title: cortical organoids, D18 and D35, scRNAseq

city: Irvine

first: Yuan-Chen

last: Tsai

address: 845 Health Sciences Road

department: Anatomy and Neurobiology

institute: University of California, Irvine

description: Samples KS30_D18, KS31_D18, KS29_D35, KS30_D35.

data_processing:
Gene expression count matrices were constructed by aligning FASTQ files using Split-pipe v0.9.6 by Parse Biosciences
Cells expressing fewer than 500 unique genes, or more than 10,000 genes were removed.
Cells with more than 5% of their total gene expression contributed by mitochondrial genes were removed.
Assembly: GRCh38
Supplementary files format and content: h5ad, csv, txt and mtx files

source_name: Brain cortical organoid

growth_protocol: At ~70-80% confluency, the H9 cells were passaged to maintain the cell line and dissociated to generate organoids. After dissociation, 9,000 cells per well were plated into low-attachment v-bottom 96-well plates (Sumitomo Bakelite, MS9096V) to form aggregates, in the medium consisting of Glasgow’s Minimal Essential Medium (GMEM, Invitrogen), 20% KSR, NEAA, 100 mg/mL of Primocin, 0.1 mM b-mercaptoethanol, sodium pyruvate (Invitrogen), Wnt inhibitor IWR-1-endo (Calbiochem), and TGF-b inhibitor SB431542 (Stemgent). ROCK inhibitor Y-27632 (20 µM, BioPioneer) was added in the medium from D0 to D6 to prevent cell death. From D0-D18, the organoids were maintained at 5% CO2, 37°C, and half of the medium was changed every 2 days. From D18-D35, the organoids were transferred to 60mm dishes and cultured in a medium consisting DMEM/F12 with N2 (Invitrogen), GlutaMAX, chemically defined lipid concentrate (CDLC, Invitrogen), and 0.4% methylcellulose (Sigma) at 5% CO2, 40% O2, and 37°C. The medium was refreshed every 2 days.

extract_protocol:
Organoids were collected at D18 (160 organoids) and D35 (25 organoids). The organoids were dissociated into single-cell suspension by using Papain Dissociation System (Worthington) following the manufacturer’s manual. The dead cells in the single-cell suspension were removed by using EasySep™ Dead Cell Removal (Annexin V) Kit (STEMCELL Technologies) following manufacturer’s manual. The cell suspension was then passed through a 40m cell strainer before assessing the cell number and viability. Samples with total cell numbers >1,000,000 and >80% viability were further processed for cell fixation and freezing following Parse Biosciences User Manual.
The samples were then sent to Genomics Research and Technology Hub, UCI, for barcoding and library preparation using Evercode WT kit (Parse Biosciences). For barcoding, the mRNA in single cells was reversed transcribed by using poly T and random hexamer primers and 3 barcodes, an Illumina adaptor and a biotin molecule were attached to the cDNA. After cell lysis, the cDNA amplification was performed by a PCR reaction to amplify double-strand cDNA using TS primer and R2 Illumina primer. The sublibrary cDNA was fragmented and ligated with a second  Illumina adaptor. A final PCR was performed to amplify the fragmented cDNA, and the fourth DNA barcode, P5 and P7 adaptors were attached.

value: Brain cortical organoid

tag: time

value: Organoids were collected at D18 and D35 (mixed samples)


title: ITGB4-NC2_raw

status: Public on Jun 07 2024

type: SRA

city: changsha

first: ruijiang

last: Zeng

address: No.139 Renmin Road Central

country: China

institute: The Second Xiangya Hospital of Central South University

library_source: transcriptomic

data_processing:
Total RNA qualification
mRNA enrichment
Double-strand cDNA synthesis
End repair, ploy-A & adaptor addition
Fragment selection and PCR
Library qualty assessement
illumina sequencing
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read count values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: bladder

growth_protocol: RT4 cells were cultured in Mycoy' s 5A medium supplemented with 10% fetal bovine serum (FBS) and incubated at 37 °C in 5% CO2.

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.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® following manufacturer's protocols.

tag: tissue

value: bladder

tag: cell line

value: RT4 cells

tag: cell type

value: bladder cancer cells

tag: group

value: the control group of overexpression of ITGB5 by plasmid

tag: treatment

value: transfection infection


title: CTL_dup1

status: Public on Jun 08 2024

city: Jiangsu

first: Boxiang

last: Qi

address: 18 Sudi north road, Xuzhou, Jiangsu

institute: Xuzhou Children Hospital

description: sham group, biological duplication#1

data_processing:
The obtained sequencing data fastq files were subjected to quality control: filtering to remove low-quality reads and trimming adapter sequences using fastp software (https://github.com/OpenGene/fastp) under the default parameters.
The clean raw data were quantified to generate an expression matrix by Salmon software (https://salmon.readthedocs.io/en/latest/salmon.html) using an index (made by salmon index command) based on the well-annotated Mus musculus transcriptome (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001635.27/) from NCBI.
Assembly: Genome assemblyGRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Mus musculus

source_name: hippocampus

extract_protocol:
High-quality total RNA from hippocampus tissues of sham, SAE, and CCLF mice were extracted using RNeasy Micro Kit (Cat: 74004, Qiagen) following the manufacturer’s instructions
For bulk sequencing libraries, the ribosomal RNAs were removed using Ribo-off rRNA Depletion Kit (Cat:#N406, Vazyme), and 200 ng obtain products were used as the input of VAHTS Universal V10 RNA-seq Library Prep Kit for Illumina (Cat: NR606, Vazyme)

value: hippocampus

value: sham group


title: ITGB4-EX1_raw

value: the treat group of overexpression of ITGB4 by plasmid


title: ITGB4-NC1_raw

value: the control group of overexpression of ITGB4 by plasmid


title: RB50 5% CO2 sample 1

city: Chapel Hill

first: Peggy

middle: A.

last: Cotter

state: North Carolina

address: 125 Mason Farm Rd, 6101 Marsico Hall Cb7290

department: Microbiology & Immunology

country: USA

institute: UNC Chapel Hill

data_processing:
Read mapping was performed using HISAT2
Read quantification was performed using featureCounts
Read counts were loaded into R, then normalized using edgeR’s Trimmed Mean of M values (TMM) algorithm
Differential expression analysis between our different conditions (5% O2 vs ambient air, 2% O2 vs ambient air, and 5% CO2 vs ambient air) was performed using edgeR’s glmQLFTest.
Assembly: NC_002927.3
Supplementary files format and content: HISAT2 reads
Supplementary files format and content: .bam files

organism: Bordetella bronchiseptica

growth_protocol: Overnight cultures were backdiluted to 1 OD600/mL in Stainer Scholte medium. These cultures were then grown for 4 hours at 37C shaking at 225 rpm on an orbital shaker while being exposed to different atmospheric conditions. Bacteria were pelleted, resuspended in RNAlater (Invitrogen AM7020), then stored at -80°C until extraction.

extract_protocol:
RNA was isolated using Trizol/chloroform extraction, followed by centrifugation in Phasemaker Tubes (Invitrogen 12183555). The aqueous phase was precipitated in isopropanol, washed in ethanol, and solubilized in RNase-free water. Samples were then cleaned using RNAeasy column purification (Qiagen 74104).
Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices.

treatment_protocol: Cultures were grown in different atmospheric conditions: ambient air, 5% O2, 2% O2, or 5% CO2

tag: strain

tag: genotype

value: WT


title: ITGB4-NC3_raw

value: the control group of overexpression of ITGB6 by plasmid


title: RB50 5% CO2 sample 2


title: RB50 5% CO2 sample 3


title: RB50 2% O2 sample 2


title: three_h, scRNAseq

city: Shanghai

first: Jun

last: Sun

state: --- Select One ---

address: siping Rd.1239

institute: School of Medicine, Tongji University

data_processing:
Cellranger standard processing
**Cell filter** Seurat allows to easily explore QC metrics and filter cells, we can visualize gene and molecule counts, plot their relationship, and exclude cells with a clear outlier number of genes detected as potential multiplets. Followed criteria were used to filter cells: 1.gene counts 500-Inf per cell. 2.UMI counts 3. the percentage of mitochondrial genes < 25% %(customized). 4.DoubletFinder for detecting doublets.
**Cell clustering** Cell clustering contains the following steps: 1)Normalizing the data After removing unwanted cells from the dataset, the next step is to normalize the data. By default, we employ a global-scaling normalization method “LogNormalize” that normalizes the gene expression measurements for each cell by the total expression.
PCA(Principal component analysis): To overcome the extensive technical noise in any single gene for scRNA-seq data, Seurat clusters cells based on their PCA scores, with each PC essentially representing a ‘metagene’ that combines information across a correlated gene set.
t-SNE (t-distributed Stochastic Neighbor Embedding) visualization: Seurat continues to use t-SNE as a powerful tool to visualize and explore these datasets. The tSNE aims to place cells with similar local neighborhoods in high-dimensional space together in low-dimensional space.
Assembly: Plasmodium falciparum 3D7 (assembly GCA_000002765); Plasmodium yoelii (assembly GCA_900002385)
Supplementary files format and content: cellranger; features.tsv.gz, barcodes.tsv.gz, matrix.mtx,gz

organism: Plasmodium yoelii

source_name: P. yoelii yoelii 17XNL

growth_protocol: In vivo experiment, when the infection rate of P. yoelii yoelii 17XNL reached 25 % - 35 %, artemether (100 mg/kg) was fed to the mice. After different time points of treatment, blood samples were collected, respectively. In vitro iron sucrose and zinc protoporphyrin IX (ZnPPIX) assay, the P. falciparum parasites (3D7 strain) were cultured in human O+ erythrocytes at 2 % haematocrit in RPMI 1640 medium supplemented with 0.5 % (w/v) Albumax I (Gibco), 0.2 mmol/L hypoxanthine (Sigma), 25 mmol/L HEPES (Gibco), 0.2 % NaHCO3, and 20 μg/mL gentamicin, and incubated under a controlled atmosphere of 5 % CO2 and 5 % O2 at 37 °C, as previously described.

