LOMUSTINE

tag: os (diagnosis)

value: Methylated


title: Sample 150_Single Dermal Fibroblast

tag: cell line

value: primary cell

tag: day of differentiation


title: Sample 148_Single Dermal Fibroblast


title: 6093

description: FFPE

value: clear cell renal cell carcinoma primary tumor

value: survival analysis only

tag: death_a=alive, c=died of ccrcc, o=death from other cause

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm

tag: _1=progress to metastatic disease in 5yrs

tag: grade


title: UCLA_S6116

value: Female

value: Bevacizumab

value: Proneural

value: Classical

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status


title: Sample 146_Single Dermal Fibroblast


title: Sample 147_Single Dermal Fibroblast


title: UCLA_S6081

tag: surgical status

value: Total resection

tag: treatment

value: Unclassified


title: EORTC_Patient_70214

tag: corticosteroids

tag: phillips subtype

value: Mesenchymal

tag: tcga subtype

tag: mmse

tag: rpa

value: Non-methylated

tag: who category

tag: dataset


title: UCLA_S5909

tag: age

tag: Sex

tag: kps

tag: os (diagnosis)


title: Sample 145_Single Dermal Fibroblast

tag: cell line

tag: day of differentiation


title: Sample 144_Single Dermal Fibroblast


title: EORTC_Patient_67246

tag: os cnsr (event = 1, censor = 0)

value: EORTC


title: UCLA_S6028

value: Male

tag: mgmt status


title: EORTC_Patient_60932

value: On

tag: surgical status

value: Missing


title: Sample 143_Single Dermal Fibroblast


title: EORTC_Patient_60934

value: Off

tag: treatment

value: BEVACIZUMAB+LOMUSTINE


title: UCLA_S5887


title: KOR848-2: Mouse_knockout_R848_rep2

city: Araçatuba

first: Flavia

middle: Lombardi

last: Lopes

state: São Paulo

address: Rua Clovis Pestana, 793

department: DAPSA

country: Brazil

institute: FMVA-UNESP

description: mRNA profile expression in BMDM of mice

hyb_protocol: Hybridization of samples to the strips was carried out at 48ºC for 20h in a GeneAtlas™ Hybridization Oven, according to the instructions of the GeneAtlas® Hybridization, Wash, and Stain Kit for mRNA Array Strips.

scan_protocol: Following hybridization, wash and stain of strips were performed using the GeneAtlas® Hybridization, Wash, and Stain Kit for mRNA Array Strips in the GeneAtlas Robotic Wash Station. Following, strips were and scanned using the GeneAtlas® Imaging System (Affymetrix).

data_processing: Raw intensity values were background corrected, log2 transformed and then quantile normalized by the software Expression Console (Affymetrix) using the Robust Multi-array Average (RMA) algorithm.

label: biotin

organism: Mus musculus

source_name: BMDM of knock out RasGEF1b mice, stimulated with R848

label_protocol: mRNA profiles were obtained from 250 ng/sample of total RNA (RIN 10) using WT PLUS Amplification and Labeling Process. First setp is first strand cDNA synthesis; second strand cDNA synthesis; cRNA amplification; 2nd-cycle ss-cDNA synthesis; template RNA removal; ss-cDNA purification and qualification; fragmentation; terminal labeling and hybridization process in Mouse Gene 2.1 ST Array Strips.

growth_protocol: Bone marrow derived macrophages (BMDM’s) were in RPMI 1640 medium supplemented with 20% heat-inactivated FBS (Gibco Invitrogen, USA), 25 mM HEPES, 2 mM glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin (Gibco, Invitrogen), 2-mercaptoethanol as well as 30% (v/v) L929 cell  conditioned medium.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Bone marrow derived macrophages (BMDM’s) from wild type and RasGEF1b knocktout mice were treated for four hours with R848, in vitro

tag: tissue

value: bone marrow derived macrophages (BMDMs)

tag: genotype

value: RasGEF1b knock-out


title: UCLA_S5908

value: Biopsy

tag: phillips subtype

tag: tcga subtype

value: Methylated


title: KOR848-3: Mouse_knockout_R848_rep3

description: mRNA profile expression in BMDM of mice


title: KOR848-1: Mouse_knockout_R848_rep1

description: mRNA profile expression in BMDM of mice


title: EORTC_Patient_60930

tag: corticosteroids

tag: mmse

tag: rpa


title: Sample 142_Single Dermal Fibroblast

value: primary cell


title: UCLA_S5821

tag: age

value: Female

value: Bevacizumab

value: Proneural


title: Sample 141_Single Dermal Fibroblast


title: UCLA_S6007

tag: Sex

value: Total resection


title: UCLA_S5817

value: Classical

tag: kps


title: KONT-3: Mouse_knockout_saline_rep3

description: mRNA profile expression in BMDM of mice

source_name: BMDM of knock out RasGEF1b mice


title: Sample 140_Single Dermal Fibroblast


title: EORTC_Patient_57830

value: Proliferative

tag: os (diagnosis)

tag: who category

tag: dataset


title: Sample 139_Single Dermal Fibroblast

tag: cell line

tag: day of differentiation


title: UCLA_S5786

tag: surgical status

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

value: Non-methylated


title: TAMIGA_05200367C0017R

value: Partial resection

tag: treatment

value: Grade NA

value: TAMIGA


title: Sample 138_Single Dermal Fibroblast


title: EORTC_Patient_60328

value: Off

tag: phillips subtype

value: Mesenchymal

value: Missing

value: EORTC


title: UCLA_S5776

tag: tcga subtype


title: TAMIGA_05200363B0011R

value: Male

tag: corticosteroids

value: On

value: Placebo

value: Grade IV


title: UCLA_S5753

value: Female

value: Bevacizumab


title: TAMIGA_05200362B0011R

value: Total resection

tag: mmse


title: KONT-2: Mouse_knockout_saline_rep2

description: mRNA profile expression in BMDM of mice

tag: tissue

value: bone marrow derived macrophages (BMDMs)

tag: genotype

value: RasGEF1b knock-out


title: KONT-1: Mouse_knockout_saline_rep1

description: mRNA profile expression in BMDM of mice


title: WTR848-3: Mouse_wildtype_R848_rep3

description: mRNA profile expression in BMDM of mice

source_name: BMDM of wild type mice, stimulated with R848

value: Wild Type


title: UCLA_S5660

tag: age

tag: Sex

value: Biopsy

value: Control

value: Proneural

value: Methylated


title: UCLA_S5682

tag: kps

tag: os (diagnosis)

value: Non-methylated


title: WTR848-2: Mouse_wildtype_R848_rep2

description: mRNA profile expression in BMDM of mice


title: WTR848-1: Mouse_wildtype_R848_rep1

description: mRNA profile expression in BMDM of mice


title: WTNT-3: Mouse_wildtype_saline_rep3

description: mRNA profile expression in BMDM of mice

source_name: BMDM of wild type mice


title: Sample 135_Single Dermal Fibroblast

value: primary cell


title: TAMIGA_05200360C0017R

value: Mesenchymal

value: Classical

tag: rpa

value: Grade V

tag: who category

tag: dataset

value: TAMIGA


title: n2_nrde4_control_late_3

city: Chapel Hill

first: Shawn

last: Ahmed

state: North Carolina

address: 216 Fordham Hall, 133 Medical Drive

institute: UNC Genetics Department

data_processing:
3’ Adapter sequence removed using bbduk.sh from the bbmap package
Reads mapped to C. elegans genome (WS251) with hisat2 using the options --max-intronlen 12000 --dta --no-mixed --no-discordant
Read counts assigned to features using Subread featureCounts with the options -M --fraction -t exon -g gene_name
Genome_build: WS251
Supplementary_files_format_and_content: Read counts for each gene

organism: Caenorhabditis elegans

source_name: whole worm (L4 larvae)

growth_protocol: Animals were grown at 20°C on 60 mm NGM plates seeded with OP50 bacteria. Early samples were taken after three-four generations. Late generation samples were taken on the generation of sterility for nrde-1/4 (F10-15), or a comparible generation for wild-type/nrde-2.

