title: K107284 (second donation from K106008)

description:
whole methylome (Methyl Capture)
K107284_MeCap

tag: race

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)


title: RNA-SEQ_A12-2-17_15-492/004_prostate tissue

status: Public on Sep 30 2021

type: SRA

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

country: USA

institute: National Cancer Institute

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A12-2-17
processed_counts.txt
processed_TPM.txt

library_source: transcriptomic

data_processing:
Base-calling was performed with CASAVA 1.9
FASTQ files were pre-processed to remove sequencing adaptors with Trimmomatic v0.36.
Paired-end trimmed FASTQ files were aligned to hg19 using STAR.
RSEM was used to estimate read counts for each genomic feature.
Genome_build: hg19
Supplementary_files_format_and_content: tab separated values, gene symbol, description, transcripts-per-million (TPM) or count

molecule: total RNA

organism: Homo sapiens

extract_protocol:
RNA was extracted from FFPE prostate tissues using the Qiagen RNeasy FFPE kit or from frozen buffy coats using the Macharay-Nagel NucleoSpin RNA Blood  kit.
Libraries were prepared with the NEBNext Globin and rRNA depletiion library construction kit and the Illumina TruSeq stranded total RNA with ribo-zero globin kit.

treatment_protocol: Patients with prostate cancer underwent radical prostatectomy with no prior therapy. Blood was drawn into EDTA tubes prior to surgery. Prostate tissues were grossed, accessioned, fixed in formalin, and embedded in paraffin.

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

value: white

tag: pathologic stage

tag: age

tag: 5-year disease status

value: remission

tag: sample type

value: normal

tag: tissue

value: prostate tissue


title: RNA-SEQ_A12-2-21_15-492/006_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A12-2-21
processed_counts.txt
processed_TPM.txt


title: K107324

city: Indianapolis

first: Natascia

last: Marino

state: IN

address: 980 W. Walnut St, R3-C238

department: Hematology/Oncology Division

institute: Indiana University School of Medicine

description:
whole methylome (Methyl Capture)
K107324_MeCap

library_source: genomic

data_processing:
The raw methyl-capture reads were cleaned using Trimmomatic version 0.36 (Bolger et al. 2014) setting the cutoff threshold for average base quality score at 20 over a window of 3 bases. Reads shorter than 20 bases post-trimming were excluded. (parameters: LEADING:20 TRAILING:20 SLIDINGWINDOW:3:20 MINLEN:20)
The cleaned reads were aligned to the human genome reference, GRCh38.p12 using bwa (version 0.7.17-r1188) (Li and Durbin, 2010).
Potential PCR duplicates were marked using Picard tools version 2.20.3 (http://broadinstitute.github.io/picard/).
Deduplicated insert alignments were inferred from the deduplicated, concordantly mapped read pair alignments using Samtools version 1.9 (Li et al. 2009).
The deduplicated insert coverage was estimated by counting the number of deduplicated inserts spanning over each base position on the reference genome and saved to the wiggle files.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Wiggle files containing deduplicated insert coverage

molecule: genomic DNA

source_name: Breast

growth_protocol: The breast tissue cores are collected by using a needle biopsy needle (Hologic, Marlborough, MA). The skin is cleaned, then numbed with lidocaine. The physician nicks the skin with a scalpel, usually in the upper-outer quadrant of the breast, and the needle is inserted into this incision. From this single incision, five sample cores are removed from the breast (approximately 200mg). A nurse/surgeon’s assistant holds pressure on the incision for 10 full minutes, then applies a pressure bandage. An ice pack is immediately placed on the breast. Within 10 min from collection the tissue cores are fresh frozen in liquid nitrogen

extract_protocol:
Total RNA was extracted using the Allprep DNA/RNA/miRNA Universal Kit (QIAGEN, Germantown, MD).
The concentration and quality of total RNA and DNA samples was first assessed using Agilent 2100 Bioanalyzer. For the RNAsequencing: cDNA library was prepared using the TruSeq Stranded Total RNA Kit (Illumina) and sequenced using Illumina HiSeq4000. For the DNA methylation analysis: Library was generated using MethylCap Library Kit (Diagenode, Denville NJ, US) according to the manufacturer′s protocols followed by single-end 75-bp sequencing on Illumina Nextseq4000

tag: age of menarche

tag: menopausal status

value: Pre

value: No

tag: blood relatives cancer

value: Yes

value: WHITE

tag: risk category

value: High


title: RNA-SEQ_A12-2-19_15-492/005_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A12-2-19
processed_counts.txt
processed_TPM.txt

tag: race

value: recurrence


title: K107298

description:
whole methylome (Methyl Capture)
K107298_MeCap

tag: hispanic

tag: bmi

tag: ever pregnant


title: GC071392_CTCCTTAC-TAAGGCGA

city: Leuven

first: Vincent

last: Pasque

address: Herestraat 49 bus 804

department: Development and Regeneration

country: Belgium

institute: KU Leuven

description: smart-seq2 protocol

data_processing:
For non-allele resulotion analyses, reads were mapped to the mouse reference genome (mm10) using STAR 2.5.3a (Dobin et al. 2013) and GENCODE vM16 annotation file. Alignment was performed with default parameters and --sjdbOverhang set to 74 and output to sorted BAM files. Uniquely aligned reads were quantified using the featureCounts function from the R Bioconductor package “Rsubread” (version 1.5.2) (Liao et al. 2019).
For allele resolution analyses, reads processed as previously described in (Janiszewski, talon et al). Briefly, reads were mapped to the same reference genome release in which SNP positions were substituted by N base (referred to as N-masked mm10). N-masking was performed with SNPsplit software (Version 0.3.2 released (29-03-2017)) (Krueger and Andrews 2016) supplied with the list of strain-specific SNPs (129S1_SvImJ and CAST_EiJ) from Sanger Mouse Genomes project database (mgp.v5.merged.snps_all.dbSNP142.vcf.gz). N-masking was done in dual hybrid mode and resulted in the identification throughout the entire genome of 20,563,466 SNP positions unique for either strain, of which 634,730 on the X Chromosome. Next, reads were aligned to the N-masked mm10 genome using STAR 2.5.3a with parameters disabling soft-clipping of incompletely aligned reads (--alignEndsType EndToEnd --outSAMattributes NH HI NM MD). Reads aligned to the N-masked reference genome were then split into two BAM files containing only strain-specific reads (on average 10.95% for Mus and 10.25% for Cast of total mapped reads) using SNPsplit (version 0.3.4). Unclassified reads were not used for subsequent allele-specific analysis. Using the allelic BAM files, variant calling files (VCF) were generated using samtools’ mpilup command (version 1.7) (ref), and merged using bcftools (ref)(version 1.5). An allelic count matrix was created by retaining counts from SNP positions and annotating these positions with their respective genes, where only genes covered by 4 SNPs or more are kept. Allelic data was size factor normalised by dividing allele-specific gene counts by total counts of that cell, this was then multiplied by 10000 and log transformed.
Genome_build: mm10
Supplementary_files_format_and_content: smartseq_norm_counts.csv: text file containing normalized read counts
Supplementary_files_format_and_content: smartseq_annotation.xlsx: spreadsheet containing additional metadata information
Supplementary_files_format_and_content: loom_XCR_5runs.loom: loom file containing both expression and gene regulatory network data together with tSNE embeddings

molecule: polyA RNA

organism: Mus musculus

source_name: MEF to iPSC reprogramming timecourse

growth_protocol: MEFs were cultured in MEF medium [DMEM (Gibco, 41966-554 052) supplemented with 10% (v/v) fetal bovine serum (FBS, Gibco, 10270-106), 1% (v/v) penicillin/streptomycin (P/S, Gibco, 15140-122), 1% (v/v) GlutaMAX (Gibco, 35050-061), 1% (v/v) non-essential amino acids (NEAA, Gibco, 11140-050), and 0.008% (v/v) beta-mercaptoethanol (Sigma-Aldrich, M7522)].   Cells undergoing reprogramming, and iPSCs were cultured in mouse ESC medium [KnockOut DMEM (Gibco, 10829-018) supplemented with 15% FBS, 1% P/S 10,000 U/mL, 1% GlutaMAX 100×, 1% NEAA 100×, 0.008% (v/v) beta-mercaptoethanol, and mouse LIF] in the presence of ascorbic acid (50 μg/ml final).

extract_protocol:
For the isolation of Day 0 time point of single-cell transcriptome analysis, 96 Xi-GFP cells were sorted into a 96-well multiwell plate with 2 µl lysis buffer, followed by initial steps of smart-seq2 protocol (see below). Remaining cells were plated for reprogramming directly after sorting, 50.000 cells per one well of a 12 well plate. Reprogramming was induced by doxycycline (2 μg/ml final) in mouse ESC medium in the presence of ascorbic acid (50 μg/ml final). The medium together with doxycycline and ascorbic acid was replaced every two days and maintained throughout entire reprogramming experiments. To derive iPSCs from picked colonies, the same conditions were used with dox and AA withdrawal after picking. Next, FUT4+ reprogramming intermediates were sorted into single wells, each with 2 µl of the lysis buffer [0,2% Triton X100, 1:20 RRI (Recombinant RNase Inhibitor Takara)] and snap-frozen in -80°C until cells from all timepoints were collected.
All samples were processed following the smart-seq2 protocol (Picelli et al). cDNA synthesis was done starting from 500 pg of input RNA, followed by library preparation from 80 pg of cDNA using the Nextera XT kit (Illumina, FC-131-1096). Indexing was performed with the Nextera XT index Kit V2 (Illumina, FC-131-2003). The quality of cDNA and individual libraries was assessed using an Agilent 2100 Bioanalyzer system.