extract_protocol:
The aorta tissue was dissected into five segments and the single cell suspension was obtained by enzymatic digestion. The cell pellet was resuspended in 50 μl of 1× PBS (0.04% BSA). The overall cell viability was confirmed by trypan blue exclusion , which needed to be above 85%, single cell suspensions were counted using a haemocytometer/ Countess II Automated Cell Counter and concentration adjusted to 700-1200 cells/μl.
Single-cell suspensions were loaded to 10x Chromium to capture 5000 single cell according to the manufacturer’s instructions of 10X Genomics Chromium Single-Cell 3’ kit (V3) .The following cDNA amplification and library construction steps were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run,150bp)

treatment_protocol: (A)After 0, 3, 9 and 24 h of artemether treatment, a blood sample containing 2-4 drops was collected from mice infected with P. yoelii yoelii 17XNL-EGFP parasites and placed in a 15 ml tube containing 10 ml RPMI 1640 media. The samples were immediately transferred onto ice along with the controls for cell sorting. Cell samples from the test and control groups were sorted on a BD FACS-Aria II cell sorter (BD Biosciences) by using UV, blue and red lasers at the wavelengths of 355, 488 and 633 nm, respectively. Positive cells were collected in RPMI 1640 medium containing 5 % BSA. After sorting, the collected erythrocytes (parasites) were used for the scRNA experiment.  (B) For the examination of the impact of DHA, DHA and iron sucrose or DFO on asynchronized P. falciparum 3D7 at 3, 9 and 24 h post-treatment, erythrocytes infected by P. falciparum 3D7 with a parasitemia of 1.5%-2% were divided into four groups as follows: (1) DHA was added to 5000 µL of asynchronized P. falciparum 3D7 culture at a final concentration of 150 nmol/L; (2) DHA and iron sucrose were added to the same culture at the final concentrations of 150 nmol/L and 0.3 mmol/L, respectively; (3) DFO was added to the same culture at the final concentration of 500 µmol/L and (4) asynchronized P. falciparum 3D7 culture without any treatment as a control. Then, 500 µL of the parasite-infected erythrocytes were mixed with 2000 µL of RPMI 1640 medium and 25 µL of Hochest 33342, and sorted and analyzed by flow cytometry on a BD FACSAria II cell sorter (BD Biosciences), as previously described. After sorting, the collected erythrocytes (parasites) were used for the scRNA experiment.

value: P. yoelii yoelii 17XNL

value: P. yoelii yoelii 17XNL sample 3 h after artemetner action


title: RB50 2% O2 sample 3


title: RB50 5% O2 sample 2


title: RB50 5% O2 sample 3


title: RB50 air sample 3

value: ambient air


title: RB50 5% O2 sample 1


title: RB50 air sample 2


title: RB50 air sample 1


title: ARNT KO 2

city: Galveston

first: Cornelis

middle: Johan

last: Elferink

state: TX

address: 301 University Boulevard

department: Pharmacology and Toxicology

institute: University of Texas Medical Branch

data_processing:
Base calling was using Illumina's bcl2fastq2-v2.20 converter
A genome index was built with STAR (v2.5.4b) using the mouse mm10 genome .
Reads were aligned to the mouse reference using the STAR software version 2.6.0c with the parameters recommended for the ENCODE consortium.
Read counts per gene were produced with the --quantMode GeneCounts function of STAR. Small non-coding RNAs were not counted.
Differential gene expression was analyzed with the R (version 3.5.1) software DESeq2 (version 1.20.0)
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited table of raw read counts per gene

source_name: ARNT KO_liver

extract_protocol:
Total cellular RNA was extracted using  Trizol Reagent (Life Technologies, CA) according to the manufacturer’s recommendations.
Poly-A plus RNA was enriched from  ~0.1 ug of total RNA and used to generate libraries using the NEBNext Ultra II Kit.

tag: strain background

tag: age

value: adult (6 months old)

tag: genotype/variation

value: ARNT KO

tag: Sex

value: female

value: high-fat diet for 13 weeks

value: liver


title: patient 631

type: RNA

city: Tampa

first: Eric

last: Welsh

state: FL

address: 12902 Magnolia Dr

department: Biostatistics and Bioinformatics

institute: H Lee Moffitt Cancer Center

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques. Arrays are hybridized for 18 hours at 45C with vigorous mixing. Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed. Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: IRON normalization was performed on the dataset, batch corrected for RNA quality using PLS

label: biotin

source_name: macrodissected primary breast tumor

label_protocol: Samples were amplified and labeled using a custom automated version of the NuGEN Ovation v2 with WB (whole blood) reagents protocol (using Ribo-SPIA amplification). The labeled molecules are biotinylated-cRNA. Sample amplification and labeling were performed by LabCorp Clinical Trials-Genomic Services in Seattle, Washington.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation. Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification. Isolated total RNA samples were assayed for quality (Agilent Bioanalyzer) and yield (Ribogreen) metrics prior to amplification.

value: macrodissected primary breast tumor

tag: subject

tag: type of surgery

value: Lumpectomy

tag: histology

value: IDC

tag: er status

value: Positive

tag: pr status

value: Negative

tag: her2 status

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

value: Yes

tag: type of radiotherapy

value: Partial breast irradiation

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

value: White

tag: chemotherapy

value: No

tag: locoregional recurrence

tag: death

value: Alive

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: RB50 2% O2 sample 1

tag: strain

tag: genotype

value: WT

tag: treatment


title: patient 637

tag: tissue

tag: subject

tag: type of surgery

value: Mastectomy

tag: histology

tag: er status

tag: pr status

tag: her2 status

tag: pt

value: External beam radiation


title: patient 634

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy


title: patient 635

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 630

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: er status


title: patient 636

tag: pr status

tag: her2 status

tag: pt

tag: pn

tag: ptnm

value: AA


title: patient 622

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race


title: patient 616

tag: chemotherapy

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: patient 617

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: bioanalyzer rin (rna integrity number)


title: patient 615

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: pn

value: Dead


title: patient 632

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)


title: patient 633

tag: race

tag: chemotherapy

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 629

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: time to death or censor from date of diagnosis (years)


title: patient 610

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: bioanalyzer rin (rna integrity number)


title: patient 624

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis


title: patient 625

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: locoregional recurrence

tag: death


title: patient 619

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 620

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: time to death or censor from date of diagnosis (years)


title: patient 623

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: bioanalyzer rin (rna integrity number)


title: patient 626

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: locoregional recurrence


title: patient 613

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: death


title: patient 618

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 611

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: time to death or censor from date of diagnosis (years)


title: patient 612

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: bioanalyzer rin (rna integrity number)


title: patient 628

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: locoregional recurrence


title: patient 621

value: ILC

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: death


title: patient 609

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 627

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

value: Unknown

tag: time to death or censor from date of diagnosis (years)


title: patient 606

tag: tissue

value: macrodissected primary breast tumor

tag: subject

tag: type of surgery

tag: histology

tag: bioanalyzer rin (rna integrity number)


title: patient 608

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: locoregional recurrence


title: patient 614

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: death


title: patient 607

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 602

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: time to death or censor from date of diagnosis (years)


title: patient 597

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: bioanalyzer rin (rna integrity number)


title: patient 599

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: locoregional recurrence


title: patient 593

value: Lumpectomy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: death


title: patient 598

tag: tissue

tag: subject

tag: type of surgery

tag: histology

value: IDC

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 601

tag: er status

value: Positive

tag: pr status

tag: her2 status

tag: pt

tag: time to death or censor from date of diagnosis (years)


title: patient 605

value: Negative

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: bioanalyzer rin (rna integrity number)


title: patient 590

value: Other

value: Yes

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: locoregional recurrence


title: patient 600

tag: tissue

tag: subject

tag: type of surgery

tag: histology

value: White

tag: death


title: patient 594

tag: er status

tag: pr status

tag: her2 status

tag: pt

value: No

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 595

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

value: Alive

tag: time to death or censor from date of diagnosis (years)


title: patient 588

value: Partial breast irradiation

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: bioanalyzer rin (rna integrity number)


title: patient 592

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: locoregional recurrence


title: patient 604

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: death


title: patient 587

value: Mastectomy

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 579

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: time to death or censor from date of diagnosis (years)


title: patient 580

tag: tissue

tag: subject

tag: type of surgery

tag: histology

value: External beam radiation

tag: bioanalyzer rin (rna integrity number)


title: patient 583

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: locoregional recurrence


title: patient 581

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: death


title: patient 585

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 589

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: time to death or censor from date of diagnosis (years)


title: patient 603

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: bioanalyzer rin (rna integrity number)


title: patient 586

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: locoregional recurrence


title: patient 582

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: death


title: patient 596

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 578

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: time to death or censor from date of diagnosis (years)


title: patient 584

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: bioanalyzer rin (rna integrity number)


title: patient 577

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

value: Hispanic, Asian & other

tag: chemotherapy

tag: locoregional recurrence


title: patient 576

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: death


title: patient 591

tag: er status

tag: pr status

tag: her2 status

tag: pt

value: AA

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 573

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

value: Dead

tag: time to death or censor from date of diagnosis (years)


title: patient 575

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: bioanalyzer rin (rna integrity number)


