title: iCLIP_SRSF6_Norm_Rep1.fq.gz

description: iCLIP


title: spt650-4alpha-MCM-IP

status: Public on Jan 03 2023

type: SRA

city: Boston

first: Catherine

middle: LW

last: Miller

state: MA

address: 77 Ave Louis Pasteur

country: USA

institute: Harvard Medical School

description: his3D200 lys2-128d ura3-52 leu2D0 bar1D::URA3 spt6-50

library_source: genomic

data_processing:
Briefly, data was aligned to a combined S. cerevisiae + S. pombe genome using Bowtie2 (Langmead and Salzberg, 2012). Sequences were trimmed with cutadapt and processed using samtools (Li et al., 2009), bedtools, and deeptools (Ramírez et al., 2016) to generate genome coverage tracks. Samples are spike-in normalized.
Assembly: S. cerevisiae R64-2-1, S. pombe ASM294v2

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol: All S. cerevisiae strains used in this study are in the S288C background. All S. cerevisiae liquid cultures were grown in YPD (1% yeast extract, 2% peptone, 2% glucose) at 30°C . For spike-in normalization, S. pombe liquid cultures were grown in YES (0.5% yeast extract, 3% glucose, 225 mg/l each of adenine, histidine, leucine, uracil, and lysine) at 32°C.

extract_protocol: Libraries were prepared with Qiagen GeneRead Kit according to manufacturers instructions.

treatment_protocol: Yeast strains were grown to an OD~0.2 and then synchronized by treatment with alpha factor for 2 hours. Visual inspection confirmed >90% of cells had shmoo-like morphology.

tag: cell type

value: S. cerevisiae (S. pombe spike-in)

tag: treatment

value: alpha arrested


title: spt650-3alpha-MCM-IP

source_name: his3D200 lys2-128d ura3-52 leu2D0 bar1D::URA3 spt6-50


title: spt650-2alpha-MCM-IP


title: iCLIP_SRSF6_Hyp24h_Rep3.fq.gz

city: Frankfurt am Main

first: Michaela

last: Müller-McNicoll

address: Max-von-Laue-Str. 13

country: Germany

institute: Goethe University Frankfurt

description: iCLIP

library_source: transcriptomic

data_processing:
iCLIP data were processed according to: Busch et al. (2020): iCLIP data analysis: A complete pipeline from sequencing reads to RBP binding sites. Methods PMID:31751605
Assembly: hg38
Supplementary files format and content: BW files containing the genomic coordinates and counts of uniquely mapped X-links for each replicate separated by strand. Bed files containing the genomic coordinates and counts of reproducible binding sites from merged replicates over all conditions.

molecule: total RNA

organism: Homo sapiens

source_name: HeLa

growth_protocol: Cells were grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum and pennicilin/streptomycin antibiotics at 37˚C with 5% CO2 and 21% oxygen (Normoxia) or 0.2% oxygen (Hypoxia).

extract_protocol:
Cells were lysed and treated with RNase I. GFP-tagged proteins were immunoprecipitated with Gamma binding beads coupled to goat anti-EGFP antibody.
After stringent washing, RNA was dephosphorylated and ligated to a 3' linker. Protein-RNA complexes were resolved by denaturing gel electrophoresis and transfered to nitrocellulose membrane. A membrane region above the expected size of the protein was cut and RNA was released by Proteinase K treatment. RNA was reverse transcribed using reverse primer containing a barcode sequence. cDNA was size selected by denaturing gel electrophoresis and circularized by ssDNA circligase. A specific oligonucleotide was annealed to create a restriction site for BamHI and cDNA was linearized by digest with BamHI. Linearized cDNA was PCR amplifiied with Solexa sequencing primers to create the final libraries. For more details see: Huppertz et al., (2014): iCLIP: protein-RNA interactions at nucleotide resolution. Methods. PMID:24184352

treatment_protocol: Cells were washed with PBS and irradiated with 254 nm UV light to crosslink proteins to nucleic acids.

tag: cell line

value: HeLa

tag: antibody

value: anti-EGFP

tag: protocol

value: SRSF6-GFP Hypoxia 24h

tag: barcode sequence


title: A23-BrainMet-2-R0i_CP-1168

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

description: HiSeq2000 (HS)

data_processing:
(If necessary) merge multiple FASTQs together
Maps the data with STAR 2.7.6a
Quantifies the expression with Salmon 1.4.0
QC: (1) Create a sorted bam with samtools sort 1.10, (2) Picard 2.22.4 CollectRnaSeqMetrics, (3) Calculate max read length, flagstat, and a few other metrics, (4) With the unsorted bam, run FastQC 0.11.9
Once all of that is done per sample, a set of summary processes create cohort-wide matrices for expression, normalized expression
Genome_build: CGRh38/hg38 genome
Supplementary_files_format_and_content: (1) Raw read counts (salmon_gene.matrix_RAP101_plus_Normals24.txt)
Supplementary_files_format_and_content: (2) Raw read counts normalized to a fixed upper quartile (salmon_gene_normalized.matrix_RAP101_plus_Normals24.txt)

molecule: polyA RNA

source_name: Brain metastasis

extract_protocol:
Tumor tissue was disrupted using roto-stator homogenization. RNA was isolated using the RNeasy Mini Kit (QUIAGEN) according to manufacturer protocol. RNA was quantified using a NanoDrop® Spectrophotometer,  and the quality of RNA was  then  analyzed  via  2100 Bioanalyzer Instrumentwhich  using the  RNA 6000 Nano  assay (Agilent)  for determination  of  an  RNA  Integrity  Number  (RIN).
Briefly, 1 μg of total RNA was converted to RNAseq libraries using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina) and sequenced on an Illumina HiSeq 2000 or HiSeq2500 using a 2x50bp configuration

value: Metastatic breast cancer

tag: tissue type

value: Fresh frozen


title: A21-LivMet-3-R0i_CP-1159

description: HiSeq2000 (HS)

source_name: Liver metastasis


title: A23-BrainMet-3-R0i_CP-1169

description: HiSeq2000 (HS)


title: iCLIP_SRSF6_Hyp24h_Rep2.fq.gz

description: iCLIP


title: iCLIP_SRSF6_Hyp24h_Rep1.fq.gz

description: iCLIP


title: A21-LivMet-2-R0i_CP-1160

description: HiSeq2000 (HS)


title: spt650-1alpha-MCM-IP


title: spt6YW-3alpha-MCM-IP

description: his3D200 lys2-128d ura3-52 leu2D0 bar1D::URA3 spt6-YW


title: A21-AdrenalMet-R0i_CP-1158

description: HiSeq2000 (HS)

source_name: Adrenal metastasis


title: A20-PrimT-FFPER0i_CP-1247

description: HiSeq2000 (HS)

source_name: Primary breast tumor

value: Primary breast cancer

value: Formalin-Fixed Paraffin-Embedded


title: spt6YW-4alpha-MCM-IP

source_name: his3D200 lys2-128d ura3-52 leu2D0 bar1D::URA3 spt6-YW


title: spt6YW-1alpha-MCM-IP


title: iCLIP_SRSF6_Hyp4h_Rep1.fq.gz

description: iCLIP

value: SRSF6-GFP Hypoxia 4h


title: WT-4alpha-MCM-IP

description: his3D200 lys2-128d ura3-52 leu2D0 bar1D::URA3


title: WT-2alpha-input

source_name: his3D200 lys2-128d ura3-52 leu2D0 bar1D::URA3


title: A19-04PrimT1-FFPER0i_CP-1244

description: HiSeq2000 (HS)


title: A19-04PrimT2-FFPER0i_CP-1245

description: HiSeq2000 (HS)


title: A18-MuscleMet-R0i_CP-1162

description: HiSeq2000 (HS)

source_name: Muscle metastasis


title: WT-1alpha-MCM-IP


title: WT-2alpha-MCM-IP


title: A17-9ChestMet-R0i_CP-1161

description: HiSeq2000 (HS)

source_name: Chest metastasis


title: TMAO-treated rep3

city: Philadelphia

first: Fatma

last: Saaoud

state: PA

address: 3500 N. Broad St

institute: Temple University

data_processing:
FASTQC were used to check the quality of sequencing data. kallisto v0.44.0 and Rstudio were used to quantify abundances of transcripts.
Sequenced reads were mapped to Homo_sapiens.GRCh38.p13.cdna.all.fa using kallisto with parameters quant -i transcripts.idx -o output -b 100 reads_1.fastq.gz reads_2.fastq.gz
Data were filtered using [rowSums(Txi_gene$counts)>=10,] as cutoff (done after DEG calculation).
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include gene counts values for each Sample ...

source_name: HAECs

extract_protocol:
HAECs were treated with TMAO and directly lysed in TRIzol, and RNA was harvested using miRNeasy Mini kit.
Total RNA libraries were prepared by using Pico Input SMARTer Stranded Total RNA-Seq Kit (Takara). In short, 250 pg -10 ng total RNA from each sample was reverse-transcribed via random priming and reverse transcriptase. Full-length cDNA was obtained with SMART (Switching Mechanism At 5' end of RNA Template) technology. The template-switching reaction was used to keep the strand orientation of the RNA. The ribosomal cDNA was hybridized to mammalian-specific R-Probes and then cleaved by ZapR. Libraries containing Illumina adapter with TruSeq HT indexes were subsequently pooled and loaded to the Hiseq 2500. Single end reads at 75 bp with 30 million reads per sample were generated for bioinformatic analysis.

value: human aortic endothelial cells (HAECs)

value: TMAO


title: A11-PrimT-FFPER0i_CP-1358

description: HiSeq2000 (HS)


title: TMAO-treated rep2


title: A8-OvaryMet-R0i_CP-1167

description: HiSeq2000 (HS)

source_name: Ovary metastasis


title: TMAO-treated rep1


title: A4-LULungMet-R0i_CP-1166

description: HiSeq2000 (HS)

source_name: Lung metastasis


title: A2-LungMet-R0i_CP-1165

description: HiSeq2000 (HS)


title: Control rep2

value: No treatment


title: A2-LN-Met-subcarinall-R0i_CP-1164

description: HiSeq2000 (HS)


title: Control rep3


title: Control rep1


title: human normal breast total RNA expression [AUR-AE5G-NT1-A-1-1-R-A742-41]

city: Pittsburgh

first: Uma

last: Chandran

address: 5150 Center Ave

department: BioMedical Informatics

institute: University of Pittsburgh

description:
Fresh frozen
AUR-AE5G-NT1-A-1-1-R-A742-41

data_processing:
Quality-control-passed reads were aligned to the human reference CGRh38/hg38 genome using STAR.
Transcript abundance estimates for each sample were performed using Salmon, an expectation-maximization algorithm using the UCSC gene definitions.
Raw read counts for all RNAseq samples were normalized to a fixed upper quartile (UQN).
Assembly: CGRh38/hg38 genome
Supplementary files format and content: Two tab-delimited text files include (1) unnormalized data (raw counts) and (2) upper quartile normalized (UQN) data for each sample.

source_name: Normal tissue

growth_protocol: Pathology quality control was performed on each tumor specimen and normal tissue specimen as an initial QC step.

extract_protocol:
RNA was extracted from frozen tissues using a modification of the AllPrep DNA/RNA kit (Qiagen). RNA was also extracted from FFPE solid tissues using a modification of the AllPrep DNA/RNA FFPE kit (Qiagen). RNA samples were quantified by measuring Abs260 with a UV spectrophotometer. RNA was analyzed via the RNA6000 Nano assay (Agilent) for the determination of an RNA Integrity Number (RIN). Only cases yielding a minimum of 500ng of tumor RNA were included in this study.
Gene expression profiles from primary and metastatic tumors for AURORA dataset were generated by RNA-sequencing using an Illumina HiSeq and a rRNA-depletion method. Briefly, 300-500ng total RNA was converted to RNAseq libraries using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina) and sequenced on an Illumina HiSeq 2500 using a 2x50bp configuration

treatment_protocol:
Hematoxylin and Eosin (H&E) stained sections from each sample were subjected to independent pathology review to confirm that the tumor specimen was histologically consistent to the reported histology
The percent rumor nuclei, percent necrosis, and other pathology annotations were also assessed. Tumor samples with ≥30% tumor nuclei, and normal tissue with 0% tumor nuclei, were submitted for nucleic acid extraction

tag: disease

value: Normal tissue

tag: tissue

value: Breast

tag: genotype

value: Female

tag: time

value: Non-Autopsy


title: A1-AxLN-Met-R0i_CP-1163

description: HiSeq2000 (HS)

source_name: Lymph node metastasis


title: A19-07-LN-Met-FFPER0i_CP-1246

description: HiSeq2000 (HS)


title: human normal lung total RNA expression [AUR-AFE6-NT1-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AFE6-NT1-A-1-1-R-A742-41

value: Lung

value: Autopsy


title: WT-3alpha-MCM-IP

value: S. cerevisiae (S. pombe spike-in)

value: alpha arrested


title: HaCaT cells, K-Chipseq

city: Changsha

first: Liao

last: yuan

state: Hunan

address: 139 renmin zhong lu, furong district

department: dermatology department

country: China

institute: Second Xiang Ya Hospital of Central South University

data_processing:
The original image data files obtained by high-throughput sequencing were transformed into original sequencing sequences by CASAVA Base Calling analysis.
The quality of raw reads was analyzed by FastQC
Fastp software was used to trim the sequencing connectors and low quality fragments of sequencing data
BWA (Burrows Wheeler Aligner) was used to match reads to the reference genome (Li, h. and r. Durbin, 2009).
For double-ended sequencing, we used RSeQC software to predict fragment sizes (fragment_sizes) for IP experiments.
Peak calling was performed using MACS2 software (Yong Zhang,Tao Liu et al., 2008) (qvalue<=0.05)
Genome_build: hg38
Supplementary_files_format_and_content: bigwig

source_name: Hacat cell

growth_protocol: cultured in DMEM (Gibco，Grand Island，USA) with 10% foetal bovine serum (FBS, HyClone) and 1% penicILlin (Solarbio ,China). The cells were mantained in a 37°C humidified air incubator with 5% CO2.