treatment_protocol: Reprogramming experiments, unless stated otherwise, were performed by conditional induction of lentivirally delivered reprogramming factors. First, passage 1 MEFs at around 70% confluency were transduced with concentrated lentiviral supernatants. Lentiviruses were generated using HEK cells separately for two constructs: tetO-FUW-OSKM, Addgene cat. 20321 (Carey et al. 2009) and FUW-M2rtTA, Addgene cat. 20342 (Hockemeyer et al. 2008) with the calcium precipitation method. Supernatants with lentiviral particles were concentrated using lenti-X-concentrator (Takara, 631231) in 1:100 ratios. Infection with a pool of equal volumes of both constructs was carried out overnight, followed by 12 hours culture in MEF medium and 1:6 split. Cells were then sorted using FACS (described below) in order to isolate homogeneous population with regard to allelic inactivation of the X-GFP transgene (either Xi-GFP or Xa-GFP).

tag: timepoint

tag: initially inactive x allele

value: Mus


title: GC071392_CTCCTTAC-GGACTCCT

description: smart-seq2 protocol


title: RNA-SEQ_A10-172-7_15-492/003_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-172-7
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

value: black

value: buffy coat


title: GC071392_CTCCTTAC-GCTCATGA

description: smart-seq2 protocol


title: GC071392_CTCCTTAC-GCGTAGTA

description: smart-seq2 protocol


title: CD8T cells #1

city: Suita

first: Kazuyo

last: Moro

state: Osaka

address: 2-2 Yamada-oka

department: Department of Microbiology and Immunology

country: Japan

institute: Osaka University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the reference genome (mm9) using Bowtie2 v2.1.0 and TopHat2 v2.0.8.
The transcript abundances were estimated as FPKM (fragments per kilobase of exon million fragments mapped) value using Cufflinks v2.1.1.
Genome_build: mm9
Supplementary_files_format_and_content: processed data.xlsx includes FPKM values for each Sample.

source_name: CD8T cells

extract_protocol:
RNA was isolated with Isogen (Nippon Gene) or TRIzol LS (Thermo Fisher Scientific)
RNA libraries were prepared using the TruSeq RNA sample preparation kit v2 (Illumina) according to the manufacturer’s “low sample” protocol.

tag: strain

value: spleen

tag: cell type

value: CD8+ T cells

tag: genotype

value: wild-type

tag: treatment


title: K107257

description:
whole methylome (Methyl Capture)
K107257_MeCap

tag: age

tag: age of menarche

tag: menopausal status

tag: life time risk (tyrer-cuzick score)

value: Average


title: RNA-SEQ_A10-184-49_15-492/002_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-184-49
processed_counts.txt
processed_TPM.txt

value: prostate cancer

value: male

tag: gleason score

tag: race

tag: pathologic stage

tag: 5-year disease status

tag: sample type

value: cancer

tag: tissue


title: GC071392_CTCCTTAC-CTCTCTAC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: GC071392_CTCCTTAC-GGAGCTAC

description: smart-seq2 protocol


title: Naïve ILC2s #1

source_name: Naïve ILC2s

value: mesentery

value: Naive ILC2s


title: RNA-SEQ_A12-2-15_15-492/003_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A12-2-15
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

value: normal

value: prostate tissue


title: K107241

description:
whole methylome (Methyl Capture)
K107241_MeCap

value: Post

value: No

tag: blood relatives cancer

value: WHITE

tag: hispanic

tag: bmi

tag: ever pregnant

value: Yes

tag: risk category


title: GC071392_CTCCTTAC-CGTACTAG

description: smart-seq2 protocol

value: Mus


title: GC071392_CTCCTTAC-CGGAGCCT

description: smart-seq2 protocol


title: K107216

description:
whole methylome (Methyl Capture)
K107216_MeCap

tag: age

tag: age of menarche

tag: menopausal status

tag: life time risk (tyrer-cuzick score)


title: K107244

description:
whole methylome (Methyl Capture)
K107244_MeCap

value: Pre

tag: race


title: RNA-SEQ_A10-184-48_15-492/002_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-184-48
processed_counts.txt
processed_TPM.txt

tag: gleason score

value: black

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type

tag: tissue


title: GC071392_CTCCTTAC-CGATCAGT

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: RNA-SEQ_A10-172-6_15-492/002_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-172-6
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

value: buffy coat


title: RNA-SEQ_A10-184-47_15-492/001_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-184-47
processed_counts.txt
processed_TPM.txt

value: white


title: GC071392_CTCCTTAC-CGAGGCTG

description: smart-seq2 protocol


title: RNA-SEQ_A10-184-46_15-492/001_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-184-46
processed_counts.txt
processed_TPM.txt

value: prostate cancer


title: K107251

description:
whole methylome (Methyl Capture)
K107251_MeCap

tag: blood relatives cancer

tag: hispanic

tag: bmi

tag: ever pregnant

tag: risk category

value: High


title: K107214

description:
whole methylome (Methyl Capture)
K107214_MeCap

tag: age

tag: age of menarche

tag: menopausal status

tag: race

tag: life time risk (tyrer-cuzick score)

value: Average


title: RNA-SEQ_A10-172-5_15-492/001_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-172-5
processed_counts.txt
processed_TPM.txt

value: male

tag: gleason score

tag: pathologic stage

tag: 5-year disease status

tag: sample type

tag: tissue


title: GC071392_CTCCTTAC-CCTAAGAC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: RNA-SEQ_A10-184-45_15-008/U47_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-184-45
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

value: cancer


title: K107170

description:
whole methylome (Methyl Capture)
K107170_MeCap

tag: blood relatives cancer

tag: hispanic

tag: bmi

tag: ever pregnant

tag: risk category


title: H1975_OR_2

type: RNA

city: Xi'an

first: Kai

last: Li

address: NO.76, West Yanta Road

country: China

institute: Xi'an Jiaotong University

hyb_protocol: 1. Resuspend the dried sample in 18 μL nuclease-free water.  2. Add 4.5 μL 10× Gene Expression Blocking Agent and 2×Hi-RPM Hybridization Buffer.  3. Incubate at 100°C for 5 minutes and immediately transfer to an ice bath for 5 minutes.  4. Load a clean gasket slide into the Agilent SureHyb chamber base with the label facing up and aligned with the rectangular section of the chamber base. Ensure that the gasket slide is flush with the chamber base and is not ajar.  5. Slowly dispense all of the volume of hybridization sample onto the gasket well in a “drag and dispense” manner.  6. Slowly place an array “active side” down onto the SureHyb gasket slide, so that the “Agilent”-labeled barcode is facing down and the numeric barcode is facing up. Verify that the sandwich-pair is properly aligned.   7. Place the SureHyb chamber cover onto the sandwiched slides and slide the clamp assembly onto both pieces.  8. Hand-tighten the clamp onto the chamber.  9. Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles.  10. Place assembled slide chamber in rotisserie in a hybridization oven set to 55°C. Set your hybridization rotator to rotate at 20 rpm.  11. Hybridize at 55°C for 20 hours.

scan_protocol: Agilent Microarray Scanner (Agilent p/n G2505C)1. Assemble the slides into a slide holder.   2. Place assembled slide holders into scanner carousel.  3. Verify scan settings for -color scans.   Parameters  Dye channel G (green)  Scan region Agilent HD (61 x 21.6 mm)  Scan resolution 3μm  Tiff file dynamic range 20bit  Green PMT gain 100%  4. Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.

data_processing: 1. Open the Agilent Feature Extraction (FE) software. 2. Add the images (.tif) to be extracted to the FE Project. 3. Set FE Project Properties. 4. Check the Extraction Set Configuration. 5. Save the FE Project (.fep) by selecting File > Save As and browse for desired location. 6. Select Project > Start Extracting and export data to txt.

label_protocol: miRNA Complete Labeling and Hyb Kit (Agilent p/n 5190-0456)

growth_protocol: We established the Osimertinib resistant H1975 cells (H1975OR) by gradually increasing concentrations of Osimertinib for 72 hours with a recovery period between treatments, and described in detail in our results section.

extract_protocol: Total RNAs were extracted by using Trizol reagent (Invitrogen, CA, USA), according to the manufacturer’s instructions

tag: cell line background

tag: phenotype

value: Osimertinib resistant


title: K107172

description:
whole methylome (Methyl Capture)
K107172_MeCap

tag: age

tag: age of menarche

tag: menopausal status

tag: race

tag: life time risk (tyrer-cuzick score)


title: H1975_OR_1


title: RNA-SEQ_A10-184-44_15-008/U47_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-184-44
processed_counts.txt
processed_TPM.txt

tag: gleason score

tag: pathologic stage

tag: 5-year disease status

tag: sample type

value: normal

tag: tissue

value: prostate tissue


title: GC071392_CTCCTTAC-ACTGAGCG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: H1975_3


title: K107188 (second donation from K105894)

description:
whole methylome (Methyl Capture)
K107188_MeCap

value: No

tag: blood relatives cancer

tag: hispanic

tag: bmi


title: RNA-SEQ_A10-184-43_15-008/U46_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-184-43
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa


title: control knockdown in pTh17, biological rep1

city: fuzhou

first: Jinpiao

last: Lin

state: fujian

address: 20 Chazhong Road, Fuzhou, Fujian, China.

