title: K105555

description:
whole methylome (Methyl Capture)
K105555_MeCap

tag: age of menarche

tag: menopausal status

tag: blood relatives cancer

value: AFRNAMER

tag: hispanic

tag: bmi

value: Average


title: K105362

status: Public on Sep 30 2021

type: SRA

city: Indianapolis

first: Natascia

last: Marino

state: IN

address: 980 W. Walnut St, R3-C238

department: Hematology/Oncology Division

country: USA

institute: Indiana University School of Medicine

description:
whole methylome (Methyl Capture)
K105362_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

organism: Homo sapiens

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

value: Post

value: Yes

tag: race

value: WHITE

value: No

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: High


title: GC071392_ATTAGACG-CGAGGCTG

city: Leuven

first: Vincent

last: Pasque

address: Herestraat 49 bus 804

department: Development and Regeneration

country: Belgium

institute: KU Leuven

description: smart-seq2 protocol

library_source: transcriptomic

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: RNA-SEQ_A10-170-24_15-008/060_buffy coat

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-170-24
processed_counts.txt
processed_TPM.txt

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

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: black

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type

value: normal

tag: tissue

value: buffy coat


title: Sample_R378-55-476946_S39_L003

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.

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: 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-ACTGAGCG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: RNA-SEQ_A10-183-57_15-008/059_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-183-57
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

value: cancer

tag: tissue

value: prostate tissue


title: RNA-SEQ_A10-183-56_15-008/059_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-183-56
processed_counts.txt
processed_TPM.txt

value: prostate cancer


title: K105254

description:
whole methylome (Methyl Capture)
K105254_MeCap

tag: age of menarche

tag: menopausal status

value: Pre

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_ATTAGACG-ACTCGCTA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: K105282

description:
whole methylome (Methyl Capture)
K105282_MeCap

value: Post


title: K105278

description:
whole methylome (Methyl Capture)
K105278_MeCap


title: GC071392_ATTAGACG-ATCTCAGG

description: smart-seq2 protocol


title: K105295

description:
whole methylome (Methyl Capture)
K105295_MeCap


title: RNA-SEQ_A10-170-23_15-008/059_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-170-23
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

value: black

value: remission

value: normal

value: buffy coat


title: Sample_R378-53-475155_S41_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

tag: death censoring

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: AO

tag: progressed tumor grade

tag: second progression date

tag: second progressed tumor pathology

value: AA

tag: second 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_R378-54-87811_S38_L003

tag: tissue

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: age

tag: gender

value: O


title: GC071392_ATTAGACG-AGGCAGAA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: Sample_R378-54-87811_S42_L006

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

tag: progressed tumor grade


title: K105173

description:
whole methylome (Methyl Capture)
K105173_MeCap

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

value: Yes

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: Average


title: Sample_R378-52-38124_S40_L005

tag: tissue

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: age

tag: date of birth

tag: vital status

tag: gender

value: M

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: RNA-SEQ_A10-183-55_15-008/058_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-183-55
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: 5-year disease status

value: remission

tag: sample type

value: cancer

value: prostate tissue


title: K105188

description:
whole methylome (Methyl Capture)
K105188_MeCap

tag: age of menarche

tag: menopausal status

value: Post

tag: blood relatives cancer

value: ASIAN

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: Sample_R378-52-38124_S36_L003

tag: tissue

value: Glioma

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: gender

tag: diagnosis date

tag: patient initial tumor grade

value: II

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: GC071392_ATTAGACG-AAGAGGCA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: K105131

description:
whole methylome (Methyl Capture)
K105131_MeCap

tag: age

tag: age of menarche

tag: menopausal status

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


title: Sample_R378-51-974748_S39_L005

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: F

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

value: III

tag: second progression date

tag: second progressed tumor pathology

tag: second progressed tumor grade


title: K105121

description:
whole methylome (Methyl Capture)
K105121_MeCap

tag: age

tag: age of menarche

tag: menopausal status

value: Pre

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: Sample_R378-51-974748_S35_L003

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

tag: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: K105138

description:
whole methylome (Methyl Capture)
K105138_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: GC071392_ATAGCCTT-TCGACGTC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: RNA-SEQ_A10-183-53_15-008/057_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-183-53
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: K105055

description:
whole methylome (Methyl Capture)
K105055_MeCap

tag: age

tag: age of menarche

tag: menopausal status

value: Post

tag: blood relatives cancer

tag: race

value: Average


title: RNA-SEQ_A10-171-24_15-008/058_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-171-24
processed_counts.txt
processed_TPM.txt

value: normal

value: buffy coat


title: Sample_R378-5-356608_S5_L001

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

tag: diagnosis date

tag: patient initial tumor grade

value: II

tag: initial tumor pathology

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: Sample_R378-53-475155_S37_L003

tag: tissue

tag: age

tag: gender

value: F

value: A

tag: progression date

tag: progressed tumor pathology

value: AO

tag: progressed tumor grade

tag: second progression date

tag: second progressed tumor pathology

value: AA

tag: second progressed tumor grade

value: III


title: K104949

description:
whole methylome (Methyl Capture)
K104949_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

value: Yes

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: Sample_R378-49-478940_S38_L005