extract_protocol:
Lysates were clarified from sonicated Hacat cell and transcription factors-DNA complexes were isolated with antibody.
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Hacat was transfected with WT1 overexpressed plasmids

value: skin

value: Hacat cell

value: Normal human skin immortalized keratinocytes

value: control

tag: chip antibody

value: DYKDDDDK Tag (D6W5B) Rabbit mAb(Cell Signaling Technology, USA,catalog #147934)


title: HaCaT cells, K input DNA


title: HaCaT cells, WT1 input DNA

value: overexpressing WT1


title: HaCaT cells, WT1-Chipseq


title: 622

city: Washington

first: Timothy

last: McCaffrey

state: DC

address: 2300 I Street NW

department: Department of Biochemisty & Molecular Biology

institute: The George Washington University

data_processing:
Concatentate 4 lanes of forward reads
Concatentate 4 lanes of reverse reads
Trim ends using trimmomatic
align to HG38 genome using STAR aligner v 2.5.2b
Use quantMode Gene Counts
Assembly: HG38
Supplementary files format and content: single Excel file .xlsx with one patient per column
Supplementary files format and content: expression level is Transcripts per Million (TPM)

source_name: Whole blood

extract_protocol:
Tempus Spin RNA Isolation Kit
Turbo DNAse treatment and RiboZero Depletion
Illumina TruSeq Stranded Total RNA kit
High-Output 2x75 bp kit on NextSeq 500

treatment_protocol: Tempus preserved whole human blood

value: Whole blood

tag: disease state

value: Coronary Artery Disease

tag: Sex

value: M

tag: age

tag: bmi

tag: sbp

tag: dbp

tag: hr

tag: ef %

tag: dyslipidemia

value: Yes

tag: hypertension

tag: diabetes mellitus

value: No

tag: family history_of_cad

tag: smoking

value: Former

tag: asa

value: Y

tag: cad

value: CAD

tag: %stenosis

tag: rnaseq group


title: human breast cancer total RNA expression [AUR-AFUG-TTM1-A-1-1-R-A743-41]

description:
Fresh frozen
AUR-AFUG-TTM1-A-1-1-R-A743-41

source_name: Metastatic tumor

tag: disease

value: Metastatic tumor

tag: tissue

value: Chest

tag: genotype

value: Female

tag: treatment

value: Metastasis

tag: time

value: Non-Autopsy


title: 496

tag: disease state

tag: Sex

value: F

tag: age

tag: bmi

tag: sbp

tag: dbp

value: Never

value: MID


title: human breast cancer total RNA expression [AUR-AD9F-TTM2-A-1-1-R-A542-39]

description:
Fresh frozen
AUR-AD9F-TTM2-A-1-1-R-A542-39

value: Lymph node

value: Autopsy


title: 621

value: Whole blood

value: Coronary Artery Disease

tag: hr

tag: ef %

tag: dyslipidemia

tag: hypertension

tag: diabetes mellitus

tag: family history_of_cad

value: N

value: LOW


title: human breast cancer total RNA expression [AUR-AD9F-TTM1-A-1-1-R-A542-39]

description:
Fresh frozen
AUR-AD9F-TTM1-A-1-1-R-A542-39

tag: disease

value: Liver


title: Cerebellum, simulated reads, GTEX-1HBPI

first: Yoseph

last: Barash

state: Pennsylvania

address: 3700 Hamilton Walk

department: Genetics

institute: University of Pennsylvania

data_processing:
Publicly available gene- and transcript-level quantifications were downloaded from the GTEx v8 portal for each of the 300 samples
Simulated paired-end fastq files were generated by the BEERS simulator (Grant et al., 2011) using the reference hg38 genome sequence, transcript models from GENCODE v26, and the publicly available TPM values for the transcripts from each donor. Simulated read depth was determined by the gene-level quantification table to count the total number of gene mapping reads for each sample. To simulate strand-specific reads with uniform coverage with no errors, substitutions, or intron retention events, we ran the BEERS simulator using the following command-line options: -strandspecific -outputfq -error 0 -subfreq 0 -indelfreq 0 -intronfreq 0 -palt 0 -fraglength 100,250,500.
Simulated fastq files were aligned to the hg38 genome assembly using STAR (v2.5.3a) and transcript abundances were estimated using Salmon (v0.14.0)
Assembly: hg38
Supplementary files format and content: tab-deliminated text files including Salmon TPM quantifications for each sample

source_name: Cerebellum (simulated)

extract_protocol: simulated RNA-seq

tag: tissue

value: Cerebellum (simulated)

value: WT


title: 494

value: M

value: Yes

value: No

tag: smoking

tag: asa

value: Y

tag: cad

tag: %stenosis

tag: rnaseq group


title: 495

tag: disease state

tag: Sex

tag: age

value: Former

value: CAD


title: human breast cancer total RNA expression [AUR-AD9F-TTM3-A-1-1-R-A542-39]

description:
Fresh frozen
AUR-AD9F-TTM3-A-1-1-R-A542-39

value: Metastatic tumor

value: Adrenal

tag: genotype

value: Female

tag: treatment

value: Metastasis

tag: time


title: human normal liver total RNA expression [AUR-AFE4-NT1-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AFE4-NT1-A-1-1-R-A742-41

value: Normal tissue

value: Autopsy


title: Brain, pMCAO, 3 days, rep2

city: Kuopio

first: Nea

last: Korvenlaita

address: Neulaniementie 2

country: Finland

institute: University of Eastern Finland

description: small RNA

data_processing:
Quality check with fastqc and extraction of reads between 18-30bp
Alignment with bowtie
Producing the count with HTSeq (GTF downloaded from miRbase)
Assembly: mm10
Supplementary files format and content: tab separated txt files containing counts for every miRNA

organism: Mus musculus

source_name: Brain, peri-ischemic cortex

extract_protocol:
Small RNAs were enriched from total RNA with the miRVana RNA extraction kit (ThermoFisher).
The Ion Total RNA-Seq Kit V2 (Life Technologies) was used to create small RNA libraries which were ligated to adapters containing a unique index barcode (Ion Xpress™ RNA-Seq Barcode 1-16 Kit, Life Technologies) according to the manufacturers’ protocol.

tag: strain

value: Balb/cOlaHsd

value: male

value: 3 months

value: Brain, peri-ischemic cortex

value: pMCAO

value: 3 days


title: Brain, pMCAO, 3 days, rep4

description: small RNA


title: human normal breast 2 total RNA expression [AUR-AFEC-NT1-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AFEC-NT1-A-1-1-R-A742-41

value: Breast


title: Brain, pMCAO, 3 days, rep3

description: small RNA


title: Brain, pMCAO, 3 days, rep5

description: small RNA


title: 493

value: Whole blood

value: Coronary Artery Disease

value: M

tag: bmi

tag: sbp

tag: dbp

tag: hr

tag: ef %

tag: dyslipidemia

value: No

tag: hypertension

value: Yes


title: Brain, pMCAO, 3 days, rep1

description: small RNA

tag: tissue


title: human breast cancer total RNA expression [AUR-AD9H-TTM2-A-1-1-R-A542-39]

description:
Fresh frozen
AUR-AD9H-TTM2-A-1-1-R-A542-39

tag: disease

value: Metastatic tumor

value: Liver


title: 492

value: F

tag: diabetes mellitus

tag: family history_of_cad

tag: smoking

value: Never

tag: asa

value: N

tag: cad

value: LOW

tag: %stenosis

tag: rnaseq group


title: human normal brain total RNA expression [AUR-AFE5-NT1-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AFE5-NT1-A-1-1-R-A742-41

value: Normal tissue

value: Brain

tag: genotype

value: Female

tag: treatment

tag: time

value: Autopsy


title: 490

tag: disease state

tag: Sex

tag: age

tag: bmi

tag: sbp

tag: dbp

value: Y

value: CAD


title: human breast cancer total RNA expression [AUR-AD9H-TTM3-A-1-1-R-A542-39]

description:
Fresh frozen
AUR-AD9H-TTM3-A-1-1-R-A542-39

tag: disease

tag: tissue

value: Metastasis


title: Brain, Sham, 3 days, rep4

description: small RNA

source_name: Brain, cortex

tag: strain

value: Balb/cOlaHsd

value: male

value: 3 months

value: Brain, cortex

value: Sham

value: 3 days


title: Brain, Sham, 3 days, rep6

description: small RNA


title: human breast cancer total RNA expression [AUR-AFUK-TTM1-A-1-0-R-A743-41]

description:
Fresh frozen
AUR-AFUK-TTM1-A-1-0-R-A743-41

value: Metastatic tumor

value: Chest

value: Non-Autopsy


title: Brain, Sham, 3 days, rep5

description: small RNA


title: 489

value: Whole blood

value: Coronary Artery Disease

value: M

tag: hr

tag: ef %

tag: dyslipidemia

value: No

tag: hypertension

tag: diabetes mellitus

tag: family history_of_cad

tag: smoking

value: Former

value: N

value: LOW


title: human breast cancer total RNA expression [AUR-AD9E-TTM2-A-1-1-R-A542-39]

description:
Fresh frozen
AUR-AD9E-TTM2-A-1-1-R-A542-39

value: Lung

tag: genotype

value: Female

tag: treatment

value: Metastasis

tag: time

value: Autopsy


title: Brain, Sham, 3 days, rep3

description: small RNA

value: Balb/cOlaHsd

tag: Sex

value: male

tag: age

value: 3 months

value: Brain, cortex


title: Brain, Sham, 3 days, rep2

description: small RNA

value: Sham

value: 3 days


title: Brain, Sham, 3 days, rep1

description: small RNA


title: 488

value: Whole blood

tag: disease state

tag: bmi

tag: sbp

value: Never

tag: asa

tag: cad

tag: %stenosis

tag: rnaseq group


title: human normal brain 2 total RNA expression [AUR-AFE9-NT1-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AFE9-NT1-A-1-1-R-A742-41

tag: disease

value: Normal tissue

tag: tissue

value: Brain


title: SAMPLE 72

type: genomic

city: Haikou

first: peng

last: Huang

address: Haikou, Hainan province

institute: Department of Pediatrics, Haikou Hospital of the Maternal and Child Health, Haikou. 570100, China.

description: peripheral blood sample

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to the Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
The minif R package was used to process the original data and calculate the raw beta (β = the signal intensity of methylated probes divided by the overall signal intensity) value. Probes with the detection P-value ≤  0.01 were retained.
Matrix_processed_data: Normalized Average Beta( the Subset-quantile Within Array Normalization algorithm was performed to extract the normalized β).
Matrix_signal_intensities: Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: genomic DNA from  peripheral blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from peripheral blood samples using  DNA purification kit (QIAGEN, USA) following the manufacturer’s instructions

tag: gender

value: obesity

value: peripheral blood


title: human breast cancer total RNA expression [AUR-AD9E-TTM4-A-1-1-R-A542-39]

description:
Fresh frozen
AUR-AD9E-TTM4-A-1-1-R-A542-39

value: Metastatic tumor

value: Liver


title: SAMPLE 71

description: peripheral blood sample


title: 486

value: Coronary Artery Disease

value: M

tag: dbp

tag: hr

tag: ef %

tag: dyslipidemia

value: Yes

tag: hypertension

tag: diabetes mellitus

value: No

tag: family history_of_cad

value: Y

value: CAD


title: 485

tag: disease state

tag: Sex

tag: age

tag: smoking

value: Former

value: N

value: LOW


title: SAMPLE 69

description: peripheral blood sample

value: male


title: human breast cancer total RNA expression [AUR-AD9H-TTM1-A-2-1-R-A542-39]

description:
Fresh frozen
AUR-AD9H-TTM1-A-2-1-R-A542-39

value: Pleura

tag: genotype

value: Female

tag: treatment

value: Metastasis

tag: time

value: Autopsy


title: SAMPLE 68

description: peripheral blood sample

value: obesity

value: peripheral blood


title: human breast cancer total RNA expression [AUR-AFUK-TTM2-A-1-0-R-A743-41]

description:
Fresh frozen
AUR-AFUK-TTM2-A-1-0-R-A743-41

tag: disease

value: Metastatic tumor

value: Lymph node

value: Non-Autopsy


title: SAMPLE 66

description: peripheral blood sample

tag: tissue


title: human breast cancer total RNA expression [AUR-AFUP-TTM1-A-1-1-R-A743-41]

description:
Fresh frozen
AUR-AFUP-TTM1-A-1-1-R-A743-41

value: Ovary


title: human breast cancer total RNA expression [AUR-AD9E-TTM1-A-1-1-R-A542-39]

description:
Fresh frozen
AUR-AD9E-TTM1-A-1-1-R-A542-39

value: Soft tissue


title: SAMPLE 65

description: peripheral blood sample

tag: gender


title: SAMPLE 63

description: peripheral blood sample


title: 483

value: Whole blood

value: Coronary Artery Disease

value: M

tag: bmi

tag: sbp

tag: dbp

value: Yes

value: No

tag: asa

tag: cad

tag: %stenosis

tag: rnaseq group


title: SAMPLE 64

description: peripheral blood sample

value: male

tag: disease state


title: SAMPLE 62

description: peripheral blood sample

value: female


title: 482

tag: Sex

tag: hr

tag: ef %

tag: dyslipidemia

tag: hypertension

tag: diabetes mellitus

tag: family history_of_cad

value: Never

value: Y

value: MID


title: SAMPLE 60

description: peripheral blood sample

value: obesity

tag: tissue


title: human breast cancer total RNA expression [AUR-AD9I-TTM3-A-1-1-R-A542-39]

description:
Fresh frozen
AUR-AD9I-TTM3-A-1-1-R-A542-39

tag: disease

value: Liver

tag: genotype

value: Female

tag: treatment

value: Metastasis

tag: time

value: Autopsy


title: 481

value: F

tag: age

tag: bmi

tag: sbp

tag: dbp

tag: smoking

tag: asa

value: N

value: LOW


title: SAMPLE 61

description: peripheral blood sample

tag: gender

tag: disease state

value: peripheral blood


title: SAMPLE 59

description: peripheral blood sample


title: SAMPLE 58

description: peripheral blood sample


title: 480

value: Whole blood

value: Coronary Artery Disease

tag: Sex

tag: hr

tag: ef %

tag: dyslipidemia

tag: cad

tag: %stenosis

tag: rnaseq group


title: 479

tag: tissue

value: Yes

tag: hypertension

tag: diabetes mellitus

tag: family history_of_cad

value: No


title: human breast cancer total RNA expression [AUR-AERY-TTM1-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AERY-TTM1-A-1-1-R-A742-41