department: The First Affiliated Hospital of Fujian Medical University

institute: Department of Laboratory Medicine,Gene Diagnosis Research Center, the First Affiliated Hospital, Fujian Medical University

description: Gene expression data from in vitro polarized-pathogenic Th17 system transfected with control shRNA lentivirus, biological rep1

hyb_protocol: Following fragmentation, cRNA were hybridized and stained using GeneChip Hybridization Wash and Stain Kit following the manufacturer’s protocol on GeneChip Hybridization Oven 645 and GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: pathogenic Th17 cells induced from human peripheral blood naïve CD4+ T cells in vitro

label_protocol: Biotinylated cRNA were prepared using of a GeneChip 3’IVT Express Kit following the manufacturer’s protocol.

growth_protocol: Human naïve CD4+ T cells from peripheral blood mononuclear cells of 3 healthy honors were purified and purified naïve CD4+ T cells at 2×105 cells per well were cultured in 96-well round-bottom plates with the following antibodies and cytokines for pTh17 subset polarizing condition in RPMI-1640 with 10% fetal bovine serum(FBS): 2 μg/ml anti-CD3/CD28, 100 U/ml IL-2, 10 ng/ml IL-6, 10 ng/ml IL-1β, 10 ng/ml IL-23, 5 μg/ml anti-IL-4, 5 μg/ml anti-IFN-γ.Cells were grown for 3 days at 37°C in 5% CO2.

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

treatment_protocol: The polarized pTh17 subsets were cultured with YY1 shRNA lentivirus (MOI=20), control lentivirus (MOI=20) after cytokines stimulation for 24 h . On day 4, cells were extracted using the standard Trizol method for microarray.

tag: cell type

value: pathogenic Th17 cells

tag: genotype/variation

value: control knockdown


title: YY1 knockdown in pTh17, biological rep3

description: Gene expression data from in vitro polarized-pathogenic Th17 system transfected with YY1 shRNA lentivirus, biological rep3

value: YY1 knockdown


title: YY1 knockdown in pTh17, biological rep1

description: Gene expression data from in vitro polarized-pathogenic Th17 system transfected with YY1 shRNA lentivirus, biological rep1


title: GC071392_CTCCTTAC-ATCTCAGG

description: smart-seq2 protocol

value: Mus


title: H1975_OR_3

tag: cell line background

tag: phenotype


title: control knockdown in pTh17, biological rep2

description: Gene expression data from in vitro polarized-pathogenic Th17 system transfected with control shRNA lentivirus, biological rep2


title: GC071392_CTCCTTAC-ATGCGCAG

description: smart-seq2 protocol


title: GC071392_CTCCTTAC-ACTCGCTA

description: smart-seq2 protocol


title: YY1 knockdown in pTh17, biological rep2

description: Gene expression data from in vitro polarized-pathogenic Th17 system transfected with YY1 shRNA lentivirus, biological rep2


title: K107225

description:
whole methylome (Methyl Capture)
K107225_MeCap

tag: age

tag: age of menarche

tag: menopausal status

value: Pre

tag: race

value: WHITE

tag: ever pregnant

value: Yes

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: RNA-SEQ_A10-184-42_15-008/U46_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-184-42
processed_counts.txt
processed_TPM.txt

tag: gleason score

value: white

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type

tag: tissue


title: control knockdown in pTh17, biological rep3

description: Gene expression data from in vitro polarized-pathogenic Th17 system transfected with control shRNA lentivirus, biological rep3


title: GC071392_CTCCTTAC-AGGCAGAA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: K107069

description:
whole methylome (Methyl Capture)
K107069_MeCap

tag: blood relatives cancer

tag: hispanic

tag: bmi

value: High


title: RNA-SEQ_A12-2-14_15-008/U45_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A12-2-14
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

tag: preoperative psa

tag: age


title: K107062

description:
whole methylome (Methyl Capture)
K107062_MeCap

tag: age of menarche

tag: menopausal status

tag: race

value: AFRNAMER

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

value: Average


title: K107092

description:
whole methylome (Methyl Capture)
K107092_MeCap

tag: risk category


title: RNA-SEQ_A10-172-2_15-008/U47_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-172-2
processed_counts.txt
processed_TPM.txt

value: male

tag: gleason score

tag: pathologic stage

tag: 5-year disease status

tag: sample type

tag: tissue

value: buffy coat


title: K107050

description:
whole methylome (Methyl Capture)
K107050_MeCap

tag: blood relatives cancer

tag: hispanic

tag: bmi


title: RNA-SEQ_A12-2-13_15-008/U45_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A12-2-13
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: gender

value: normal

value: prostate tissue


title: K107203

description:
whole methylome (Methyl Capture)
K107203_MeCap

tag: age

tag: age of menarche

value: Post

value: No


title: RNA-SEQ_A10-172-1_15-008/U46_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-172-1
processed_counts.txt
processed_TPM.txt

tag: preoperative psa

tag: race


title: RNA-SEQ_A10-184-41_15-008/U44_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-184-41
processed_counts.txt
processed_TPM.txt

value: unknown

value: cancer


title: H1975_2

tag: cell line background


title: K107021 (second donation from K106734)

description:
whole methylome (Methyl Capture)
K107021_MeCap

tag: menopausal status

value: Don‚Äôt know

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: RNA-SEQ_A10-170-22_15-008/U45_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-170-22
processed_counts.txt
processed_TPM.txt

tag: gleason score

tag: pathologic stage

tag: 5-year disease status

tag: sample type


title: Sample_S-09-40561_S22_L003merged

city: Houston

first: Akdes

last: Serin Harmanci

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Raw reads from the RNA-seq data were processed using an in-house pipeline that uses STAR for read alignment; FastQC and RSeQC (for read and alignment quality assessment) and FeatureCount for expression count. Samples with degraded RNA or unique mapping rates lower than 30% were excluded. The reads were aligned to GRCh38 Human reference genome and mapping to the human transcriptome according to UCSC gene annotations. We then normalized the RNA-seq read counts for genes, applied a variance stabilizing transformation, and identified differentially expressed genes using the DESeq2 package. Differential gene expression determined by a false discovery rate cutoff of 0.05.
Genome_build: hg38
Supplementary_files_format_and_content: raw counts

source_name: Glioma

extract_protocol:
Total RNA was isolated from formalin-fixed, paraffin-embedded (FFPE) glioma tissue using MasterPure kit (Epicentre).
RNA libraries were prepared for sequencing using standard Illumina protocols.Paired-end RNA sequencing was performed.

tag: tissue

value: Glioma

tag: unique sample id

tag: patient id

tag: grade

value: HGG

tag: batch

tag: idh status prediction

value: Mutant

tag: date of birth

tag: vital status

tag: death censoring

value: F

tag: diagnosis date

tag: patient initial tumor grade

value: II

tag: initial tumor pathology

value: O

tag: progression date

tag: progressed tumor pathology

value: AA

tag: progressed tumor grade

value: III

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: K107140

description:
whole methylome (Methyl Capture)
K107140_MeCap

tag: age

tag: age of menarche

tag: menopausal status

value: Pre

tag: blood relatives cancer

tag: race

value: AFRNAMER

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: High


title: GC071392_CTAGTCGA-TCGACGTC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: GC071392_CTCCTTAC-AAGAGGCA

description: smart-seq2 protocol


title: Sample_S-07-28414_S22_L003merged

tag: tissue

tag: unique sample id

tag: patient id

tag: grade

value: LGG

tag: batch

tag: idh status prediction

tag: date of birth

tag: vital status

tag: death censoring

tag: gender

value: M

tag: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

value: A

tag: progression date

tag: progressed tumor pathology

tag: progressed tumor grade


title: Sample_S-13-16523_S22_L003merged

tag: age

value: AO

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: GC071392_CTAGTCGA-TGCAGCTA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: Sample_S-10-33895_S22_L003merged

tag: tissue

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: idh status prediction

tag: date of birth

value: OA

value: AOA


title: GC071392_CTAGTCGA-TACGCTGC

description: smart-seq2 protocol


title: H1975_1

tag: cell line background


title: K107043

description:
whole methylome (Methyl Capture)
K107043_MeCap

tag: age of menarche

tag: menopausal status

value: No

tag: blood relatives cancer

value: Yes

tag: race

value: WHITE

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: RNA-SEQ_A10-170-21_15-008/U44_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-170-21
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

value: unknown

tag: pathologic stage

tag: age

tag: 5-year disease status

value: remission

tag: sample type

value: normal

tag: tissue

value: buffy coat


title: RNA-SEQ_A10-184-40_15-008/U44_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-184-40
processed_counts.txt
processed_TPM.txt

value: prostate tissue


title: GC071392_CTAGTCGA-TAAGGCGA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: Sample_S-06-7905_S22_L003merged