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

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_A10-183-54_15-008/058_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-183-54
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: prostate tissue


title: GC071392_ATAGCCTT-TAGGCATG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: Sample_R378-50-481380_S34_L003

tag: tissue

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

value: M

tag: diagnosis date

tag: patient initial tumor grade

value: II

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


title: GC071392_ATAGCCTT-TGCAGCTA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: K104986

description:
whole methylome (Methyl Capture)
K104986_MeCap

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: High


title: GC071392_ATAGCCTT-TACGCTGC

description: smart-seq2 protocol


title: RNA-SEQ_A10-171-23_15-008/057_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-171-23
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

tag: pathologic stage

tag: age

tag: 5-year disease status

tag: sample type

value: normal

tag: tissue

value: buffy coat


title: RNA-SEQ_A10-183-52_15-008/057_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-183-52
processed_counts.txt
processed_TPM.txt


title: K104932

description:
whole methylome (Methyl Capture)
K104932_MeCap

tag: age of menarche

tag: menopausal status

value: Pre

value: No

tag: blood relatives cancer

value: WHITE

value: Average


title: RNA-SEQ_A10-183-51_15-008/056_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-183-51
processed_counts.txt
processed_TPM.txt

value: prostate cancer

value: male

tag: race

value: cancer


title: GC071392_ATAGCCTT-TCCTGAGC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: K104934

description:
whole methylome (Methyl Capture)
K104934_MeCap

tag: hispanic

tag: bmi

tag: ever pregnant

value: Yes

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: K104924

description:
whole methylome (Methyl Capture)
K104924_MeCap


title: GC071392_ATAGCCTT-TAGCGCTC

description: smart-seq2 protocol

value: Mus


title: RNA-SEQ_A10-184-2_15-008/U24_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-184-2
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

value: white

value: remission

value: prostate tissue


title: Sample_R378-49-478940_S33_L003

tag: tissue

value: Glioma

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

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: RNA-SEQ_A10-183-50_15-008/056_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-183-50
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: 5-year disease status

tag: sample type

value: normal

tag: tissue


title: GC071392_ATAGCCTT-TAAGGCGA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: Sample_R378-48-475866_S37_L005

tag: unique sample id

tag: patient id

tag: grade

value: HGG

tag: batch

tag: idh status prediction

value: Mutant

tag: age

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


title: RNA-SEQ_A10-171-22_15-008/056_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-171-22
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: 5-year disease status

tag: sample type

tag: tissue

value: buffy coat


title: K104910

description:
whole methylome (Methyl Capture)
K104910_MeCap

tag: age

tag: age of menarche

tag: menopausal status

value: Post

value: No

tag: blood relatives cancer

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_ATAGCCTT-GGAGCTAC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: RNA-SEQ_A10-183-49_15-008/055_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-183-49
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

value: unknown

value: remission

value: cancer

value: prostate tissue


title: RNA-SEQ_A10-183-48_15-008/055_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-183-48
processed_counts.txt
processed_TPM.txt

tag: race

tag: pathologic stage

tag: 5-year disease status

tag: sample type

value: normal

tag: tissue


title: Sample_R378-42-322918_S34_L005

value: Glioma

tag: unique sample id

tag: patient id

tag: grade

value: HGG

tag: batch

tag: idh status prediction

tag: age

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: 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: RNA-SEQ_A10-171-21_15-008/055_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-171-21
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

tag: race

tag: pathologic stage

tag: age

tag: 5-year disease status

tag: sample type

tag: tissue

value: buffy coat


title: K104904

description:
whole methylome (Methyl Capture)
K104904_MeCap

tag: age of menarche

tag: menopausal status

value: Post

value: No

tag: blood relatives cancer

value: WHITE

tag: hispanic

tag: bmi

tag: ever pregnant

value: Yes

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: Average


title: Sample_R378-45-479502_S35_L005

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

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: K104797

description:
whole methylome (Methyl Capture)
K104797_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: K104830

description:
whole methylome (Methyl Capture)
K104830_MeCap

value: High


title: GC071392_ATAGCCTT-GTAGAGGA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: K104782

description:
whole methylome (Methyl Capture)
K104782_MeCap


title: RNA-SEQ_A10-183-45_15-008/053_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-183-45
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

value: black

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type

value: cancer

tag: tissue

value: prostate tissue


title: Sample_R378-4-629979_S4_L001

value: Glioma

tag: unique sample id

tag: patient id

tag: grade

value: LGG

tag: batch

tag: idh status prediction

tag: age

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: 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: GC071392_ATAGCCTT-GCGTAGTA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: K104591

description:
whole methylome (Methyl Capture)
K104591_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: K104780

description:
whole methylome (Methyl Capture)
K104780_MeCap

tag: age

value: Pre


title: K104531 (second donation from K102516)

description:
whole methylome (Methyl Capture)
K104531_MeCap

value: High


title: RNA-SEQ_A10-183-46_15-008/054_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-183-46
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

tag: sample type

value: normal

tag: tissue


title: GC071392_ATAGCCTT-CTCTCTAC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: GC071392_ATAGCCTT-CGTACTAG

description: smart-seq2 protocol


title: Sample_R378-38-53636_S32_L004

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

tag: initial tumor pathology

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: RNA-SEQ_A10-183-47_15-008/054_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-183-47
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

value: remission

tag: sample type

value: cancer

tag: tissue

value: prostate tissue


title: Sample_R378-41-878541_S33_L005

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: 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: GBM

value: IV

tag: second progression date

tag: second progressed tumor pathology

tag: second progressed tumor grade


title: Sample_R378-36-480467_S30_L004

tag: tissue

tag: age

tag: gender

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_ATAGCCTT-CGAGGCTG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: GC071392_ATAGCCTT-CGGAGCCT

description: smart-seq2 protocol


title: Sample_R378-33-91963_S28_L004

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: diagnosis date

tag: patient initial tumor grade


title: RNA-SEQ_A10-183-44_15-008/053_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-183-44
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: black

tag: pathologic stage

tag: age

tag: 5-year disease status

tag: sample type

tag: tissue


title: RNA-SEQ_A10-183-42_15-008/052_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-183-42
processed_counts.txt
processed_TPM.txt

value: white

value: normal


title: GC071392_ATAGCCTT-GCTCATGA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: Sample_R378-46-493319_S36_L005