title: patient 570

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: locoregional recurrence


title: patient 568

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: death


title: patient 552

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 574

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: time to death or censor from date of diagnosis (years)


title: patient 565

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: bioanalyzer rin (rna integrity number)


title: patient 560

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: locoregional recurrence


title: patient 566

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: death


title: patient 556

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 569

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: time to death or censor from date of diagnosis (years)


title: patient 571

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: bioanalyzer rin (rna integrity number)


title: patient 561

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: locoregional recurrence


title: patient 564

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

value: Unknown

tag: death


title: patient 546

tag: tissue

value: macrodissected primary breast tumor

tag: subject

tag: type of surgery

tag: histology

value: ILC

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 557

value: IDC

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: time to death or censor from date of diagnosis (years)


title: patient 562

value: Lumpectomy

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: bioanalyzer rin (rna integrity number)


title: patient 548

value: Negative

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: locoregional recurrence


title: patient 567

tag: tissue

tag: subject

tag: type of surgery

tag: histology

value: Positive

tag: death


title: patient 547

tag: er status

tag: pr status

tag: her2 status

tag: pt

value: Yes

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 553

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

value: White

tag: time to death or censor from date of diagnosis (years)


title: patient 558

value: No

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: bioanalyzer rin (rna integrity number)


title: patient 545

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: locoregional recurrence

value: Alive


title: patient 554

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: death


title: patient 550

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 572

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: time to death or censor from date of diagnosis (years)


title: patient 559

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: bioanalyzer rin (rna integrity number)


title: patient 563

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: locoregional recurrence


title: patient 551

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: death


title: patient 549

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 555

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: time to death or censor from date of diagnosis (years)


title: patient 544

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: bioanalyzer rin (rna integrity number)


title: patient 535

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: locoregional recurrence


title: patient 543

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: death


title: patient 538

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 534

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: time to death or censor from date of diagnosis (years)


title: patient 530

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

value: Partial breast irradiation

tag: bioanalyzer rin (rna integrity number)


title: patient 537

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: locoregional recurrence


title: patient 539

tag: tissue

tag: subject

tag: type of surgery

value: Mastectomy

tag: histology

tag: death


title: patient 541

tag: er status

tag: pr status

tag: her2 status

tag: pt

value: External beam radiation

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 523

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: time to death or censor from date of diagnosis (years)


title: patient 531

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: bioanalyzer rin (rna integrity number)


title: patient 522

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: locoregional recurrence


title: patient 524

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: death


title: patient 516

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 527

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: time to death or censor from date of diagnosis (years)


title: patient 532

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: bioanalyzer rin (rna integrity number)


title: patient 515

tag: er status

tag: pr status

tag: her2 status

tag: pt

value: Hispanic, Asian & other

tag: locoregional recurrence


title: patient 517

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: death


title: patient 533

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 521

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: time to death or censor from date of diagnosis (years)


title: patient 529

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: bioanalyzer rin (rna integrity number)


title: patient 519

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: locoregional recurrence


title: patient 536

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: death


title: patient 518

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 525

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: time to death or censor from date of diagnosis (years)


title: patient 526

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: bioanalyzer rin (rna integrity number)


title: patient 528

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: locoregional recurrence


title: patient 520

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: death


title: patient 540

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 514

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: time to death or censor from date of diagnosis (years)


title: patient 513

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

value: AA

tag: chemotherapy

tag: bioanalyzer rin (rna integrity number)


title: patient 512

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: locoregional recurrence


title: patient 510

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: death


title: patient 511

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

value: Dead

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 507

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: time to death or censor from date of diagnosis (years)


title: patient 509

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: bioanalyzer rin (rna integrity number)


title: patient 508

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: locoregional recurrence


title: patient 506

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: death


title: patient 504

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 502

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: time to death or censor from date of diagnosis (years)


title: patient 499

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: bioanalyzer rin (rna integrity number)


title: patient 501

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: locoregional recurrence


title: patient 503

value: Other

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: death


title: patient 497

tag: tissue

value: macrodissected primary breast tumor

tag: subject

tag: type of surgery

tag: histology

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 490

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: time to death or censor from date of diagnosis (years)


title: patient 491

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: bioanalyzer rin (rna integrity number)


title: patient 495

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: locoregional recurrence


title: patient 493

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: death


title: patient 489

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 496

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: time to death or censor from date of diagnosis (years)


title: patient 488

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: bioanalyzer rin (rna integrity number)


title: patient 500

tag: tissue

tag: subject

tag: type of surgery

tag: histology

value: ILC

tag: locoregional recurrence


title: patient 494

value: IDC

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: death


title: patient 487

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 485

value: Lumpectomy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: time to death or censor from date of diagnosis (years)


title: patient 486

tag: tissue

tag: subject

tag: type of surgery

tag: histology

value: Negative

tag: bioanalyzer rin (rna integrity number)


title: patient 505

tag: er status

tag: pr status

tag: her2 status

value: Positive

tag: pt

tag: locoregional recurrence


title: patient 492

tag: pn

tag: ptnm

tag: radiotherapy

value: Yes

tag: type of radiotherapy

tag: death


title: patient 498

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

value: White

tag: chemotherapy

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 484

tag: tissue

tag: subject

tag: type of surgery

tag: histology

value: No

tag: time to death or censor from date of diagnosis (years)


title: patient 480

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: bioanalyzer rin (rna integrity number)


title: patient 482

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: locoregional recurrence


title: patient 479

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: death

value: Alive


title: patient 542

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 475

tag: er status

tag: pr status

tag: her2 status

tag: pt

value: Unknown

tag: time to death or censor from date of diagnosis (years)


title: patient 472

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: bioanalyzer rin (rna integrity number)


title: patient 478

value: Mastectomy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: locoregional recurrence


title: patient 476

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: death


title: patient 477

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 473

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: time to death or censor from date of diagnosis (years)


title: patient 471

value: Partial breast irradiation

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: bioanalyzer rin (rna integrity number)


title: patient 483

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: locoregional recurrence


title: patient 468

tag: er status

tag: pr status

tag: her2 status

tag: pt

value: Hispanic, Asian & other

tag: death


title: patient 474

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

value: External beam radiation

value: AA

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 466

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

value: Dead

tag: time to death or censor from date of diagnosis (years)


title: patient 456

tag: tissue

value: macrodissected primary breast tumor

tag: subject

tag: type of surgery

tag: histology

tag: bioanalyzer rin (rna integrity number)


title: patient 463

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: locoregional recurrence


title: patient 458

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: death


title: patient 452

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 462

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: time to death or censor from date of diagnosis (years)


title: patient 470

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: bioanalyzer rin (rna integrity number)


title: patient 481

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: locoregional recurrence


title: patient 460

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: death


title: patient 465

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 451

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: time to death or censor from date of diagnosis (years)


title: patient 457

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: bioanalyzer rin (rna integrity number)


title: patient 469

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: locoregional recurrence


title: patient 464

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: death


title: patient 467

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 453

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: time to death or censor from date of diagnosis (years)


title: patient 449

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: bioanalyzer rin (rna integrity number)


title: patient 461

tag: tissue

tag: subject

tag: type of surgery

tag: histology

value: Other

tag: locoregional recurrence


title: patient 459

value: IDC

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: death


title: patient 455

value: Lumpectomy

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 450

value: ILC

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: time to death or censor from date of diagnosis (years)


title: patient 445

tag: tissue

tag: subject

tag: type of surgery

tag: histology

value: Positive

value: Negative

tag: bioanalyzer rin (rna integrity number)


title: PMC, Ribotag, 24hrs, Isotype control [E2_P6_30_IP]

city: Freiburg

first: Michael

last: Mihlan

address: Stuebeweg 51

country: Germany

institute: MPI Immunobiology & Epigenetics

data_processing:
RNA-seq data was analyzed using the RNA-seq module from the snakePipes package. Mouse gene annotation (genome build mm10) from Gencode release m9 was used as reference for mapping and read counting.
Differential gene expression analysis was done using DESeq2.
Heatmaps were generated using gplots package in R.
Genome_build: mm10
Supplementary_files_format_and_content: table with raw counts per gene

source_name: PMC WT

growth_protocol: Mast cells from mouse peritoneum (PMC) were cultured for 5-6 weeks in OptiMEM Medium containing 5% supernatant of CHO transfectants secreting mouse SCF and 10% FCS. Mouse neutrophils were isolated freshly from bone marrow cells. PMC and neutrophils were co-cultured in RPMI Medium cntaining 10% FCS, 5% supernatant of CHO transfectants secreting mouse SCF and 1% Penicillin/Streptamycin.

extract_protocol:
60,000 MIT and PMC per sample were lysed in HBS buffer (cyclohexamide 100ug/ml, Protease inhibitor cocktail, Heparin 1mg/ml, RNAsin 1:200, DTT 1mM, NP-40 1%, KCl 100mM, Tris 30mM pH 7.4, MgCl2 82mM). After centrifugation, 10% of supernatant was saved as an input control and 130ul were used for the pulldown of HA-tagged ribosomes using 4ug of anti-HA antibodies or an isotype control (xxxx) (2,5 hrs 4°C). Next, we add 30ul of magnetic Potein A/G Beads (ThermoFisher) for 1 hr at 4°C. Unbound proteins were washed away with high salt buffer (KCl 350mM, NP-40 1%, MgCl2 82mM, DTT 0,5mM, Tris 30mM pH 7.4) three times 10 minutes, 4°C. Precipitated proteins were eluted with 350ul RLT buffer (Qiagen) containing b-mercaptoethanol (1:100).  Subsequently precipitated mRNA species were isolated with a RNeasy Plus Micro Kit (Qiagen) and eluted in 12ul water.
cDNA libraries were prepared with 7ul RNA using a Low Input RNA Library Prep Kit for Illumina (NEB).