extract_protocol:
RNA was extracted using Trizol (Ambion)  followed by isopropanol precipitation.
Library preparation and sequencing was performed at the UNC School of Medicine High-Throughput Sequencing Facility (HTSF). RNA-seq libraries were prepared using the NEXTflex Small RNA Library Prep Kit for Illumina (Bioo Scientific). Samples were depleted of ribosomes before library preparation. Libraries were sequenced on an Illumina HiSeq 2500.

tag: Stage

value: L4 larvae

value: whole worm

tag: genotype/variation

value: WT


title: Sample 134_Single Dermal Fibroblast

tag: cell line

tag: day of differentiation


title: Sample 136_Single Dermal Fibroblast


title: TAMIGA_05200359B0011R

value: Male

value: On

tag: surgical status

value: Partial resection

tag: treatment

tag: phillips subtype

value: Grade IV

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status


title: UCLA_S5583

value: Total resection

tag: tcga subtype

value: Unclassified


title: Sample 133_Single Dermal Fibroblast


title: Sample 137_Single Dermal Fibroblast


title: TAMIGA_05200357B0011R

tag: age

tag: corticosteroids

value: Proneural

tag: mmse


title: n2_nrde4_control_late_2

tag: tissue


title: UCLA_S5565

tag: Sex

value: Bevacizumab

tag: kps

tag: os (diagnosis)


title: n2_nrde4_control_late_1

tag: Stage


title: Sample 132_Single Dermal Fibroblast


title: UCLA_S5348


title: Sample 131_Single Dermal Fibroblast


title: n2_nrde4_control_early_2

tag: genotype/variation


title: TAMIGA_05200361B0011R

value: Female

value: Off

tag: rpa

tag: who category

tag: dataset


title: n2_nrde4_control_early_1


title: UCLA_S5317

tag: surgical status

tag: treatment

value: Methylated


title: UCLA_S5292

tag: phillips subtype

value: Proliferative

value: Mesenchymal

tag: os cnsr (event = 1, censor = 0)


title: nrde4_late_3

value: nrde-4 mutant


title: UCLA_S5325

value: Control

tag: tcga subtype

value: Classical

tag: mgmt status

value: Non-methylated


title: WTNT-1: Mouse_wildtype_saline_rep1

description: mRNA profile expression in BMDM of mice

value: bone marrow derived macrophages (BMDMs)

tag: genotype

value: Wild Type


title: UCLA_S5286

tag: age


title: Sample 130_Single Dermal Fibroblast

tag: cell line

value: primary cell

tag: day of differentiation


title: nrde4_late_2

value: L4 larvae

tag: tissue

value: whole worm


title: TAMIGA_05200343B0011R

tag: Sex

value: Male

tag: corticosteroids

value: Partial resection

tag: kps

tag: mmse

value: Grade III

tag: os (diagnosis)

value: TAMIGA


title: WTNT-2: Mouse_wildtype_saline_rep2

description: mRNA profile expression in BMDM of mice


title: TAMIGA_05200342N0011R

value: Off

value: Total resection

value: Bevacizumab

value: Proneural

tag: rpa

value: Grade IV

tag: who category

tag: dataset


title: Sample 127_Single Dermal Fibroblast


title: Sample 128_Single Dermal Fibroblast


title: UCLA_S5255

tag: surgical status

tag: treatment

tag: phillips subtype

value: Mesenchymal

value: Methylated


title: nrde4_late_1

tag: Stage

tag: genotype/variation

value: nrde-4 mutant


title: Sample 126_Single Dermal Fibroblast


title: TAMIGA_05200355C0017R

tag: age

value: Female

tag: tcga subtype

value: Grade V

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status


title: Sample 129_Single Dermal Fibroblast

tag: cell line

value: primary cell

tag: day of differentiation


title: UCLA_S5192

tag: Sex

value: Control

value: Proliferative

value: Classical

tag: kps


title: TAMIGA_05200331B0011R

value: Male

tag: corticosteroids

value: On

value: Biopsy

tag: mmse

tag: os (diagnosis)


title: Sample 125_Single Dermal Fibroblast


title: TAMIGA_05200353C0017R

value: Off

value: Partial resection

tag: rpa

value: Grade III

tag: who category

tag: dataset

value: TAMIGA


title: TAMIGA_05200338C0017R

tag: surgical status

tag: treatment

value: Placebo

tag: phillips subtype

value: Grade IV


title: UCLA_S5084

tag: age

value: Bevacizumab


title: UCLA_S5051

value: Total resection

value: Proneural

tag: tcga subtype

value: Non-methylated


title: TAMIGA_05200326C0007R

value: Unclassified

value: Mesenchymal

tag: os cnsr (event = 1, censor = 0)


title: Sample 124_Single Dermal Fibroblast

value: primary cell


title: nrde4_early_1

tag: Stage

value: L4 larvae

tag: tissue

value: whole worm

tag: genotype/variation

value: nrde-4 mutant


title: Sample 123_Single Dermal Fibroblast

tag: cell line

tag: day of differentiation


title: TAMIGA_05200356C0017R

tag: Sex

value: Male

tag: corticosteroids

value: Biopsy

value: Proliferative

value: Classical

tag: kps

value: Grade V

tag: mgmt status


title: nrde1_yp4_late

value: nrde-1 mutant


title: UCLA_S5028

tag: os (diagnosis)


title: nrde1_yp4_early


title: UCLA_S5004

value: Partial resection


title: n2_nrde4_control_early_3

value: WT


title: Sample 121_Single Dermal Fibroblast


title: Sample 122_Single Dermal Fibroblast


title: TAMIGA_05200318B0011R

value: Off

value: Total resection

value: Bevacizumab

tag: mmse

tag: rpa

value: Grade IV

tag: who category

tag: dataset

value: TAMIGA


title: nrde1_yp5_late


title: TAMIGA_05200319B0011R

tag: age

value: Female

value: On

tag: surgical status

tag: treatment

tag: phillips subtype

value: Proneural


title: Sample 120_Single Dermal Fibroblast

value: primary cell


title: UCLA_S4902

value: Mesenchymal

tag: tcga subtype

tag: os cnsr (event = 1, censor = 0)


title: nrde4_early_3

tag: Stage

value: L4 larvae

tag: tissue

value: whole worm

tag: genotype/variation

value: nrde-4 mutant


title: TAMIGA_05200320B0011R

tag: Sex

tag: corticosteroids

value: Unclassified

value: Classical


title: TAMIGA_05200334C0007R

value: Male

value: Biopsy

tag: kps

value: Grade V

tag: mgmt status


title: nrde1_yp5_early

value: nrde-1 mutant


title: Sample 119_Single Dermal Fibroblast

tag: cell line

tag: day of differentiation


title: UCLA_S4873

value: Partial resection

value: Bevacizumab

tag: os (diagnosis)


title: nrde4_early_2


title: Sample 118_Single Dermal Fibroblast


title: n2_nrde1_control

value: WT


title: TAMIGA_05200276B001R

value: Placebo

tag: mmse

tag: rpa

value: Grade IV

tag: who category

tag: dataset

value: TAMIGA


title: nrde2_late

value: nrde-2 mutant


title: Sample 117_Single Dermal Fibroblast

value: primary cell


title: TAMIGA_05200277B0011R

tag: age

value: Female

value: On

tag: surgical status

tag: treatment

tag: phillips subtype

value: Proneural


title: UCLA_S4883

value: Total resection

value: Mesenchymal

tag: tcga subtype

tag: os cnsr (event = 1, censor = 0)