tag: disease

value: Metastatic tumor

tag: genotype

tag: treatment

tag: time

value: Non-Autopsy


title: SAMPLE 57

description: peripheral blood sample

tag: gender

value: female


title: human breast cancer total RNA expression [AUR-ADCB-TTM1-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-ADCB-TTM1-A-1-1-R-A742-41

value: Lung


title: SAMPLE 67

description: peripheral blood sample

tag: disease state

value: obesity


title: 484

tag: Sex

value: M

tag: age

tag: bmi

tag: sbp

tag: dbp

tag: smoking

value: Never

tag: asa


title: 478

tag: tissue

tag: hr

tag: ef %

tag: dyslipidemia

value: Former

tag: cad

tag: %stenosis

tag: rnaseq group


title: SAMPLE 54

description: peripheral blood sample


title: 477

tag: hypertension

tag: diabetes mellitus

tag: family history_of_cad

value: Y

value: MID


title: SAMPLE 70

description: peripheral blood sample

tag: gender

tag: disease state


title: human breast cancer total RNA expression [AUR-AFUO-TTP1-A-1-0-R-A741-41]

description:
FFPE
AUR-AFUO-TTP1-A-1-0-R-A741-41

source_name: Primary tumor

tag: disease

value: Primary tumor

value: Breast

tag: genotype

value: Female

tag: treatment

value: Pre-treatment

tag: time


title: SAMPLE 53

description: peripheral blood sample

value: male

value: peripheral blood


title: SAMPLE 52

description: peripheral blood sample


title: SAMPLE 51

description: peripheral blood sample


title: human breast cancer total RNA expression [AUR-AD9J-TTP1-B-4-0-R-A584-39]

description:
FFPE
AUR-AD9J-TTP1-B-4-0-R-A584-39

value: Autopsy


title: SAMPLE 56

description: peripheral blood sample


title: SAMPLE 50

description: peripheral blood sample


title: 476

value: Whole blood

value: Coronary Artery Disease

tag: Sex

tag: age

tag: bmi

tag: sbp

tag: dbp

value: Yes

value: No

tag: smoking

tag: asa


title: A_PFC_WT_3677

city: Stockholm

first: Anastasios

middle: Erik

last: Damdimopoulos

state: Huddinge

address: Hälsovägen 7c

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

data_processing:
The fastq files were generated after BCL conversion and demultiplexing using the bcl2fastq (v2.20.0.422) from Illumina
Fastq files were aligned to mus musculus reference genome (mm10 obtained from UCSC) using STAR_2.5.2b.
Reads in exons were counted using featureCounts v1.5.1 with mm10 entrez annotations obtained from UCSC
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text file with raw gene counts

source_name: PFC AAV-Cre WT

growth_protocol: Mice were maintained in a 129Ola/ICR/C57bl6 mixed genetic background. The mice were group-housed in a specific pathogen free stage with ad libitum access to food and water under a 12-h light-dark cycle (lights on at 6 a.m.) at relative humidity of 50-60 % and room temperature 21±1 °C. Bedding (aspen chips, Tapvei) and nest material (Tapvei) were changed weekly and wooden blocks (Tapvei) were provided for enrichment.

extract_protocol:
Adult male mice were deeply anesthetized with CO2, followed by cervical dislocation and decapitation. The brain was quickly dissected and immersed in ice-cold PBS. Brain regions of interest were isolated from 2-mm slices cut using a brain matrix. Samples were snap frozen and stored at -80 °C. Total RNA was isolated using Trizol Reagent (Thermo Fisher Scientific) according to manufacturer's recommendations. Total RNA was quality checked on an Agilent 2200 TapeStation system. RNA quantity was measured using a NanoDrop ND-1000 Spectrophotometer.Tissue collection and processing were performed by researchers blinded to the genotypes of the animals. In all experiments, wild-type littermates were used as controls.
200 ng RNA/sample was used for library preparation using TruSeq Stranded mRNA protocol (Illumina). The yield and quality of the amplified libraries was analysed using Qubit (Thermo Fisher) and the Agilent 2200 TapeStation system. The indexed cDNA libraries were normalised and combined, and the pools were sequenced on the Illumina Nextseq for a 75-cycle v2.5 sequencing run, generating 75 bp single-end reads.

tag: strain background

value: 129Ola/ICR/C57bl6 mixed

tag: strain

value: GDNF cKU +AAV-Cre

value: 5-7 months

value: wt/wt

value: bilateral striatal AAV-Cre injection at 3-5 months

tag: tissue

value: Brain

tag: tissue subtype

value: prefrontal cortex


title: SAMPLE 49

description: peripheral blood sample

tag: gender

value: female

value: obesity


title: human breast cancer total RNA expression [AUR-AFKD-TTP1-A-1-1-R-A742-41]

description:
FFPE
AUR-AFKD-TTP1-A-1-1-R-A742-41

value: Primary tumor

value: Breast

value: Female

value: Post-treatment


title: 474

value: Whole blood

tag: disease state

value: M

tag: hr

tag: ef %

tag: dyslipidemia

tag: hypertension

tag: diabetes mellitus

tag: family history_of_cad

value: Former

value: N

tag: cad

value: LOW

tag: %stenosis

tag: rnaseq group


title: SAMPLE 47

description: peripheral blood sample

value: peripheral blood


title: 475

value: Coronary Artery Disease

tag: Sex

tag: age

tag: bmi

tag: sbp

tag: dbp

value: Yes

value: No

tag: smoking

value: Y

value: MID


title: SAMPLE 46

description: peripheral blood sample

tag: gender

value: male

tag: tissue


title: human breast cancer total RNA expression [AUR-AFR2-TTP1-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AFR2-TTP1-A-1-1-R-A742-41

tag: disease

tag: genotype

tag: treatment

value: Pre-treatment

tag: time

value: Non-Autopsy


title: SAMPLE 44

description: peripheral blood sample

tag: disease state

value: obesity


title: SAMPLE 45

description: peripheral blood sample

value: female


title: human breast cancer total RNA expression [AUR-AER4-TTP1-A-1-0-R-A741-41]

description:
FFPE
AUR-AER4-TTP1-A-1-0-R-A741-41

value: Primary tumor

value: Breast

value: Female

value: Post-treatment

value: Autopsy


title: 472

value: Whole blood

value: F

tag: hr

tag: ef %

tag: dyslipidemia

tag: hypertension

tag: diabetes mellitus

tag: family history_of_cad

value: Never

tag: asa


title: human breast cancer total RNA expression [AUR-AE6X-TTP1-A-1-0-R-A741-41]

description:
FFPE
AUR-AE6X-TTP1-A-1-0-R-A741-41


title: SAMPLE 43

description: peripheral blood sample

value: peripheral blood


title: 473

value: Coronary Artery Disease

tag: Sex

value: M

tag: age

tag: bmi

tag: sbp

value: No

value: Yes

value: Former

tag: cad

value: CAD

tag: %stenosis

tag: rnaseq group


title: SAMPLE 48

description: peripheral blood sample

tag: gender

value: male

value: obesity

tag: tissue


title: SAMPLE 41

description: peripheral blood sample

value: female

tag: disease state


title: human breast cancer total RNA expression [AUR-AFR4-TTM1-A-1-1-R-A743-41]

description:
Fresh frozen
AUR-AFR4-TTM1-A-1-1-R-A743-41

tag: disease

value: Metastatic tumor

value: Brain

tag: genotype

tag: treatment

value: Metastasis

tag: time

value: Non-Autopsy


title: SAMPLE 55

description: peripheral blood sample


title: SAMPLE 40

description: peripheral blood sample


title: 471

value: Whole blood

tag: dbp

tag: hr

tag: ef %

tag: dyslipidemia

tag: hypertension

tag: diabetes mellitus

tag: smoking

value: Y


title: human breast cancer total RNA expression [AUR-AFR4-TTP1-A-1-1-R-A743-41]

description:
Fresh frozen
AUR-AFR4-TTP1-A-1-1-R-A743-41

value: Primary tumor

value: Breast

value: Female

value: Post-treatment


title: human breast cancer total RNA expression [AUR-AE6X-TTM1-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AE6X-TTM1-A-1-1-R-A742-41

value: Liver


title: 470

value: Coronary Artery Disease

tag: Sex

value: M

tag: age

tag: bmi

tag: sbp

value: No

value: Yes

tag: family history_of_cad

value: Never

tag: asa

tag: cad


title: SAMPLE 39

description: peripheral blood sample

tag: gender

value: female

tag: disease state

value: obesity

tag: tissue

value: peripheral blood


title: SAMPLE 42

description: peripheral blood sample

value: male


title: SAMPLE 36

description: peripheral blood sample


title: SAMPLE 37

description: peripheral blood sample


title: human breast cancer total RNA expression [AUR-AFE6-TTM2-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AFE6-TTM2-A-1-1-R-A742-41

tag: disease

value: Metastatic tumor

value: Lung

tag: genotype

tag: treatment

value: Metastasis

tag: time

value: Autopsy


title: 469

value: Whole blood

tag: dbp

tag: hr

tag: ef %

tag: dyslipidemia

tag: hypertension

value: N

value: LOW

tag: %stenosis

tag: rnaseq group


title: 468

tag: Sex

value: F

tag: age

tag: bmi

tag: sbp

tag: diabetes mellitus

tag: family history_of_cad

tag: smoking

value: Former


title: SAMPLE 34

description: peripheral blood sample

tag: gender

tag: disease state

tag: tissue


title: SAMPLE 33

description: peripheral blood sample


title: human breast cancer total RNA expression [AUR-AFE6-TTP1-A-1-0-R-A741-41]

description:
FFPE
AUR-AFE6-TTP1-A-1-0-R-A741-41

tag: disease

value: Primary tumor

value: Breast

tag: genotype

value: Female

tag: treatment

value: Post-treatment

tag: time


title: SAMPLE 31

description: peripheral blood sample

value: normal


title: human breast cancer total RNA expression [AUR-AER2-TTM1-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AER2-TTM1-A-1-1-R-A742-41

value: Liver


title: SAMPLE 32

description: peripheral blood sample

value: female

value: obesity

value: peripheral blood


title: human breast cancer total RNA expression [AUR-AER2-TTM3-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AER2-TTM3-A-1-1-R-A742-41

value: Metastatic tumor

value: Soft tissue


title: 467

value: Coronary Artery Disease

value: M

tag: dbp

tag: hr

tag: ef %

tag: dyslipidemia

value: Yes

tag: hypertension

value: No

tag: asa

value: Y

tag: cad

value: CAD


title: SAMPLE 30

description: peripheral blood sample

value: male


title: 466

value: Whole blood

tag: Sex

tag: age

tag: bmi

tag: sbp

tag: diabetes mellitus

value: Never

value: MID

tag: %stenosis

tag: rnaseq group


title: human breast cancer total RNA expression [AUR-AER2-TTP1-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AER2-TTP1-A-1-1-R-A742-41

tag: disease

value: Primary tumor

tag: tissue

value: Breast

tag: genotype

value: Female

value: Post-treatment

value: Autopsy


title: 465

tag: disease state

value: F

tag: dbp

tag: family history_of_cad

tag: smoking

value: Former

value: N

value: LOW


title: 464

value: Coronary Artery Disease

value: M

tag: hr

tag: ef %

tag: dyslipidemia

tag: hypertension

value: Yes

value: Current


title: SAMPLE 28

description: peripheral blood sample

tag: gender

value: female

value: normal

value: peripheral blood


title: SAMPLE 27

description: peripheral blood sample

value: male


title: SAMPLE 25

description: peripheral blood sample


title: 463

value: Whole blood

tag: Sex

tag: age

tag: bmi

value: No

value: Never

tag: asa

tag: cad


title: human breast cancer total RNA expression [AUR-AFE6-TTM1-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AFE6-TTM1-A-1-1-R-A742-41

tag: disease

value: Metastatic tumor

value: Chest

value: Female

tag: treatment

value: Metastasis

tag: time


title: human breast cancer total RNA expression [AUR-AFE9-TTM2-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AFE9-TTM2-A-1-1-R-A742-41

tag: tissue

value: Lung

tag: genotype

value: Autopsy


title: SAMPLE 35

description: peripheral blood sample

tag: disease state

value: obesity


title: SAMPLE 24

description: peripheral blood sample


title: SAMPLE 23

description: peripheral blood sample


title: 462

value: Coronary Artery Disease

value: M

tag: sbp

tag: dbp

tag: diabetes mellitus

tag: family history_of_cad

tag: smoking

value: Y

value: MID

tag: %stenosis

tag: rnaseq group


title: human breast cancer total RNA expression [AUR-AFE9-TTM4-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AFE9-TTM4-A-1-1-R-A742-41

value: Liver


title: 461

tag: Sex

value: F

tag: age

tag: hr

tag: ef %

tag: dyslipidemia

tag: hypertension

value: Yes

value: N

value: LOW


title: SAMPLE 21

description: peripheral blood sample

tag: gender

value: female

value: normal

value: peripheral blood


title: SAMPLE 29

description: peripheral blood sample

tag: tissue


title: SAMPLE 22

description: peripheral blood sample


title: human breast cancer total RNA expression [AUR-AFE9-TTM1-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AFE9-TTM1-A-1-1-R-A742-41

tag: disease

value: Metastatic tumor

value: Brain

tag: genotype

value: Female

tag: treatment

tag: time


title: SAMPLE 26

description: peripheral blood sample

value: male

tag: disease state


title: 460

value: Whole blood

tag: bmi

tag: sbp

tag: dbp

value: No

tag: diabetes mellitus

tag: family history_of_cad

value: Former

tag: asa

tag: cad

value: CAD


title: SAMPLE 19

description: peripheral blood sample


title: SAMPLE 17

description: peripheral blood sample


title: human breast cancer total RNA expression [AUR-AFE9-TTM3-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AFE9-TTM3-A-1-1-R-A742-41