treatment_protocol: Before co-culturing with neutrophils, PMC were treated over night with 0.5ug/ml  anti-DNP IgE. PMC-Neutrophil co-cultures were treated with 100ng DNP-HSA to degranulate mast cells. Two hours later cells were FACS sorted to isolate MIT and PMC. Sorted MIT and PMC were cultured in RPMI medium for 12 or 24 hrs.

tag: condition

value: 24hrs after PMC degranulation

tag: tag

value: PMC Ribotag positive

tag: antibody precipitation

value: IgG Isotype control


title: PMC, Ribotag, 24hrs, anti-HA [E2_P5_30_IP]

value: anti-HA


title: patient 454

value: Mastectomy

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: pn

tag: ptnm

value: No

value: White

tag: locoregional recurrence

tag: death

value: Alive


title: patient 447

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: PMC, Ribotag, 24hrs, Isotype control [E2_P4_30_IP]

tag: condition

tag: tag

tag: antibody precipitation


title: PMC, Ribotag, 24hrs, anti-HA [E2_P3_30_IP]


title: patient 443

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: er status

tag: pr status

tag: her2 status

value: Yes

value: External beam radiation

tag: bioanalyzer rin (rna integrity number)


title: patient 444

value: macrodissected primary breast tumor

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: locoregional recurrence

tag: death

value: Dead


title: patient 448

value: IDC

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: patient 446

tag: tissue

tag: subject

tag: type of surgery

value: Lumpectomy

tag: histology

tag: er status


title: PMC, no Ribotag, 24hrs, anti-HA [E2_P3_25_IP]

tag: condition

tag: tag

value: PMC WT - no Ribotag control

tag: antibody precipitation


title: PMC, Ribotag, 12hrs, Isotype control [E2_P2_30_IP]

value: 12hrs after PMC degranulation


title: MIT, Ribotag, 24hrs, anti-HA [E2_M3_30_IP]

source_name: PMC Ribotag+Neutrophil


title: PMC, Ribotag, 12hrs, anti-HA [E2_P1_30_IP]


title: MIT, Ribotag, 24hrs, anti-HA [E2_M5_30_IP]


title: MIT, Ribotag, 24hrs, Isotype control [E2_M6_30_IP]


title: patient 441

value: Positive

tag: pr status

tag: her2 status

value: Negative

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: bioanalyzer rin (rna integrity number)


title: MIT, Ribotag, 12hrs, Isotype control [E2_M2_30_IP]

value: PMC Ribotag positive


title: patient 440

value: Partial breast irradiation

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: MIT, no Ribotag, 24hrs, anti-HA [E2_M3_25_IP]

source_name: PMC WT+Neutrophil

tag: condition

value: 24hrs after PMC degranulation

tag: tag

tag: antibody precipitation

value: anti-HA


title: patient 442

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: er status

tag: pr status

tag: her2 status

tag: pt

value: No


title: PMC, no Ribotag, 12hrs, anti-HA [E2_P1_25_IP]


title: MIT, Ribotag, 24hrs, Isotype control [E2_M4_30_IP]

value: IgG Isotype control


title: patient 437

value: Mastectomy

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

value: White

value: Alive

tag: bioanalyzer rin (rna integrity number)


title: MIT, Ribotag, 12hrs, anti-HA [E2_M1_30_IP]

tag: condition

tag: tag

tag: antibody precipitation


title: MIT, no Ribotag, 12hrs, anti-HA [E2_M1_25_IP]


title: PMC, Ribotag, 24hrs, Isotype control [E1_P4_30_IP]


title: PMC, Ribotag, 24hrs, anti-HA [E1_P3_30_IP]


title: PMC, no Ribotag, 24hrs, anti-HA [E1_P3_25_IP]


title: PMC, Ribotag, 12hrs, Isotype control [E1_P2_30_IP]


title: patient 439

tag: tissue

value: macrodissected primary breast tumor

tag: subject

tag: type of surgery

value: Yes

value: External beam radiation

tag: chemotherapy

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: patient 432

tag: histology

value: ILC

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy


title: patient 431

value: IDC

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: bioanalyzer rin (rna integrity number)


title: patient 430

tag: tissue

tag: subject

tag: type of surgery

tag: chemotherapy

tag: locoregional recurrence


title: PMC, Ribotag, 12hrs, anti-HA [E1_P1_30_IP]

tag: condition

value: 12hrs after PMC degranulation

tag: tag

tag: antibody precipitation


title: patient 433

tag: histology

tag: er status

value: Positive

tag: pr status

tag: her2 status

tag: pt

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: patient 429

value: Negative

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

value: Dead

tag: bioanalyzer rin (rna integrity number)


title: patient 434

tag: tissue

tag: subject

tag: type of surgery

tag: chemotherapy

tag: locoregional recurrence


title: patient 428

tag: histology

tag: er status

tag: pr status

tag: her2 status

tag: pt

value: Hispanic, Asian & other


title: patient 438

tag: pn

tag: ptnm

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: patient 425

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race


title: patient 426

tag: tissue

tag: subject

tag: type of surgery

value: Lumpectomy

tag: chemotherapy

tag: bioanalyzer rin (rna integrity number)


title: patient 427

tag: histology

tag: er status

tag: pr status

tag: her2 status

tag: locoregional recurrence


title: patient 436

tag: pt

tag: pn

tag: ptnm

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 435

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: time to death or censor from date of diagnosis (years)


title: patient 424

tag: tissue

tag: subject

tag: type of surgery

tag: race

tag: chemotherapy


title: MIT, Ribotag, 24hrs, anti-HA [E1_M3_30_IP]

tag: condition

value: 24hrs after PMC degranulation

tag: tag

value: PMC Ribotag positive

tag: antibody precipitation

value: anti-HA


title: PMC, no Ribotag, 12hrs, anti-HA [E1_P1_25_IP]

value: PMC WT - no Ribotag control


title: MIT, Ribotag, 24hrs, Isotype control [E1_M4_30_IP]

value: IgG Isotype control


title: MIT, no Ribotag, 24hrs, anti-HA [E1_M3_25_IP]


title: patient 422

tag: histology

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: pn

value: AA

tag: locoregional recurrence

value: No

value: Alive

tag: bioanalyzer rin (rna integrity number)


title: patient 421

value: macrodissected primary breast tumor

value: Mastectomy

value: Other

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

value: Yes

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: MIT, Ribotag, 12hrs, Isotype control [E1_M2_30_IP]

tag: condition

value: 12hrs after PMC degranulation

tag: tag

tag: antibody precipitation


title: MIT, Ribotag, 12hrs, anti-HA [E1_M1_30_IP]


title: MIT, no Ribotag, 12hrs, anti-HA [E1_M1_25_IP]


title: MML-1 ChIP DNA replicate A

city: London

first: Ruben

last: Esse

address: Guy's Hospital, Great Maze Pond

department: Department of Medical and Molecular Genetics

country: United Kingdom

institute: King’s College London

description: ChIP sample for MML-1 ChIP-seq, replicate A

library_source: genomic

data_processing:
Libraries were sequenced on a NextSeq500 Illumina sequencer and FASTQ files were downloaded from Illumina BaseSpace.
Reads were mapped to the Caenorhabditis elegans genome (WS220/ce10 assembly) using Bowtie for Illumina (Galaxy Version 1.1.2) with default parameters, except: --best --maxbts 800 --strata.
Peak calling was performed using MACS2 (Galaxy Version 2.1.0.20151222.0) with parameters: --gsize 93260000 --bw 175 --qvalue 0.05 --bdg.
Genome_build: WS220/ce10 assembly
Supplementary_files_format_and_content: Coverage files in bedGraph format were generated by MACS2. Peak coordinate files in tabular and BED formats were generated by MACS2.

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: MML-1 ChIP DNA

growth_protocol: Strains were maintained at 20°C under standard conditions. Hypochlorite-synchronized first larval (L1) stage animals were grown for 36 hours post-hatching at 20ºC on standard NGM plates with OP-50 E. coli.

extract_protocol:
Synchronized L3 larvae were washed off the plates using isotonic M9 solution. Fixation was performed for 30 min at 20°C in crosslinking solution (2% paraformaldehyde in M9 buffer), and excess formaldehyde was quenched with 0.1 M Tris-HCl pH 7.5. The pellet was then washed twice with M9 buffer at 4°C. The worm pellet was resuspended in 1 mL ice-cold RIPA buffer (10 mM Tris-HCl pH 8.0, 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate, 1 mM EDTA, 0.15 M NaCl) supplemented with Halt™ Protease Inhibitor Cocktail (Thermo Fisher Scientific). The suspension was then transferred to a Covaris milliTUBE 1 mL with AFA® fiber and shearing was performed using the following settings in SonoLab7: Peak Incident Power (PIP) = 240W; Duty Factor = 20%; Cycles per burst (cpb) = 200; time = 480 seconds. After shearing, the crude extract was spun for 10 min at 10,000 x g and the supernatant was collected. Protein concentration was determined by the Bradford method. Extract corresponding to 2.5 mg protein was diluted to 500 μl with ice-cold RIPA buffer supplemented with Halt™ Protease Inhibitor Cocktail (Thermo Fisher Scientific). Antibody specific for MML-1 (a kind gift from Dr. Donald Ayer, 1 μl) was added and, after incubation overnight at 4°C for 1 h, 50 μl of Dynabeads™ Protein G suspension (Thermo Fisher Scientific) were added and the mixture was incubated at 4°C for 1 h on rotation. Beads were recovered with a Dynal® Magnetic Particle Concentrator (Invitrogen) and washed at 4°C with: 0.5 mL buffer TSE-150 (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 150 mM NaCl), 2 X 0.5 mL buffer TSE-500 (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 500 mM NaCl), 0.5 mL buffer TSE-1M (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 1 M NaCl), 0.5 mL buffer LiCl (250 mM LiCl, 1% NP40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.1), 2 X 0.5 mL buffer TE (10 mM Tris pH 8.0, 1 mM EDTA). Antibody-bound chromatin was recovered in 2 X 0.2 mL elution buffer (1% SDS, 0.1 M NaHCO3) by shaking at room temperature for 15 min. Elution buffer was added to input samples (5%) to a total volume of 0.4 mL. Input and ChIP chromatin samples were subsequently processed in parallel. After 20 μl of 5 M NaCl was added to each sample, cross-links were reversed overnight at 65°C. 10 μl of 0.5 M EDTA, 20 μl of 1 M Tris-HCl pH 6.5 and 0.5 μl of 20 mg/mL Proteinase K (Thermo Fisher Scientific) were added and each sample was incubated for 1 h at 42°C. DNA was recovered using the QIAquick PCR Purification Kit (Qiagen) in accordance with the manufacturer's instructions.
Immunoprecipitated DNA and input libraries were prepared using TruSeq ChIP Library Preparation kit following the manufacturer's instructions (Illumina) and checked for concentration and quality on DNA chips with a Bioanalyzer (Agilent). 75-bp single read sequences were generated on the NextSeq 500 sequencer according to manufacturer’s instructions (Illumina).