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

value: F

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: Sample_R378-32-638178_S27_L004

tag: tissue

tag: age

tag: death censoring

tag: gender

tag: diagnosis date

tag: patient initial tumor grade

value: AO

value: III


title: Sample_R378-34-493226_S29_L004

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: idh status prediction

value: M

value: II

value: OA

value: AA


title: RNA-SEQ_A10-171-19_15-008/052_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-171-19
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

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: GC071392_ATAGCCTT-GGACTCCT

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: Sample_R378-30-355527_S25_L004

tag: tissue

tag: age

tag: date of birth

tag: vital status

tag: death censoring

tag: gender

tag: diagnosis date

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: RNA-SEQ_A10-183-40_15-008/051_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-183-40
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

value: male

tag: preoperative psa

tag: gleason score

tag: race

value: unknown

tag: pathologic stage

tag: 5-year disease status

tag: sample type

value: normal

value: prostate tissue


title: GC071392_ATAGCCTT-ACTGAGCG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: Sample_R378-3-662112_S3_L001

tag: tissue

value: Glioma

tag: unique sample id

tag: patient id

tag: grade

value: LGG

tag: batch

tag: idh status prediction

value: Mutant

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: A

tag: progression date


title: K104444

description:
whole methylome (Methyl Capture)
K104444_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: Average


title: GC071392_ATAGCCTT-ATGCGCAG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: GC071392_ATAGCCTT-ATCTCAGG

description: smart-seq2 protocol


title: GC071392_ATAGCCTT-ACTCGCTA

description: smart-seq2 protocol


title: K102516

description:
whole methylome (Methyl Capture)
K102516_MeCap

tag: age

value: Pre

value: High


title: RNA-SEQ_A10-183-41_15-008/051_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-183-41
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type

value: cancer

tag: tissue


title: GC071392_ATAGCCTT-CCTAAGAC

description: smart-seq2 protocol


title: GC071392_ATAGCCTT-AAGAGGCA

description: smart-seq2 protocol


title: RNA-SEQ_A10-171-20_15-008/053_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-171-20
processed_counts.txt
processed_TPM.txt

value: male

tag: race

value: black

value: normal

value: buffy coat


title: Sample_R378-27-474275_S23_L003

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

value: F

tag: diagnosis date

tag: patient initial tumor grade

value: II

tag: initial tumor pathology

value: OA

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_A10-183-43_15-008/052_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-183-43
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: gender

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_ATAGAGAG-TGCAGCTA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: GC071392_ATAGCCTT-AGGCAGAA

description: smart-seq2 protocol


title: K102551

description:
whole methylome (Methyl Capture)
K102551_MeCap

tag: age of menarche

tag: menopausal status

value: Pre

value: No

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

value: High


title: COADM_1

city: Nanjing

first: Cun-en

last: Wu

address: no.155 Hanzhong Road

country: China

institute: Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine

description: miRNA sequencing

data_processing:
miRNA-Seq: Unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
miRNA-Seq: Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
miRNA-Seq: The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3pderived miRNA candidates.
miRNA-Seq: The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
miRNA-Seq: The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes, and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software (http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤20). (6) number of nucleotides in one bulge in mature region (≤8) (7) number of biased errors in one bulge in mature region (≤4) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤7) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Supplementary_files_format_and_content: excel,expression profiles

source_name: plasma from patient of COAD with liver metastasis

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
The libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol.

tag: diagnosis

value: COAD with liver metastasis


title: COADM_3

description: miRNA sequencing


title: RNA-SEQ_A10-171-18_15-008/051_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-171-18
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: unknown

value: remission

value: normal

value: buffy coat


title: RNA-SEQ_A12-2-10_15-008/050_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A12-2-10
processed_counts.txt
processed_TPM.txt

tag: pathologic stage

tag: age

tag: 5-year disease status

tag: sample type

value: cancer

tag: tissue


title: RNA-SEQ_A12-2-9_15-008/050_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A12-2-9
processed_counts.txt
processed_TPM.txt


title: GC071392_ATAGCCTT-CGATCAGT

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: RNA-SEQ_A10-183-39_15-008/049_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-183-39
processed_counts.txt
processed_TPM.txt


title: RNA-SEQ_A10-183-38_15-008/049_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-183-38
processed_counts.txt
processed_TPM.txt


title: K104335

description:
whole methylome (Methyl Capture)
K104335_MeCap

tag: age of menarche

tag: menopausal status

value: Post

tag: blood relatives cancer

tag: hispanic

tag: bmi

tag: ever pregnant


title: GC071392_ATAGAGAG-TCCTGAGC

description: smart-seq2 protocol


title: GC071392_ATAGAGAG-TAGGCATG

description: smart-seq2 protocol


title: COAD_1

description: miRNA sequencing

source_name: plasma from patient of COAD

tag: diagnosis

value: COAD


title: COAD_3

description: miRNA sequencing


title: Sample_R378-28-474461_S24_L003

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

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: Sample_R378-26-720984_S22_L003

tag: tissue

tag: unique sample id

tag: patient id

tag: grade

tag: age

value: A

value: AA


title: RNA-SEQ_A10-183-37_15-008/048_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-183-37
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: unknown

tag: pathologic stage

tag: 5-year disease status

value: recurrence

tag: sample type

value: prostate tissue


title: Sample_R378-31-496519_S26_L004

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: OA

tag: progression date

tag: progressed tumor pathology

value: GBM

tag: progressed tumor grade

value: IV

tag: percentage of total mapped reads


title: RNA-SEQ_A10-183-36_15-008/048_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-183-36
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: preoperative psa