value: Adrenal

value: Metastasis

value: Autopsy


title: human breast cancer total RNA expression [AUR-AFE9-TTP1-A-1-0-R-A741-41]

description:
FFPE
AUR-AFE9-TTP1-A-1-0-R-A741-41

value: Primary tumor

value: Breast

value: Pre-treatment


title: SAMPLE 16

description: peripheral blood sample

value: female


title: SAMPLE 20

description: peripheral blood sample

value: normal


title: human breast cancer total RNA expression [AUR-AFUM-TTM1-A-1-1-R-A743-41]

description:
Fresh frozen
AUR-AFUM-TTM1-A-1-1-R-A743-41

value: Bone

value: Non-Autopsy


title: SAMPLE 13

description: peripheral blood sample

value: peripheral blood


title: human breast cancer total RNA expression [AUR-AFUM-TTP1-A-1-0-R-A741-41]

description:
FFPE
AUR-AFUM-TTP1-A-1-0-R-A741-41

value: Female

value: Post-treatment


title: SAMPLE 15

description: peripheral blood sample

value: male


title: SAMPLE 14

description: peripheral blood sample


title: 457

value: Whole blood

value: Coronary Artery Disease

tag: Sex

value: M

tag: age

tag: hr

tag: ef %

value: No

value: Yes

tag: smoking

value: Never

value: N

value: LOW

tag: %stenosis

tag: rnaseq group


title: 458

tag: tissue

tag: dyslipidemia

tag: hypertension

value: Y

value: CAD


title: SAMPLE 12

description: peripheral blood sample

tag: gender

tag: disease state

value: normal


title: SAMPLE 11

description: peripheral blood sample


title: human breast cancer total RNA expression [AUR-AFKF-TTM1-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AFKF-TTM1-A-1-1-R-A742-41

tag: disease

value: Metastatic tumor

value: Brain

tag: genotype

tag: treatment

value: Metastasis

tag: time


title: 456

tag: bmi

tag: sbp

tag: dbp

tag: diabetes mellitus

tag: family history_of_cad

value: Former

tag: asa

tag: cad

value: MID


title: SAMPLE 18

description: peripheral blood sample

value: female

value: peripheral blood


title: human breast cancer total RNA expression [AUR-AFKF-TTP1-A-10-0-R-A741-41]

description:
FFPE
AUR-AFKF-TTP1-A-10-0-R-A741-41

value: Primary tumor

value: Breast

value: Female

value: Unknown

value: Non-Autopsy


title: 459

value: Whole blood

value: Coronary Artery Disease

tag: Sex

value: M

tag: age

tag: hr

tag: ef %

value: Yes

value: No

tag: smoking

tag: %stenosis

tag: rnaseq group


title: 455

tag: tissue

tag: disease state

tag: dyslipidemia

tag: hypertension

value: N

value: LOW


title: SAMPLE 8

description: peripheral blood sample

tag: gender

value: normal


title: SAMPLE 9

description: peripheral blood sample

value: male


title: SAMPLE 7

description: peripheral blood sample


title: SAMPLE 6

description: peripheral blood sample


title: 454

tag: bmi

tag: sbp

tag: dbp

value: Former

value: Y

value: CAD


title: SAMPLE 5

description: peripheral blood sample

value: female

value: peripheral blood


title: SAMPLE 4

description: peripheral blood sample


title: 453

tag: diabetes mellitus

tag: family history_of_cad

tag: asa


title: human breast cancer total RNA expression [AUR-AER8-TTP1-A-1-0-R-A741-41]

description:
FFPE
AUR-AER8-TTP1-A-1-0-R-A741-41

tag: disease

value: Primary tumor

value: Breast

tag: genotype

value: Female

tag: treatment

value: Post-treatment

tag: time

value: Autopsy


title: human breast cancer total RNA expression [AUR-AER8-TTM2-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AER8-TTM2-A-1-1-R-A742-41

value: Metastatic tumor

value: Liver

value: Metastasis


title: SAMPLE 3

description: peripheral blood sample


title: 452

value: Whole blood

value: Coronary Artery Disease

tag: Sex

value: M

tag: age

tag: hr

tag: ef %

value: No

value: Yes

tag: smoking

value: Never

value: N

tag: cad

tag: %stenosis


title: SAMPLE 2

description: peripheral blood sample

tag: gender

value: male

tag: disease state

value: normal

tag: tissue


title: 451

tag: bmi

tag: sbp

tag: dbp

tag: dyslipidemia

tag: hypertension

tag: diabetes mellitus

value: Former

value: Y

value: MID

tag: rnaseq group


title: SAMPLE 1

description: peripheral blood sample

value: peripheral blood


title: human breast cancer total RNA expression [AUR-AEPZ-TTM1-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AEPZ-TTM1-A-1-1-R-A742-41

tag: disease

value: Ovary

tag: genotype

value: Female

tag: treatment

tag: time

value: Non-Autopsy


title: human breast cancer total RNA expression [AUR-AEPZ-TTP1-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AEPZ-TTP1-A-1-1-R-A742-41

value: Primary tumor

value: Breast

value: Pre-treatment


title: 450

value: Whole blood

value: Coronary Artery Disease

tag: Sex

value: F

tag: age

tag: hr

tag: ef %

tag: family history_of_cad

tag: smoking

tag: asa

value: LOW


title: human breast cancer total RNA expression [AUR-AFKB-TTP1-A-10-0-R-A741-41]

description:
FFPE
AUR-AFKB-TTP1-A-10-0-R-A741-41

tag: tissue


title: SAMPLE 10

description: peripheral blood sample

tag: gender

value: female

tag: disease state


title: human breast cancer total RNA expression [AUR-AFKB-TTM1-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AFKB-TTM1-A-1-1-R-A742-41

value: Metastatic tumor

value: Bone

value: Metastasis


title: XpressRef Universal Total RNA

city: Meldola

first: Tania

last: Rossi

state: FC

address: Via Piero Maroncelli 40

department: Biosciences Laboratory

country: Italy

institute: IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori"

description: Cell barcodes are proprietary;  raw data can be re-analyzed using cell_IDs with the CLC Genomics Workbench Biomedical Plugin

data_processing:
CLC Genomics Workbench version 22.0.1
Demultiplex of QIAseq UPX 3' reads was performed using CLC Genomics Workbench Biomedical Plugin using default parameters.
Quantification was performed was performed using CLC Genomics Workbench Biomedical Plugin using default parameters.
Assembly: hg38
Supplementary files format and content: comma-separated values files reporting TPM, RPKM and gene expression levels for each gene

source_name: 20 different human adult and fetal normal major organs

growth_protocol: OE33 commercial cells were cultured RPMI 1640 + 2mM Glutamine + 10% Foetal Bovine Serum (FBS). For sample preparation, OE33 cells were dissociated through trypsinization, then cellular pellet was split in two for CSF and EtOH fixation respectively.

extract_protocol:
For RNA samples, RNA was extracted using RNEasy Mini Kit while the other samples were subjected to cell lysis during library preparation.
Libraries were prepared using the QIAseq 3’ UPX Transcriptome kit (384 reactions, QIAGEN) starting from the above-mentioned single cells and 10-cell pools isolated using DEPArray, and 8 replicates of each RNA sample extracted from fixed (CSF and EtOH) and unfixed OE33 cell pellet. In addition, we included in library preparation the XPress Ref Universal Total RNA (QIAGEN) (8 replicates) as a reference sample.

treatment_protocol: CSF fixation was performed using the fixative contained in CellSave Preservative tubes. More specifically, fixation was performed with 100 µl of preservative diluted 1:10 in PBS1X at room temperature. EtOH fixation was performed by adding 200 µl of ice-cold PBS1X and 800 µl of ice-cold EtOH dropwise. Fixation was carried out on ice for 15 minutes

tag: replicates


title: OE33 cells, RNA, EtOH fixed

tag: cell line

value: EtOH fixation


title: OE33 cells, RNA, CSF fixed

value: CSF fixation


title: 449

value: M

tag: bmi

tag: sbp

tag: dbp

tag: dyslipidemia

value: Yes

tag: hypertension

tag: diabetes mellitus

value: No

value: Never

value: Y

tag: cad

value: CAD

tag: %stenosis

tag: rnaseq group


title: human breast cancer total RNA expression [AUR-AFUL-TTM1-A-1-1-R-A743-41]

description:
Fresh frozen
AUR-AFUL-TTM1-A-1-1-R-A743-41

tag: disease

value: Ovary

tag: genotype

value: Female

tag: treatment

tag: time

value: Non-Autopsy


title: 448

tag: tissue

value: Whole blood

value: Coronary Artery Disease

tag: Sex

value: F

tag: age

tag: hr

tag: ef %

tag: family history_of_cad

tag: smoking

tag: asa

value: N


title: OE33 cells, 10-cell pools, EtOH fixed

tag: cell line

tag: replicates


title: 446

tag: disease state

tag: bmi

tag: sbp

tag: dbp

tag: dyslipidemia

tag: hypertension

tag: diabetes mellitus

tag: cad

value: LOW


title: OE33 cells, 10-cell pools, unfixed

tag: treatment

value: No fixation


title: human breast cancer total RNA expression [AUR-AFUN-TTM1-A-1-0-R-A743-41]

description:
Fresh frozen
AUR-AFUN-TTM1-A-1-0-R-A743-41

tag: disease

value: Metastatic tumor

tag: tissue

value: Uterus

tag: genotype

value: Metastasis

tag: time


title: 445

tag: Sex

value: M

tag: age

tag: hr

tag: ef %

tag: family history_of_cad

tag: smoking

value: Former

tag: %stenosis

tag: rnaseq group


title: OE33 cells, 10-cell pools, CSF fixed

tag: cell line

value: CSF fixation

tag: replicates


title: 444

tag: disease state

tag: bmi

tag: sbp

tag: dbp

tag: dyslipidemia

value: Yes

tag: hypertension

value: No

tag: diabetes mellitus

value: Current

tag: asa


title: neuron, vehicle, rep2

description: nascent nuclear RNA

data_processing:
Libraries were sequenced for 51 cycles (single-end) on an Illumina HiSeq 2000, according to the manufacturer’s instructions.
GRO-Seq and RNA-Seq results were trimmed to remove A-stretches originating from the library preparation using the Homer software (homerTools trim) and from resulting sequences those shorter than 25 bp were discarded.  Sequence reads were further quality filtered with the FASTX software (-q 10 -p 97)
GRO-seq reads were aligned to the mm9 genome assembly using Bowtie version 0.12.9 (-v 2 -k 3 -m 1 --best)
Bedgraphs were generated using the HOMER software. Data analysis was performed using HOMER and custom scripts http://biowhat.ucsd.edu/homer/
Assembly: mm9
Supplementary files format and content: bedGraph GRO-seq signal files
Library strategy: GRO-seq

source_name: Cortical neuron

extract_protocol:
Five to 16 million cells were incubated in swelling buffer (10 mM Tris–HCl, 2 mM MgCl2, 3 mM CaCl2 and 2 U/ml SUPERase In RNAse inhibitor) for 5 min on ice. Cells were pelleted for 10 min at 400 × g and resuspended in 500 μl of swelling buffer supplemented with 10% glycerol. Subsequently, 500 μl of swelling buffer supplemented with 10% glycerol and 1% Igepal was added drop by drop to the cells under gentle vortexing. Nuclei were washed twice with lysis buffer (10 ml of swelling buffer supplemented with 0.5% Igepal and 10% glycerol), and once with 1 ml of freezing buffer (50 mM Tris–HCl pH 8.3, 40% glycerol, 5 mM MgCl2 and 0.1 mM ethylenediaminetetraacetic acid). Nuclei were counted, centrifuged at 900 × g for 6 min and suspended to a concentration of 5 million nuclei per 100 μl of freezing buffer, snap-frozen in LN2 and stored −80°C until run-on reactions
The nuclear run-on reactions were performed for 5 minutes at 30°C in the presence of Sarkosyl and BrUTP. RNA was extracted with Trizol, DNase-treated, base-hydrolyzed and dephosphorylated with PNK. BrUTP-labeled run-on RNA was immunopurified with anti-BrdUTP-coated agarose beads and precipitated overnight. Poly(A)-tailing was followed by cDNA synthesis using complementary poly(T)-primers. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified. The recovered cDNA was circularized, linearized, amplified for 11-14 cycles. The final product was ran on 10% TBE gel, gel purified and cleaned-up using ChIP DNA clean & Concentrator Kit. The final libraries were sequenced using an Illumina HiSeq 2000

treatment_protocol: Neurons were treated with 400 µM glutamate or vehicle for 6 hours prior to the extraction of nuclei.

tag: strain

tag: age

value: embryonic day 15

tag: cell type

value: Cortical neuron

tag: treatment

value: vehicle

tag: time

value: 6 hours


title: 443

tag: tissue

value: Whole blood

value: Coronary Artery Disease

tag: Sex

tag: hr

tag: ef %

tag: family history_of_cad

tag: smoking

value: Never

tag: cad

tag: %stenosis


title: human breast cancer total RNA expression [AUR-AFUN-TTP1-A-1-0-R-A741-41]

description:
FFPE
AUR-AFUN-TTP1-A-1-0-R-A741-41

tag: disease

value: Primary tumor

value: Breast

tag: genotype

value: Female

value: Pre-treatment

value: Non-Autopsy


title: OE33 cells, single cells, unfixed

tag: cell line

value: No fixation

tag: replicates


title: human breast cancer total RNA expression [AUR-AFE4-TTM5-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AFE4-TTM5-A-1-1-R-A742-41

value: Metastatic tumor

value: Pericardium

value: Metastasis

value: Autopsy


title: OE33 cells, single cells, EtOH-fixed

value: EtOH fixation


title: neuron, vehicle, rep1

description: nascent nuclear RNA

tag: strain

value: embryonic day 15

value: Cortical neuron


title: OE33 cells, single cells, CSF-fixed

value: CSF fixation


title: neuron, glutamate, rep2

description: nascent nuclear RNA

tag: age

value: glutamate 400 microM

value: 6 hours


title: OE33 cells, RNA, unfixed


title: SAMPLE 38

description: peripheral blood sample

tag: gender

value: female

tag: disease state

value: obesity

value: peripheral blood


title: human breast cancer total RNA expression [AUR-AFE4-TTM1-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AFE4-TTM1-A-1-1-R-A742-41

value: Lung

value: Female

tag: treatment

tag: time


title: human breast cancer total RNA expression [AUR-AFE4-TTM6-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AFE4-TTM6-A-1-1-R-A742-41

tag: tissue

value: Liver


title: 441

value: Whole blood

value: Coronary Artery Disease

tag: Sex

value: M

tag: bmi

tag: sbp

tag: dbp

tag: hr

tag: dyslipidemia

value: No

tag: hypertension

tag: diabetes mellitus

value: Yes

value: Never

tag: asa

value: Y

value: MID

tag: rnaseq group


title: neuron, glutamate, rep1

description: nascent nuclear RNA

tag: strain

value: embryonic day 15

tag: cell type

value: Cortical neuron


title: PPO1_P131

city: CINCINNATI

first: Richard

middle: Q.