value: Glioma

tag: unique sample id

tag: patient id

tag: grade

value: LGG

tag: batch

tag: idh status prediction

value: Mutant

tag: date of birth

tag: vital status

tag: death censoring

value: F

tag: diagnosis date

tag: patient initial tumor grade

value: II

tag: initial tumor pathology

value: O

tag: progression date

tag: progressed tumor pathology

tag: progressed tumor grade

value: III

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: Sample_S-12-53702_S22_L003merged

tag: tissue

tag: unique sample id

tag: patient id

value: HGG

value: WT

tag: age

tag: gender

value: A

value: GBM

value: IV

tag: second progression date

tag: second progressed tumor pathology

tag: second progressed tumor grade


title: K106979 (second donation from K107339)

description:
whole methylome (Methyl Capture)
K106979_MeCap

tag: age of menarche

tag: menopausal status

value: Post

value: No

tag: blood relatives cancer

value: Yes

tag: race

value: WHITE

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: High


title: Sample_S-11-31466_S22_L003merged

tag: tissue

value: Glioma

tag: grade

tag: batch

tag: idh status prediction

tag: date of birth

tag: vital status

tag: death censoring

value: M

tag: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

tag: progression date

tag: progressed tumor pathology

tag: progressed tumor grade

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: GC071392_CTAGTCGA-TAGGCATG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: RNA-SEQ_A10-184-38_15-008/U43_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-184-38
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

tag: race

value: white

tag: pathologic stage

tag: age

tag: 5-year disease status

value: recurrence

tag: sample type

value: normal

tag: tissue

value: prostate tissue


title: GC071392_CTAGTCGA-GGAGCTAC

description: smart-seq2 protocol


title: Sample_S-11-46862_S22_L003merged

tag: unique sample id

tag: patient id

tag: grade

value: HGG

tag: batch

tag: idh status prediction

value: Mutant

tag: date of birth

tag: vital status

tag: death censoring

tag: diagnosis date

tag: patient initial tumor grade

value: II

tag: initial tumor pathology

value: A

tag: progression date

tag: progressed tumor pathology

tag: progressed tumor grade

tag: second progression date

tag: second progressed tumor pathology

tag: second progressed tumor grade

tag: percentage of total mapped reads


title: Sample_S-05-29379_S22_L003merged

tag: tissue

tag: unique sample id

tag: patient id

value: LGG

tag: age

tag: gender

value: AA

value: III

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: K106980

description:
whole methylome (Methyl Capture)
K106980_MeCap

tag: age of menarche

tag: menopausal status

value: Pre

value: No

tag: blood relatives cancer

value: Yes

tag: race

value: WHITE

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: High


title: RNA-SEQ_A10-184-39_15-008/U43_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-184-39
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

value: male

tag: preoperative psa

tag: gleason score

tag: pathologic stage

tag: 5-year disease status

tag: sample type

value: cancer

tag: tissue


title: K106845

description:
whole methylome (Methyl Capture)
K106845_MeCap

tag: age

tag: age of menarche

value: Post

value: Average


title: Sample_S-07-18021_S22_L003merged

value: Glioma

tag: unique sample id

tag: patient id

tag: grade

value: HGG

tag: batch

tag: idh status prediction

tag: date of birth

tag: vital status

tag: death censoring

tag: gender

value: M

tag: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

value: O

tag: progression date

tag: progressed tumor pathology

value: GBM

tag: progressed tumor grade

value: IV

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: Sample_S-03-45665_S22_L003merged

tag: tissue

tag: unique sample id

tag: patient id

tag: grade

value: Mutant

tag: age

value: II

value: AO

value: III


title: GC071392_CTAGTCGA-GTAGAGGA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: K106863 (second donation from K106169)

description:
whole methylome (Methyl Capture)
K106863_MeCap

tag: age of menarche

tag: menopausal status

value: Pre

value: No

tag: blood relatives cancer

tag: race

value: WHITE

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: GC071392_CTAGTCGA-CTCTCTAC

description: smart-seq2 protocol


title: K107016

description:
whole methylome (Methyl Capture)
K107016_MeCap

value: Yes


title: GC071392_CTAGTCGA-TAGCGCTC

description: smart-seq2 protocol


title: K106889

description:
whole methylome (Methyl Capture)
K106889_MeCap

value: Asian

value: High


title: Sample_S-05-9894_S22_L003merged

value: Glioma

value: LGG

tag: batch

tag: idh status prediction

tag: date of birth

tag: vital status

tag: death censoring

tag: gender

tag: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

tag: progression date

tag: progressed tumor pathology

tag: progressed tumor grade

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: K107041

description:
whole methylome (Methyl Capture)
K107041_MeCap

tag: age

tag: age of menarche

tag: menopausal status

value: Post

tag: blood relatives cancer

tag: race

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: Average


title: GC071392_CTAGTCGA-GCTCATGA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: RNA-SEQ_A10-184-34_15-008/U41_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-184-34
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

value: white

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type

value: normal

tag: tissue

value: prostate tissue


title: RNA-SEQ_A10-170-19_15-008/U42_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-170-19
processed_counts.txt
processed_TPM.txt

tag: race

tag: age

value: buffy coat


title: RNA-SEQ_A10-184-37_15-008/U42_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-184-37
processed_counts.txt
processed_TPM.txt

value: cancer


title: RNA-SEQ_A10-170-20_15-008/U43_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-170-20
processed_counts.txt
processed_TPM.txt

value: recurrence


title: K106841

description:
whole methylome (Methyl Capture)
K106841_MeCap

tag: age of menarche

tag: menopausal status

value: Pre

value: No

tag: blood relatives cancer

value: WHITE

tag: hispanic

tag: bmi


title: RNA-SEQ_A10-184-36_15-008/U42_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-184-36
processed_counts.txt
processed_TPM.txt


title: RNA-SEQ_A10-170-18_15-008/U41_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-170-18
processed_counts.txt
processed_TPM.txt


title: RNA-SEQ_A10-184-35_15-008/U41_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-184-35
processed_counts.txt
processed_TPM.txt


title: Sample_S-03-60591_S22_L003merged

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: idh status prediction

value: Mutant

tag: date of birth

tag: vital status

tag: death censoring

value: F

tag: diagnosis date

tag: patient initial tumor grade

value: II

tag: initial tumor pathology

value: O

tag: progression date

tag: progressed tumor pathology

value: AO

tag: progressed tumor grade

value: III

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: GC071392_CTAGTCGA-CGGAGCCT

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: GC071392_CTAGTCGA-GCGTAGTA

description: smart-seq2 protocol


title: Sample_22-274878_S46_L005

tag: tissue

value: Glioma

tag: unique sample id

tag: patient id

tag: grade

value: HGG

tag: batch

tag: age

tag: gender

value: M

value: A

value: AA


title: Sample_S-02-37047_S22_L003merged

value: LGG

tag: idh status prediction

tag: date of birth

tag: vital status

tag: death censoring

tag: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology


title: K106801

description:
whole methylome (Methyl Capture)
K106801_MeCap

tag: age of menarche

tag: menopausal status

value: Post

tag: blood relatives cancer

value: Yes

tag: race

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: Average


title: GC071392_CTAGTCGA-GGACTCCT

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: RNA-SEQ_A10-184-32_15-008/U40_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-184-32
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

value: white

tag: pathologic stage

tag: age

tag: 5-year disease status

value: remission

tag: sample type

value: normal

tag: tissue

value: prostate tissue


title: GC071392_CTAGTCGA-CGTACTAG

description: smart-seq2 protocol


title: GC071392_CTAGTCGA-TCCTGAGC

description: smart-seq2 protocol


title: Sample_S-11-85908_S49_L008

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: idh status prediction

value: WT

tag: date of birth

tag: vital status

tag: death censoring

tag: diagnosis date

tag: patient initial tumor grade

value: II

tag: initial tumor pathology

tag: progression date

tag: progressed tumor pathology

value: GBM

tag: progressed tumor grade

value: IV

tag: second progression date

tag: second progressed tumor pathology

tag: second progressed tumor grade

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: K106713

description:
whole methylome (Methyl Capture)
K106713_MeCap

tag: age

tag: age of menarche

tag: menopausal status

value: Pre

tag: blood relatives cancer

tag: race

value: AFRNAMER

tag: hispanic

value: No

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: High


title: Sample_S-10-6956_S56_L008

tag: tissue

value: Glioma

tag: unique sample id

tag: patient id

tag: grade

value: HGG

tag: batch

tag: idh status prediction

value: Mutant

tag: date of birth

tag: vital status

tag: death censoring

tag: gender

value: F

tag: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

value: O

tag: progression date

tag: progressed tumor pathology

value: AO

tag: progressed tumor grade

value: III

tag: second progression date


title: RNA-SEQ_A10-184-31_15-008/U39_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-184-31
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

value: male

tag: preoperative psa

tag: gleason score

tag: race

value: white

tag: pathologic stage

tag: age

tag: 5-year disease status

value: remission

tag: sample type

value: cancer

tag: tissue


title: K106766

description:
whole methylome (Methyl Capture)
K106766_MeCap

tag: age of menarche

tag: menopausal status

value: Post

tag: blood relatives cancer

value: Yes

value: WHITE

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: Sample_S-13-44668_S52_L008