tag: genotype/variation

value: wild type

tag: developmental stage

value: Third larval stage

tag: tissue

value: Synchronized L3 larvae

tag: antibody

value: Antibody specific for MML-1 (a kind gift from Dr. Donald Ayer)


title: MML-1 ChIP DNA replicate B

description: ChIP sample for MML-1 ChIP-seq, replicate B


title: Input DNA replicate B

description: Input sample for MML-1 ChIP-seq, replicate B

source_name: Input DNA


title: Input DNA replicate A

description: Input sample for MML-1 ChIP-seq, replicate A


title: patient 420

tag: subject

tag: type of surgery

tag: histology

value: IDC

tag: er status

value: Positive

tag: pr status

tag: her2 status

tag: pt

tag: pn

tag: race

value: White

tag: chemotherapy

tag: locoregional recurrence


title: patient 423

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 414

tag: tissue

tag: subject

tag: type of surgery

value: Lumpectomy

tag: histology

tag: er status

value: Negative

value: External beam radiation


title: patient 419

tag: pr status

tag: her2 status

tag: pt

tag: pn

value: Partial breast irradiation

tag: race

value: No

value: Dead


title: dot-1.1(knu339);ced-3 mut H3K9me2 ChIP-seq repl 1

description: ChIP sample for H3K9me2 ChIP-seq in dot-1.1;ced-3 mutant, replicate 1.

data_processing:
Libraries were sequenced on a NextSeq500 Illumina sequencer and FASTQ files were downloaded from Illumina BaseSpace.
Reads were mapped to the C. elegans genome (ce10 assembly) using QuasR (version 1.16.0).
Read counting in regions was performed with package GenomicAlignments (version 1.16.0), using only reads with mapping quality 20 or higher. Regions without reads in all samples were removed.
Counts were normalized using the TMM method, which takes RNA composition bias into account, using the edgeR package (version 1.16.0).
For each region, coverage was first expressed as RPKM (reads per kilobase per million mapped) and log2-transformed, and then the value in the non-immunoprecipitated (input) DNA was subtracted from that in the immunoprecipitated DNA sample. Only regions in which the normalized count value in the immunoprecipitated DNA sample was higher than that in the corresponding input DNA in at least one sample in the set were considered.
Genome_build: ce10
Supplementary_files_format_and_content: Coverage files in bedGraph format were generated by counting reads at 25 bp bins. Counts were normalized using the TMM method implemented in the edgeR package (version 1.16.0) and expressed as CPM (counts per million). Bin-level coverage in each input sample was subtracted from that in the corresponding ChIP sample.

source_name: Third larval stage animals

growth_protocol: Strains were maintained at 20°C under standard conditions. Hypochlorite-synchronized L1 stage animals were grown for 36 hours post-hatching at 20ºC on standard NGM plates with OP-50 E. coli.

extract_protocol:
Synchronized L3 larvae were washed off the plates using isotonic M9 solution. Fixation was performed for 30 min at 20°C in crosslinking solution (2% paraformaldehyde in M9 buffer), and excess formaldehyde was quenched with 0.1 M Tris-HCl pH 7.5. The pellet was then washed twice with M9 buffer at 4°C. The worm pellet was resuspended in 1 mL ice-cold RIPA buffer (10 mM Tris-HCl pH 8.0, 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate, 1 mM EDTA, 0.15 M NaCl) supplemented with Halt™ Protease Inhibitor Cocktail (Thermo Fisher Scientific). The suspension was then transferred to a Covaris milliTUBE 1 mL with AFA® fiber and shearing was performed using the following settings in SonoLab7: Peak Incident Power (PIP) = 240W; Duty Factor = 20%; Cycles per burst (cpb) = 200; time = 480 seconds. After shearing, the crude extract was spun for 10 min at 10,000 x g and the supernatant was collected. Protein concentration was determined by the Bradford method. Extract corresponding to 1 mg protein was diluted to 500 μl with ice-cold RIPA buffer supplemented with Halt™ Protease Inhibitor Cocktail (Thermo Fisher Scientific). Antibody specific for H3K9me2 (Abcam, ab1220, 5 μg) was added and, after incubation at 4°C for 1 h, 50 μl of Dynabeads™ Protein G suspension (Thermo Fisher Scientific) were added and the mixture was incubated at 4°C for 1 h on rotation. Beads were recovered with a Dynal® Magnetic Particle Concentrator (Invitrogen) and washed at 4°C with: 0.5 mL buffer TSE-150 (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 150 mM NaCl), 2 X 0.5 mL buffer TSE-500 (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 500 mM NaCl), 0.5 mL buffer TSE-1M (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 1 M NaCl), 0.5 mL buffer LiCl (250 mM LiCl, 1% NP40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.1), 2 X 0.5 mL buffer TE (10 mM Tris pH 8.0, 1 mM EDTA). Antibody-bound chromatin was recovered in 2 X 0.2 mL elution buffer (1% SDS, 0.1 M NaHCO3) by shaking at room temperature for 15 min. Elution buffer was added to input samples (5%) to a total volume of 0.4 mL. Input and ChIP chromatin samples were subsequently processed in parallel. After 20 μl of 5 M NaCl was added to each sample, cross-links were reversed overnight at 65°C. 10 μl of 0.5 M EDTA, 20 μl of 1 M Tris-HCl pH 6.5 and 0.5 μl of 20 mg/mL Proteinase K (Thermo Fisher Scientific) were added and each sample was incubated for 1 h at 42°C. DNA was recovered using the QIAquick PCR Purification Kit (Qiagen) in accordance with the manufacturer's instructions.
Immunoprecipitated DNA and input libraries were prepared using TruSeq ChIP Library Preparation kit following the manufacturer's instructions (Illumina) and checked for concentration and quality on DNA chips with a Bioanalyzer (Agilent). 75-bp single read sequences were generated on the NextSeq 500 sequencer according to manufacturer’s instructions (Illumina).

tag: genotype

tag: antibody

tag: antibody catalog#

tag: antibody manufacturer

value: Abcam


title: dot-1.1(knu339);ced-3 mut H3K9me2 ChIP-seq repl 2

description: ChIP sample for H3K9me2 ChIP-seq in dot-1.1;ced-3 mutant, replicate 2.


title: patient 415

value: macrodissected primary breast tumor

value: ILC

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: chemotherapy

tag: locoregional recurrence

tag: death

value: Alive

tag: time to locoregional recurrence from date of diagnosis (years)


title: dot-1.1(knu339);ced-3 mut input DNA repl 2

description: Input sample for H3K9me2 ChIP-seq in dot-1.1;ced-3 mutant, replicate 2.


title: patient 412

tag: tissue

tag: subject

tag: type of surgery

value: Mastectomy

tag: histology

tag: er status

tag: pr status

tag: her2 status

value: Yes

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 416

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

tag: race


title: patient 413

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: chemotherapy

tag: locoregional recurrence


title: patient 411

tag: tissue

tag: subject

tag: type of surgery

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 410

tag: histology

tag: er status

tag: pr status

tag: her2 status

tag: time to death or censor from date of diagnosis (years)


title: dot-1.1(knu339);ced-3 mut input DNA repl 1

description: Input sample for H3K9me2 ChIP-seq in dot-1.1;ced-3 mutant, replicate 1.

tag: genotype

tag: antibody

tag: antibody catalog#

tag: antibody manufacturer


title: patient 417

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: bioanalyzer rin (rna integrity number)


title: ced-3 mut H3K9me2 ChIP-seq repl 2

description: ChIP sample for H3K9me2 ChIP-seq in ced-3 mutant, replicate 2.


title: ced-3 mut H3K9me2 ChIP-seq repl 1

description: ChIP sample for H3K9me2 ChIP-seq in ced-3 mutant, replicate 1.


title: patient 408

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: er status

tag: chemotherapy

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)


title: ced-3 mut input DNA repl 2

description: Input sample for H3K9me2 ChIP-seq in ced-3 mutant, replicate 2.

tag: genotype

tag: antibody

tag: antibody catalog#

tag: antibody manufacturer


title: patient 418

tag: pr status

tag: her2 status

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: time to death or censor from date of diagnosis (years)


title: ced-3 mut input DNA repl 1

description: Input sample for H3K9me2 ChIP-seq in ced-3 mutant, replicate 1.