title: TAMIGA_05200274C0007R

tag: Sex

value: Classical


title: nrde2_early

tag: Stage

value: L4 larvae

tag: tissue

value: whole worm

tag: genotype/variation


title: Sample 116_Single Dermal Fibroblast

tag: cell line


title: Sample 115_Single Dermal Fibroblast

tag: day of differentiation


title: Sample 114_Single Dermal Fibroblast


title: TAMIGA_05200249B0011R

value: Male

tag: corticosteroids

value: Off

tag: kps

value: Grade V

tag: os (diagnosis)

tag: mgmt status


title: TAMIGA_05200242B0011R

value: Partial resection

tag: mmse

tag: rpa

tag: who category

tag: dataset


title: UCLA_S4417

tag: age

tag: surgical status

tag: treatment

value: Bevacizumab

tag: phillips subtype

value: Proliferative


title: TAMIGA_05200252C007R

tag: Sex

tag: tcga subtype

value: Grade IV

tag: os cnsr (event = 1, censor = 0)

value: TAMIGA


title: UCLA_S4293


title: Vehicle 24hr Rep 2

city: Boulder

first: William

middle: Marland

last: Old

state: CO

address: 1945 Colorado Ave.

department: MCDB

institute: University of Colorado Boulder

description: Single read 50 cycles (1x50)

data_processing:
Adapter sequences were trimmed at sequencing facility.  Cutting of low scoring reads was done using Trimmomatic-0.36.  Settings were a sliding window of 4bp and minimum PHRED score of 15.  Minimum allowable read length 35.
FastQC was run to verify adapter sequence removal and assess read quality.
Lanes were concatenated  together per condition/replicate using a linux bash command.
Read alignment to HG19 was done using Tophat 2.2.1.
Cufflinks was run on each condition/replicate to obtain a normalized FPKM read count per gene.
Cuffdiff was run by time point to obtain gene specific differential expression estimates.
The 4 resulting cuffdiff output were meged using a Python script.
Genome_build: Most recent available UCSC HG19 build downloaded from Johns Hopkins Tophat download page.
Supplementary_files_format_and_content: tab delimited cuffdiff output files

molecule: polyA RNA

source_name: SK-N-BE(2) neuroblastoma line

growth_protocol: SK-N-BE(2) cells were plated on 6-well dishes at a density of 2E6 cells per well and allowed to attach overnight. The following morning, cells were treated.

extract_protocol:
For RNA extraction, media was aspirated and cells were washed gently with PBS with subsequent aspiration. 400ul of cold TRIzol reagent was added to each well, cells were scraped with a cell lifter, and lifted cells were pipetted briefly to homogenize the suspension. RNA was prepared according to the TRIzol manufacturer?s instructions and RNA pellets were solubilized in 100ul of RNase free water. For cleanup, RNA was bound to a Qiagen RNeasy column and underwent on-column DNase I digestion according to the manufacturer?s instructions. RNAs were subsequently eluted in 50ul RNase-free water, quantified on a NanoDrop, and used for RNA-seq analysis.
500ng was used in the Nugen mRNA library protocol. Libraries were run on the Illumina HiSEQ 4000 with single read, 50bp length. All 32 samples were uniquely tagged, pooled, and then run across 7 lanes. FASTQ files were merged for subsequent analysis.

treatment_protocol: SK-N-BE(2) cells were treated with either 20µM CBD in ethanol or vehicle (0.1% ethanol) for the indicated time points above.

tag: cell line

tag: cell type

value: neuroblastoma

value: Vehicle

tag: time (hours)


title: Vehicle 24hr Rep 1

description: Single read 50 cycles (1x50)


title: Vehicle 24hr Rep 4

description: Single read 50 cycles (1x50)


title: TAMIGA_05200259C0007R

tag: corticosteroids

value: On

tag: kps


title: Sample 113_Single Dermal Fibroblast

value: primary cell

tag: day of differentiation


title: UCLA_S4837

value: Total resection

tag: os (diagnosis)

tag: mgmt status


title: TAMIGA_05200269B0021R

value: Proneural

tag: mmse

tag: rpa

tag: who category


title: Sample 112_Single Dermal Fibroblast


title: UCLA_S4224

tag: age

tag: surgical status

value: Mesenchymal


title: Vehicle 24hr Rep 3

description: Single read 50 cycles (1x50)

tag: treatment


title: CBD 24hr Rep 4

description: Single read 50 cycles (1x50)

value: CBD


title: TAMIGA_05200232B0016R

tag: Sex

tag: phillips subtype

tag: dataset


title: Sample 111_Single Dermal Fibroblast

tag: cell line


title: UCLA_S4188

tag: tcga subtype

tag: os cnsr (event = 1, censor = 0)


title: Sample 110_Single Dermal Fibroblast


title: TAMIGA_05200229B0016R

value: Female

tag: corticosteroids

value: Classical


title: CBD 24hr Rep 3

description: Single read 50 cycles (1x50)

tag: cell type

tag: time (hours)


title: UCLA_S4146

value: Male

tag: kps

tag: os (diagnosis)


title: UCLA_S4330

value: Unclassified

tag: mgmt status


title: UCLA_S4720

value: Control


title: CBD 24hr Rep 2

description: Single read 50 cycles (1x50)


title: TAMIGA_05200221B0021R

value: Off

tag: mmse

tag: rpa

value: Grade NA


title: UCLA_S4109

tag: age

value: Proliferative


title: Sample 109_Single Dermal Fibroblast

tag: day of differentiation


title: TAMIGA_05200220B0021R

tag: surgical status

value: Partial resection

tag: treatment

value: Grade IV

tag: who category

value: TAMIGA


title: CBD 24hr Rep 1

description: Single read 50 cycles (1x50)

value: neuroblastoma


title: UCLA_S4670

tag: Sex

value: Bevacizumab

tag: phillips subtype


title: UCLA_S4063

tag: tcga subtype


title: TAMIGA_05200219B0011R

value: Total resection

tag: os cnsr (event = 1, censor = 0)

tag: dataset


title: Sample 106_Single Dermal Fibroblast

tag: cell line

value: primary cell


title: Vehicle 12hr Rep 3

description: Single read 50 cycles (1x50)

tag: cell type

value: Vehicle

tag: time (hours)


title: Vehicle 12hr Rep 4

description: Single read 50 cycles (1x50)


title: Sample 104_Single Dermal Fibroblast


title: Sample 107_Single Dermal Fibroblast


title: Sample 108_Single Dermal Fibroblast


title: Vehicle 12hr Rep 2

description: Single read 50 cycles (1x50)


title: Sample 105_Single Dermal Fibroblast


title: Vehicle 12hr Rep 1

description: Single read 50 cycles (1x50)


title: UCLA_S3830

tag: kps

tag: os (diagnosis)

value: Non-methylated


title: UCLA_S3860

value: Mesenchymal

tag: mgmt status


title: UCLA_S3869

value: Proneural


title: CBD 12hr Rep 3

description: Single read 50 cycles (1x50)

value: CBD


title: Sample 102_Single Dermal Fibroblast


title: CBD 12hr Rep 4

description: Single read 50 cycles (1x50)


title: TAMIGA_05200218B0011R

value: Female

tag: corticosteroids

value: On

value: Placebo

tag: mmse

tag: rpa

value: Grade III


title: UCLA_S3766

tag: age

value: Male

tag: surgical status


title: TAMIGA_05200216B0011R

value: Partial resection

tag: treatment

value: Proliferative

value: Classical

value: Grade V

tag: who category


title: Sample 103_Single Dermal Fibroblast

tag: day of differentiation


title: Sample 101_Single Dermal Fibroblast


title: UCLA_S3778

tag: Sex

value: Control

tag: phillips subtype

tag: tcga subtype


title: TAMIGA_05200213B0021R

value: Grade IV

tag: os cnsr (event = 1, censor = 0)