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: idh status prediction

tag: date of birth

tag: vital status

tag: death censoring

tag: gender

tag: diagnosis date

tag: patient initial tumor grade

value: II

tag: initial tumor pathology

tag: progression date

tag: progressed tumor pathology

tag: progressed tumor grade

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: K106757

description:
whole methylome (Methyl Capture)
K106757_MeCap

tag: age

tag: age of menarche

tag: menopausal status

value: Pre

tag: blood relatives cancer

tag: race

tag: hispanic

value: No

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: High


title: GC071392_CTAGTCGA-ATCTCAGG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: K106684

description:
whole methylome (Methyl Capture)
K106684_MeCap

value: AFRNAMER

value: Average


title: K106734

description:
whole methylome (Methyl Capture)
K106734_MeCap

value: Don‚Äôt know


title: GC071392_CTAGTCGA-CGAGGCTG

description: smart-seq2 protocol


title: Sample_S-13-13785_S55_L008

tag: tissue

value: Glioma

tag: unique sample id

tag: patient id

tag: grade

value: HGG

tag: batch

tag: idh status prediction

value: Mutant

tag: date of birth

tag: vital status

tag: death censoring

tag: gender

value: F

tag: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

value: A

tag: progression date

tag: progressed tumor pathology

value: GBM

tag: progressed tumor grade

value: IV


title: RNA-SEQ_A10-184-29_15-008/U38_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-184-29
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

value: male

tag: preoperative psa

tag: gleason score

tag: race

value: white

tag: pathologic stage

tag: age

tag: 5-year disease status

value: remission

tag: sample type

value: cancer

value: prostate tissue


title: Sample_S-12-31070_S46_L008

tag: tissue

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: idh status prediction

tag: date of birth

tag: vital status

tag: death censoring

value: II

value: O

value: AO

value: III

tag: second progression date

tag: second progressed tumor pathology

tag: second progressed tumor grade

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: K106678

description:
whole methylome (Methyl Capture)
K106678_MeCap

tag: age

tag: age of menarche

tag: menopausal status

value: Post

tag: blood relatives cancer

value: Yes

tag: race

value: WHITE

tag: hispanic

value: No

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: Average


title: RNA-SEQ_A10-184-33_15-008/U40_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-184-33
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

tag: pathologic stage

tag: 5-year disease status

tag: sample type

tag: tissue


title: GC071392_CTAGTCGA-ACTGAGCG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: K106730 (second donation from K106642)

description:
whole methylome (Methyl Capture)
K106730_MeCap

tag: age

tag: age of menarche

tag: menopausal status

value: Pre

tag: blood relatives cancer

tag: race


title: GC071392_CTAGTCGA-CCTAAGAC

description: smart-seq2 protocol


title: Sample_S-12-91302_S54_L008

value: Glioma

tag: unique sample id

tag: patient id

tag: grade

value: HGG

tag: batch

tag: idh status prediction

value: Mutant

tag: date of birth

tag: vital status

tag: death censoring

value: M

tag: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

value: A

tag: progression date

tag: progressed tumor pathology

value: AA

tag: progressed tumor grade

tag: second progression date

tag: second progressed tumor pathology

value: GBM

tag: second progressed tumor grade

value: IV

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: Sample_S-07-54479_S59_L008

tag: tissue

tag: unique sample id

tag: patient id

tag: grade

value: LGG

tag: batch

tag: idh status prediction

tag: age

tag: gender

value: F

value: II


title: K106655

description:
whole methylome (Methyl Capture)
K106655_MeCap

tag: age of menarche

tag: menopausal status

tag: blood relatives cancer

value: Yes

tag: race

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: High


title: RNA-SEQ_A10-170-17_15-008/U40_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-170-17
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

value: male

tag: preoperative psa

tag: gleason score

value: white

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type

value: normal

tag: tissue

value: buffy coat


title: GC071392_CTAGTCGA-CGATCAGT

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: RNA-SEQ_A10-170-15_15-008/U38_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-170-15
processed_counts.txt
processed_TPM.txt

tag: gender

tag: age


title: Sample_S-06-53660_S57_L008

value: Glioma

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: idh status prediction

value: Mutant

tag: date of birth

tag: vital status

tag: death censoring

tag: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

value: O

tag: progression date

tag: progressed tumor pathology

value: AO

tag: progressed tumor grade

value: III

tag: second progression date

tag: second progressed tumor pathology

tag: second progressed tumor grade

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: K106695

description:
whole methylome (Methyl Capture)
K106695_MeCap

tag: age

tag: age of menarche

tag: menopausal status

value: Pre

tag: blood relatives cancer

value: No

tag: race

value: WHITE

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: Average


title: RNA-SEQ_A10-184-27_15-008/U37_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-184-27
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

value: unknown

tag: pathologic stage

tag: 5-year disease status

tag: sample type

value: cancer

tag: tissue

value: prostate tissue


title: GC071392_CGGAGAGA-TGCAGCTA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: K106642

description:
whole methylome (Methyl Capture)
K106642_MeCap

tag: age

tag: age of menarche

tag: menopausal status

tag: blood relatives cancer

tag: race

value: Yes


title: Sample_S-02-4483_S47_L008

tag: unique sample id

tag: patient id

tag: grade

value: LGG

tag: batch

tag: idh status prediction

tag: date of birth

tag: vital status

tag: death censoring

value: M

tag: diagnosis date

tag: patient initial tumor grade

value: II

tag: initial tumor pathology

value: A

tag: progression date

tag: progressed tumor pathology

value: AA

tag: progressed tumor grade

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: Sample_S-10-10520_S50_L008

tag: tissue

value: Glioma

tag: unique sample id

tag: patient id

value: Mutant

tag: age

tag: gender

value: GBM

value: IV

tag: second progression date

tag: second progressed tumor pathology

tag: second progressed tumor grade


title: K106733

description:
whole methylome (Methyl Capture)
K106733_MeCap

tag: age of menarche

tag: menopausal status

value: Pre

tag: blood relatives cancer

tag: race

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: Sample_R378-8-330216_S8_L001

tag: tissue

tag: grade

tag: batch

tag: idh status prediction

tag: date of birth

tag: vital status

tag: death censoring

value: F

tag: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

value: O

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: RNA-SEQ_A10-184-30_15-008/U39_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-184-30
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

tag: race

value: white

tag: pathologic stage

tag: age

tag: 5-year disease status

value: remission

tag: sample type

value: normal


title: GC071392_CTAGTCGA-AGGCAGAA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: RNA-SEQ_A10-184-28_15-008/U38_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-184-28
processed_counts.txt
processed_TPM.txt

tag: tissue

value: prostate tissue


title: Sample_R378-78-834403_S61_L006

tag: unique sample id

tag: patient id

tag: grade

value: HGG

tag: batch

tag: date of birth

tag: vital status

tag: death censoring

value: M

tag: diagnosis date

tag: patient initial tumor grade

value: III

tag: initial tumor pathology

tag: progression date

tag: progressed tumor pathology

tag: progressed tumor grade

tag: percentage of total mapped reads


title: GC071392_CGGAGAGA-TAGCGCTC

description: smart-seq2 protocol

tag: timepoint


title: GC071392_CTAGTCGA-ATGCGCAG

description: smart-seq2 protocol

tag: initially inactive x allele


title: RNA-SEQ_A10-170-16_15-008/U39_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-170-16
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

tag: race

tag: pathologic stage

tag: age

tag: 5-year disease status

tag: sample type

tag: tissue

value: buffy coat


title: K106656

description:
whole methylome (Methyl Capture)
K106656_MeCap

tag: age of menarche

tag: menopausal status

tag: blood relatives cancer

value: No

value: WHITE

tag: hispanic

tag: bmi

tag: ever pregnant

value: Yes

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: Average


title: GC071392_CTAGTCGA-ACTCGCTA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: Sample_S-09-3532_S53_L008

value: Glioma

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: idh status prediction

value: Mutant

tag: date of birth

tag: vital status

tag: death censoring

tag: gender

tag: diagnosis date

tag: patient initial tumor grade

value: II

tag: initial tumor pathology

value: A

tag: progression date

tag: progressed tumor pathology

value: AA

tag: progressed tumor grade

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: Sample_S-08-30786_S58_L008

tag: tissue

tag: unique sample id

tag: patient id

tag: grade

value: LGG

tag: age

tag: second progression date

tag: second progressed tumor pathology

value: GBM

tag: second progressed tumor grade

value: IV


title: RNA-SEQ_A10-170-13_15-008/U36_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-170-13
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

tag: race

value: white

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type

value: normal


title: Sample_R378-78-834403_S56_L007

tag: tissue

value: HGG

tag: batch

tag: date of birth

tag: vital status

tag: death censoring

value: M

tag: diagnosis date

tag: patient initial tumor grade

value: III

tag: initial tumor pathology

tag: progression date

tag: progressed tumor pathology

tag: progressed tumor grade

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: Sample_S-05-861_S51_L008

tag: unique sample id

tag: patient id

tag: grade

tag: idh status prediction

tag: age

tag: gender

value: OA


title: RNA-SEQ_A10-184-26_15-008/U37_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-184-26
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: preoperative psa