last: Lu

state: OH

address: 3333 Burnet Avenue

department: CBDI

institute: Cincinnati Childrens Hosp Med Ctrl

data_processing:
RNA-seq reads in FASTQ format were first subjected to quality control to assess the need for trimming of adapter sequences or bad quality segments. The programs used in these steps were FastQC v0.11.7 (1), Trim Galore! v0.4.2 (2) and cutadapt v1.8.1 (3). The trimmed reads were aligned to the reference mouse genome version mm9 with the program STAR v2.6.1e (4). Aligned reads were stripped of duplicate reads with the program sambamba v0.6.8 (5). Gene-level expression was assessed by counting features for each gene, as defined in the NCBI's RefSeq database (6). Read counting was done with the program featureCounts v1.6.2 from the Rsubread package (7). Raw counts were normalized as transcripts per million (TPM).
The differential expression analysis is done by R using DESeq2 package using raw read as input. The significant gene is defined with atleast log2 fold change of atleast2 and FDR <0.05 value
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values

source_name: Brain

extract_protocol: RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.

value: Brain

tag: genotype

tag: stain

value: Mixed

tag: age (days)

tag: tumor stage

value: End stage


title: P13_Cortex3

tag: tissue

value: WT


title: P13_Cortex2


title: human breast cancer total RNA expression [AUR-AFUL-TTP1-A-1-1-R-A743-41]

description:
Fresh frozen
AUR-AFUL-TTP1-A-1-1-R-A743-41

tag: disease

value: Primary tumor

value: Breast

tag: treatment

value: Pre-treatment

tag: time

value: Non-Autopsy


title: PPO1_P120


title: PPO1_P91

value: Late


title: 440

value: Whole blood

tag: disease state

value: Coronary Artery Disease

tag: Sex

value: M

tag: age

tag: bmi

tag: sbp

tag: dbp

tag: ef %

tag: family history_of_cad

tag: smoking

value: Former

value: N

tag: cad

value: LOW

tag: %stenosis


title: PPO1_P68

tag: genotype

tag: stain

tag: age (days)

value: Early


title: human breast cancer total RNA expression [AUR-AF94-TTM1-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AF94-TTM1-A-1-1-R-A742-41

tag: disease

value: Metastatic tumor

tag: tissue

value: Liver

value: Female

value: Metastasis


title: PPO1_P52

value: Brain

value: Mixed

tag: tumor stage


title: human breast cancer total RNA expression [AUR-AF94-TTP1-A-1-0-R-A741-41]

description:
FFPE
AUR-AF94-TTP1-A-1-0-R-A741-41

value: Primary tumor

value: Breast

tag: treatment

tag: time


title: 438

tag: disease state

tag: Sex

tag: age

tag: hr

tag: dyslipidemia

value: No

tag: hypertension

tag: diabetes mellitus

value: Yes

value: Never

tag: asa

tag: rnaseq group


title: VARI-Control-4-IMR90-A-5

description: VAI control sample for QC purposes

hyb_protocol: DNA was bisulfite-converted using the Zymo EZ DNA Methylation Kit (Zymo Research), cleaned using the Zymo-Spin binding columns, and processed through the EPIC array protocol. For FFPE samples, BS converted eluate from the spin columns was used as input for the Infinium HD FFPE DNA Restore kit and processed through the separate restoration workflow. BS converted DNA was denatured, amplified, and hybridized to the EPIC bead chip.

scan_protocol: Array BeadChips were scanned on the Illumina iScan system to produce IDAT files.

data_processing: IDATs were processed with the R Bioconductor (release 3.8) package sesame (version 1.0.0) using the default openSesame pipeline. Probe masking was performed using the standard mask list in sesame, including probes that overlap with SNPs and repeat elements. De-identified files were generated by removing data from the SNP probes using the deidentify function in sesame.

label: Cy3 and Cy5

source_name: IMR-90 fibroblast cell line

label_protocol: An extension reaction was performed using fluorophore-labeled nucleotides per the manufacturer’s protocol.

extract_protocol: DNA was extracted from frozen tissues and FFPE solid tissues using a modification of the AllPrep DNA/RNA kit (Qiagen) and the AllPrep DNA/RNA FFPE kit (Qiagen), respectively. DNA was quantified by Qubit fluorimetry (Life Technologies). Only cases yielding a minimum of 250ng of tumor DNA were included in this study.

tag: cell line

value: IMR-90 fibroblast


title: 442

value: Whole blood

value: Coronary Artery Disease

value: M

tag: bmi

tag: sbp

tag: dbp

tag: ef %

tag: family history_of_cad

tag: smoking

value: Y

tag: cad

value: CAD

tag: %stenosis


title: VARI-Control-3-IMR90-A-3

description: VAI control sample for QC purposes


title: 437

tag: tissue

tag: disease state

tag: Sex

value: N

value: LOW


title: human breast cancer total RNA expression [AUR-AE5G-TTM1-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AE5G-TTM1-A-1-1-R-A742-41

tag: disease

value: Metastatic tumor

tag: genotype

value: Female

tag: treatment

tag: time

value: Non-Autopsy


title: 439

tag: age

tag: hr

tag: dyslipidemia

tag: hypertension

tag: diabetes mellitus

tag: asa

tag: rnaseq group


title: 436

value: F

tag: bmi

tag: sbp

tag: dbp

tag: ef %

tag: family history_of_cad

tag: smoking


title: VARI-Control-3-HCT116-A-2

description: VAI control sample for QC purposes

source_name: HCT116 colon cancer cell line

tag: cell line

value: HCT116 colon cancer


title: VARI-Control-3-IMR90-A-4

description: VAI control sample for QC purposes


title: P13_Cortex1

tag: tissue

value: Brain

tag: genotype

value: WT

tag: stain

value: Mixed

tag: age (days)


title: VARI-Control-2-IMR90-A-2

description: VAI control sample for QC purposes


title: 435

tag: disease state

tag: Sex

tag: age

tag: hr

value: No

value: Yes

value: Former

tag: cad

tag: %stenosis


title: VARI-Control-1-GM12878-A-1

description: VAI control sample for QC purposes

source_name: GM12878 lymphoblastoid cell line

value: GM12878 lymphoblastoid


title: VARI-Control-1-IMR90-A-1

description: VAI control sample for QC purposes

value: IMR-90 fibroblast


title: AUR-AG0N-TTP1-A-1-0-D-A746-37

source_name: FFPE primary breast tumor

tag: sample type

value: Primary tumor

value: Breast

tag: tissue type

value: FFPE

tag: autopsy

tag: treatment (primary tumor)

value: Pre-treatment


title: human breast cancer total RNA expression [AUR-AFE4-TTP1-A-1-0-R-A741-41]

description:
FFPE
AUR-AFE4-TTP1-A-1-0-R-A741-41

tag: disease

tag: treatment

tag: time

value: Autopsy


title: human breast cancer total RNA expression [AUR-AE5G-TTP1-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AE5G-TTP1-A-1-1-R-A742-41

tag: tissue

value: Female


title: human breast cancer total RNA expression [AUR-AFR3-TTP1-A-2-1-R-A743-41]

description:
Fresh frozen
AUR-AFR3-TTP1-A-2-1-R-A743-41

tag: genotype

value: Non-Autopsy


title: human breast cancer total RNA expression [AUR-AFR3-TTM1-A-1-1-R-A743-41]

description:
Fresh frozen
AUR-AFR3-TTM1-A-1-1-R-A743-41

value: Metastatic tumor

value: Metastasis


title: 434

value: Whole blood

value: Coronary Artery Disease

value: M

tag: bmi

tag: sbp

tag: dbp

tag: ef %

tag: dyslipidemia

tag: hypertension

tag: diabetes mellitus

tag: family history_of_cad

tag: smoking

value: Never

tag: asa

value: Y

value: CAD

tag: rnaseq group


title: AUR-AG0N-TTM1-A-1-1-D-A746-37

source_name: Fresh frozen metastatic breast tumor

tag: Sex

tag: sample type

value: Lymph node

tag: tissue type

value: Fresh frozen

tag: autopsy


title: AUR-AG0M-TTM1-A-2-1-D-A746-37

tag: tissue

value: Chest


title: human breast cancer total RNA expression [AUR-AFSO-TTM1-A-8-0-R-A741-41]

description:
FFPE
AUR-AFSO-TTM1-A-8-0-R-A741-41

tag: disease

value: Brain

tag: genotype

tag: treatment

tag: time


title: AUR-AG0J-TTP1-A-1-0-D-A746-37

value: Primary tumor

value: Breast

value: FFPE

tag: treatment (primary tumor)


title: 433

tag: disease state

tag: age

tag: bmi

tag: sbp

tag: dbp

tag: hr

tag: ef %

tag: dyslipidemia

value: No

value: Former

value: N

tag: cad

value: LOW

tag: %stenosis


title: AUR-AG0J-TTM1-A-1-0-D-A746-37

tag: Sex

value: Female

tag: sample type

value: Metastatic tumor

value: Soft tissue

tag: tissue type

tag: autopsy

value: Non-Autopsy


title: VARI-Control-3-HCT116-A-1

description: VAI control sample for QC purposes

tag: cell line

value: HCT116 colon cancer


title: 432

tag: tissue

value: Whole blood

value: Coronary Artery Disease

value: M

tag: hypertension

value: Yes

tag: diabetes mellitus

tag: family history_of_cad

tag: smoking

tag: asa

value: Y

value: MID

tag: rnaseq group


title: AUR-AFUP-TTP1-A-1-0-D-A746-37

value: Primary tumor

value: Breast

tag: treatment (primary tumor)

value: Post-treatment


title: AUR-AFUP-TTM1-A-1-1-D-A746-37

value: Ovary

value: Fresh frozen


title: AUR-AFUN-TTP1-A-1-0-D-A746-37

value: FFPE

value: Pre-treatment


title: 429

tag: disease state

tag: age

tag: bmi

tag: sbp

tag: dbp

tag: hr

tag: ef %

value: No

value: Former


title: AUR-AFUN-TTM1-A-1-0-D-A746-37

tag: Sex

value: Female

tag: sample type

value: Metastatic tumor

value: Uterus

tag: tissue type

tag: autopsy

value: Non-Autopsy


title: AUR-AFUL-TTP1-A-1-1-D-A746-37

source_name: Fresh frozen primary breast tumor

tag: tissue


title: 431

source_name: Whole blood

value: Whole blood

value: Coronary Artery Disease

value: M

tag: dyslipidemia

tag: hypertension

tag: diabetes mellitus

tag: family history_of_cad

value: Never

tag: cad

tag: %stenosis


title: AUR-AFUM-TTM1-A-1-1-D-A746-37

value: Bone


title: human breast cancer total RNA expression [AUR-AERX-TTM1-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AERX-TTM1-A-1-1-R-A742-41

source_name: Metastatic tumor

tag: disease

value: Liver

tag: genotype

tag: treatment

value: Metastasis

tag: time


title: 430

tag: disease state

tag: age

tag: bmi

tag: sbp

tag: dbp

tag: hr

value: Yes

tag: smoking

tag: asa

value: Y

value: CAD

tag: rnaseq group


title: AUR-AFUK-TTP1-A-1-0-D-A746-37

tag: Sex

tag: sample type

value: Primary tumor

tag: tissue

value: Breast

tag: tissue type

value: FFPE

tag: autopsy

tag: treatment (primary tumor)

value: Pre-treatment


title: AUR-AFUK-TTM2-A-1-0-D-A746-37

value: Female

value: Metastatic tumor

value: Lymph node

value: Fresh frozen


title: human breast cancer total RNA expression [AUR-AERW-TTM1-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AERW-TTM1-A-1-1-R-A742-41

tag: disease

value: Skin

tag: genotype

tag: treatment

value: Non-Autopsy


title: AUR-AFUK-TTM1-A-1-0-D-A746-37

value: Chest


title: AUR-AFUI-TTP1-A-1-0-D-A746-37


title: human breast cancer total RNA expression [AUR-AG12-TTM1-A-1-1-R-A743-41]

description:
Fresh frozen
AUR-AG12-TTM1-A-1-1-R-A743-41

tag: time


title: 426

value: Whole blood

tag: disease state

value: Coronary Artery Disease

value: M

tag: age

tag: bmi

tag: ef %

tag: dyslipidemia

tag: hypertension

tag: diabetes mellitus

value: No

tag: family history_of_cad

value: Current

value: N

tag: cad

value: LOW

tag: %stenosis


title: AUR-AFUI-TTM1-A-1-0-D-A746-37

tag: Sex

tag: sample type

tag: tissue

tag: tissue type


title: 428

value: F

tag: sbp

tag: dbp

tag: hr

value: Yes

tag: smoking

value: Never

tag: asa

value: Y

value: MID

tag: rnaseq group


title: human breast cancer total RNA expression [AUR-AG12-TTP1-A-1-0-R-A741-41]