tag: dataset

value: TAMIGA


title: TAMIGA_05200215B0011R

value: Off

value: Total resection


title: UCLA_S3763

value: Bevacizumab

value: Mesenchymal

value: Methylated


title: TAMIGA_05200211B0021R


title: CBD 12hr Rep 2

description: Single read 50 cycles (1x50)

tag: cell line

tag: cell type

value: neuroblastoma

value: CBD

tag: time (hours)


title: TAMIGA_05200207B0031R

value: Female

value: Proneural

tag: kps

tag: os (diagnosis)

tag: mgmt status


title: TAMIGA_05200209B0021R

tag: corticosteroids

tag: mmse

tag: rpa


title: TAMIGA_05200206B0016R

tag: age

value: Male

value: On

tag: surgical status

tag: treatment


title: UCLA_S3835

tag: Sex

value: Partial resection


title: Sample 100_Single Dermal Fibroblast

value: primary cell

tag: day of differentiation


title: CBD 12hr Rep 1

description: Single read 50 cycles (1x50)


title: Sample 99_Single Dermal Fibroblast


title: Vehicle 6hr Rep 4

description: Single read 50 cycles (1x50)

value: Vehicle


title: UCLA_S3749

tag: phillips subtype

tag: tcga subtype


title: UCLA_S3762

value: Control

tag: os cnsr (event = 1, censor = 0)


title: Vehicle 6hr Rep 3

description: Single read 50 cycles (1x50)

tag: cell line


title: Vehicle 6hr Rep 2

description: Single read 50 cycles (1x50)

tag: cell type


title: Vehicle 6hr Rep 1

description: Single read 50 cycles (1x50)

tag: time (hours)


title: TAMIGA_05200199B0016R

value: Placebo

value: Classical

tag: kps

value: Grade IV

tag: who category

tag: dataset


title: Sample 97_Single Dermal Fibroblast


title: Sample 98_Single Dermal Fibroblast


title: Sample 95_Single Dermal Fibroblast


title: UCLA_S3688

value: Proliferative

tag: os (diagnosis)

tag: mgmt status


title: TAMIGA_05200202B0021R

tag: corticosteroids

value: Total resection

value: Bevacizumab

tag: mmse

tag: rpa

value: Grade III

value: TAMIGA


title: CBD 6hr Rep 3

description: Single read 50 cycles (1x50)

value: neuroblastoma

tag: treatment

value: CBD


title: TAMIGA_05200198B0016R

tag: age

tag: Sex

tag: surgical status

value: Mesenchymal


title: UCLA_S3695

value: Female

tag: phillips subtype

tag: tcga subtype

value: Non-methylated


title: TAMIGA_05200196C0017R

value: On

value: Proneural

tag: os cnsr (event = 1, censor = 0)


title: Sample 96_Single Dermal Fibroblast

tag: cell line

value: primary cell

tag: day of differentiation


title: CBD 6hr Rep 4

description: Single read 50 cycles (1x50)

tag: cell type

tag: time (hours)


title: TAMIGA_05200197B0016R

value: Male

value: Off

value: Partial resection

tag: kps

tag: who category

tag: dataset


title: UCLA_S3457

tag: os (diagnosis)

tag: mgmt status


title: UCLA_S3481

value: Classical

value: Methylated


title: Sample 94_Single Dermal Fibroblast


title: CBD 6hr Rep 2

description: Single read 50 cycles (1x50)


title: UCLA_S3439

value: Total resection

value: Unclassified


title: Sample 93_Single Dermal Fibroblast


title: TAMIGA_05200186C0007R

tag: corticosteroids

tag: mmse

tag: rpa

value: Grade IV


title: UCLA_S3712

tag: age

tag: Sex

tag: treatment

value: Control


title: UCLA_S3427

tag: surgical status

value: Bevacizumab

tag: phillips subtype

value: Proliferative

tag: tcga subtype


title: Vehicle 3hr Rep 4

description: Single read 50 cycles (1x50)

tag: cell line

value: neuroblastoma

value: Vehicle


title: TAMIGA_05200181C0007R

value: Female

value: Biopsy

value: Grade V

tag: os cnsr (event = 1, censor = 0)

value: TAMIGA


title: Sample 91_Single Dermal Fibroblast

value: primary cell

tag: day of differentiation


title: Sample 92_Single Dermal Fibroblast


title: TAMIGA_05200173B0016R

value: Male

value: Off

value: Mesenchymal

value: Proneural

tag: kps


title: Vehicle 3hr Rep 3

description: Single read 50 cycles (1x50)

tag: cell type

tag: time (hours)


title: TAMIGA_05200189C0007R

value: Partial resection

value: Classical

tag: os (diagnosis)

tag: who category

tag: dataset


title: TAMIGA_05200172B0016R

tag: corticosteroids

tag: mmse

tag: mgmt status


title: UCLA_S3371

tag: age

tag: Sex

value: Total resection

value: Non-methylated


title: Vehicle 3hr Rep 2

description: Single read 50 cycles (1x50)

tag: treatment


title: TAMIGA_05200171B0016R

tag: surgical status

value: Bevacizumab

tag: phillips subtype

tag: rpa

value: Grade III


title: Sample 89_Single Dermal Fibroblast

tag: cell line


title: Vehicle 3hr Rep 1

description: Single read 50 cycles (1x50)

value: neuroblastoma


title: Sample 88_Single Dermal Fibroblast

tag: day of differentiation


title: Sample 87_Single Dermal Fibroblast


title: CBD 3hr Rep 4

description: Single read 50 cycles (1x50)

value: CBD


title: TAMIGA_05200170B0016R

tag: tcga subtype

tag: kps

tag: os cnsr (event = 1, censor = 0)


title: UCLA_S3330

value: Female

tag: os (diagnosis)

value: Methylated


title: CBD 6hr Rep 1

description: Single read 50 cycles (1x50)

tag: cell type

tag: time (hours)


title: UCLA_S3231

value: Proliferative


title: CBD 3hr Rep 3

description: Single read 50 cycles (1x50)


title: Sample 86_Single Dermal Fibroblast


title: TAMIGA_05200168B0016R

tag: corticosteroids

value: On

value: Grade V

tag: who category

tag: dataset

value: TAMIGA


title: UCLA_S3401

tag: age

value: Male

tag: mgmt status


title: CBD 3hr Rep 2

description: Single read 50 cycles (1x50)

tag: treatment


title: Sample 85_Single Dermal Fibroblast

value: primary cell


title: Sample 90_Single Dermal Fibroblast


title: TAMIGA_05200165B0016R

tag: Sex

value: Off

tag: surgical status

value: Mesenchymal

tag: mmse


title: CBD 3hr Rep 1

description: Single read 50 cycles (1x50)

tag: cell line


title: Sample 84_Single Dermal Fibroblast

tag: day of differentiation


title: UCLA_S3206

value: Partial resection

tag: phillips subtype

value: Proneural

tag: tcga subtype


title: TAMIGA_05200164B0016R

value: Classical

tag: kps

tag: rpa

value: Grade IV

tag: os cnsr (event = 1, censor = 0)


title: UCLA_S3216

value: Bevacizumab

tag: os (diagnosis)


title: TAMIGA_05200169B0016R

tag: corticosteroids

value: Placebo


title: Glut DFAT tet-shRSPO3_dox_3

city: Oxford

first: Nellie

middle: Yen

last: Loh

state: OXON

address: OCDEM, Churchill Hospital, Headington

department: Radcliffe Dept of Medicine

institute: University of Oxford

data_processing:
The sequencing quality was assessed with FASTQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads were aligned to the human reference genome (GRCh37) using HISAT2
Duplicate reads removed using the Picard ‘MarkDuplicates’ tool (http://broadinstitute.github.io/picard)
Reads mapping uniquely to Ensembl-annotated genes were summarised using featureCounts
Genome_build: human reference genome (GRCh37)
Supplementary_files_format_and_content: P190228_gene_count_table.txt