title: DNA methylation data of ccRCC tumor 119

type: genomic

city: Lyon

first: James

last: Mckay

address: 25 Av. Tony Garnier

country: France

institute: IARC - International Agency for Research on Cancer

description:
clear clear renal carcinoma tumor, high-quality sample
206419180153_R08C01

hyb_protocol: The DNA (600 ng) of samples underwent pre-processing steps as follows: bisulfite-conversion, whole-genome amplification, fragmentation, and hybridization with complementary probes sequences on The Infinium MethylationEPIC BeadChip v1 using standard Illumina protocol.

scan_protocol: iScan system scanner (Ilumina) and probe intensities were obtained by GenomeStudio Software ((Ilumina)

data_processing:
The processing steps of probes were performed using the implemented functions in methylkey R package (https://github.com/IARCbioinfo/methylkey). Version 0.1.1.9000
tab-delimited file with a matrix of 121 samples as cols and 792,697 normalised (Funnorm) average beta values as rows. File named as 'MatrixProcessed.tsv',
Unmethylated and methylated signal intensities uploaded as 'rawdata2Geo.tsv' and unprocessed betas as 'betas2Geo.tsv'

label: Cy5 and Cy3

source_name: ccRCC tumor 119

label_protocol: Standard Illumina Protocol

growth_protocol: Not applicable.

extract_protocol: DNA was isolated from tumor samples using the Flexigene DNA isolation kit from Qiagen as per manufacturer’s protocol and stored in aliquots at −20 °C.

treatment_protocol: Not applicable.

tag: tissue

value: ccRCC tumor 119

tag: age

tag: Sex

value: Male

tag: batch


title: DNA methylation data of ccRCC tumor 121

description:
clear clear renal carcinoma tumor, high-quality sample
206419180169_R02C01

source_name: ccRCC tumor 121

value: ccRCC tumor 121

value: Female


title: DNA methylation data of ccRCC tumor 120

description:
clear clear renal carcinoma tumor, Excluded from original study, outlier based on unmethylated and methylation global levels
206419180169_R01C01

source_name: ccRCC tumor 120

value: ccRCC tumor 120


title: patient 405

tag: subject

tag: type of surgery

tag: histology

tag: er status

value: Positive

tag: age at diagnosis (dichotomized)

tag: race

value: White

tag: chemotherapy

value: Unknown

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: DNA methylation data of ccRCC tumor 117

description:
clear clear renal carcinoma tumor, high-quality sample
206419180153_R02C01

source_name: ccRCC tumor 117

value: ccRCC tumor 117


title: DNA methylation data of ccRCC tumor 116

description:
clear clear renal carcinoma tumor, high-quality sample
206419180153_R01C01

source_name: ccRCC tumor 116

value: ccRCC tumor 116


title: patient 406

value: IDC

tag: pr status

tag: her2 status

value: Negative

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

value: No

tag: type of radiotherapy

tag: age at diagnosis


title: patient 403

tag: tissue

value: macrodissected primary breast tumor

tag: subject

tag: type of surgery

value: Lumpectomy

tag: histology

value: Partial breast irradiation

tag: time to death or censor from date of diagnosis (years)


title: patient 402

value: Mastectomy

tag: er status

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: locoregional recurrence

value: Alive


title: patient 409

value: ILC

tag: pr status

tag: her2 status

value: Yes

value: External beam radiation

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: DNA methylation data of ccRCC tumor 115

description:
clear clear renal carcinoma tumor, high-quality sample
206419180144_R08C01

source_name: ccRCC tumor 115

value: ccRCC tumor 115

tag: age

tag: Sex

value: Male

tag: batch


title: patient 401

tag: tissue

tag: subject

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

value: White


title: patient 399

tag: type of surgery

tag: histology

tag: er status

value: Positive

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: locoregional recurrence

tag: time to death or censor from date of diagnosis (years)


title: patient 407

tag: pr status

tag: her2 status

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 404

tag: tissue

tag: subject

value: Other

tag: pt

tag: pn

tag: ptnm

value: Dead


title: patient 400

tag: type of surgery

tag: histology

value: IDC

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis


title: DNA methylation data of ccRCC tumor 112

description:
clear clear renal carcinoma tumor, high-quality sample
206419180144_R05C01

source_name: ccRCC tumor 112

value: ccRCC tumor 112

tag: age

tag: Sex

tag: batch


title: DNA methylation data of ccRCC tumor 113

description:
clear clear renal carcinoma tumor, high-quality sample
206419180144_R06C01

source_name: ccRCC tumor 113

value: ccRCC tumor 113


title: DNA methylation data of ccRCC tumor 118

description:
clear clear renal carcinoma tumor, high-quality sample
206419180153_R03C01

source_name: ccRCC tumor 118

value: ccRCC tumor 118

value: Female


title: patient 398

value: macrodissected primary breast tumor

value: Lumpectomy

tag: er status

tag: pr status

value: Negative

tag: her2 status

value: Partial breast irradiation

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: locoregional recurrence

tag: time to death or censor from date of diagnosis (years)


title: DNA methylation data of ccRCC tumor 109

description:
clear clear renal carcinoma tumor, high-quality sample
206419180144_R02C01

source_name: ccRCC tumor 109

tag: tissue

value: ccRCC tumor 109


title: DNA methylation data of ccRCC tumor 110

description:
clear clear renal carcinoma tumor, high-quality sample
206419180144_R03C01

source_name: ccRCC tumor 110

value: ccRCC tumor 110


title: patient 397

source_name: macrodissected primary breast tumor

tag: subject

tag: type of surgery

value: Mastectomy

tag: pt

tag: pn

tag: ptnm

value: No

value: Yes

tag: death

value: Alive

tag: time to locoregional recurrence from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: DNA methylation data of ccRCC tumor 114

description:
clear clear renal carcinoma tumor, high-quality sample
206419180144_R07C01

source_name: ccRCC tumor 114

value: ccRCC tumor 114

tag: age

tag: Sex

value: Male

tag: batch


title: patient 395

tag: histology

value: IDC

tag: er status

value: Positive

tag: pr status

tag: her2 status

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

value: White


title: DNA methylation data of ccRCC tumor 108

description:
clear clear renal carcinoma tumor, high-quality sample
206419180144_R01C01

source_name: ccRCC tumor 108

tag: tissue

value: ccRCC tumor 108


title: DNA methylation data of ccRCC tumor 111

description:
clear clear renal carcinoma tumor, high-quality sample
206419180144_R04C01

source_name: ccRCC tumor 111

value: ccRCC tumor 111


title: patient 396

value: macrodissected primary breast tumor

tag: subject

tag: type of surgery

tag: pt

tag: pn

tag: race

tag: chemotherapy

tag: locoregional recurrence

tag: time to death or censor from date of diagnosis (years)


title: DNA methylation data of ccRCC tumor 107

description:
clear clear renal carcinoma tumor, high-quality sample
206419180142_R08C01

source_name: ccRCC tumor 107

value: ccRCC tumor 107

tag: age

tag: Sex

tag: batch


title: DNA methylation data of ccRCC tumor 105

description:
clear clear renal carcinoma tumor, high-quality sample
206419180142_R06C01

source_name: ccRCC tumor 105

value: ccRCC tumor 105

value: Female


title: DNA methylation data of ccRCC tumor 104

description:
clear clear renal carcinoma tumor, high-quality sample
206419180142_R05C01

source_name: ccRCC tumor 104

value: ccRCC tumor 104


title: DNA methylation data of ccRCC tumor 106

description:
clear clear renal carcinoma tumor, high-quality sample
206419180142_R07C01

source_name: ccRCC tumor 106

value: ccRCC tumor 106


title: patient 393

value: Lumpectomy

tag: histology

tag: er status

tag: pr status

value: Negative

tag: her2 status

tag: ptnm

value: External beam radiation

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 392

tag: tissue

tag: subject

tag: type of surgery

tag: pt

tag: radiotherapy

value: Yes

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

value: AA

value: No

value: Alive


title: patient 394

value: Mastectomy

value: IDC

value: Positive

tag: pn

tag: race

tag: chemotherapy

tag: locoregional recurrence

tag: time to death or censor from date of diagnosis (years)


title: DNA methylation data of ccRCC tumor 100

description:
clear clear renal carcinoma tumor, high-quality sample
206419180142_R01C01

source_name: ccRCC tumor 100

value: ccRCC tumor 100

tag: age

tag: Sex

value: Male

tag: batch


title: DNA methylation data of ccRCC tumor 99

description:
clear clear renal carcinoma tumor, high-quality sample
206419180137_R08C01

source_name: ccRCC tumor 99

value: ccRCC tumor 99


title: patient 390

value: macrodissected primary breast tumor

tag: histology

value: ILC

tag: er status

tag: pr status

tag: her2 status

tag: ptnm

value: White

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: DNA methylation data of ccRCC tumor 103

description:
clear clear renal carcinoma tumor, high-quality sample
206419180142_R04C01

source_name: ccRCC tumor 103

tag: tissue

value: ccRCC tumor 103

value: Female


title: patient 389

tag: subject

tag: type of surgery

value: Lumpectomy

tag: pt

tag: pn

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)


title: DNA methylation data of ccRCC tumor 98

description:
clear clear renal carcinoma tumor, high-quality sample
206419180137_R07C01

source_name: ccRCC tumor 98

value: ccRCC tumor 98

tag: age

tag: Sex

tag: batch


title: DNA methylation data of ccRCC tumor 97

description:
clear clear renal carcinoma tumor, high-quality sample
206419180137_R06C01