tag: gleason score

tag: race

tag: age

value: normal

tag: tissue


title: GC071392_ATAGAGAG-TCGACGTC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: COAD_2

description: miRNA sequencing

tag: diagnosis

value: COAD


title: COADM_2

description: miRNA sequencing

value: COAD with liver metastasis


title: pDC_C

city: Boston

first: Andrew

last: Lane

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

data_processing:
The raw FASTQ data were analyzed by the VIPER pipeline which combines STAR alignment and gene expression analysis such as unsupervised clustering, PCA based on Cufflinks and differential expression with DESEq2
Genome_build: hg19
Supplementary_files_format_and_content: RNA abundance expressed as fragments per kilobase of transcript per million mapped reads (FPKM)

source_name: pDC

extract_protocol:
Arcturus PicoPure RNA Isolation Kit (Life Technologies)
Ovation kit (Nugen, #0340) using 50 ng of input total RNA and 20 cycles of amplificaftion


title: pDC_B


title: GC071392_ATAGAGAG-TAGCGCTC

description: smart-seq2 protocol


title: Sample_R378-23-728542_S20_L003

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

value: II

tag: second progression date

tag: second progressed tumor pathology

tag: second progressed tumor grade

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: RNA-SEQ_A10-171-16_15-008/048_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-171-16
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

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

tag: tissue

value: buffy coat


title: Sample_R378-22-274878_S19_L003

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

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


title: pDC_A

tag: tissue


title: RNA-SEQ_A12-2-7_15-008/047_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A12-2-7
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: age

tag: 5-year disease status

value: remission

tag: sample type

value: cancer

value: prostate tissue


title: Sample_R378-25-494228_S21_L003

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

value: O

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: Sample_R378-19-473907_S16_L002

tag: tissue

value: WT

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


title: GC071392_ATAGAGAG-TAAGGCGA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: RNA-SEQ_A10-171-17_15-008/050_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-171-17
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: age

tag: 5-year disease status

tag: sample type

value: normal


title: Sample_R378-2-663713_S2_L001

tag: tissue

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

tag: gender

value: M

tag: diagnosis date

tag: patient initial tumor grade

value: II

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: pDC_D


title: Sample_R378-21-473295_S18_L003

value: HGG

tag: age

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


title: GC071392_ATAGAGAG-GGAGCTAC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: Sample_R378-20-474126_S17_L003

tag: tissue

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: idh status prediction

tag: date of birth

value: F


title: RNA-SEQ_A12-2-8_15-008/047_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A12-2-8
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: prostate tissue


title: Pt_10

source_name: BPDCN

value: tumor


title: K102424

description:
whole methylome (Methyl Capture)
K102424_MeCap

tag: age

tag: age of menarche

tag: menopausal status

value: Post

value: No

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

value: High


title: GC071392_ATAGAGAG-TACGCTGC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: Pt_11

tag: tissue


title: Sample_R378-16-773952_S14_L002

value: Glioma

tag: unique sample id

tag: patient id

tag: grade

value: HGG

tag: batch

tag: idh status prediction

value: WT

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

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: GC071392_ATAGAGAG-GGACTCCT

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: RNA-SEQ_A10-171-15_15-008/047_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-171-15
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

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

tag: tissue

value: buffy coat


title: RNA-SEQ_A10-183-35_15-008/046_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-183-35
processed_counts.txt
processed_TPM.txt

tag: gender

value: white

value: remission

value: cancer

value: prostate tissue


title: Pt_9

value: tumor


title: Sample_R378-15-49530_S13_L002

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

tag: initial tumor pathology

value: A

tag: progression date

tag: progressed tumor pathology

tag: progressed tumor grade

tag: percentage of total mapped reads


title: GC071392_ATAGAGAG-GTAGAGGA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: Pt_8

tag: tissue


title: GC071392_ATAGAGAG-GCGTAGTA

description: smart-seq2 protocol


title: RNA-SEQ_A10-183-34_15-008/046_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-183-34
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


title: Pt_7


title: RNA-SEQ_A10-183-32_15-008/045_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-183-32
processed_counts.txt
processed_TPM.txt


title: Pt_5


title: GC071392_ATAGAGAG-CTCTCTAC

description: smart-seq2 protocol


title: Sample_R378-17-329452_S15_L002

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: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

tag: progression date

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: Pt_6

tag: tissue


title: Sample_R378-11-493155_S10_L002

tag: age

tag: gender

value: II

value: O

tag: progressed tumor pathology

value: GBM

tag: progressed tumor grade

tag: percentage of total mapped reads


title: Sample_R378-13-480248_S11_L002

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: idh status prediction

value: AA

value: III


title: RNA-SEQ_A10-183-33_15-008/045_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-183-33
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

value: male

tag: preoperative psa

tag: gleason score

tag: race

tag: pathologic stage

tag: 5-year disease status

tag: sample type


title: GC071392_ATAGAGAG-CGGAGCCT

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: Sample_R378-10-130792_S9_L002

tag: tissue

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

tag: progression date

tag: progressed tumor pathology

value: AOA

tag: progressed tumor grade

tag: second progression date

tag: second progressed tumor pathology

value: AO

tag: second progressed tumor grade

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: RNA-SEQ_A10-171-14_15-008/045_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-171-14
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: age

tag: 5-year disease status

value: remission

tag: sample type

value: normal

tag: tissue

value: buffy coat


title: GC071392_ATAGAGAG-GCTCATGA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: Pt_4

value: tumor


title: RNA-SEQ_A10-183-31_15-008/044_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-183-31
processed_counts.txt
processed_TPM.txt

tag: gender

value: Hawaiian/Pacific Islander

value: cancer

value: prostate tissue


title: Sample_R378-1-854739_S1_L001

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: M

tag: diagnosis date

tag: patient initial tumor grade

value: II

tag: initial tumor pathology

value: A

tag: percentage of total mapped reads


title: Pt_3


title: GC071392_ATAGAGAG-CGATCAGT

description: smart-seq2 protocol

value: Mus


title: GC071392_ATAGAGAG-CGAGGCTG

description: smart-seq2 protocol


title: RNA-SEQ_A10-183-30_15-008/044_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-183-30
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