source_name: gluteal adipose progenitor cells

growth_protocol: DFAT tet-shRSPO3 and tet-shCON preadipocytes were maintained in tetracycline-free media [DMEM-F12 supplemented with 10% FBS (ThermoFisher Scientific Gibco, #26140079), 2 mM L-glutamine, 0.25 ng ml-1 fibroblast growth factor, 100 units ml-1 penicillin and 100 µg ml-1 streptomycin, and 2 µg ml-1 puromycin]. For differentiation to adipocytes, 200K/well cells were seeded in 6-well plates and two days later, confluent cells were differentiated for 13 days in standard adipogenic media (DMEM-F12 containing 2 mM L-glutamine, 100 units ml-1 penicillin, 100 µg ml-1 streptomycin, 17 µM pantothenate, 100 nM human insulin, 10 nM 3,3’,5-triiodo-L-thyronine, 33 µM biotin, 10 µg ml-1 human transferrin and 1 µM dexamethasone). For the first 4 days, 250 µM 3-isobutyl-1-methylxanthine and 4 μM troglitazone were added to the adipogenic medium.

extract_protocol:
Total RNA purification and on-column DNaseI-treatment were performed using the RNeasy Mini kit (Qiagen).
Library preparation, cDNA sequencing and analysis were performed at the Oxford Genomics Centre (Wellcome Trust Centre for Human Genetics, Oxford, UK). Polyadenylated transcript enrichment and strand specific library preparation was completed using NEBNext Ultra II mRNA kit (NEB) following manufacturer’s instructions. Libraries were amplified on a Tetrad (Bio-Rad) using in-house unique dual indexing primers (based on DOI: 10.1186/1472-6750-13-104). Individual libraries were normalized using Qubit, and the size profile was analysed on the 2200 or 4200 TapeStation. Individual libraries were normalised and pooled together accordingly. The pooled library was diluted to ~10 nM for storage. The 10 nM library was denatured and further diluted prior to loading on the sequencer. Paired end sequencing was performed using a HiSeq4000 75bp platform (Illumina, HiSeq 3000/4000 PE Cluster Kit and 150 cycle SBS Kit), generating a raw read count of 20-25 million reads per sample.

treatment_protocol: Differentiated cells were incubated in hormone-free basal media (DMEM-F12 supplemented with 2 mM L-glutamine, 100 units ml-1 penicillin, 100 µg ml-1 streptomycin, 17 µM pantothenate, 33 µM biotin, 10 µg ml-1 human transferrin) containing either vehicle or 0.05 µg ml-1 doxycycline (to induce shRNA-expression) for 48 hours prior to harvesting for RNA.

tag: tissue

value: gluteal adipose

tag: cell type

value: immortalized gluteal DFAT cells

tag: vector

value: dox (0.05 µg/ml)


title: UCLA_S3198

tag: age

value: Female

value: Total resection

tag: mgmt status

value: Non-methylated


title: UCLA_S3367

tag: Sex

tag: treatment


title: TAMIGA_05200167B0016R

value: On

tag: surgical status

value: Biopsy

tag: mmse

value: Grade V

tag: who category

tag: dataset

value: TAMIGA


title: Glut DFAT tet-shRSPO3_nodox_3

value: vehicle


title: Sample 82_Single Dermal Fibroblast

tag: cell line

value: primary cell

tag: day of differentiation


title: Sample 81_Single Dermal Fibroblast


title: Glut DFAT tet-shCON_dox_3

value: tet-pLKO-puro-shCON


title: UCLA_S3192

value: Male

value: Partial resection

tag: phillips subtype

value: Proliferative

tag: tcga subtype

value: Classical

tag: kps

value: Methylated


title: Sample 80_Single Dermal Fibroblast


title: UCLA_S3194

value: Bevacizumab

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)


title: Glut DFAT tet-shCON_nodox_3

tag: tissue

value: gluteal adipose

tag: cell type

value: immortalized gluteal DFAT cells


title: Glut DFAT tet-shRSPO3_dox_2

tag: vector

value: dox (0.05 µg/ml)


title: TAMIGA_0520016380016R

tag: age

tag: corticosteroids

value: Mesenchymal

tag: rpa

tag: mgmt status


title: Sample 79_Single Dermal Fibroblast


title: UCLA_S3213

tag: Sex

value: Female

tag: surgical status

value: Total resection

tag: treatment

value: Control

value: Unclassified

value: Non-methylated


title: UCLA_S3106

value: Proneural


title: UCLA_S3112


title: TAMIGA_05200160B0016R

value: Off

tag: mmse

value: Grade IV

tag: who category

tag: dataset

value: TAMIGA


title: TAMIGA_05200161B0016R

value: Male

value: Partial resection

value: Placebo

tag: phillips subtype

tag: tcga subtype


title: Sample 78_Single Dermal Fibroblast

tag: cell line

value: primary cell

tag: day of differentiation


title: Sample 83_Single Dermal Fibroblast


title: Glut DFAT tet-shRSPO3_nodox_2

tag: tissue

value: gluteal adipose

value: vehicle


title: TAMIGA_05200159B0016R

tag: kps

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)


title: Glut DFAT tet-shCON_dox_2

tag: cell type

value: immortalized gluteal DFAT cells

tag: vector

value: tet-pLKO-puro-shCON

value: dox (0.05 µg/ml)


title: Glut DFAT tet-shCON_nodox_2


title: Sample 76_Single Dermal Fibroblast


title: UCLA_S3046

tag: age

value: Biopsy

tag: mgmt status


title: UCLA_S3073

tag: Sex

tag: surgical status

value: Bevacizumab


title: TAMIGA_05200162B0016R

tag: corticosteroids

value: Total resection

tag: treatment

value: Mesenchymal

tag: mmse

tag: rpa

value: Grade III


title: TAMIGA_05200157B0016R

value: On

tag: phillips subtype

value: Proneural

tag: tcga subtype

value: Classical

tag: who category

tag: dataset


title: Glut DFAT tet-shRSPO3_dox_1

tag: tissue


title: Sample 74_Single Dermal Fibroblast

tag: cell line

tag: day of differentiation


title: Glut DFAT tet-shRSPO3_nodox_1

tag: cell type


title: TAMIGA_05200156B0016R

value: Male

tag: kps

value: Grade IV

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

value: TAMIGA


title: UCLA_S3005

tag: age

tag: Sex

value: Female

value: Partial resection

tag: mgmt status

value: Methylated


title: Sample 73_Single Dermal Fibroblast

value: primary cell


title: Glut DFAT tet-shCON_dox_1

value: gluteal adipose

value: immortalized gluteal DFAT cells

tag: vector

value: tet-pLKO-puro-shCON

tag: treatment


title: Sample 72_Single Dermal Fibroblast


title: Glut DFAT tet-shCON_nodox_1

value: vehicle


title: TAMIGA_05200155C0007R

tag: corticosteroids

value: Off

tag: surgical status

value: Total resection

value: Unclassified

tag: mmse

tag: rpa


title: UCLA_S3096

value: Control

tag: phillips subtype

value: Proliferative

tag: tcga subtype

value: Mesenchymal


title: Sample 77_Single Dermal Fibroblast

tag: cell line


title: TAMIGA_05200158B0016R

value: Male

value: On

value: Grade V

tag: who category

tag: dataset


title: UCLA_S2982

value: Female

value: Bevacizumab

value: Proneural

tag: kps


title: TAMIGA_05200152B0016R

value: Classical

value: Grade IV

tag: os (diagnosis)

value: TAMIGA


title: Abdo DFAT tet-shRSPO3_dox_3

source_name: subcutaneous abdominal adipose progenitor cells

tag: tissue

value: subcutaneous abdominal adipose

tag: cell type

value: immortalized abdominal DFAT cells

value: dox (0.05 µg/ml)