source_name: ccRCC tumor 97

value: ccRCC tumor 97


title: patient 391

tag: histology

tag: er status

tag: pr status

tag: her2 status

value: Negative

value: Yes

value: External beam radiation

tag: race

tag: chemotherapy

tag: locoregional recurrence

tag: time to death or censor from date of diagnosis (years)


title: DNA methylation data of ccRCC tumor 101

description:
clear clear renal carcinoma tumor, high-quality sample
206419180142_R02C01

source_name: ccRCC tumor 101

tag: tissue

value: ccRCC tumor 101


title: patient 387

tag: subject

tag: type of surgery

value: Mastectomy

value: IDC

tag: pt

tag: pn

tag: ptnm

value: AA

tag: death

value: Dead

tag: time to locoregional recurrence from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 382

tag: histology

value: Positive

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

value: No

value: Alive


title: patient 384

value: macrodissected primary breast tumor

tag: er status

tag: pr status

tag: her2 status

tag: race

value: White

tag: chemotherapy


title: patient 385

tag: tissue

tag: subject

tag: type of surgery

value: Partial breast irradiation

tag: locoregional recurrence

tag: time to death or censor from date of diagnosis (years)


title: DNA methylation data of ccRCC tumor 102

description:
clear clear renal carcinoma tumor, high-quality sample
206419180142_R03C01

source_name: ccRCC tumor 102

value: ccRCC tumor 102

tag: age

tag: Sex

value: Male

tag: batch


title: patient 386

value: Lumpectomy

tag: histology

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: DNA methylation data of ccRCC tumor 96

description:
clear clear renal carcinoma tumor, high-quality sample
206402350177_R08C01

source_name: ccRCC tumor 96

value: ccRCC tumor 96


title: DNA methylation data of ccRCC tumor 95

description:
clear clear renal carcinoma tumor, high-quality sample
206402350177_R07C01

source_name: ccRCC tumor 95

value: ccRCC tumor 95


title: patient 388

source_name: macrodissected primary breast tumor

value: Other

tag: er status

value: Negative

tag: pr status

tag: her2 status

value: Yes

tag: type of radiotherapy

value: External beam radiation

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy


title: DNA methylation data of ccRCC tumor 94

description:
clear clear renal carcinoma tumor, high-quality sample
206402350177_R06C01

source_name: ccRCC tumor 94

tag: tissue

value: ccRCC tumor 94

tag: age

tag: Sex

tag: batch


title: patient 380

tag: subject

tag: type of surgery

tag: histology

value: IDC

tag: pt

tag: pn

tag: ptnm

tag: locoregional recurrence

tag: time to death or censor from date of diagnosis (years)


title: patient 381

value: Mastectomy

value: ILC

tag: er status

value: Positive

tag: pr status

tag: her2 status

tag: radiotherapy

tag: type of radiotherapy

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 378

tag: tissue

value: macrodissected primary breast tumor

value: No

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

value: Alive


title: patient 383

tag: subject

tag: type of surgery

tag: histology

tag: pt

tag: pn

value: White

value: Dead


title: patient 379

value: Lumpectomy

tag: er status

tag: pr status

tag: ptnm

value: Partial breast irradiation

tag: locoregional recurrence

tag: time to death or censor from date of diagnosis (years)


title: patient 377

tag: her2 status

tag: radiotherapy

tag: type of radiotherapy

value: Hispanic, Asian & other

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)


title: DNA methylation data of ccRCC tumor 93

description:
clear clear renal carcinoma tumor, high-quality sample
206402350177_R05C01

source_name: ccRCC tumor 93

tag: tissue

value: ccRCC tumor 93

tag: age

tag: Sex

value: Female

tag: batch


title: patient 376

tag: subject

tag: type of surgery

tag: histology

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: bioanalyzer rin (rna integrity number)


title: DNA methylation data of ccRCC tumor 91

description:
clear clear renal carcinoma tumor, high-quality sample
206402350177_R03C01

source_name: ccRCC tumor 91

value: ccRCC tumor 91


title: DNA methylation data of ccRCC tumor 89

description:
clear clear renal carcinoma tumor, high-quality sample
206402350177_R01C01

source_name: ccRCC tumor 89

value: ccRCC tumor 89

value: Male


title: DNA methylation data of ccRCC tumor 90

description:
clear clear renal carcinoma tumor, high-quality sample
206402350177_R02C01

source_name: ccRCC tumor 90

value: ccRCC tumor 90


title: DNA methylation data of ccRCC tumor 92

description:
clear clear renal carcinoma tumor, high-quality sample
206402350177_R04C01

source_name: ccRCC tumor 92

value: ccRCC tumor 92


title: patient 375

value: Mastectomy

value: IDC

tag: er status

tag: pr status

tag: her2 status

value: Negative

tag: pt

tag: pn

tag: ptnm

tag: locoregional recurrence

tag: time to death or censor from date of diagnosis (years)


title: DNA methylation data of ccRCC tumor 88

description:
clear clear renal carcinoma tumor, high-quality sample
206402350163_R08C01

source_name: ccRCC tumor 88

tag: tissue

value: ccRCC tumor 88

tag: age

tag: Sex

tag: batch


title: DNA methylation data of ccRCC tumor 86

description:
clear clear renal carcinoma tumor, high-quality sample
206402350163_R06C01

source_name: ccRCC tumor 86

value: ccRCC tumor 86


title: DNA methylation data of ccRCC tumor 85

description:
clear clear renal carcinoma tumor, high-quality sample
206402350163_R05C01

source_name: ccRCC tumor 85

value: ccRCC tumor 85


title: patient 374

value: macrodissected primary breast tumor

tag: subject

tag: type of surgery

tag: histology

value: Positive

tag: radiotherapy

value: Yes

tag: type of radiotherapy

tag: age at diagnosis

value: White

value: No

tag: death

value: Alive

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 373

value: Lumpectomy

tag: er status

tag: pr status

tag: her2 status

tag: pt

value: Partial breast irradiation

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: bioanalyzer rin (rna integrity number)


title: DNA methylation data of ccRCC tumor 84

description:
clear clear renal carcinoma tumor, high-quality sample
206402350163_R04C01

source_name: ccRCC tumor 84

tag: tissue

value: ccRCC tumor 84

tag: age

tag: Sex

value: Female

tag: batch


title: DNA methylation data of ccRCC tumor 80

description:
clear clear renal carcinoma tumor, high-quality sample
206402350158_R08C01

source_name: ccRCC tumor 80

value: ccRCC tumor 80


title: DNA methylation data of ccRCC tumor 83

description:
clear clear renal carcinoma tumor, high-quality sample
206402350163_R03C01

source_name: ccRCC tumor 83

value: ccRCC tumor 83


title: DNA methylation data of ccRCC tumor 81

description:
clear clear renal carcinoma tumor, high-quality sample
206402350163_R01C01

source_name: ccRCC tumor 81

value: ccRCC tumor 81

value: Male


title: DNA methylation data of ccRCC tumor 87

description:
clear clear renal carcinoma tumor, high-quality sample
206402350163_R07C01

source_name: ccRCC tumor 87

value: ccRCC tumor 87


title: patient 372

tag: subject

tag: type of surgery

tag: histology

value: IDC

tag: pn

tag: ptnm

tag: radiotherapy

value: External beam radiation

tag: locoregional recurrence

tag: time to death or censor from date of diagnosis (years)


title: patient 368

value: macrodissected primary breast tumor

tag: er status

tag: pr status

tag: her2 status

value: Negative

tag: pt

tag: type of radiotherapy

tag: age at diagnosis

tag: death

value: Dead

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 370

tag: tissue

value: Positive

value: Yes

tag: age at diagnosis (dichotomized)

tag: race

value: White

tag: chemotherapy

tag: bioanalyzer rin (rna integrity number)


title: DNA methylation data of ccRCC tumor 79

description:
clear clear renal carcinoma tumor, high-quality sample
206402350158_R07C01

source_name: ccRCC tumor 79

value: ccRCC tumor 79

tag: age

tag: Sex

tag: batch


title: DNA methylation data of ccRCC tumor 77

description:
clear clear renal carcinoma tumor, high-quality sample
206402350158_R05C01

source_name: ccRCC tumor 77

value: ccRCC tumor 77


title: patient 364

source_name: macrodissected primary breast tumor

tag: subject

tag: type of surgery

value: Lumpectomy

tag: histology

tag: pn

tag: ptnm

tag: radiotherapy

value: Partial breast irradiation

value: No

tag: locoregional recurrence

tag: time to death or censor from date of diagnosis (years)


title: DNA methylation data of ccRCC tumor 78

description:
clear clear renal carcinoma tumor, high-quality sample
206402350158_R06C01

source_name: ccRCC tumor 78

value: ccRCC tumor 78

value: Female


title: patient 366

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: type of radiotherapy

tag: age at diagnosis

tag: death

value: Alive

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 369

tag: tissue

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: bioanalyzer rin (rna integrity number)


title: patient 371

tag: subject

tag: type of surgery

value: Mastectomy

tag: histology

tag: pn

tag: ptnm


title: patient 367

value: IDC

tag: er status

tag: pr status

tag: radiotherapy

tag: locoregional recurrence

tag: time to death or censor from date of diagnosis (years)


title: patient 363

value: Other

tag: her2 status

tag: pt

tag: type of radiotherapy

tag: age at diagnosis

tag: death


title: patient 362

tag: tissue

value: macrodissected primary breast tumor

value: External beam radiation

tag: age at diagnosis (dichotomized)

tag: race

value: AA

tag: chemotherapy

tag: time to locoregional recurrence from date of diagnosis (years)


title: DNA methylation data of ccRCC tumor 74

description:
clear clear renal carcinoma tumor, high-quality sample
206402350158_R02C01