description:
FFPE
AUR-AG12-TTP1-A-1-0-R-A741-41

tag: disease

value: Primary tumor

value: Breast

tag: genotype

value: Female

tag: treatment

value: Pre-treatment

tag: time


title: AUR-AFUL-TTM1-A-1-1-D-A746-37

value: Metastatic tumor

value: Ovary

value: Fresh frozen

tag: autopsy

value: Non-Autopsy


title: human breast cancer total RNA expression [AUR-AFSO-TTP1-A-8-0-R-A741-41]

description:
FFPE
AUR-AFSO-TTP1-A-8-0-R-A741-41


title: AUR-AFSO-TTP1-A-8-0-D-A746-37

value: FFPE

tag: treatment (primary tumor)


title: human breast cancer total RNA expression [AUR-AFEC-TTM6-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AFEC-TTM6-A-1-1-R-A742-41

value: Pleura

value: Metastasis

value: Autopsy


title: human breast cancer total RNA expression [AUR-AERW-TTP1-B-1-0-R-A741-41]

description:
FFPE
AUR-AERW-TTP1-B-1-0-R-A741-41

value: Post-treatment


title: AUR-AFSO-TTM1-A-8-0-D-A78F-37

description: Replicate data merged with AUR-AFSO-TTM1-A-8-0-D-A746-37 in the processed data file

source_name: FFPE metastatic breast tumor

value: Brain


title: AUR-AFSO-TTM1-A-8-0-D-A746-37


title: human breast cancer total RNA expression [AUR-AFEC-TTM4-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AFEC-TTM4-A-1-1-R-A742-41

value: Lymph node


title: AUR-AFSL-TTP1-A-8-0-D-A746-37


title: human breast cancer total RNA expression [AUR-AERX-TTP1-A-1-0-R-A741-41]

description:
FFPE
AUR-AERX-TTP1-A-1-0-R-A741-41


title: 422

value: Whole blood

tag: disease state

value: Coronary Artery Disease

value: F

tag: age

tag: bmi

tag: ef %

tag: dyslipidemia

value: No

tag: hypertension

value: Yes

tag: diabetes mellitus

tag: family history_of_cad

value: Never

value: Y

tag: cad

tag: %stenosis


title: human breast cancer total RNA expression [AUR-AFEC-TTM3-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AFEC-TTM3-A-1-1-R-A742-41

value: Metastatic tumor

tag: tissue

value: Liver

value: Female


title: AUR-AFSL-TTM1-A-8-0-D-A746-37

tag: Sex

tag: sample type

tag: tissue type

value: FFPE

value: Non-Autopsy


title: AUR-AFR5-TTM1-A-1-1-D-A746-37

value: Fresh frozen


title: human breast cancer total RNA expression [AUR-AFEC-TTP2-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AFEC-TTP2-A-1-1-R-A742-41

tag: disease

value: Primary tumor

value: Breast

tag: genotype

tag: treatment

tag: time

value: Autopsy


title: AUR-AFUG-TTM1-A-1-1-D-A746-37

value: Chest

tag: autopsy


title: human breast cancer total RNA expression [AUR-AER6-TTM1-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AER6-TTM1-A-1-1-R-A742-41

value: Skin

value: Metastasis


title: AUR-AFR2-TTP1-A-1-1-D-A746-37

tag: treatment (primary tumor)

value: Pre-treatment


title: 419

value: Whole blood

tag: disease state

value: Coronary Artery Disease

value: F

tag: age

tag: bmi

tag: sbp

tag: dbp

tag: hr

tag: ef %

value: No

tag: smoking

tag: asa

value: CAD

tag: rnaseq group


title: 420

tag: tissue

tag: Sex

value: M

tag: dyslipidemia

tag: hypertension

value: Yes

tag: diabetes mellitus

tag: family history_of_cad

value: Never

value: Y

tag: cad

value: MID

tag: %stenosis


title: AUR-AFR3-TTP1-A-2-1-D-A746-37

value: Female

tag: sample type

value: Primary tumor

tag: tissue type

value: Fresh frozen

tag: autopsy

value: Non-Autopsy

tag: treatment (primary tumor)


title: AUR-AFKF-TTP1-A-10-0-D-A746-37

value: Breast

value: FFPE

value: Unknown


title: AUR-AFR3-TTM1-A-1-1-D-A746-37

value: Metastatic tumor

value: Brain


title: 425

value: Whole blood

tag: disease state

value: Coronary Artery Disease

value: F

tag: age

tag: bmi

tag: sbp

tag: dbp

tag: hr


title: AUR-AFR2-TTM1-A-1-1-D-A746-37

tag: Sex

tag: tissue


title: human breast cancer total RNA expression [AUR-AER6-TTM5-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AER6-TTM5-A-1-1-R-A742-41

tag: disease

value: Stomach

tag: genotype

tag: treatment

value: Metastasis

tag: time

value: Autopsy


title: human breast cancer total RNA expression [AUR-AER6-TTM10-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AER6-TTM10-A-1-1-R-A742-41

value: Peritoneum


title: 418

tag: ef %

tag: dyslipidemia

value: Yes

tag: hypertension

tag: diabetes mellitus

tag: family history_of_cad

value: No

tag: smoking

value: Never

tag: asa

value: N

tag: cad

value: LOW

tag: %stenosis

tag: rnaseq group


title: 423

tag: disease state

value: M

tag: age

tag: bmi

tag: sbp

tag: dbp

tag: hr

value: Y

value: MID


title: 417

tag: tissue

tag: Sex

value: Current

value: CAD


title: AUR-AFR4-TTM1-A-1-1-D-A746-37

value: Female

tag: sample type

value: Metastatic tumor

value: Brain

tag: tissue type

value: Fresh frozen

tag: autopsy

value: Non-Autopsy


title: AUR-AFKF-TTM1-A-1-1-D-A746-37


title: AUR-AFKD-TTP1-A-1-1-D-A746-37

value: Primary tumor

value: Breast

value: FFPE

value: Autopsy

tag: treatment (primary tumor)

value: Post-treatment


title: human breast cancer total RNA expression [AUR-AER6-TTM6-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AER6-TTM6-A-1-1-R-A742-41

tag: disease

value: Rectum

tag: genotype

tag: treatment

value: Metastasis

tag: time


title: 421

value: Whole blood

value: Coronary Artery Disease

value: M

tag: ef %

tag: dyslipidemia

value: Yes

tag: hypertension

tag: diabetes mellitus

value: No

tag: family history_of_cad

tag: smoking

value: Former

tag: asa

tag: cad

tag: %stenosis

tag: rnaseq group


title: AUR-AFKB-TTP1-A-10-0-D-A746-37

tag: Sex

value: Female

tag: sample type

tag: tissue

tag: tissue type

value: Pre-treatment


title: AUR-AFR5-TTP1-A-1-1-D-A746-37

value: Fresh frozen

tag: autopsy

tag: treatment (primary tumor)


title: AUR-AFKD-TTM1-A-1-1-D-A746-37

value: Metastatic tumor

value: Liver


title: human breast cancer total RNA expression [AUR-AER6-TTM9-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AER6-TTM9-A-1-1-R-A742-41

tag: disease

tag: genotype

tag: treatment

tag: time


title: AUR-AFKB-TTM1-A-1-1-D-A746-37

value: Bone

value: Non-Autopsy


title: 415

tag: disease state

tag: age

tag: bmi

tag: sbp

tag: dbp

tag: hr

tag: ef %

tag: dyslipidemia

tag: hypertension

tag: diabetes mellitus

value: Y

value: CAD


title: human breast cancer total RNA expression [AUR-AER6-TTM7-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AER6-TTM7-A-1-1-R-A742-41

tag: tissue

value: Soft tissue

value: Autopsy


title: 414

value: Whole blood

tag: Sex

value: F

tag: family history_of_cad

tag: smoking

value: Never

tag: asa

value: N

tag: cad

value: LOW

tag: %stenosis

tag: rnaseq group


title: AUR-AFEC-TTM4-A-1-1-D-A746-37

tag: sample type

value: Lymph node

tag: tissue type

tag: autopsy


title: AUR-AFEC-TTP1-A-1-0-D-A746-37

value: Female

value: Primary tumor

value: Breast

value: FFPE

tag: treatment (primary tumor)


title: AUR-AFEC-TTM3-A-1-1-D-A746-37

value: Metastatic tumor

value: Liver

value: Fresh frozen


title: AUR-AFEC-TTM6-A-1-1-D-A746-37

value: Pleura


title: human breast cancer total RNA expression [AUR-AER6-TTM3-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AER6-TTM3-A-1-1-R-A742-41

tag: disease

value: Diaphragm

tag: genotype

tag: treatment

value: Metastasis

tag: time


title: 413

tag: disease state

value: Coronary Artery Disease

tag: age

tag: bmi

tag: sbp

tag: dbp

tag: hr

tag: ef %

tag: dyslipidemia

value: Yes

tag: hypertension

value: No

tag: diabetes mellitus


title: human breast cancer total RNA expression [AUR-AER6-TTM2-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AER6-TTM2-A-1-1-R-A742-41

tag: tissue

value: Thyroid

value: Autopsy


title: AUR-AFEA-TTP2-A-1-0-D-A746-37

tag: Sex

tag: sample type

tag: tissue type

tag: autopsy

value: Post-treatment


title: AUR-AFEC-TTM1-A-1-1-D-A746-37


title: human breast cancer total RNA expression [AUR-AER6-TTP1-A-1-0-R-A741-41]

description:
FFPE
AUR-AER6-TTP1-A-1-0-R-A741-41

tag: disease

tag: genotype

tag: treatment


title: 412

value: Whole blood

tag: disease state

value: F

tag: age

tag: family history_of_cad

tag: smoking

value: Never

tag: asa

value: N

tag: cad

value: LOW

tag: %stenosis

tag: rnaseq group


title: 410

value: M

tag: bmi

tag: sbp

tag: dbp

tag: hr

tag: ef %

tag: dyslipidemia

tag: hypertension

tag: diabetes mellitus

value: Y

value: CAD


title: AUR-AFEA-TTM6-A-1-0-D-A746-37

tag: Sex

value: Female

tag: sample type

value: Metastatic tumor

tag: tissue

value: Lymph node

tag: tissue type

value: Fresh frozen

tag: autopsy


title: 416

tag: disease state

value: Coronary Artery Disease

tag: age

value: Yes

tag: family history_of_cad

tag: smoking

tag: asa


title: human breast cancer total RNA expression [AUR-AER7-TTM4-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AER7-TTM4-A-1-1-R-A742-41

tag: disease

tag: genotype

tag: treatment

value: Metastasis

tag: time


title: AUR-AFEA-TTM3-A-1-1-D-A746-37

value: Lung

value: Autopsy


title: human breast cancer total RNA expression [AUR-AER7-TTP1-A-1-0-R-A741-41]

description:
FFPE
AUR-AER7-TTP1-A-1-0-R-A741-41

value: Primary tumor

value: Breast

value: Pre-treatment


title: AUR-AFEA-TTM4-A-1-1-D-A746-37


title: AUR-AFEA-TTM2-A-1-1-D-A746-37

value: Brain


title: AUR-AFEA-TTM1-A-1-1-D-A746-37


title: AUR-AFE9-TTM4-A-1-1-D-A746-37

value: Liver


title: human breast cancer total RNA expression [AUR-AFUI-TTM1-A-1-0-R-A743-41]

description:
Fresh frozen
AUR-AFUI-TTM1-A-1-0-R-A743-41

value: Chest

value: Non-Autopsy


title: 408

value: Whole blood

value: F

tag: bmi

tag: sbp

tag: dbp

tag: hr

tag: ef %

tag: dyslipidemia

value: No

value: Never

value: N

tag: cad

value: LOW

tag: %stenosis

tag: rnaseq group


title: 407

tag: tissue

tag: disease state

value: Coronary Artery Disease

tag: Sex

value: M

tag: age

value: Yes

tag: hypertension

tag: diabetes mellitus

value: Y

value: CAD


title: AUR-AFE9-TTM3-A-1-1-D-A746-37

value: Female

tag: sample type

value: Metastatic tumor

value: Adrenal

tag: tissue type

value: Fresh frozen

tag: autopsy

value: Autopsy


title: AUR-AFEA-TTM6-A-1-0-D-A78F-37

description: Replicate data merged with AUR-AFEA-TTM6-A-1-0-D-A746-37 in the processed data file

value: Lymph node


title: 406

value: Whole blood

tag: bmi

tag: sbp

tag: family history_of_cad

tag: smoking

tag: asa

value: MID


title: human breast cancer total RNA expression [AUR-AE5H-TTM1-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AE5H-TTM1-A-1-1-R-A742-41

tag: disease

value: Skin

tag: genotype

tag: treatment

value: Metastasis

tag: time

value: Non-Autopsy


title: AUR-AFE7-TTP2-A-1-1-D-A746-37

value: Primary tumor

tag: tissue

value: Breast

tag: treatment (primary tumor)

value: Post-treatment


title: human breast cancer total RNA expression [AUR-AE6Y-TTM1-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AE6Y-TTM1-A-1-1-R-A742-41

value: Lung


title: 405

tag: disease state

value: Coronary Artery Disease

tag: Sex

value: M

tag: age

tag: dbp

tag: hr

tag: ef %

tag: dyslipidemia

value: Yes

value: No

value: Never

value: Y

tag: cad

tag: %stenosis

tag: rnaseq group


title: human breast cancer total RNA expression [AUR-AFUI-TTP1-A-1-0-R-A743-41]

description:
FFPE
AUR-AFUI-TTP1-A-1-0-R-A743-41

value: Female

value: Pre-treatment


title: human breast cancer total RNA expression [AUR-AE5H-TTP1-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AE5H-TTP1-A-1-1-R-A742-41