title: Sample 71_Single Dermal Fibroblast

value: primary cell

tag: day of differentiation


title: TAMIGA_05200151C0007R

tag: age

tag: Sex

value: Partial resection

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status


title: UCLA_S2940

tag: surgical status

tag: treatment

value: Methylated


title: TAMIGA_05200148B0016R

tag: corticosteroids

value: Off

tag: mmse

tag: rpa


title: UCLA_S2936

value: Biopsy

tag: phillips subtype

value: Proliferative

tag: tcga subtype


title: Abdo DFAT tet-shRSPO3_nodox_3

tag: vector

value: vehicle


title: UCLA_S2934

value: Male

value: Total resection

tag: kps


title: Sample 75_Single Dermal Fibroblast

tag: cell line


title: Sample 70_Single Dermal Fibroblast


title: UCLA_S3044

value: Female

value: Bevacizumab

value: Mesenchymal

tag: os (diagnosis)

value: Non-methylated


title: TAMIGA_05200146B0016R

value: On

value: Placebo

value: Grade IV

tag: who category

tag: dataset

value: TAMIGA


title: Abdo DFAT tet-shCON_dox_3

tag: tissue

value: subcutaneous abdominal adipose

tag: cell type

value: immortalized abdominal DFAT cells

value: tet-pLKO-puro-shCON

value: dox (0.05 µg/ml)


title: UCLA_S2928

tag: age

tag: Sex

value: Classical

tag: os cnsr (event = 1, censor = 0)


title: Abdo DFAT tet-shCON_nodox_3

tag: treatment


title: UCLA_S2896

tag: surgical status

value: Partial resection

value: Control

value: Unclassified

tag: mgmt status


title: TAMIGA_05200144B0016R

tag: corticosteroids

value: Biopsy

value: Proliferative

tag: mmse

tag: rpa

value: Grade V


title: Sample 68_Single Dermal Fibroblast

value: primary cell

tag: day of differentiation


title: TAMIGA_05200143B0016R

value: Female

value: Total resection

tag: phillips subtype

value: Proneural

tag: tcga subtype

tag: kps


title: Abdo DFAT tet-shRSPO3_dox_2

tag: vector


title: Sample 67_Single Dermal Fibroblast

tag: cell line


title: TAMIGA_05200142B0016R

value: On

value: Mesenchymal

value: Grade III

tag: os (diagnosis)

tag: who category

tag: dataset


title: Abdo DFAT tet-shRSPO3_nodox_2

tag: tissue

value: subcutaneous abdominal adipose

tag: cell type

value: immortalized abdominal DFAT cells

value: vehicle


title: UCLA_S2861

tag: age

tag: Sex

tag: treatment

tag: os cnsr (event = 1, censor = 0)


title: TAMIGA_05200141B0016R

value: Male

tag: corticosteroids

tag: surgical status

value: Placebo

tag: mmse

value: Grade IV

tag: mgmt status

value: TAMIGA


title: Abdo DFAT tet-shCON_dox_2

value: tet-pLKO-puro-shCON

value: dox (0.05 µg/ml)


title: Sample 66_Single Dermal Fibroblast

tag: day of differentiation


title: UCLA_S2833

value: Biopsy

value: Bevacizumab

tag: phillips subtype

tag: tcga subtype

value: Unclassified

tag: kps


title: TAMIGA_05200140B0016R

value: Off

value: Total resection

tag: rpa

tag: os (diagnosis)


title: Sample 65_Single Dermal Fibroblast

tag: cell line

value: primary cell


title: Abdo DFAT tet-shCON_nodox_2

tag: tissue

tag: vector


title: UCLA_S2769

tag: age

value: Female

value: Partial resection

value: Proneural

value: Non-methylated


title: Abdo DFAT tet-shRSPO3_dox_1

value: subcutaneous abdominal adipose

tag: cell type

value: immortalized abdominal DFAT cells


title: Sample 63_Single Dermal Fibroblast


title: TAMIGA_05200130B0021R

tag: Sex

value: Male

tag: treatment

value: Grade V

tag: who category

tag: dataset


title: TAMIGA_05200134B0021R

tag: corticosteroids

tag: surgical status

tag: mmse

tag: os cnsr (event = 1, censor = 0)

value: TAMIGA


title: Sample 64_Single Dermal Fibroblast

tag: day of differentiation


title: Sample 69_Single Dermal Fibroblast


title: Sample 62_Single Dermal Fibroblast


title: TAMIGA_05200126B0016R

tag: phillips subtype

tag: tcga subtype

tag: kps

value: Grade IV

tag: mgmt status


title: Abdo DFAT tet-shRSPO3_nodox_1

tag: tissue

value: vehicle


title: UCLA_S2710

value: Mesenchymal

tag: os (diagnosis)


title: Abdo DFAT tet-shCON_dox_1

tag: vector

value: tet-pLKO-puro-shCON

value: dox (0.05 µg/ml)


title: UCLA_S2746

tag: age

value: Control


title: UCLA_S2646

tag: Sex

value: Proliferative


title: UCLA_S2621

value: Total resection

tag: treatment

value: Bevacizumab


title: UCLA_S2749

value: Female

value: Partial resection

value: Unclassified

value: Classical

value: Methylated


title: Abdo DFAT tet-shCON_nodox_1

value: subcutaneous abdominal adipose

tag: cell type

value: immortalized abdominal DFAT cells


title: collagen 240h [10-CO_240h]

city: Philadelphia

first: Ali

last: Naji

state: PA

address: 3400 Civic Ctr Blvd

department: Transplant Surgery

institute: University of Pennsylvania

data_processing:
Read were trimmed with cutadapt version 1.9.1 with parameters -m 36 –max-n 1 -a AGATCGGAAGAGCACACGTCT
UMI extraction was carried out with custom R code (R version 3.5.1)
Alignments were done with bowtie version 0.12.7 using parameters -k 4 --best --sam --norc
Quantification was done using custom R code (R  version 3.5.1)
Reads were convereted to CPM by adding pseudocount of 1,normalizing to total counts, then taking log2
Genome_build: RefSeq 2012
Genome_build: mirBase 21
Genome_build: trna downloaded 2008
Supplementary_files_format_and_content: human.mirna.tsv.xls contains raw mirna UMI-count expression for each sample
Supplementary_files_format_and_content: human.mirna.tsv.de.cpm.tsv.xls contains mirna CPM normalized values for each sample
Supplementary_files_format_and_content: human.refseq.tsv.xls contains raw refseq transcript UMI-count expression for each sample
Supplementary_files_format_and_content: human.refseq.tsv.de.cpm.tsv.xls contains refseq transcript CPM normalized values  for each sample

source_name: human specific exoxomes from mouse plasma

extract_protocol:
RNA was extracted using TRIzol reagent(  ambion life thecnology).
Exoxomal RNA samples were assayed for quantity and quality with an Agilent 2100 Bioanalyzer instrument using the Agilent RNA 6000 Pico Kit (Agilent Technologies, Part number 5067-1513). Libraries were prepared using QIAseq miRNA Library Kit (QIAGEN, cat #331502) as per standard protocol in the kit’s sample prep guide.