source_name: ccRCC tumor 74

value: ccRCC tumor 74

tag: age

tag: Sex

value: Male

tag: batch


title: patient 361

tag: subject

tag: type of surgery

tag: histology

tag: er status

value: Positive

tag: pr status

value: Negative

tag: pn

tag: ptnm

value: White

tag: bioanalyzer rin (rna integrity number)


title: DNA methylation data of ccRCC tumor 82

description:
clear clear renal carcinoma tumor, high-quality sample
206402350163_R02C01

source_name: ccRCC tumor 82

value: ccRCC tumor 82


title: patient 360

value: Lumpectomy

tag: her2 status

tag: pt

tag: radiotherapy

value: Yes

tag: type of radiotherapy

tag: age at diagnosis

tag: locoregional recurrence

tag: death

tag: time to death or censor from date of diagnosis (years)


title: patient 365

tag: tissue

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

value: No

value: Dead

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 359

tag: subject

tag: type of surgery

tag: histology

tag: er status

tag: pr status

value: Alive


title: DNA methylation data of ccRCC tumor 76

description:
clear clear renal carcinoma tumor, high-quality sample
206402350158_R04C01

source_name: ccRCC tumor 76

value: ccRCC tumor 76

tag: age

tag: Sex

value: Female

tag: batch


title: DNA methylation data of ccRCC tumor 73

description:
clear clear renal carcinoma tumor, high-quality sample
206402350158_R01C01

source_name: ccRCC tumor 73

value: ccRCC tumor 73


title: DNA methylation data of ccRCC tumor 72

description:
clear clear renal carcinoma tumor, high-quality sample
206402350156_R08C01

source_name: ccRCC tumor 72

value: ccRCC tumor 72


title: DNA methylation data of ccRCC tumor 75

description:
clear clear renal carcinoma tumor, high-quality sample
206402350158_R03C01

source_name: ccRCC tumor 75

value: ccRCC tumor 75


title: DNA methylation data of ccRCC tumor 71

description:
clear clear renal carcinoma tumor, high-quality sample
206402350156_R07C01

source_name: ccRCC tumor 71

value: ccRCC tumor 71


title: patient 356

value: macrodissected primary breast tumor

value: IDC

tag: her2 status

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: bioanalyzer rin (rna integrity number)


title: DNA methylation data of ccRCC tumor 69

description:
clear clear renal carcinoma tumor, high-quality sample
206402350156_R05C01

source_name: ccRCC tumor 69

tag: tissue

value: ccRCC tumor 69


title: patient 358

tag: subject

value: Mastectomy

value: Positive

value: Negative

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: DNA methylation data of ccRCC tumor 70

description:
clear clear renal carcinoma tumor, high-quality sample
206402350156_R06C01

source_name: ccRCC tumor 70

value: ccRCC tumor 70

tag: age

tag: Sex

value: Male

tag: batch


title: patient 357

tag: type of surgery

tag: histology

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: pn

tag: ptnm

value: No

value: White


title: patient 355

tag: tissue

tag: subject

value: Lumpectomy

tag: radiotherapy

value: Yes

tag: type of radiotherapy

value: External beam radiation

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

value: Alive

tag: bioanalyzer rin (rna integrity number)


title: patient 354

value: Hispanic, Asian & other

tag: chemotherapy

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: DNA methylation data of ccRCC tumor 68

description:
clear clear renal carcinoma tumor, high-quality sample
206402350156_R04C01

source_name: ccRCC tumor 68

value: ccRCC tumor 68

tag: age

tag: Sex

tag: batch


title: DNA methylation data of ccRCC tumor 67

description:
clear clear renal carcinoma tumor, high-quality sample
206402350156_R03C01

source_name: ccRCC tumor 67

value: ccRCC tumor 67

value: Female


title: DNA methylation data of ccRCC tumor 65

description:
clear clear renal carcinoma tumor, high-quality sample
206402350156_R01C01

source_name: ccRCC tumor 65

value: ccRCC tumor 65


title: DNA methylation data of ccRCC tumor 64

description:
clear clear renal carcinoma tumor, high-quality sample
206402350153_R08C01

source_name: ccRCC tumor 64

value: ccRCC tumor 64


title: DNA methylation data of ccRCC tumor 66

description:
clear clear renal carcinoma tumor, high-quality sample
206402350156_R02C01

source_name: ccRCC tumor 66

value: ccRCC tumor 66


title: patient 352

value: macrodissected primary breast tumor

tag: type of surgery

tag: histology

value: IDC

tag: er status

value: Positive

tag: pr status

tag: her2 status

tag: pt

tag: pn

tag: ptnm


title: patient 353

tag: tissue

tag: subject

value: Negative

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: bioanalyzer rin (rna integrity number)


title: patient 351

value: Mastectomy

value: No

tag: chemotherapy

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: patient 350

tag: type of surgery

tag: histology

tag: er status

tag: pr status

tag: her2 status

value: White


title: DNA methylation data of ccRCC tumor 61

description:
clear clear renal carcinoma tumor, high-quality sample
206402350153_R05C01

source_name: ccRCC tumor 61

tag: tissue

value: ccRCC tumor 61

tag: age

tag: Sex

value: Male

tag: batch


title: DNA methylation data of ccRCC tumor 63

description:
clear clear renal carcinoma tumor, high-quality sample
206402350153_R07C01

source_name: ccRCC tumor 63

value: ccRCC tumor 63


title: DNA methylation data of ccRCC tumor 62

description:
clear clear renal carcinoma tumor, high-quality sample
206402350153_R06C01

source_name: ccRCC tumor 62

value: ccRCC tumor 62


title: patient 349

source_name: macrodissected primary breast tumor

tag: subject

value: Lumpectomy

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

value: Yes

tag: type of radiotherapy

value: Partial breast irradiation

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

value: Alive


title: DNA methylation data of ccRCC tumor 60

description:
clear clear renal carcinoma tumor, high-quality sample
206402350153_R04C01

source_name: ccRCC tumor 60

value: ccRCC tumor 60


title: DNA methylation data of ccRCC tumor 59

description:
clear clear renal carcinoma tumor, high-quality sample
206402350153_R03C01

source_name: ccRCC tumor 59

value: ccRCC tumor 59

value: Female


title: DNA methylation data of ccRCC tumor 58

description:
clear clear renal carcinoma tumor, high-quality sample
206402350153_R02C01

source_name: ccRCC tumor 58

value: ccRCC tumor 58


title: DNA methylation data of ccRCC tumor 57

description:
clear clear renal carcinoma tumor, high-quality sample
206402350153_R01C01

source_name: ccRCC tumor 57

value: ccRCC tumor 57


title: DNA methylation data of ccRCC tumor 56

description:
clear clear renal carcinoma tumor, high-quality sample
206402350152_R08C01

source_name: ccRCC tumor 56

value: ccRCC tumor 56


title: patient 348

value: macrodissected primary breast tumor

tag: type of surgery

value: Other

value: Positive

value: Negative

tag: race

tag: chemotherapy

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: DNA methylation data of ccRCC tumor 54

description:
clear clear renal carcinoma tumor, high-quality sample
206402350152_R06C01

source_name: ccRCC tumor 54

tag: tissue

value: ccRCC tumor 54

tag: age

tag: Sex

value: Male

tag: batch


title: patient 341

tag: subject

value: Mastectomy

tag: histology

value: IDC

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: pn

tag: ptnm

value: External beam radiation

value: White

value: No


title: patient 342

tag: type of surgery

value: ILC

tag: radiotherapy

value: Yes

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: locoregional recurrence

value: Alive


title: patient 344

tag: tissue

value: Lumpectomy

value: Partial breast irradiation

tag: death

value: Dead

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 346

value: macrodissected primary breast tumor

tag: subject

tag: histology

tag: er status

tag: pr status

tag: her2 status


title: patient 340

tag: type of surgery

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy


title: patient 337

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy


title: patient 343

tag: tissue

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: patient 336

tag: subject

tag: histology

tag: er status

tag: pr status

tag: bioanalyzer rin (rna integrity number)


title: patient 345

tag: type of surgery

tag: her2 status

tag: pt

tag: pn

tag: ptnm


title: DNA methylation data of ccRCC tumor 50

description:
clear clear renal carcinoma tumor, high-quality sample
206402350152_R02C01

source_name: ccRCC tumor 50

value: ccRCC tumor 50

tag: age

tag: Sex

tag: batch


title: patient 335

tag: tissue

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: locoregional recurrence


title: DNA methylation data of ccRCC tumor 51

description:
clear clear renal carcinoma tumor, high-quality sample
206402350152_R03C01

source_name: ccRCC tumor 51

value: ccRCC tumor 51

value: Female


title: DNA methylation data of ccRCC tumor 48

description:
clear clear renal carcinoma tumor, high-quality sample
206402350151_R08C01

source_name: ccRCC tumor 48

value: ccRCC tumor 48


title: DNA methylation data of ccRCC tumor 52

description:
clear clear renal carcinoma tumor, high-quality sample
206402350152_R04C01

source_name: ccRCC tumor 52

value: ccRCC tumor 52

value: Male


title: DNA methylation data of ccRCC tumor 55

description:
clear clear renal carcinoma tumor, high-quality sample
206402350152_R07C01

source_name: ccRCC tumor 55

value: ccRCC tumor 55


title: DNA methylation data of ccRCC tumor 53

description:
clear clear renal carcinoma tumor, high-quality sample
206402350152_R05C01

source_name: ccRCC tumor 53

value: ccRCC tumor 53


title: patient 334

tag: subject

tag: histology

value: IDC

tag: er status

value: Positive

tag: pr status

value: White

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)