title: AUR-AFE6-TTM2-A-1-1-D-A746-37

tag: sample type

value: Metastatic tumor

tag: tissue type

value: Fresh frozen

tag: autopsy

value: Autopsy


title: AUR-AFE9-TTM1-A-1-1-D-A746-37

value: Brain


title: AUR-AFE7-TTM3-A-1-1-D-A746-37


title: AUR-AFE7-TTM1-A-1-1-D-A746-37

value: Lymph node


title: 404

value: Whole blood

value: F

tag: bmi

tag: sbp

tag: hypertension

tag: diabetes mellitus

tag: family history_of_cad

tag: smoking

tag: asa

value: CAD


title: AUR-AFEC-NT1-A-1-1-D-A746-37

source_name: Fresh frozen normal breast

tag: Sex

value: Normal tissue

tag: tissue

value: Breast


title: AUR-AFE7-TTM2-A-1-1-D-A746-37


title: AUR-AFE7-NT1-A-1-1-D-A746-37


title: AUR-AFE6-TTM1-A-1-1-D-A746-37

value: Chest


title: human breast cancer total RNA expression [AUR-AE6Y-TTP1-A-1-0-R-A741-41]

description:
FFPE
AUR-AE6Y-TTP1-A-1-0-R-A741-41

tag: disease

value: Primary tumor

tag: genotype

tag: treatment

tag: time

value: Non-Autopsy


title: AUR-AFE5-TTM9-A-1-1-D-A745-37

value: Spleen


title: human breast cancer total RNA expression [AUR-AFR5-TTM1-A-1-1-R-A743-41]

description:
Fresh frozen
AUR-AFR5-TTM1-A-1-1-R-A743-41

value: Metastasis


title: 403

tag: disease state

value: Coronary Artery Disease

tag: age

tag: dbp

tag: hr

tag: ef %

tag: dyslipidemia

value: Yes

value: No

value: Never

value: N

tag: cad

value: LOW

tag: %stenosis

tag: rnaseq group


title: 409

value: M

tag: bmi

tag: sbp

tag: hypertension

tag: diabetes mellitus

tag: family history_of_cad

tag: smoking

value: Current


title: AUR-AFE5-TTP1-A-1-0-D-A745-37

tag: Sex

value: Female

tag: sample type

tag: tissue

tag: tissue type

value: FFPE

tag: autopsy

value: Autopsy

tag: treatment (primary tumor)

value: Post-treatment


title: 402

value: Whole blood

tag: disease state

tag: age

tag: dbp

tag: hr

tag: ef %

tag: asa


title: human breast cancer total RNA expression [AUR-AFR5-TTP1-A-1-1-R-A743-41]

description:
Fresh frozen
AUR-AFR5-TTP1-A-1-1-R-A743-41

tag: disease

value: Primary tumor

value: Breast

tag: genotype

tag: treatment

tag: time


title: 401

tag: bmi

tag: sbp

tag: dyslipidemia

tag: hypertension

tag: diabetes mellitus

tag: family history_of_cad

tag: smoking

value: Y

tag: cad

value: CAD

tag: %stenosis

tag: rnaseq group


title: AUR-AFE5-TTM8-A-1-1-D-A745-37

tag: Sex

tag: sample type

value: Metastatic tumor

tag: tissue

value: Liver

tag: tissue type

value: Fresh frozen

tag: autopsy


title: AUR-AFE5-TTM7-A-1-1-D-A745-37

value: Peritoneum


title: 400

tag: disease state

value: Coronary Artery Disease

value: F

tag: age

tag: dbp

tag: hr

tag: ef %

value: Yes

value: Former

tag: asa


title: human breast cancer total RNA expression [AUR-AFSL-TTM1-A-8-0-R-A741-41]

description:
FFPE
AUR-AFSL-TTM1-A-8-0-R-A741-41

tag: disease

value: Lymph node

tag: genotype

value: Female

tag: treatment

value: Metastasis

tag: time

value: Non-Autopsy


title: AUR-AFE5-TTM5-A-1-1-D-A745-37

value: Diaphragm

value: Autopsy


title: AUR-AFE5-TTM4-A-1-1-D-A745-37


title: AUR-AFE5-TTM2-A-1-1-D-A745-37

value: Brain


title: AUR-AFE5-TTM10-A-1-1-D-A745-37

value: Kidney


title: human breast cancer total RNA expression [AUR-AFSL-TTP1-A-8-0-R-A741-41]

description:
FFPE
AUR-AFSL-TTP1-A-8-0-R-A741-41

value: Primary tumor

value: Breast

value: Post-treatment


title: human breast cancer total RNA expression [AUR-AF95-TTM1-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AF95-TTM1-A-1-1-R-A742-41

value: Metastatic tumor

value: Chest


title: 396

value: Whole blood

value: Coronary Artery Disease

value: M

tag: bmi

tag: sbp

tag: dyslipidemia

value: No

tag: hypertension

tag: diabetes mellitus

tag: family history_of_cad

tag: smoking

value: Y

tag: cad

value: CAD

tag: %stenosis


title: 395

tag: tissue

tag: disease state

tag: Sex

tag: age

tag: dbp

value: Yes

value: Never

value: N

value: LOW

tag: rnaseq group


title: AUR-AFE4-TTM5-A-1-1-D-A745-37

value: Female

tag: sample type

value: Pericardium

tag: tissue type

value: Fresh frozen

tag: autopsy

value: Autopsy


title: AUR-AFE5-TTM1-A-1-1-D-A745-37

value: Bone


title: human breast cancer total RNA expression [AUR-AF98-TTM1-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AF98-TTM1-A-1-1-R-A742-41

tag: disease

value: Metastatic tumor

tag: genotype

tag: treatment

value: Metastasis

tag: time

value: Non-Autopsy


title: human breast cancer total RNA expression [AUR-AF95-TTP1-A-1-0-R-A741-41]

description:
FFPE
AUR-AF95-TTP1-A-1-0-R-A741-41

value: Primary tumor

value: Breast

value: Pre-treatment


title: AUR-AFE5-TTM6-A-1-1-D-A745-37

value: Lung


title: AUR-AFE4-TTM2-A-1-1-D-A745-37

value: Lymph node


title: human breast cancer total RNA expression [AUR-AF98-TTP1-A-1-0-R-A741-41]

description:
FFPE
AUR-AF98-TTP1-A-1-0-R-A741-41

value: Post-treatment


title: 392

value: Whole blood

value: Coronary Artery Disease

value: F

tag: bmi

tag: sbp

tag: hr

tag: ef %

tag: dyslipidemia

value: No

tag: hypertension

value: Yes

tag: diabetes mellitus

tag: family history_of_cad

value: Former

tag: asa


title: 394

tag: tissue

tag: disease state

tag: Sex

value: M

tag: age

tag: dbp

tag: smoking

value: Never

value: N

tag: cad

value: LOW

tag: %stenosis

tag: rnaseq group


title: AUR-AFE4-TTM3-A-1-1-D-A745-37

value: Female

tag: sample type

value: Metastatic tumor

tag: tissue type

value: Fresh frozen

tag: autopsy

value: Autopsy


title: human breast cancer total RNA expression [AUR-AF9A-TTM1-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AF9A-TTM1-A-1-1-R-A742-41

tag: disease

value: Liver

tag: genotype

tag: treatment

value: Metastasis

tag: time

value: Non-Autopsy


title: AUR-AFE4-TTM4-A-1-1-D-A745-37

value: Pancreas


title: 393

value: Whole blood

value: Coronary Artery Disease

tag: bmi

tag: sbp

tag: hr

tag: ef %

tag: dyslipidemia

tag: hypertension

tag: diabetes mellitus

tag: family history_of_cad

tag: asa

value: Y

value: MID


title: AUR-AFE4-TTM1-A-1-1-D-A745-37

tag: Sex

tag: tissue

value: Lung


title: 398

tag: disease state

value: M

tag: age

tag: dbp

value: No

tag: smoking

value: Former

tag: cad

tag: %stenosis

tag: rnaseq group


title: AUR-AF9A-TTP1-A-1-0-D-A745-37

tag: sample type

value: Primary tumor

value: Breast

tag: tissue type

value: FFPE

tag: autopsy

tag: treatment (primary tumor)

value: Post-treatment


title: AUR-AF99-TTM1-A-1-1-D-A745-37

value: Female

value: Metastatic tumor

value: Soft Tissue

value: Fresh frozen


title: 391

tag: bmi

tag: sbp

tag: hr

tag: ef %

tag: dyslipidemia

tag: hypertension

value: Yes

value: N

value: LOW


title: human breast cancer total RNA expression [AUR-AF9A-TTP1-A-1-0-R-A741-41]

description:
FFPE
AUR-AF9A-TTP1-A-1-0-R-A741-41

tag: disease

tag: tissue

tag: genotype

tag: treatment

tag: time

value: Non-Autopsy


title: AUR-AF98-TTP1-A-1-0-D-A745-37

tag: Sex


title: AUR-AFE4-TTM6-A-1-1-D-A745-37

value: Liver

value: Autopsy


title: AUR-AF98-TTM1-A-1-1-D-A745-37

value: Chest


title: AUR-AF95-TTP1-A-1-0-D-A745-37

value: Pre-treatment


title: 390

value: Whole blood

tag: disease state

value: Coronary Artery Disease

value: F

tag: age

tag: dbp

tag: diabetes mellitus

value: No

tag: family history_of_cad

tag: smoking

value: Former

tag: asa

value: Y

tag: cad

value: CAD

tag: %stenosis

tag: rnaseq group


title: AUR-AF95-TTM1-A-1-1-D-A745-37

value: Female

tag: sample type

value: Metastatic tumor

tag: tissue type

tag: autopsy


title: 388

tag: tissue

value: M

tag: bmi

tag: sbp

tag: hr

tag: ef %

tag: dyslipidemia

value: Yes

tag: hypertension

value: Current

value: MID


title: AUR-AF94-TTP1-A-1-0-D-A78F-37

description: Replicate data merged with AUR-AF94-TTP1-A-1-0-D-A745-37 in the processed data file

tag: Sex

value: Primary tumor

value: Breast

value: FFPE

value: Non-Autopsy

tag: treatment (primary tumor)


title: 389

value: Whole blood

tag: disease state

tag: age

tag: dbp

tag: diabetes mellitus

tag: family history_of_cad

tag: smoking


title: human breast cancer total RNA expression [AUR-AFSP-TTM1-A-8-0-R-A741-41]

description:
FFPE
AUR-AFSP-TTM1-A-8-0-R-A741-41

tag: disease

value: Pleura

tag: genotype

tag: treatment

value: Metastasis

tag: time


title: human breast cancer total RNA expression [AUR-AFSP-TTP1-A-8-0-R-A741-41]

description:
FFPE
AUR-AFSP-TTP1-A-8-0-R-A741-41

tag: tissue

value: Pre-treatment


title: AUR-AF9A-TTM1-A-1-1-D-A745-37

tag: sample type

value: Liver

tag: tissue type

value: Fresh frozen

tag: autopsy


title: AUR-AF94-TTP1-A-1-0-D-A745-37


title: AUR-AF94-TTM1-A-1-1-D-A745-37


title: AUR-AERX-TTP1-A-1-0-D-A78F-37

description: Replicate data merged with AUR-AERX-TTP1-A-1-0-D-A745-37 in the processed data file


title: human breast cancer total RNA expression [AUR-AG0M-TTM1-A-2-1-R-A743-41]

description:
Fresh frozen
AUR-AG0M-TTM1-A-2-1-R-A743-41

value: Chest


title: AUR-AERY-TTM1-A-1-1-D-A745-37

value: Female


title: 387

value: Coronary Artery Disease

value: F

tag: bmi

tag: sbp

tag: hr

tag: ef %

tag: dyslipidemia

tag: hypertension

value: No

value: Former

tag: asa

value: Y

tag: cad

tag: %stenosis

tag: rnaseq group


title: AUR-AERX-TTP1-A-1-0-D-A745-37

tag: Sex

value: Primary tumor

tag: treatment (primary tumor)


title: 386

tag: disease state

tag: age

tag: dbp

value: Yes

tag: diabetes mellitus

tag: family history_of_cad

tag: smoking

value: Never

value: MID


title: human breast cancer total RNA expression [AUR-AG0M-TTP1-A-2-0-R-A741-41]

description:
FFPE
AUR-AG0M-TTP1-A-2-0-R-A741-41

tag: disease

tag: tissue

value: Breast

tag: genotype

tag: treatment

tag: time

value: Non-Autopsy


title: AUR-AERW-TTP1-B-1-0-D-A745-37

tag: sample type

tag: tissue type

value: FFPE

tag: autopsy

value: Post-treatment


title: 385

value: Whole blood

tag: bmi

tag: sbp

tag: hr

tag: ef %

tag: dyslipidemia

tag: hypertension

tag: asa

tag: cad

value: CAD

tag: %stenosis

tag: rnaseq group


title: human breast cancer total RNA expression [AUR-AG0J-TTM1-A-1-0-R-A743-41]

description:
Fresh frozen
AUR-AG0J-TTM1-A-1-0-R-A743-41

tag: disease

value: Metastatic tumor

tag: tissue

value: Soft tissue

value: Metastasis


title: AUR-AER8-TTM2-A-1-1-D-A745-37

tag: Sex

value: Female

value: Liver

value: Fresh frozen

value: Autopsy


title: human breast cancer total RNA expression [AUR-AG0J-TTP1-A-1-0-R-A741-41]

description:
FFPE
AUR-AG0J-TTP1-A-1-0-R-A741-41

value: Primary tumor

tag: genotype

tag: treatment

value: Pre-treatment

tag: time


title: AUR-AF98-TTP1-A-1-0-D-A78F-37

description: Replicate data merged with AUR-AF98-TTP1-A-1-0-D-A745-37 in the processed data file

tag: sample type

tag: tissue type

tag: autopsy

tag: treatment (primary tumor)


title: 384

tag: disease state

value: Coronary Artery Disease

value: M

tag: age

tag: bmi

tag: sbp

tag: dbp

tag: hr

tag: ef %

value: Yes

value: No

tag: diabetes mellitus

tag: family history_of_cad

tag: smoking

value: Former

value: Y


title: AUR-AER8-TTM1-A-1-1-D-A745-37

tag: Sex

tag: tissue


title: human breast cancer total RNA expression [AUR-AG0N-TTM1-A-1-1-R-A743-41]