treatment_protocol: human islets treated with collagen/ no collagen were subcutaneously transplanted into B6/SCID mouse

value: Human islet

value: collagen

tag: host strain

tag: molecule subtype

value: Exosomal RNA


title: TAMIGA_05200110C0007R

value: Male

tag: corticosteroids

value: Off

tag: surgical status

value: Placebo

value: Mesenchymal

tag: rpa

value: Grade IV

tag: who category

tag: dataset

value: TAMIGA


title: TAMIGA_05200122C0007R

value: On

tag: phillips subtype

value: Proneural

tag: tcga subtype

tag: mmse

tag: os cnsr (event = 1, censor = 0)


title: collagen 072h [8-CO_072h]

tag: tissue


title: No_collagen_240h [9-NOCO_240h]

value: no collagen


title: Sample 58_Single Dermal Fibroblast

tag: cell line

value: primary cell

tag: day of differentiation


title: TAMIGA_05200119C0007R

tag: age

tag: Sex

value: Partial resection

value: Proliferative

value: Classical

tag: kps

tag: os (diagnosis)

tag: mgmt status


title: UCLA_S2585

tag: treatment

value: Bevacizumab

value: Methylated


title: Sample 60_Single Dermal Fibroblast


title: No_collagen _072h [7-NOCO_072h]

value: Human islet

tag: host strain

tag: molecule subtype


title: Sample 56_Single Dermal Fibroblast


title: Sample 61_Single Dermal Fibroblast


title: TAMIGA_05200105C0007R

tag: corticosteroids

tag: surgical status

tag: rpa

tag: who category


title: UCLA_S10827

value: Control

tag: phillips subtype

tag: tcga subtype

value: Non-methylated


title: TAMIGA_05200102B0016R

value: Female

value: Off

value: Total resection

tag: mmse

tag: os cnsr (event = 1, censor = 0)

tag: dataset


title: UCLA_S10693

tag: age

value: Male

value: Mesenchymal


title: TAMIGA_05200101C0007R

tag: Sex

value: missing

value: Biopsy

value: Grade V

value: TAMIGA


title: UCLA_S10794

value: Proneural

tag: kps


title: collagen 24h [6-CO_024h]

tag: tissue

value: collagen

value: Exosomal RNA


title: Sample 57_Single Dermal Fibroblast

tag: cell line

value: primary cell

tag: day of differentiation


title: Sample 55_Single Dermal Fibroblast


title: UCLA_S10690

tag: treatment

tag: os (diagnosis)

tag: mgmt status


title: TAMIGA_05200098C0007R

tag: corticosteroids

tag: surgical status

value: Partial resection

value: Bevacizumab

value: Grade IV


title: No_collagen_24h [5-NOCO_024h]

value: Human islet

value: no collagen

tag: host strain

tag: molecule subtype


title: Sample 59_Single Dermal Fibroblast


title: TAMIGA_05200107C0017R

value: Off

tag: phillips subtype

value: Unclassified

tag: tcga subtype

value: Classical

tag: rpa

tag: who category


title: Sample 54_Single Dermal Fibroblast


title: Sample 53_Single Dermal Fibroblast


title: collagen 12h [4-CO_012h]


title: TAMIGA_05200091B0016R

tag: age

value: Female

value: Mesenchymal

tag: mmse

tag: os cnsr (event = 1, censor = 0)

tag: dataset


title: UCLA_S10506

tag: Sex

value: Male

value: Biopsy

value: Control

tag: kps

value: Non-methylated


title: No_collagen_12h [3-NOCO_012h]

tag: tissue

tag: treatment


title: UCLA_S10824

value: Total resection

value: Proliferative

tag: os (diagnosis)

tag: mgmt status


title: Sample 52_Single Dermal Fibroblast

tag: cell line

value: primary cell

tag: day of differentiation


title: collagen 6h [2-CO006h]

value: collagen

tag: host strain

tag: molecule subtype

value: Exosomal RNA


title: TAMIGA_05200090C0007R

tag: corticosteroids

value: On

tag: surgical status

tag: phillips subtype

tag: tcga subtype

value: Grade V

value: TAMIGA


title: UCLA_S10485

tag: age

value: Methylated


title: Sample 51_Single Dermal Fibroblast


title: Sample 50_Single Dermal Fibroblast


title: No_collagen_6h [1-NOCO006h]

value: Human islet

value: no collagen


title: UCLA_S10477

value: Partial resection

value: Classical

tag: os cnsr (event = 1, censor = 0)


title: UCLA_S10402

value: Male

value: Unclassified


title: ERCC3WT/R109X irofulven_biological replicate 7

city: New York

first: Sabine

last: Topka

state: NY

address: 417 E. 68Th St.Zuckerman Research Bldg.

department: Medicine

institute: MSKCC

description:
HMLE cell line-derived ERCC3WT/R109X tumor from irofulven treated mouse, biological replicate 7
Proj_08988_htseq_all_samples.csv

data_processing:
On average, 86 million paired reads were generated per sample and 36% of the data mapped to the transcriptome.
The output data (FASTQ files) were mapped to the human genome, converted to BAM format and expression count matrix generated from the mapped reads using HTSeq (https://htseq.readthedocs.io/en/release_0.11.1/).
Read counts were normalized for individual transcript lengths, log transformed, and differential gene expression analysis was performed using the R package DeSeq2
Genome_build: hg19
Supplementary_files_format_and_content: csv files containing gene counts and differnetial gene expression results

source_name: HMLE

growth_protocol: Isogenic cell line xenografts were generated by injecting 10 million hRAS-V12 driven ERCC3 wildtype or heterozygous R109X mutant HMLE cells together with matrigel (50:50) subcutaneously in 6-week-old athymic female mice.

extract_protocol:
Fresh frozen tumor tissues were subsequently preserved in RNAlater (Invitrogen) and RNA was extracted using the RNeasy Midi Kit (Qiagen). After RiboGreen quantification and quality control by Agilent BioAnalyzer, 0.99-1ug of total RNA with an RNA integrity number varying from 3.8-10 underwent ribosomal depletion.
Library preparation was performed using the TruSeq Stranded Total RNA LT Kit (Illumina catalog # RS-122-1202) according to instructions provided by the manufacturer with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000 in a 100bp/100bp paired end run, using the HiSeq 3000/4000 SBS Kit (Illumina).

treatment_protocol: Once tumors reached an average volume of 100 mm3, mice (8-10 mice/group) were randomized to receive either vehicle or irofulven 3.5 mg/kg i.p. for 5 consecutive days. The treatment cycle was repeated every 21 days for a total of three cycles.

tag: cell type

value: mammary epithelial cells

tag: genotype

value: ERCC3 WT/R109X

value: Irofulven 3.5 mg/kg i.p


title: TAMIGA_05200076B0017R

tag: Sex

value: Bevacizumab

value: Proneural

tag: kps

tag: mmse

tag: rpa

value: Grade IV

tag: who category

tag: dataset


title: TAMIGA_05200075B0016R

tag: treatment

tag: os (diagnosis)

tag: mgmt status


title: UCLA_S10366

value: Total resection

value: Control

value: Non-methylated


title: Sample 49_Single Dermal Fibroblast

tag: cell line

value: primary cell

tag: day of differentiation


title: ERCC3WT/R109X irofulven_biological replicate 6

description:
HMLE cell line-derived ERCC3WT/R109X tumor from irofulven treated mouse, biological replicate 6
Proj_08988_htseq_all_samples.csv


title: Sample 48_Single Dermal Fibroblast


title: Sample 47_Single Dermal Fibroblast


title: ERCC3WT/R109X irofulven_biological replicate 5

description:
HMLE cell line-derived ERCC3WT/R109X tumor from irofulven treated mouse, biological replicate 5
Proj_08988_htseq_all_samples.csv


title: TAMIGA_05200074C0007R

tag: corticosteroids

value: Off

tag: surgical status

tag: phillips subtype

value: Proliferative

value: TAMIGA


title: UCLA_S10273

tag: age

tag: tcga subtype

tag: os cnsr (event = 1, censor = 0)


title: TAMIGA_05200070B0011R

tag: Sex

value: Grade III


title: UCLA_S10087

value: Mesenchymal

tag: kps

value: Methylated


title: Sample 46_Single Dermal Fibroblast


title: ERCC3WT/R109X irofulven_biological replicate 4

description:
HMLE cell line-derived ERCC3WT/R109X tumor from irofulven treated mouse, biological replicate 4
Proj_08988_htseq_all_samples.csv