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


title: Sample_R378-14-133900_S12_L002

tag: tissue

tag: unique sample id

tag: patient id

tag: grade

value: HGG

tag: batch

tag: idh status prediction

value: WT

tag: gender

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

value: GBM

tag: second progressed tumor grade

value: IV

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: Sample_9-494457_S50_L006

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: AA

tag: percentage of total mapped reads


title: Pt_2

tag: tissue

value: tumor


title: GC071392_ATAGAGAG-CGTACTAG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: GC071392_ATAGAGAG-CCTAAGAC

description: smart-seq2 protocol


title: Sample_9-493777_S33_L004

value: Glioma

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: idh status prediction

tag: gender

tag: progression date

tag: progressed tumor pathology

tag: progressed tumor grade


title: RNA-SEQ_A10-183-28_15-008/043_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-183-28
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: age

tag: 5-year disease status

value: recurrence

tag: sample type

value: normal

value: prostate tissue


title: Pt_1

tag: tissue


title: Sample_8-653019_S63_L007

tag: unique sample id

tag: patient id

tag: grade

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: OA

value: AOA

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: Sample_R378-37-129347_S31_L004

tag: tissue

value: HGG

tag: batch

tag: idh status prediction

tag: age

tag: gender

value: A

tag: progression date

tag: progressed tumor pathology

tag: progressed tumor grade


title: RNA-SEQ_A10-171-13_15-008/043_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-171-13
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

value: male

tag: preoperative psa

tag: gleason score

tag: race

tag: pathologic stage

tag: 5-year disease status

tag: sample type

value: buffy coat


title: RNA-SEQ_A10-183-27_15-008/042_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-183-27
processed_counts.txt
processed_TPM.txt

value: remission

value: cancer


title: GC071392_ATAGAGAG-AGGCAGAA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: GC071392_ATAGAGAG-ATCTCAGG

description: smart-seq2 protocol


title: ML8

city: New york

first: Miguel

middle: A

last: Lopez-Lago

state: NY

address: 1275 york avenue

department: Surgery

institute: Memorial Sloan-kettering cancer center

data_processing:
CutAdapt version cutadapt-1.6 was used to trim and filter reads. Adapters were trimmed with minimum overlap of 10 bases and reads of less than half original read length were filtered out.
STAR version STAR-STAR_2.5.0a was run using the 2-pass method. First pass was run with the following parameters: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All --outSAMunmapped Within. Genome database was then generated using the minimum read length of half desired read length and second pass was run against the new genome file with the same parameters as pass 1.
Expression count matrix was computed using HTSeq version HTSeq-0.5.3. Parameters set were: -m intersection-strict -s reverse -t exon
Raw count matrix was processed using the R/Bioconductor package DESeq, version [UNKNOWN], which is used to both normalize the full dataset and analyze differential expression between sample groups.
Genome_build: hg19

source_name: MGM variant-2

growth_protocol: MSTO cells were cultured in RPMI+10% serum

extract_protocol:
Whole RNA was isolated from  cells using the RNeasy Mini Kit (Qiagen) and subsequently submitted to the Integrated Genomics Operation at Memorial Sloan Kettering Cancer Center for further analysis
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 500ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102), with 8 cycles of PCR.
Samples were barcoded and run on a HiSeq 2500 in High Output mode in a PE50 end run, using the TruSeq SBS Kit v4 (Illumina).  An average of 40 million paired reads was generated per sample. At the most the ribosomal reads represented 1.2% of the total reads generated and the percent of mRNA bases averaged 70%.

tag: cell type

value: Mesothelioma

tag: phenotype

value: variant


title: Sample_8-330216_S32_L003

tag: tissue

value: Glioma

tag: unique sample id

tag: patient id

tag: grade

value: LGG

tag: batch

tag: idh status prediction

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: O

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: Sample_7-496402_S31_L003

tag: tissue

value: Mutant

tag: gender

value: F

tag: progression date

tag: progressed tumor pathology

value: AA

tag: progressed tumor grade

value: III


title: Sample_7-40636_S61_L007

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: idh status prediction

value: II

value: OA

value: AOA

tag: second progression date

tag: second progressed tumor pathology

value: GBM

tag: second progressed tumor grade

value: IV


title: GC071392_ATAGAGAG-ACTGAGCG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: ML7

source_name: MGM variant-1

tag: cell type

tag: phenotype


title: RNA-SEQ_A10-183-29_15-008/043_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-183-29
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: recurrence

tag: sample type

tag: tissue

value: prostate tissue


title: RNA-SEQ_A10-183-26_15-008/042_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-183-26
processed_counts.txt
processed_TPM.txt

tag: gender

value: remission

value: normal


title: ML5

source_name: MGM wt-1

value: Mesothelioma

value: parental


title: GC071392_ATAGAGAG-ACTCGCTA

description: smart-seq2 protocol

value: Mus


title: GC071392_ATAGAGAG-ATGCGCAG

description: smart-seq2 protocol


title: RNA-SEQ_A10-171-12_15-008/042_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-171-12
processed_counts.txt
processed_TPM.txt

value: buffy coat


title: Sample_6-934656_S60_L007

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

value: III

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: RNA-SEQ_A10-183-25_15-008/041_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-183-25
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: unknown