tag: gleason score

tag: race

value: unknown

tag: pathologic stage

tag: 5-year disease status

tag: sample type

tag: tissue

value: prostate tissue


title: GC071392_CTAGTCGA-AAGAGGCA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: K106647

description:
whole methylome (Methyl Capture)
K106647_MeCap

tag: age of menarche

tag: menopausal status

value: Post

tag: blood relatives cancer

value: Yes

value: WHITE

tag: hispanic

value: No

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: Average


title: RNA-SEQ_A12-2-12_15-008/U35_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A12-2-12
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

tag: preoperative psa

tag: age

value: cancer


title: K106641

description:
whole methylome (Methyl Capture)
K106641_MeCap

value: Pre

tag: race

value: AFRNAMER

value: High


title: Sample_R378-76-497763_S59_L006

tag: tissue

value: Glioma

tag: unique sample id

tag: patient id

tag: grade

value: HGG

tag: batch

tag: date of birth

tag: vital status

tag: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

value: AA

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: Sample_R378-76-497763_S55_L007

tag: gender

value: M

value: III


title: GC071392_CGGAGAGA-GGAGCTAC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: K106531 (second donation from K105926)

description:
whole methylome (Methyl Capture)
K106531_MeCap

tag: age

tag: age of menarche

tag: menopausal status

tag: blood relatives cancer

tag: race

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: Sample_R378-75-359415_S58_L006

tag: tissue

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: date of birth

tag: vital status

tag: death censoring

tag: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

tag: percentage of total mapped reads


title: GC071392_CGGAGAGA-TCGACGTC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: RNA-SEQ_A10-170-14_15-008/U37_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-170-14
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

tag: race

value: unknown

tag: pathologic stage

tag: age

tag: 5-year disease status

value: remission

tag: sample type

value: normal

value: buffy coat


title: GC071392_CGGAGAGA-GGACTCCT

description: smart-seq2 protocol

value: Mus


title: RNA-SEQ_A10-184-25_15-008/U36_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-184-25
processed_counts.txt
processed_TPM.txt

value: white

tag: tissue

value: prostate tissue


title: RNA-SEQ_A10-184-22_15-008/U34_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-184-22
processed_counts.txt
processed_TPM.txt

value: prostate cancer


title: GC071392_CGGAGAGA-GCTCATGA

description: smart-seq2 protocol


title: K106620

description:
whole methylome (Methyl Capture)
K106620_MeCap

tag: age of menarche

tag: menopausal status

value: Pre

tag: blood relatives cancer

value: No

tag: hispanic

tag: bmi

tag: ever pregnant

value: Yes

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: Average


title: Sample_R378-77-538288_S60_L006

value: Glioma

tag: unique sample id

tag: patient id

tag: batch

tag: vital status

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: GC071392_CGGAGAGA-TACGCTGC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: GC071392_CGGAGAGA-TCCTGAGC

description: smart-seq2 protocol


title: K106609

description:
whole methylome (Methyl Capture)
K106609_MeCap

tag: age

tag: age of menarche

tag: menopausal status

tag: race

value: WHITE


title: GC071392_CGGAGAGA-GTAGAGGA

description: smart-seq2 protocol


title: K106578

description:
whole methylome (Methyl Capture)
K106578_MeCap

tag: blood relatives cancer

tag: hispanic

tag: bmi

tag: ever pregnant

value: High


title: GC071392_CGGAGAGA-TAAGGCGA

description: smart-seq2 protocol


title: RNA-SEQ_A10-184-24_15-008/U36_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-184-24
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

tag: pathologic stage

tag: 5-year disease status

tag: sample type

tag: tissue


title: Sample_R378-75-359415_S54_L007

tag: unique sample id

tag: patient id

tag: grade

value: HGG

tag: batch

tag: age

tag: date of birth

tag: vital status

tag: death censoring

value: M

tag: diagnosis date

tag: patient initial tumor grade

value: III

tag: initial tumor pathology

value: AA

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: GC071392_CGGAGAGA-GCGTAGTA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: K106517

description:
whole methylome (Methyl Capture)
K106517_MeCap

tag: age of menarche

tag: menopausal status

tag: blood relatives cancer

tag: race

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: Sample_R378-74-329244_S57_L006

tag: tissue

tag: unique sample id

tag: patient id

tag: grade

value: LGG

tag: batch

tag: age

tag: date of birth

tag: vital status

tag: death censoring

tag: diagnosis date

tag: patient initial tumor grade


title: Sample_S-01-8474_S48_L008

tag: idh status prediction

value: Mutant

tag: gender

value: II

tag: initial tumor pathology

value: O

tag: progression date

tag: progressed tumor pathology

value: GBM

tag: progressed tumor grade

value: IV

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: K106301

description:
whole methylome (Methyl Capture)
K106301_MeCap

tag: age of menarche

tag: menopausal status

value: Post

tag: blood relatives cancer

tag: race

value: AFRNAMER

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: GC071392_CGGAGAGA-CTCTCTAC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: Sample_R378-74-329244_S53_L007

tag: tissue

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: age

tag: date of birth

tag: vital status

tag: death censoring

tag: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology


title: K106629

description:
whole methylome (Methyl Capture)
K106629_MeCap

tag: age of menarche

tag: menopausal status

value: Pre

tag: blood relatives cancer

value: No

tag: race

tag: hispanic

tag: bmi

tag: ever pregnant

value: Average


title: GC071392_CGGAGAGA-TAGGCATG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: GC071392_CGGAGAGA-CGGAGCCT

description: smart-seq2 protocol


title: RNA-SEQ_A10-170-10_15-008/U33_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-170-10
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

value: unknown

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type

value: normal

tag: tissue

value: buffy coat


title: Sample_R378-73-202304_S56_L006

value: Glioma

tag: unique sample id

tag: patient id

tag: grade

value: LGG

tag: batch

tag: age

tag: date of birth

tag: vital status

value: F

tag: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

tag: progression date

tag: progressed tumor pathology

value: AO

tag: progressed tumor grade

value: III

tag: second progression date

tag: second progressed tumor pathology

tag: second progressed tumor grade

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: K106597

description:
whole methylome (Methyl Capture)
K106597_MeCap

tag: age of menarche

tag: menopausal status

value: Post

tag: blood relatives cancer

value: Yes

tag: race

value: WHITE

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: Sample_R378-72-128135_S62_L006

tag: tissue

tag: unique sample id

tag: patient id

tag: grade

value: HGG

tag: batch

tag: age

tag: date of birth

tag: vital status

tag: death censoring

tag: gender

tag: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

value: AA

tag: progression date


title: RNA-SEQ_A12-2-11_15-008/U35_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A12-2-11
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: preoperative psa

tag: gleason score

tag: race

value: white

tag: pathologic stage

tag: 5-year disease status

tag: sample type

value: prostate tissue


title: K106507

description:
whole methylome (Methyl Capture)
K106507_MeCap

tag: age

tag: age of menarche

tag: menopausal status

value: Pre

tag: blood relatives cancer

value: No

value: AFRNAMER

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: Average


title: K106201

description:
whole methylome (Methyl Capture)
K106201_MeCap


title: K106169

description:
whole methylome (Methyl Capture)
K106169_MeCap


title: RNA-SEQ_A10-184-18_15-008/U32_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-184-18
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: gender

value: male

value: remission

value: normal

tag: tissue


title: RNA-SEQ_A10-170-9_15-008/U32_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-170-9
processed_counts.txt
processed_TPM.txt

tag: patientid

tag: preoperative psa

tag: gleason score

value: buffy coat


title: RNA-SEQ_A10-170-12_15-008/U35_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-170-12
processed_counts.txt
processed_TPM.txt

tag: race

tag: pathologic stage

tag: 5-year disease status


title: RNA-SEQ_A10-184-23_15-008/U34_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-184-23
processed_counts.txt
processed_TPM.txt

tag: age

tag: sample type

value: cancer


title: GC071392_CGGAGAGA-CGATCAGT

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: GC071392_CGGAGAGA-ATGCGCAG

description: smart-seq2 protocol


title: K106157

description:
whole methylome (Methyl Capture)
K106157_MeCap

tag: age of menarche

tag: menopausal status

tag: blood relatives cancer

tag: hispanic

tag: bmi

value: Yes


title: K106221

description:
whole methylome (Methyl Capture)
K106221_MeCap

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: Sample_R378-70-96899_S54_L005

tag: tissue

value: Glioma

tag: unique sample id

tag: patient id

tag: grade

value: LGG

tag: batch

tag: date of birth

tag: vital status

tag: death censoring

tag: gender

value: F

tag: diagnosis date

tag: patient initial tumor grade

value: II

tag: initial tumor pathology

value: O

tag: progression date

tag: progressed tumor pathology

value: AO

tag: progressed tumor grade

value: III

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: K106139

description:
whole methylome (Methyl Capture)
K106139_MeCap

tag: age

tag: age of menarche

tag: menopausal status

value: Pre

tag: blood relatives cancer

tag: race

value: WHITE

tag: hispanic

value: No

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: High


title: K106481

description:
whole methylome (Methyl Capture)
K106481_MeCap

value: AFRNAMER

value: Average


title: RNA-SEQ_A10-184-16_15-008/U31_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-184-16
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