tag: cell type

tag: genotype


title: TAMIGA_05200087C0007R

value: Female

value: Biopsy

value: Classical

tag: mmse

tag: rpa

value: Grade V

tag: who category


title: Sample 45_Single Dermal Fibroblast


title: ERCC3WT/R109X irofulven_biological replicate 2

description:
HMLE cell line-derived ERCC3WT/R109X tumor from irofulven treated mouse, biological replicate 2
Proj_08988_htseq_all_samples.csv

value: mammary epithelial cells

value: ERCC3 WT/R109X

tag: treatment

value: Irofulven 3.5 mg/kg i.p


title: TAMIGA_05200069C0007R

value: Male

value: Partial resection

tag: os (diagnosis)

tag: mgmt status

tag: dataset


title: ERCC3WT/R109X irofulven_biological replicate 1

description:
HMLE cell line-derived ERCC3WT/R109X tumor from irofulven treated mouse, biological replicate 1
Proj_08988_htseq_all_samples.csv


title: Sample 44_Single Dermal Fibroblast

tag: cell line

tag: day of differentiation


title: ERCC3WT/R109X irofulven_biological replicate 3

description:
HMLE cell line-derived ERCC3WT/R109X tumor from irofulven treated mouse, biological replicate 3
Proj_08988_htseq_all_samples.csv


title: Sample 43_Single Dermal Fibroblast


title: Glarius_GLARIUS_9_10

hyb_protocol: Per NanoString Total RNA Standard Protocol for formalin-fixed, paraffin-embedded (FFPE) samples

data_processing:
Raw data were preprocessed using functions from NanoStringQCPro R package in particular positive control normalisation, background correction (using both water samples and negative control probes) and RNA content normalisation (median normalisation). Prior to clustering analysis, sample-wise normalization was performed by transforming counts to the log2 scale and subtracting the sample-wise mean of housekeeping genes.
Water samples (used for the normalisation) using the NanoStringQCPro package on Bioconductor.

tag: surgical status

value: Total resection

value: TEMOZOLOMIDE

tag: phillips subtype

value: Unclassified

value: Non-methylated


title: Glarius_GLARIUS_9_12

tag: age

tag: tcga subtype


title: TAMIGA_05200064B0016R

tag: Sex

tag: corticosteroids

value: Off

value: Bevacizumab

value: Proliferative

tag: os cnsr (event = 1, censor = 0)

value: TAMIGA


title: ERCC3WT/R109X vehicle_biological replicate 8

description:
HMLE cell line-derived ERCC3WT/R109X tumor from vehicle treated mouse, biological replicate 8
Proj_08988_htseq_all_samples.csv

tag: cell type

tag: genotype

value: vehicle:1% EtOH in D5W


title: UCLA_S10336

value: Female

value: Control

value: Mesenchymal

tag: kps


title: TAMIGA_05200065B0016R

value: On

value: Biopsy

value: Classical

tag: mmse

tag: rpa

value: Grade V

tag: who category


title: TAMIGA_05200066B0016R

value: Male

value: Partial resection

tag: treatment

value: Proneural

tag: os (diagnosis)

tag: mgmt status


title: Sample 42_Single Dermal Fibroblast

tag: cell line

value: primary cell

tag: day of differentiation


title: ERCC3WT/R109X vehicle_biological replicate 7

description:
HMLE cell line-derived ERCC3WT/R109X tumor from vehicle treated mouse, biological replicate 7
Proj_08988_htseq_all_samples.csv

value: mammary epithelial cells

value: ERCC3 WT/R109X


title: Sample 41_Single Dermal Fibroblast


title: Glarius_GLARIUS_9_09

tag: surgical status

value: Total resection

value: TEMOZOLOMIDE

tag: phillips subtype

value: Non-methylated


title: TAMIGA_05200063B0016R

tag: age

value: Off

tag: tcga subtype

value: Grade IV

tag: dataset

value: TAMIGA


title: TAMIGA_05200062C0007R

tag: Sex

tag: corticosteroids

tag: os cnsr (event = 1, censor = 0)


title: Sample 40_Single Dermal Fibroblast


title: Glarius_GLARIUS_9_07

value: BEVACIZUMAB+IRINOTECAN


title: TAMIGA_05200058C0007R

value: Female

value: On

tag: kps


title: Sample 39_Single Dermal Fibroblast


title: TAMIGA_05200055B0016R

value: Mesenchymal

value: Classical

tag: mmse


title: Glarius_GLARIUS_9_11

value: Male


title: Glarius_GLARIUS_9_06

value: Partial resection


title: ERCC3WT/R109X vehicle_biological replicate 4

description:
HMLE cell line-derived ERCC3WT/R109X tumor from vehicle treated mouse, biological replicate 4
Proj_08988_htseq_all_samples.csv

tag: cell type

tag: genotype

value: vehicle:1% EtOH in D5W


title: TAMIGA_05200054B0016R

tag: treatment

value: Bevacizumab

tag: rpa

value: Grade III

tag: who category


title: Glarius_GLARIUS_8_11

tag: os (diagnosis)

tag: mgmt status


title: ERCC3WT/R109X vehicle_biological replicate 3

description:
HMLE cell line-derived ERCC3WT/R109X tumor from vehicle treated mouse, biological replicate 3
Proj_08988_htseq_all_samples.csv

value: mammary epithelial cells

value: ERCC3 WT/R109X


title: ERCC3WT/R109X vehicle_biological replicate 2

description:
HMLE cell line-derived ERCC3WT/R109X tumor from vehicle treated mouse, biological replicate 2
Proj_08988_htseq_all_samples.csv


title: Glarius_GLARIUS_9_08

tag: surgical status

value: Total resection

value: Proliferative


title: Glarius_GLARIUS_8_10

tag: phillips subtype

value: Non-methylated


title: TAMIGA_05200050C0007R

tag: age

value: Off

value: Unclassified

value: Grade V


title: ERCC3WT/R109X vehicle_biological replicate 1

description:
HMLE cell line-derived ERCC3WT/R109X tumor from vehicle treated mouse, biological replicate 1
Proj_08988_htseq_all_samples.csv


title: Glarius_GLARIUS_8_09

value: BEVACIZUMAB+IRINOTECAN

value: Proneural

tag: tcga subtype


title: Sample 36_Single Dermal Fibroblast

tag: cell line

value: primary cell

tag: day of differentiation


title: Sample 35_Single Dermal Fibroblast


title: ERCC3WT/WT irofulven_biological replicate 7

description:
HMLE cell line-derived ERCC3WT/WT tumor from irofulven treated mouse, biological replicate 7
Proj_08988_htseq_all_samples.csv

value: ERCC3 WT/WT

value: Irofulven 3.5 mg/kg i.p


title: Glarius_GLARIUS_8_08

tag: Sex

value: Male

value: Partial resection

value: Classical


title: ERCC3WT/R109X vehicle_biological replicate 6

description:
HMLE cell line-derived ERCC3WT/R109X tumor from vehicle treated mouse, biological replicate 6
Proj_08988_htseq_all_samples.csv

value: vehicle:1% EtOH in D5W


title: Sample 34_Single Dermal Fibroblast


title: ERCC3WT/R109X vehicle_biological replicate 5

description:
HMLE cell line-derived ERCC3WT/R109X tumor from vehicle treated mouse, biological replicate 5
Proj_08988_htseq_all_samples.csv

value: mammary epithelial cells


title: TAMIGA_05200038B0016R

value: Female

tag: corticosteroids

tag: os cnsr (event = 1, censor = 0)

tag: dataset

value: TAMIGA


title: TAMIGA_05200037C0017R

value: Total resection

value: Placebo

tag: kps

tag: mmse

value: Grade NA