description:
Fresh frozen
AUR-AG0N-TTM1-A-1-1-R-A743-41

tag: disease

value: Lymph node

tag: genotype

tag: treatment

tag: time

value: Non-Autopsy


title: AUR-AER8-NT1-A-1-1-D-A745-37

tag: sample type

value: Normal tissue

value: Breast

tag: tissue type

tag: autopsy


title: 383

value: Whole blood

tag: disease state

value: F

tag: age

tag: bmi

tag: dyslipidemia

tag: hypertension

tag: asa

value: N

tag: cad

value: LOW

tag: %stenosis

tag: rnaseq group


title: AUR-AER7-TTM4-A-1-1-D-A745-37

tag: Sex

value: Female

value: Metastatic tumor

tag: tissue

value: Fresh frozen

value: Autopsy


title: 382

value: Coronary Artery Disease

tag: sbp

tag: dbp

tag: hr

tag: ef %

tag: diabetes mellitus

tag: family history_of_cad

tag: smoking

value: Never

value: CAD


title: 381

tag: disease state

value: M

tag: age

value: Yes

value: No

value: Former


title: human breast cancer total RNA expression [AUR-AFE5-TTM9-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AFE5-TTM9-A-1-1-R-A742-41

tag: disease

value: Spleen

tag: genotype

tag: treatment

value: Metastasis

tag: time


title: AUR-AER6-TTP1-A-1-0-D-A745-37

tag: sample type

value: Primary tumor

value: Breast

tag: tissue type

value: FFPE

tag: autopsy

tag: treatment (primary tumor)

value: Post-treatment


title: AUR-AER7-TTM1-A-1-1-D-A745-37

tag: Sex

value: Female

tag: tissue

value: Liver


title: AUR-AER7-TTM2-A-1-1-D-A745-37

value: Metastatic tumor

value: Lung

value: Fresh frozen


title: AUR-AER8-TTP1-A-1-0-D-A745-37

value: Autopsy


title: 379

value: Whole blood

value: Coronary Artery Disease

tag: bmi

tag: sbp

tag: dbp

tag: hr

tag: dyslipidemia

tag: hypertension

value: Never

tag: asa

value: Y

tag: cad

value: CAD

tag: %stenosis

tag: rnaseq group


title: AUR-AER6-TTM7-A-1-1-D-A745-37

value: Soft tissue


title: AUR-AER6-TTM9-A-1-1-D-A745-37


title: human breast cancer total RNA expression [AUR-AFE5-TTP1-A-1-0-R-A741-41]

description:
FFPE
AUR-AFE5-TTP1-A-1-0-R-A741-41

tag: disease

tag: genotype

tag: treatment

tag: time


title: 378

tag: disease state

value: F

tag: age

tag: ef %

value: No

tag: diabetes mellitus

tag: family history_of_cad

tag: smoking

value: Former

value: N

value: LOW


title: AUR-AER6-TTM5-A-1-1-D-A745-37

tag: Sex

value: Female

tag: sample type

tag: tissue

value: Stomach

tag: tissue type

tag: autopsy


title: AUR-AER6-TTM3-A-1-1-D-A745-37

value: Metastatic tumor

value: Diaphragm


title: AUR-AER6-TTM10-A-1-1-D-A745-37

value: Peritoneum

value: Fresh frozen


title: AUR-AER6-TTM2-A-1-1-D-A745-37

value: Thyroid

value: Autopsy


title: human breast cancer total RNA expression [AUR-AD9G-TTM2-A-1-1-R-A542-39]

description:
Fresh frozen
AUR-AD9G-TTM2-A-1-1-R-A542-39

value: Liver

value: Metastasis


title: 377

value: Whole blood

value: Coronary Artery Disease

value: M

tag: bmi

tag: sbp

tag: dbp

tag: hr

tag: dyslipidemia

value: Yes

tag: hypertension

value: Never

tag: asa

value: Y

tag: cad

value: MID

tag: %stenosis


title: human breast cancer total RNA expression [AUR-AD9G-TTM3-A-1-1-R-A542-39]

description:
Fresh frozen
AUR-AD9G-TTM3-A-1-1-R-A542-39

tag: disease

value: Adrenal

tag: genotype

value: Female

tag: treatment

tag: time


title: 376

tag: disease state

tag: Sex

value: F

tag: age

tag: ef %

value: No

tag: diabetes mellitus

tag: family history_of_cad

tag: smoking

value: N

value: LOW

tag: rnaseq group


title: AUR-AER6-TTM1-A-1-1-D-A745-37

tag: sample type

value: Metastatic tumor

tag: tissue

value: Skin

tag: tissue type

value: Fresh frozen

tag: autopsy


title: human breast cancer total RNA expression [AUR-AD9G-TTP1-B-4-0-R-A584-39]

description:
FFPE
AUR-AD9G-TTP1-B-4-0-R-A584-39

value: Primary tumor

value: Breast

value: Pre-treatment

value: Autopsy


title: AUR-AER5-TTP2-A-1-1-D-A745-37

tag: treatment (primary tumor)

value: Post-treatment


title: human breast cancer total RNA expression [AUR-AG0N-TTP1-A-1-0-R-A741-41]

description:
FFPE
AUR-AG0N-TTP1-A-1-0-R-A741-41

tag: disease

value: Non-Autopsy


title: 374

value: Whole blood

value: Coronary Artery Disease

tag: bmi

tag: sbp

tag: dbp

tag: hr

tag: dyslipidemia

tag: hypertension

value: Yes

value: Former

tag: asa

tag: cad

tag: %stenosis


title: human breast cancer total RNA expression [AUR-AFE7-TTM3-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AFE7-TTM3-A-1-1-R-A742-41

value: Lung

tag: genotype

value: Female

tag: treatment

value: Metastasis

tag: time


title: AUR-AER5-TTM5-A-1-1-D-A745-37

tag: Sex

tag: sample type

tag: tissue


title: human breast cancer total RNA expression [AUR-AFE5-TTM4-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AFE5-TTM4-A-1-1-R-A742-41

value: Lymph node


title: AUR-AER4-TTM2-A-1-1-D-A745-37

value: Metastatic tumor

value: Liver

tag: tissue type

tag: autopsy


title: AUR-AER6-TTM6-A-1-1-D-A745-37

value: Rectum

value: Fresh frozen


title: human breast cancer total RNA expression [AUR-AFE7-TTM1-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AFE7-TTM1-A-1-1-R-A742-41

tag: disease


title: AUR-AER2-TTP1-A-1-1-D-A745-37

value: Primary tumor

value: Breast

tag: treatment (primary tumor)


title: AUR-AER4-TTM1-A-1-1-D-A745-37

value: Autopsy


title: 372

tag: disease state

value: M

tag: age

tag: bmi

tag: sbp

tag: dbp

tag: ef %

value: No

tag: diabetes mellitus

tag: family history_of_cad

tag: smoking

value: Never

value: N

value: LOW

tag: rnaseq group


title: 370

value: Whole blood

value: Coronary Artery Disease

tag: Sex

tag: hr

tag: dyslipidemia

value: Yes

tag: hypertension

tag: asa

tag: cad

tag: %stenosis


title: 373

tag: tissue

tag: disease state

value: Former


title: human breast cancer total RNA expression [AUR-AFE7-TTP2-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AFE7-TTP2-A-1-1-R-A742-41

tag: disease

tag: genotype

value: Female

tag: treatment

value: Post-treatment

tag: time


title: 369

tag: age

tag: bmi

tag: sbp

tag: dbp

tag: ef %

tag: diabetes mellitus

value: Current

value: Y

value: MID


title: human breast cancer total RNA expression [AUR-AFE7-TTM2-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AFE7-TTM2-A-1-1-R-A742-41

value: Metastatic tumor

value: Lymph node

value: Metastasis


title: AUR-AEPZ-TTM1-A-1-1-D-A745-37

tag: Sex

tag: sample type

value: Ovary

tag: tissue type

value: Fresh frozen

tag: autopsy

value: Non-Autopsy


title: AUR-AER2-TTM1-A-1-1-D-A745-37

value: Liver

value: Autopsy


title: AUR-AE6Y-TTP1-A-1-0-D-A745-37

value: Primary tumor

value: Breast

value: FFPE

tag: treatment (primary tumor)

value: Pre-treatment


title: human breast cancer total RNA expression [AUR-AFEA-TTM6-A-1-0-R-A741-41]

description:
Fresh frozen
AUR-AFEA-TTM6-A-1-0-R-A741-41

tag: tissue

value: Female


title: AUR-AER2-TTM3-A-1-1-D-A745-37

value: Soft tissue


title: AUR-AER5-TTP3-A-1-0-D-A745-37

value: Post-treatment


title: 368

value: Whole blood

tag: disease state

value: Coronary Artery Disease

value: F

tag: hr

tag: dyslipidemia

value: Yes

tag: hypertension

value: No

tag: family history_of_cad

tag: smoking

value: Former

tag: asa

value: Y

tag: cad

tag: %stenosis

tag: rnaseq group


title: AUR-AE6Y-TTM1-A-1-1-D-A745-37

value: Metastatic tumor

value: Lung

value: Fresh frozen

value: Non-Autopsy


title: human breast cancer total RNA expression [AUR-AFEA-TTM3-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AFEA-TTM3-A-1-1-R-A742-41

tag: disease

tag: genotype

tag: treatment

value: Metastasis

tag: time

value: Autopsy


title: AUR-AE6X-TTM1-A-1-1-D-A745-37

tag: Sex

tag: sample type

value: Liver

tag: tissue type

tag: autopsy


title: human breast cancer total RNA expression [AUR-AFEA-TTM1-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AFEA-TTM1-A-1-1-R-A742-41

tag: tissue

value: Brain

value: Female


title: AUR-AE5H-TTP1-A-1-1-D-A745-37

value: Primary tumor

value: Breast

tag: treatment (primary tumor)

value: Pre-treatment


title: AUR-AER5-TTM4-A-1-1-D-A745-37


title: 366

value: Whole blood

tag: disease state

value: Coronary Artery Disease

value: F

tag: age

tag: bmi

tag: sbp

tag: dbp

tag: hr

tag: ef %

tag: dyslipidemia

tag: hypertension

tag: diabetes mellitus

value: Never

value: N

value: LOW


title: AUR-AE5G-TTP1-A-1-1-D-A745-37


title: human breast cancer total RNA expression [AUR-AFEA-TTM2-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AFEA-TTM2-A-1-1-R-A742-41

tag: disease

value: Metastatic tumor

tag: genotype

tag: treatment

tag: time


title: 365

tag: Sex

value: M

value: No

value: Yes

tag: family history_of_cad

tag: smoking

value: Current

tag: asa

tag: cad

tag: %stenosis

tag: rnaseq group


title: AUR-AE5G-TTM1-A-1-1-D-A745-37

tag: sample type

tag: tissue

tag: tissue type

value: Fresh frozen

tag: autopsy

value: Non-Autopsy


title: AUR-AE5G-NT1-A-1-1-D-A745-37

value: Female

value: Normal tissue


title: 364

tag: disease state

tag: age

tag: bmi

tag: sbp

tag: dbp

tag: hr

tag: ef %

tag: dyslipidemia

tag: hypertension

value: Former


title: AUR-AEPZ-TTP1-A-1-1-D-A745-37

tag: Sex

value: Primary tumor

value: Breast

tag: treatment (primary tumor)

value: Pre-treatment


title: human breast cancer total RNA expression [AUR-AFEA-TTP1-A-1-0-R-A741-41]

description:
FFPE
AUR-AFEA-TTP1-A-1-0-R-A741-41

tag: disease

tag: genotype

tag: treatment

tag: time

value: Autopsy


title: AUR-AD9I-TTM3-A-1-1-D-A531-37

tag: sample type

tag: tissue

value: Liver

tag: tissue type


title: 9830-020185A-R0i_CP-3046

description: HiSeq2500 HO

source_name: Normal Breast tissue

tag: cell type

value: Healty tissue


title: AUR-ADCB-TTP1-A-13-0-D-A745-37

value: FFPE

tag: autopsy


title: AUR-AD9I-NT1-A-1-1-D-A531-37

source_name: Fresh frozen normal liver


title: AUR-AD9H-TTM3-A-1-1-D-A531-37

value: Metastatic tumor


title: AUR-ADCB-TTP1-A-13-0-D-A78F-37

description: Replicate data merged with AUR-ADCB-TTP1-A-13-0-D-A745-37 in the processed data file


title: human breast cancer total RNA expression [AUR-AFEA-TTM4-A-1-1-R-A742-41]

description:
Fresh frozen
AUR-AFEA-TTM4-A-1-1-R-A742-41

value: Lymph node

value: Metastasis


title: 361

value: Whole blood

tag: disease state

value: Coronary Artery Disease

value: M

tag: age

tag: bmi

tag: sbp

value: Yes

tag: diabetes mellitus

value: No

tag: family history_of_cad

tag: smoking

tag: asa

value: N

tag: cad

value: LOW

tag: %stenosis

tag: rnaseq group


title: 363

tag: Sex

value: F

tag: dbp

tag: hr

tag: ef %

tag: dyslipidemia

tag: hypertension

value: Never


title: 9830-010214A-R0i_CP-3045

description: HiSeq2500 HO

tag: cell type

tag: tissue type

value: Fresh frozen


title: A4-Breast-NL-R0i_CP-3047

description: HiSeq2500 HO


title: AUR-ADCB-TTM1-A-1-1-D-A745-37

value: Female

tag: sample type

tag: tissue

value: Lung

tag: autopsy

value: Non-Autopsy


title: AUR-AD9H-TTM1-A-2-1-D-A531-37

value: Pleura

value: Autopsy


title: 367

tag: disease state

tag: age

tag: bmi

tag: sbp

tag: diabetes mellitus

tag: family history_of_cad


title: AUR-AE5H-TTM1-A-1-1-D-A745-37

tag: Sex

value: Metastatic tumor

value: Skin


title: 362

value: Whole blood

tag: dbp

tag: smoking

tag: asa

tag: cad

tag: %stenosis

tag: rnaseq group


title: AUR-AD9G-TTP1-B-4-0-D-A585-37

value: Primary tumor

value: Breast

tag: tissue type

value: FFPE

tag: treatment (primary tumor)

value: Pre-treatment


title: AUR-AD9H-TTM2-A-1-1-D-A531-37

tag: sample type

tag: tissue

value: Liver