value: white

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type

value: normal

tag: tissue

value: prostate tissue


title: Sample_R378-71-38765_S51_L007

value: Glioma

tag: unique sample id

tag: patient id

tag: grade

value: HGG

tag: batch

tag: age

tag: date of birth

tag: vital status

tag: death censoring

tag: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

value: A

tag: progression date

tag: progressed tumor pathology

value: GBM

tag: progressed tumor grade

value: IV

tag: second progression date

tag: second progressed tumor pathology

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: RNA-SEQ_A10-184-20_15-008/U33_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-184-20
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

tag: race

value: unknown

tag: pathologic stage

tag: 5-year disease status

tag: sample type

tag: tissue


title: GC071392_CGGAGAGA-CGAGGCTG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: RNA-SEQ_A10-184-15_15-008/U30_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-184-15
processed_counts.txt
processed_TPM.txt

tag: age

value: recurrence

value: cancer


title: RNA-SEQ_A10-184-21_15-008/U33_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-184-21
processed_counts.txt
processed_TPM.txt


title: K106060

description:
whole methylome (Methyl Capture)
K106060_MeCap

tag: age of menarche

tag: menopausal status

value: Pre

tag: blood relatives cancer

value: Yes

value: WHITE

tag: hispanic

value: No

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: High


title: K106295

description:
whole methylome (Methyl Capture)
K106295_MeCap

value: Don‚Äôt know

value: Average


title: RNA-SEQ_A10-170-11_15-008/U34_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-170-11
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

value: white

value: remission

value: normal

value: buffy coat


title: GC071392_CGGAGAGA-CGTACTAG

description: smart-seq2 protocol


title: RNA-SEQ_A10-184-19_15-008/U32_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-184-19
processed_counts.txt
processed_TPM.txt

tag: race

tag: pathologic stage

tag: 5-year disease status

tag: sample type

tag: tissue

value: prostate tissue


title: GC071392_CGGAGAGA-CCTAAGAC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: RNA-SEQ_A10-184-14_15-008/U30_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-184-14
processed_counts.txt
processed_TPM.txt

tag: age

value: recurrence


title: Sample_R378-68-730769_S52_L005

value: Glioma

tag: unique sample id

tag: patient id

tag: grade

value: LGG

tag: batch

tag: date of birth

tag: vital status

tag: death censoring

value: M

tag: diagnosis date

tag: patient initial tumor grade

value: II

tag: initial tumor pathology

value: O

tag: progression date

tag: progressed tumor pathology

value: AA

tag: progressed tumor grade

value: III

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: K106020

description:
whole methylome (Methyl Capture)
K106020_MeCap

tag: age

tag: age of menarche

tag: menopausal status

value: Pre

tag: blood relatives cancer

value: Yes

tag: race

value: WHITE

tag: hispanic

value: No

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: Average


title: GC071392_CGGAGAGA-ACTCGCTA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: K106009

description:
whole methylome (Methyl Capture)
K106009_MeCap


title: RNA-SEQ_A10-184-17_15-008/U31_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-184-17
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

value: white

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type

value: cancer

tag: tissue


title: K106208

description:
whole methylome (Methyl Capture)
K106208_MeCap

tag: age

tag: age of menarche

tag: menopausal status

tag: blood relatives cancer

tag: race

value: High


title: Sample_R378-66-344104_S50_L007

value: Glioma

tag: unique sample id

tag: patient id

tag: grade

value: LGG

tag: batch

tag: date of birth

tag: vital status

tag: death censoring

tag: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

tag: progression date

tag: progressed tumor pathology

value: AO

tag: progressed tumor grade

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: Sample_R378-72-128135_S52_L007

tag: tissue

tag: unique sample id

value: HGG

tag: age

tag: gender

value: F


title: RNA-SEQ_A10-184-13_15-008/U29_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-184-13
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: preoperative psa

tag: gleason score

tag: race

value: unknown

tag: pathologic stage

tag: 5-year disease status

tag: sample type

value: prostate tissue


title: GC071392_ATTAGACG-TGCAGCTA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: Sample_R378-71-38765_S55_L005

tag: patient id

tag: grade

tag: batch

tag: date of birth

tag: vital status

tag: death censoring

tag: diagnosis date

tag: patient initial tumor grade

value: II

tag: initial tumor pathology

value: A

tag: progression date

tag: progressed tumor pathology

value: GBM

tag: progressed tumor grade

value: IV

tag: second progression date

tag: second progressed tumor pathology

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads


title: RNA-SEQ_A10-184-12_15-008/U29_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-184-12
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

tag: race

tag: pathologic stage

tag: age

tag: 5-year disease status

tag: sample type

value: normal

tag: tissue


title: Sample_R378-66-344104_S50_L005

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: date of birth

tag: vital status

tag: death censoring

value: M

tag: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

value: O

tag: progression date

tag: progressed tumor pathology

value: III

tag: progress free survival (months)

tag: overall survival (months)


title: Sample_R378-65-649720_S49_L007

value: Glioma

value: LGG

tag: age

tag: gender

tag: progressed tumor grade

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads


title: K106071

description:
whole methylome (Methyl Capture)
K106071_MeCap

tag: age of menarche

tag: menopausal status

value: Pre

tag: blood relatives cancer

value: Yes

tag: race

value: WHITE

tag: hispanic

value: No

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: High


title: RNA-SEQ_A10-170-6_15-008/U29_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-170-6
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: preoperative psa

tag: gleason score

value: unknown

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type

tag: tissue

value: buffy coat


title: GC071392_CGGAGAGA-AGGCAGAA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: GC071392_ATTAGACG-TCCTGAGC

description: smart-seq2 protocol


title: Sample_R378-7-496402_S7_L001

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: idh status prediction

value: Mutant

tag: age

tag: date of birth

tag: vital status

tag: death censoring

tag: gender

value: F

tag: diagnosis date

tag: patient initial tumor grade

value: II

tag: initial tumor pathology

value: A

tag: progression date

tag: progressed tumor pathology

value: AA

tag: progressed tumor grade

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: GC071392_CGGAGAGA-ATCTCAGG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: Sample_R378-69-831094_S53_L005

tag: tissue

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: age

value: O

value: AO

value: III


title: GC071392_CGGAGAGA-AAGAGGCA

description: smart-seq2 protocol


title: RNA-SEQ_A10-170-7_15-008/U30_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-170-7
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

tag: race

value: white

tag: pathologic stage

tag: 5-year disease status

value: recurrence

tag: sample type

value: normal


title: Sample_R378-64-750328_S48_L004

value: Glioma

value: LGG

tag: date of birth

tag: vital status

tag: death censoring

value: M

tag: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

tag: progression date

tag: progressed tumor pathology

tag: progressed tumor grade

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: Sample_R378-67-790770_S51_L005

tag: tissue

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: age

tag: gender


title: GC071392_CGGAGAGA-ACTGAGCG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: RNA-SEQ_A10-170-8_15-008/U31_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-170-8
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: preoperative psa

tag: gleason score

tag: race

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type

value: buffy coat


title: RNA-SEQ_A10-184-10_15-008/U28_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-184-10
processed_counts.txt
processed_TPM.txt

value: black

tag: tissue

value: prostate tissue


title: GC071392_ATTAGACG-TACGCTGC

description: smart-seq2 protocol


title: Sample_R378-62-45880_S46_L004

tag: unique sample id

tag: date of birth

tag: vital status

value: F

tag: diagnosis date

tag: patient initial tumor grade

value: II

tag: initial tumor pathology

tag: progression date

tag: progressed tumor pathology

tag: progressed tumor grade

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: RNA-SEQ_A10-184-11_15-008/U28_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-184-11
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

tag: race

tag: pathologic stage

tag: age

value: cancer


title: GC071392_ATTAGACG-TCGACGTC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: GC071392_ATTAGACG-TAGGCATG

description: smart-seq2 protocol


title: K106008

description:
whole methylome (Methyl Capture)
K106008_MeCap

tag: age of menarche

tag: menopausal status

value: Pre

tag: blood relatives cancer

value: Yes

value: WHITE

tag: hispanic

value: No

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: High


title: Sample_R378-61-137803_S47_L006

tag: tissue

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: date of birth

tag: vital status

tag: death censoring

tag: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

value: A

tag: progression date

tag: progressed tumor pathology

value: AA

tag: progressed tumor grade

value: III

tag: second progression date

tag: second progressed tumor pathology

value: GBM

tag: second progressed tumor grade

value: IV

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: GC071392_ATTAGACG-TAAGGCGA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: K105898

description:
whole methylome (Methyl Capture)
K105898_MeCap

tag: age

tag: age of menarche

tag: menopausal status

tag: blood relatives cancer

tag: race

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: Average


title: K105980

description:
whole methylome (Methyl Capture)
K105980_MeCap

value: Don‚Äôt know

value: AFRNAMER


title: RNA-SEQ_A10-184-9_15-008/U27_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-184-9
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

value: unknown

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type

tag: tissue

value: prostate tissue


title: Sample_R378-65-649720_S49_L005

value: Glioma

tag: unique sample id

tag: patient id

tag: grade

value: LGG

tag: batch

tag: age

tag: date of birth

tag: vital status

value: M

tag: diagnosis date

tag: patient initial tumor grade

value: II

tag: initial tumor pathology

tag: progression date

tag: progressed tumor pathology

tag: progressed tumor grade

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: K106006 (second donation from K104932)