tag: pathologic stage

tag: age

tag: 5-year disease status

tag: sample type

value: cancer

tag: tissue


title: ML9

source_name: MGM variant-3

tag: cell type

tag: phenotype

value: variant


title: GC071392_ATAGAGAG-AAGAGGCA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: RNA-SEQ_A10-183-24_15-008/041_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-183-24
processed_counts.txt
processed_TPM.txt

value: recurrence

value: normal

value: prostate tissue


title: AB12ShNF2-21

data_processing:
CutAdapt version cutadapt-1.6 was used to trim and filter reads. Adapters were trimmed with minimum overlap of 10 bases and reads of less than half original read length were filtered out.
STAR version STAR-STAR_2.5.0a was run using the 2-pass method. First pass was run with the following parameters: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All --outSAMunmapped Within. Genome database was then generated using the minimum read length of half desired read length and second pass was run against the new genome file with the same parameters as pass 1.
Expression count matrix was computed using HTSeq version HTSeq-0.5.3. Parameters set were: -m intersection-strict -s reverse -t exon
Raw count matrix was processed using the R/Bioconductor package DESeq, version 1.22.1, which is used to both normalize the full dataset and analyze differential expression between sample groups.
Genome_build: mm10

growth_protocol: AB12 cells were cultured in RPMI+10% serum

value: Mesothelioma

tag: treatment

tag: cell line


title: Sample_6-496697_S30_L003

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: diagnosis date

tag: patient initial tumor grade

value: II

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: AB12ShNF2-20

tag: cell type

tag: treatment


title: GC071392_AGGCTTAG-TGCAGCTA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: Sample_5-493354_S54_L006

tag: tissue

value: Glioma

tag: unique sample id

tag: patient id

tag: grade

value: Mutant

tag: age

tag: gender

value: M

tag: progression date

tag: progressed tumor pathology

tag: progressed tumor grade


title: RNA-SEQ_A10-183-23_15-008/040_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-183-23
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: preoperative psa

tag: gleason score

tag: race

value: black

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type


title: AB12ShSC

tag: cell type

tag: treatment

value: shSC

tag: cell line


title: ML6

source_name: MGM wt-2

tag: phenotype

value: parental


title: GC071392_AGGCTTAG-TCGACGTC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: Sample_48-475866_S72_L008

tag: tissue

tag: unique sample id

tag: patient id

tag: grade

value: HGG

tag: batch

tag: idh status prediction

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

tag: progression date

value: AO

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_5-356608_S29_L003

tag: tissue

tag: unique sample id

tag: patient id

value: F


title: RNASET2HippocampusKO5000nucleiSakib_K4_L004

city: Göttingen

first: Andre

last: Fischer

state: NDS

address: Von-Siebold-Str. 3a

department: Epigenetics and Systems Medicine in Neurodegenerative Diseases

country: Germany

institute: DZNE Göttingen

description:
Sample Title format: sample_sequencing run_lane
Processed data file: RNASET2HippocampusKO5000nucleiSakib_processed_data_files.tar.gz

data_processing:
Cellranger-4.0.0 mkfastq was used for adapter trimming and converting the base calls
Cellranger-4.0.0 counts was used to align the reads on the pre-mRNA and create the read count matrices
Genome_build: mm10
Supplementary_files_format_and_content: count matrices, barcode tables, feature tables (in a tar.gz archive)

source_name: Hippocampus, tissue from adult mice brain

extract_protocol:
10X Chromium v3.1 kit (NextGEM) and 5000 nuclei out of 300000 sorted nuclei were barcoded
Mice were deeply anesthetized with ketamine and medetomidine and transcardially perfused with phosphate buffered saline (PBS, pH 7.4). After cervical dislocation, the whole brain was removed from the skull and the preparation of the hippocampus and caudate putamen was performed in a petri dish filled with ice cold PBS buffer under a binocular. Tissue sample from two hemispheres of different mice were pooled and immediately frozen on liquid nitrogen and stored at -80°C until further processing. Nuclei from frozen mouse brain tissues were isolated according to previously published protocol with modifications.65 Isolated total nuclei were stained with 7AAD (Invitrogen, Cat: 00-6993-50) and single nuclei were sorted using BD FACS Aria III sorter. Sorted nuclei were counted in Countess II FL Automated Counter.
Around 5000 single nuclei per sample were used for GEM generation, barcoding, and cDNA libraries according to 10X Chromium Next GEM Single Cell 3′ Reagent v3.1 protocol. Pooled libraries were sequenced in Illumina NextSeq 550 in order to achieve >50,000 reads/nuclei.
10X genomics single-cell seq

tag: strain

tag: genotype

value: RNT2AB KO

tag: developmental stage

value: adult

value: Hippocampus


title: RNA-SEQ_A10-171-11_15-008/040_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-171-11
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

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: buffy coat


title: RNA-SEQ_A10-183-22_15-008/040_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-183-22
processed_counts.txt
processed_TPM.txt

tag: gender

value: prostate tissue


title: GC071392_AGGCTTAG-TCCTGAGC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: GC071392_AGGCTTAG-TAGCGCTC

description: smart-seq2 protocol


title: RNASET2HippocampusKO5000nucleiSakib_K4_L003

tag: tissue


title: RNA-SEQ_A12-2-5_15-008/039_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A12-2-5
processed_counts.txt
processed_TPM.txt

value: white


title: RNA-SEQ_A12-2-6_15-008/039_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A12-2-6
processed_counts.txt
processed_TPM.txt

value: remission

value: cancer


title: GC071392_AGGCTTAG-TACGCTGC

description: smart-seq2 protocol


title: RNASET2HippocampusKO5000nucleiSakib_K4_L002


title: Sample_46-493319_S70_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

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: RNASET2HippocampusKO5000nucleiSakib_K4_L001

tag: strain

tag: genotype

value: RNT2AB KO

tag: age

tag: developmental stage

value: adult

tag: tissue


title: RNASET2HippocampusKO5000nucleiSakib_K3_L004

value: Hippocampus


title: Sample_45-479502_S69_L008

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: gender

value: F

value: AO

value: III


title: GC071392_AGGCTTAG-TAGGCATG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: Sample_44-856139_S68_L008

tag: death censoring

tag: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

value: AA

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

tag: percentage of uniquely mapped reads

tag: progress free survival (months)


title: Sample_47-92626_S71_L008

tag: tissue

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: idh status prediction

tag: age

tag: date of birth

tag: vital status

value: M

value: A

tag: overall survival (months)


title: GC071392_AGGCTTAG-GTAGAGGA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: RNA-SEQ_A10-171-10_15-008/039_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-171-10
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

tag: race

value: white

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type

value: normal

value: buffy coat


title: RNA-SEQ_A10-183-21_15-008/038_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-183-21
processed_counts.txt
processed_TPM.txt

value: black

value: cancer

tag: tissue

value: prostate tissue


title: GC071392_AGGCTTAG-TAAGGCGA

description: smart-seq2 protocol


title: RNASET2HippocampusKO5000nucleiSakib_K3_L003

tag: strain

tag: genotype

value: RNT2AB KO

tag: developmental stage

value: adult

value: Hippocampus


title: Sample_42-322918_S66_L008

value: Glioma

tag: unique sample id

tag: patient id

tag: grade

value: HGG

tag: batch

tag: idh status prediction

value: Mutant

tag: age

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: 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)


title: Sample_43-653001_S67_L008

tag: tissue

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: idh status prediction

tag: gender

value: M

value: OA

value: AOA

tag: overall survival (months)


title: GC071392_AGGCTTAG-GGAGCTAC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: RNASET2HippocampusKO5000nucleiSakib_K3_L002

tag: strain

tag: genotype

tag: age

tag: developmental stage


title: RNA-SEQ_A10-171-9_15-008/038_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-171-9
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: black

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type

value: normal

value: buffy coat


title: Sample_41-878541_S65_L008

tag: tissue

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: 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: second progressed tumor grade

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)


title: GC071392_AGGCTTAG-GGACTCCT

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: RNA-SEQ_A10-183-20_15-008/038_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-183-20
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: prostate tissue


title: RNA-SEQ_A10-183-19_15-008/037_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-183-19
processed_counts.txt
processed_TPM.txt

value: unknown

value: cancer


title: GC071392_AGGCTTAG-GCTCATGA

description: smart-seq2 protocol


title: Sample_40-836221_S64_L007

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: 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: overall survival (months)


title: RNA-SEQ_A10-183-18_15-008/037_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-183-18
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

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


title: GC071392_AGGCTTAG-GCGTAGTA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: RNASET2HippocampusKO5000nucleiSakib_K2_L004

tag: strain

tag: genotype

value: RNT2AB KO

tag: developmental stage

value: adult

tag: tissue

value: Hippocampus


title: RNASET2HippocampusKO5000nucleiSakib_K2_L002


title: Sample_4-928505_S53_L006

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: diagnosis date

tag: patient initial tumor grade

value: III

tag: initial tumor pathology

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_AGGCTTAG-CTCTCTAC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: GC071392_AGGCTTAG-CGTACTAG

description: smart-seq2 protocol


title: RNA-SEQ_A10-171-8_15-008/037_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-171-8
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

tag: race

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_A12-2-4_15-008/036_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A12-2-4
processed_counts.txt
processed_TPM.txt

value: white

value: prostate tissue


title: Sample_4-629979_S28_L003

value: Glioma

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: 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: percentage of total mapped reads


title: RNASET2HippocampusKO5000nucleiSakib_K2_L001

tag: strain

tag: genotype

tag: age

tag: developmental stage


title: RNASET2HippocampusKO5000nucleiSakib_K2_L003

tag: tissue


title: Sample_39-481640_S63_L007

tag: unique sample id

tag: patient id

tag: grade

value: HGG

tag: batch

value: Mutant

tag: gender

value: M

value: II

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: GC071392_AGGCTTAG-CGGAGCCT

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: RNASET2HippocampusKO5000nucleiSakib_K1_L004

value: RNT2AB KO

value: adult

value: Hippocampus


title: RNA-SEQ_A10-171-7_15-008/036_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-171-7
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

value: male

tag: preoperative psa

tag: gleason score

tag: race

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type

value: normal


title: RNA-SEQ_A12-2-3_15-008/036_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A12-2-3
processed_counts.txt
processed_TPM.txt

value: white

tag: age

tag: tissue

value: prostate tissue


title: RNASET2HippocampusKO5000nucleiSakib_K3_L001

tag: strain

tag: genotype

tag: developmental stage


title: RNA-SEQ_A10-183-17_15-008/035_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-183-17
processed_counts.txt
processed_TPM.txt

tag: gender

value: cancer


title: RNA-SEQ_A10-183-16_15-008/035_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-183-16
processed_counts.txt
processed_TPM.txt


title: Sample_36-480467_S60_L007

value: Glioma

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: 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: Sample_38-53636_S62_L007

tag: tissue

tag: unique sample id

tag: patient id

value: HGG

value: Mutant

tag: age

tag: gender

value: F


title: RNASET2HippocampusKO5000nucleiSakib_K1_L003

description:
Sample Title format: sample_sequencing run_lane
Processed data file: RNASET2HippocampusKO5000nucleiSakib_processed_data_files.tar.gz

tag: strain

tag: genotype

value: RNT2AB KO

tag: developmental stage


title: Sample_35-288330_S59_L007

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

value: II

value: AO


title: GC071392_AGGCTTAG-CGAGGCTG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: GC071392_AGGCTTAG-ATGCGCAG

description: smart-seq2 protocol


title: RNA-SEQ_A10-171-6_15-008/035_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-171-6
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

value: male

tag: preoperative psa

tag: gleason score

tag: race

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type

tag: tissue

value: buffy coat


title: RNASET2HippocampusKO5000nucleiSakib_K1_L002

tag: strain

tag: genotype

tag: age

tag: developmental stage

value: adult

value: Hippocampus


title: RNA-SEQ_A10-183-14_15-008/034_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-183-14
processed_counts.txt
processed_TPM.txt

tag: gender

value: white

value: normal

value: prostate tissue


title: Sample_37-129347_S61_L007

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: 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: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: Sample_33-91963_S57_L007

tag: tissue

tag: unique sample id

tag: patient id

value: Mutant

tag: age

tag: gender

value: F

value: II

value: AA

value: III


title: Sample_30-355527_S54_L006

tag: grade

tag: batch

tag: idh status prediction

tag: date of birth

tag: vital status

value: M


title: RNASET2HippocampusControl5000nucleiSakib_C4_L002

description:
Sample Title format: sample_sequencing run_lane
Processed data file: RNASET2HippocampusControl5000nucleiSakib_processed_data_files.tar.gz

tag: strain

tag: genotype

value: WT

tag: developmental stage


title: GC071392_AGGCTTAG-ACTCGCTA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: RNASET2HippocampusControl5000nucleiSakib_C4_L001

value: adult

value: Hippocampus


title: RNA-SEQ_A10-183-12_15-008/033_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-183-12
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: 5-year disease status

value: remission

tag: sample type

value: normal


title: GC071392_AGGCTTAG-CCTAAGAC

description: smart-seq2 protocol


title: RNASET2HippocampusControl5000nucleiSakib_C3_L004

tag: age

tag: tissue


title: RNA-SEQ_A10-183-15_15-008/034_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-183-15
processed_counts.txt
processed_TPM.txt

tag: gender

value: cancer

value: prostate tissue


title: GC071392_AGGCTTAG-CGATCAGT

description: smart-seq2 protocol


title: GC071392_AGGCTTAG-AGGCAGAA

description: smart-seq2 protocol


title: Sample_34-493226_S58_L007

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: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

value: OA

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_29-347647_S53_L006

tag: tissue

tag: unique sample id

tag: patient id

tag: age

tag: gender

value: II

value: O

value: AO

value: III


title: Sample_3-662112_S27_L003

tag: grade

value: LGG

tag: batch

tag: idh status prediction

tag: date of birth

tag: vital status

value: M

value: A

value: GBM

value: IV


title: GC071392_AGCTAGAA-TGCAGCTA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: GC071392_AGCTAGAA-TCGACGTC

description: smart-seq2 protocol


title: RNASET2HippocampusControl5000nucleiSakib_C4_L004

tag: strain

tag: genotype

value: WT

tag: developmental stage

value: adult

value: Hippocampus


title: GC071392_AGGCTTAG-ATCTCAGG

description: smart-seq2 protocol


title: RNA-SEQ_A10-183-13_15-008/033_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-183-13
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: 5-year disease status

value: remission

tag: sample type

value: cancer

value: prostate tissue


title: RNASET2HippocampusControl5000nucleiSakib_C3_L003

tag: age

tag: tissue


title: RNASET2HippocampusControl5000nucleiSakib_C4_L003


title: RNA-SEQ_A10-171-4_15-008/032_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-171-4
processed_counts.txt
processed_TPM.txt

tag: gender

value: normal

value: buffy coat


title: Sample_28-474461_S52_L006

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: 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: RNA-SEQ_A10-183-11_15-008/032_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-183-11
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

tag: 5-year disease status

tag: sample type

tag: tissue


title: GC071392_AGGCTTAG-ACTGAGCG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: Sample_3-37065_S45_L005

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

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


title: RNA-SEQ_A10-183-9_15-008/031_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-183-9
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

tag: race

value: white

tag: pathologic stage

tag: age

tag: 5-year disease status

value: remission

tag: sample type

value: cancer

tag: tissue


title: RNASET2HippocampusControl5000nucleiSakib_C3_L002

tag: strain

tag: genotype

value: WT

tag: developmental stage

value: adult

value: Hippocampus


title: GC071392_AGCTAGAA-TCCTGAGC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: RNASET2HippocampusKO5000nucleiSakib_K1_L001

value: RNT2AB KO


title: RNA-SEQ_A10-183-10_15-008/032_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-183-10
processed_counts.txt
processed_TPM.txt

value: normal

value: prostate tissue


title: RNASET2HippocampusControl5000nucleiSakib_C3_L001


title: RNA-SEQ_A10-171-5_15-008/033_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-171-5
processed_counts.txt
processed_TPM.txt

value: buffy coat


title: RNASET2HippocampusControl5000nucleiSakib_C2_L004


title: RNASET2HippocampusControl5000nucleiSakib_C2_L003


title: Sample_26-720984_S50_L006

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

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: RNA-SEQ_A10-183-8_15-008/031_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-183-8
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

tag: tissue


title: Sample_25-494228_S49_L006

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: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

value: O

tag: progression date

tag: progressed tumor pathology

value: AA


title: GC071392_AGGCTTAG-AAGAGGCA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: GC071392_AGCTAGAA-TAGCGCTC

description: smart-seq2 protocol


title: GC071392_AGCTAGAA-TAGGCATG

description: smart-seq2 protocol


title: RNA-SEQ_A10-183-7_15-008/030_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-183-7
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: gender

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


title: GC071392_AGCTAGAA-TACGCTGC

description: smart-seq2 protocol