description:
whole methylome (Methyl Capture)
K106006_MeCap

tag: age of menarche

tag: menopausal status

value: Pre

tag: blood relatives cancer

value: Yes

tag: race

value: WHITE

tag: hispanic

value: No

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: GC071392_ATTAGACG-GGAGCTAC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: K105970

description:
whole methylome (Methyl Capture)
K105970_MeCap

tag: age

value: Average


title: RNA-SEQ_A10-184-7_15-008/U26_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-184-7
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

value: white

tag: pathologic stage

tag: 5-year disease status

tag: sample type

value: cancer

tag: tissue


title: RNA-SEQ_A10-170-5_15-008/U28_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-170-5
processed_counts.txt
processed_TPM.txt

value: prostate cancer

tag: race

value: black

value: recurrence

value: normal

value: buffy coat


title: Sample_R378-60-140037_S44_L004

value: Glioma

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: date of birth

tag: vital status

tag: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

value: A

tag: progression date

tag: progressed tumor pathology

value: AA

tag: progressed tumor grade

value: III

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: K105813

description:
whole methylome (Methyl Capture)
K105813_MeCap

tag: age

tag: age of menarche

tag: menopausal status

value: Pre

tag: blood relatives cancer

tag: race

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: Sample_R378-6-496697_S6_L001

tag: tissue

tag: unique sample id

tag: patient id

tag: grade

value: LGG

tag: batch

tag: idh status prediction

value: Mutant

tag: date of birth

tag: vital status

tag: death censoring

tag: gender

value: M

tag: diagnosis date

tag: patient initial tumor grade

value: II

tag: initial tumor pathology

value: O


title: RNA-SEQ_A10-170-3_15-008/U26_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-170-3
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

value: male

tag: preoperative psa

tag: gleason score

tag: race

value: white

tag: pathologic stage

tag: age

tag: 5-year disease status

value: remission

tag: sample type


title: GC071392_ATTAGACG-GCGTAGTA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: GC071392_ATTAGACG-TAGCGCTC

description: smart-seq2 protocol


title: K105894

description:
whole methylome (Methyl Capture)
K105894_MeCap

tag: age of menarche

tag: menopausal status

tag: blood relatives cancer

value: Yes

value: WHITE

tag: hispanic

value: No

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: High


title: RNA-SEQ_A10-170-4_15-008/U27_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-170-4
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

tag: preoperative psa

value: unknown

value: normal

tag: tissue

value: buffy coat


title: GC071392_ATTAGACG-CTCTCTAC

description: smart-seq2 protocol


title: K105906

description:
whole methylome (Methyl Capture)
K105906_2_MeCap

tag: age

value: Pre

tag: race


title: Sample_R378-63-856277_S48_L006

value: Glioma

tag: unique sample id

tag: patient id

tag: grade

value: LGG

tag: batch

tag: date of birth

tag: vital status

tag: death censoring

value: F

tag: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

tag: progression date

tag: progressed tumor pathology

value: GBM

tag: progressed tumor grade

value: IV

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: K105938

description:
whole methylome (Methyl Capture)
K105938_MeCap

tag: age

tag: age of menarche

tag: menopausal status

tag: blood relatives cancer

tag: race

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: Average


title: Sample_R378-60-140037_S46_L006

tag: tissue

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: date of birth

tag: vital status

tag: gender

value: M

tag: diagnosis date

tag: patient initial tumor grade

value: II

tag: initial tumor pathology

value: A

tag: progression date

value: AA

value: III


title: RNA-SEQ_A10-184-4_15-008/U25_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-184-4
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

value: male

tag: preoperative psa

tag: gleason score

tag: race

value: white

tag: pathologic stage

tag: age

tag: 5-year disease status

value: remission

tag: sample type

value: prostate tissue


title: GC071392_ATTAGACG-GTAGAGGA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: K105926

description:
whole methylome (Methyl Capture)
K105926_MeCap

tag: age of menarche

tag: menopausal status

value: Pre

tag: blood relatives cancer

value: No

value: AFRNAMER

tag: hispanic

tag: bmi

tag: ever pregnant

value: Yes

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: RNA-SEQ_A10-184-8_15-008/U27_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-184-8
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

tag: preoperative psa

value: unknown

value: normal

tag: tissue


title: K105717

description:
whole methylome (Methyl Capture)
K105717_MeCap

tag: age

value: Post

tag: race

value: WHITE

value: High


title: GC071392_ATTAGACG-CGGAGCCT

description: smart-seq2 protocol

tag: timepoint


title: K105643

description:
whole methylome (Methyl Capture)
K105643_MeCap

value: Average


title: GC071392_ATTAGACG-CGATCAGT

description: smart-seq2 protocol

tag: initially inactive x allele


title: GC071392_ATTAGACG-GGACTCCT

description: smart-seq2 protocol


title: K105883

description:
whole methylome (Methyl Capture)
K105883_MeCap

tag: age of menarche

value: ASIAN


title: K105437

description:
whole methylome (Methyl Capture)
K105437_MeCap

tag: menopausal status


title: RNA-SEQ_A10-184-5_15-008/U25_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-184-5
processed_counts.txt
processed_TPM.txt

value: male

tag: gleason score

tag: pathologic stage

tag: 5-year disease status

tag: sample type

value: cancer


title: K105688

description:
whole methylome (Methyl Capture)
K105688_MeCap

tag: blood relatives cancer

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)


title: Sample_R378-56-849040_S40_L003

value: Glioma

tag: unique sample id

tag: patient id

tag: grade

value: LGG

tag: batch

tag: date of birth

tag: vital status

tag: death censoring

tag: gender

value: M

tag: diagnosis date

tag: patient initial tumor grade

value: II

tag: initial tumor pathology

value: O

tag: progression date

tag: progressed tumor pathology

value: GBM

tag: progressed tumor grade

value: IV

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: RNA-SEQ_A10-170-1_15-008/U24_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-170-1
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

tag: preoperative psa

tag: gleason score

tag: race

value: white

tag: pathologic stage

tag: age

tag: 5-year disease status

value: remission

tag: sample type

tag: tissue

value: buffy coat


title: Sample_R378-61-137803_S45_L004

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: date of birth

tag: vital status

tag: death censoring

tag: gender

value: F

tag: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

value: A

tag: progression date

value: AA

value: III

tag: second progression date

tag: second progressed tumor pathology

tag: second progressed tumor grade


title: Sample_R378-58-526276_S42_L004

tag: age

tag: progressed tumor pathology

tag: progressed tumor grade

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: GC071392_ATTAGACG-GCTCATGA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: Sample_R378-59-117815_S45_L006

tag: tissue

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: date of birth

tag: vital status

tag: death censoring

tag: gender

value: AO


title: RNA-SEQ_A10-184-6_15-008/U26_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-184-6
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

value: male

tag: preoperative psa

tag: gleason score

tag: race

tag: pathologic stage

tag: age

tag: 5-year disease status

tag: sample type

value: normal

value: prostate tissue


title: RNA-SEQ_A10-170-2_15-008/U25_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-170-2
processed_counts.txt
processed_TPM.txt

tag: tissue


title: Sample_R378-57-476964_S41_L004

value: Glioma

tag: unique sample id

tag: patient id

value: LGG

tag: diagnosis date

tag: patient initial tumor grade

value: II

tag: initial tumor pathology

tag: progression date

tag: progressed tumor pathology

tag: progressed tumor grade

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: GC071392_ATTAGACG-CGTACTAG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: Sample_R378-57-476964_S44_L006

tag: grade

tag: batch

tag: age

tag: date of birth

tag: vital status

tag: death censoring

tag: gender

value: GBM

value: IV


title: GC071392_ATTAGACG-ATGCGCAG

description: smart-seq2 protocol


title: RNA-SEQ_A10-183-58_15-008/060_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-183-58
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

tag: preoperative psa

tag: gleason score

tag: race

value: black

tag: pathologic stage

tag: 5-year disease status

tag: sample type

tag: tissue


title: Sample_R378-59-117815_S43_L004

tag: unique sample id

tag: patient id

value: M

tag: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

value: O

tag: progression date

tag: progressed tumor pathology

tag: progressed tumor grade

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: RNA-SEQ_A10-184-1_15-008/060_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-184-1
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

tag: race

tag: age

value: remission

value: cancer


title: Sample_R378-55-476946_S43_L006

tag: tissue

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: date of birth

tag: vital status

tag: death censoring

tag: diagnosis date

value: A

value: AA

value: III

tag: second progression date

tag: second progressed tumor pathology

tag: second progressed tumor grade


title: K105727

description:
whole methylome (Methyl Capture)
K105727_MeCap

tag: age of menarche

tag: menopausal status

value: Post

tag: blood relatives cancer

value: Yes

value: WHITE

tag: hispanic

value: No

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: High


title: RNA-SEQ_A10-184-3_15-008/U24_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-184-3
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

tag: race

value: white

tag: pathologic stage

tag: age

tag: 5-year disease status

tag: sample type

tag: tissue

value: prostate tissue


title: GC071392_ATTAGACG-CCTAAGAC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus