title: DNA_METHYLATION_15-008/U27_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/U27
A10-170-28_BUFFYCOAT

tag: disease state

tag: patientid

value: unknown


title: DNA_METHYLATION_15-008/U26_TUMOR

status: Public on Sep 30 2021

type: genomic

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

country: USA

institute: National Cancer Institute

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/U26
A10-180-10_TUMOR

hyb_protocol: Bisulfite converted DNA was fragmented and hybridized to Illumina EPIC arrays using standard Illumina protocol

scan_protocol: Arrays were imaged using HiScanSQ using standard recommended Illumina scanner setting

data_processing:
IDAT files were processed using Minfi (R version 4.1) using the preprocessRaw and preprocessSWAN functions. Methyated and unmethylated intensity values were acquired using the getMeth and getUnmeth functions. Detection P values were acquired using the detectionP function. SWAN-normalized beta values were acquired using the ratioConvert and getBeta functions.
matrix_processed.txt:  SWAN normalized Average Beta
matrix_signal_intensities.txt:  Unmethylated and methylated signal intensities

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina labelling protocol

extract_protocol: Genomic DNA was purifed from ribbons of FFPE tissues using the QIAamp DNA FFPE Tissue Kit, or from buffy coat aliquots using the DNeasy Blood and Tissue Kit, according to the manufacturer's instructions.

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.

value: prostate cancer

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

value: prostate tissue


title: GC071392_TATGCAGT-TCGACGTC

type: SRA

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: GC071392_TCGCATAA-ACTGAGCG

description: smart-seq2 protocol


title: K105362_RNASeq

city: Indianapolis

first: Natascia

last: Marino

state: IN

address: 980 W. Walnut St, R3-C238

department: Hematology/Oncology Division

institute: Indiana University School of Medicine

description:
transcriptome profile
K105362_RNASeq

data_processing:
The raw RNA-seq 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 STAR (version STAR_2.5.2b) (Dobin et al. 2013).
Individual gene expression was quantified by counting the number reads mapping to the exon regions of each of the annotated genes from gencode v.28 using featureCounts tool of subread package (version 2.0.0) (Liao et al. 2014). Those reads that mapped to antisense strand, or mapped to multiple regions on the genome or those reads that overlapped with multiple genes were excluded. (parameters: -s 2 -p -B -C)
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Wiggle files containing deduplicated insert coverage

molecule: total RNA

source_name: Breast

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

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

tag: age of menarche

tag: menopausal status

value: Post

tag: blood relatives cancer

value: Yes

value: WHITE

tag: hispanic

value: No

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: High


title: K105254_RNASeq

description:
transcriptome profile
K105254_RNASeq

value: Pre

value: Average


title: K105173_RNASeq

description:
transcriptome profile
K105173_RNASeq


title: K105055_RNASeq

description:
transcriptome profile
K105055_RNASeq


title: K105131_RNASeq

description:
transcriptome profile
K105131_RNASeq


title: DNA_METHYLATION_15-008/U24_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/U24
A10-177-46_BENIGN

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

value: normal


title: GC071392_TATGCAGT-TACGCTGC

description: smart-seq2 protocol


title: GC071392_TATGCAGT-GGAGCTAC

description: smart-seq2 protocol


title: 948OctoPos

city: Oklahoma City

first: Michael

last: Stout

state: OK

address: 825 N.E. 13th Street

department: Aging and Metabolism

institute: Oklahoma Medical Research Foundation

data_processing:
Following sequencing, reads were trimmed, aligned, differential expression statistics and correlation analyses were performed in Strand NGS software package (v4.0) (Strand Life Sciences).
Alignment and filtering criteria included: adapter trimming, fixed 2bp trim from 5’ and 2bp from 3’ ends, a maximum number of one novel splice allowed per read, a minimum of 90% identity with the reference sequence, a maximum of 5% gap, trimming of 3’ end with Q<30.
Alignment was performed directionally with Read 1 aligned in reverse and Read 2 in forward orientation. Normalization was performed with the DESeq2 algorithm.
Transcripts with an average read count value >5 in at least 100% of the samples in at least one group were considered expressed at a level sufficient for quantitation per tissue and those transcripts below this level were considered not detected/not expressed and excluded, as these low levels of reads are close to background and are highly variable.
For statistical analysis of differential expression, a one-way ANOVA or two-way ANOVA with the factors of TRAP fraction and treatment and a Benjamini-Hochberg Multiple Testing Correction followed by Student-Newman Keuls post hoc test were used (FDR<0.1). For those transcripts meeting this statistical criterion, a fold change >|2| cutoff was used to eliminate those genes which were statistically significant but unlikely to be biologically significant and orthogonally confirmable due to their very small magnitude of change.
Genome_build: Mm10 build of the mouse genome (2014.11.26)
Supplementary_files_format_and_content: Data matrix with raw and normalized counts of all expressed genes.

source_name: brain

extract_protocol:
Purification of ribosomal-bound, microglial-specific RNA was performed as previously described (Chucair-Elliott et al., 2020; Kang et al., 2018; Roh et al., 2018) with slight modifications. For TRAP from whole tissue, a hemisected half-brain was minced into small pieces and homogenized in 1.5 ml ice-cold complete homogenization buffer (50 mM Tris, pH 7.4; 12 mM MgCl2; 100 mM KCl; 1% NP-40; 1 mg/ml sodium heparin; 1 mM DTT; 100 µg/mL cycloheximide (#C4859-1ML, Millipore Sigma); 200 units/ml RNaseOUT Recombinant Ribonuclease Inhibitor (#10777019; Thermofisher); 0.5 mM Spermidine (#S2626, Sigma), 1X complete EDTA-free Protease Inhibitor Cocktail (#11836170001; Millipore Sigma)) with a glass dounce tissue grinder set (#D8938; 15 times with pestle A). For TRAP from cells, microglial cells were sorted by a variety of methods (FACSAria, AutoMACS, Tyto, AutoMACS to Tyto). After pelleting cells at 1000 x g for 10 min at 4°C, cells were resuspended in 400 ul of complete ice-cold homogenization buffer, transferred to a glass dounce tissue grinder set, and homogenized 15 times with pestle A. Volume was brought up to 1.5 mL with complete homogenization buffer. Homogenates (from tissue or cells) were transferred to 2 mL round-bottom tubes and centrifuged at 12,000 x g for 10 minutes at 4°C. After centrifugation, 100 µL of the supernatant was saved as “RNA” input. The remaining supernatant was transferred to a 2 mL round-bottom tube and incubated with 5 µg/µl of anti-GFP antibody (ab290; Abcam) at 4°C with end-over-end rotation for one hour. Dynabeads Protein G for Immunoprecipitation (#10003D; Thermofisher) were washed three times in 1 ml ice-cold low-salt wash buffer (50mM Tris, pH 7.5; 12mM MgCl2; 100mM KCl; 1% NP-40; 100μg/ml cycloheximide; 1mM DTT). After removal of the last wash, the homogenate/antibody mixture was transferred to the 2 ml round-bottom tube containing the washed Protein-G Dynabeads and incubated at 4°C with end-over-end rotation overnight. Magnetic beads were collected using a DynaMag-2 magnet and the unbound- ribosomes and associated RNA discarded. Beads and GFP-bound polysomes were then washed three times with 0.5 ml of high-salt wash buffer (50mM Tris, pH 7.5; 12mM MgCl2; 300mM KCl; 1% NP-40; 100μg/ml cycloheximide; 2mM DTT). Following the last wash, 350 µL of Buffer RLT (Qiagen) supplemented with 3.5 µl 2-β mercaptoethanol (#444203, Sigma) was added directly to the beads and incubated with mixing on a ThermoMixer (Eppendorf) for 10 minutes at room temperature. The beads were magnetically separated and the supernatant containing the target bead-bound polysomes and associated RNA was transferred to a new tube. 350 µl of 100% ethanol was added to the tube (“TRAP” fraction: enriched in transcriptome associated to EGFP-tagged ribosomes) and then loaded onto a RNeasy MinElute column. RNA was isolated using RNeasy Mini Kit (#74104, Qiagen), according to manufacturer’s instructions. RNA was quantified with a Nanodrop 2000c spectrophotometer (Thermofisher Scientific) and its quality assessed by HSRNA screentape with a 2200 Tapestation analyzer (Agilent Technologies).
Directional RNA-Seq libraries were made from 5-100 ng RNA, as previously described (Chucair-Elliott et al., 2020; Chucair-Elliott et al., 2019). Briefly, poly-adenylated RNA was captured using NEBNext Poly(A) mRNA Magnetic Isolation Module (#NEBE7490L; New England Biolabs, Ipswich, MA) and then processed using NEBNext Ultra II Directional Library Prep Kit for Illumina (#NEBE7760L; New England Biolabs) for the creation of cDNA libraries, according to the manufacturer’s instruction. Library sizing was performed with HS RNA ScreenTape (#5067-5579; Agilent Technologies) and libraries were quantified by Qubit HSDNA (#Q32851, Thermo). The libraries for each sample were pooled at 4 nM concentration and sequenced using an Illumina NovaSeq 6000 system (SP PE50bp) at the Oklahoma Medical Research Foundation Clinical Genomics Center.

treatment_protocol: At ~3 months of age, Cx3cr1-NuTRAP mice received a daily intraperitoneal (ip) injection of tamoxifen (Tam) solubilized in 100% sunflower seed oil by sonication (100 mg/kg body weight) to induce cre recombination in microglia (Cx3cr1+).

tag: genotype

tag: sort method

value: Cell suspension (no sort)

tag: trap fraction

value: TRAP Pos Fraction

tag: experiment

value: Sort Comparison

tag: inhibitors

value: brain


title: K104949_RNASeq

description:
transcriptome profile
K104949_RNASeq

tag: age

tag: age of menarche

tag: menopausal status

tag: race


title: DNA_METHYLATION_15-008/U26_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/U26
A10-177-50_BENIGN

value: prostate cancer

value: male

value: white

tag: pathologic stage

tag: 5-year disease status

tag: sample type

tag: tissue


title: GC071392_TATGCAGT-GCTCATGA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: 948OctoInput

value: TRAP Input


title: GC071392_TATGCAGT-GCGTAGTA

description: smart-seq2 protocol

value: Mus


title: K105121_RNASeq

description:
transcriptome profile
K105121_RNASeq

tag: blood relatives cancer

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: DNA_METHYLATION_15-008/060_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/060
A12-3-15_BENIGN

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

value: black

value: remission

value: prostate tissue


title: GC071392_TATGCAGT-GTAGAGGA

description: smart-seq2 protocol


title: 949OctoInput

tag: genotype

tag: sort method

tag: trap fraction

tag: experiment

tag: inhibitors


title: K104986_RNASeq

description:
transcriptome profile
K104986_RNASeq

tag: age

tag: age of menarche

tag: menopausal status

value: Post

value: No

value: Yes

tag: race

value: WHITE


title: DNA_METHYLATION_15-008/060_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/060
A10-170-48_BUFFYCOAT

tag: pathologic stage

tag: 5-year disease status

tag: sample type

value: normal

tag: tissue

value: buffy coat


title: DNA_METHYLATION_15-008/U25_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/U25
A10-177-49_TUMOR

tag: disease state

tag: patientid

value: cancer


title: 991LFACSInput

value: FACSAria FACS

value: Sort Comparison


title: 947TissueInput

value: Tissue Homogenate (no sort)

value: brain


title: DNA_METHYLATION_15-008/060_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/060
A12-3-16_TUMOR

value: prostate cancer

tag: gender

value: male

tag: preoperative psa


title: DNA_METHYLATION_15-008/059_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/059
A10-177-42_BENIGN

tag: gleason score


title: DNA_METHYLATION_15-008/U24_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/U24
A10-170-25_BUFFYCOAT

value: white


title: 947TissuePos

tag: genotype

tag: sort method

value: TRAP Pos Fraction


title: GC071392_TATGCAGT-CGTACTAG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: DNA_METHYLATION_15-008/059_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/059
A10-170-47_BUFFYCOAT

value: black

tag: age

value: remission


title: GC071392_TATGCAGT-CGATCAGT

description: smart-seq2 protocol


title: DNA_METHYLATION_15-008/U24_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/U24
A10-177-47_TUMOR

value: prostate tissue


title: GC071392_TATGCAGT-GGACTCCT

description: smart-seq2 protocol


title: K104932_RNASeq

description:
transcriptome profile
K104932_RNASeq

tag: age of menarche

value: Pre

value: No

tag: blood relatives cancer

value: Yes

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: Average


title: K104924_RNASeq

description:
transcriptome profile
K104924_RNASeq

tag: menopausal status

value: Post

tag: race

value: WHITE


title: 948TissuePos

tag: trap fraction

tag: experiment

value: Sort Comparison

tag: inhibitors

tag: tissue


title: K104830_RNASeq

description:
transcriptome profile
K104830_RNASeq

value: High


title: GC071392_TATGCAGT-CTCTCTAC

description: smart-seq2 protocol


title: 948TissueInput

tag: genotype

tag: sort method

value: Tissue Homogenate (no sort)

value: TRAP Input

value: brain


title: 946OctoPos

value: Cell suspension (no sort)


title: K104797_RNASeq

description:
transcriptome profile
K104797_RNASeq


title: K104904_RNASeq

description:
transcriptome profile
K104904_RNASeq


title: DNA_METHYLATION_15-008/059_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/059
A10-177-43_TUMOR

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

tag: pathologic stage

tag: 5-year disease status

tag: sample type

value: cancer


title: 947OctoInput


title: 947OctoPos

value: TRAP Pos Fraction


title: 946TissueInput


title: GC071392_TATGCAGT-CGGAGCCT

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: K104934_RNASeq

description:
transcriptome profile
K104934_RNASeq

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: DNA_METHYLATION_15-008/058_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/058
A10-177-40_BENIGN

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

value: white

value: remission

value: normal

tag: tissue

value: prostate tissue


title: K104910_RNASeq

description:
transcriptome profile
K104910_RNASeq

value: Post

value: No

value: WHITE

value: Yes

value: Average


title: 946OctoInput

tag: genotype

tag: sort method

tag: trap fraction

value: TRAP Input

tag: experiment

value: Sort Comparison

tag: inhibitors

value: brain


title: K104591_RNASeq

description:
transcriptome profile
K104591_RNASeq

tag: age

tag: age of menarche

tag: menopausal status

tag: blood relatives cancer

value: High


title: GC071392_TATGCAGT-ATGCGCAG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: 945RTytoPos

value: Tyto FACS


title: DNA_METHYLATION_15-008/058_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/058
A10-177-41_TUMOR

value: prostate cancer

value: male

tag: gleason score

tag: race

tag: pathologic stage

tag: 5-year disease status

tag: sample type

value: cancer


title: DNA_METHYLATION_15-008/058_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/058
A10-171-48_BUFFYCOAT

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

value: white

tag: tissue

value: buffy coat


title: GC071392_TATGCAGT-ATCTCAGG

description: smart-seq2 protocol

value: Mus


title: 946TissuePos

tag: genotype

tag: sort method

value: Tissue Homogenate (no sort)

tag: trap fraction

value: TRAP Pos Fraction

tag: experiment

tag: inhibitors


title: GC071392_TATGCAGT-AGGCAGAA

description: smart-seq2 protocol

tag: timepoint


title: DNA_METHYLATION_15-008/057_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/057
A10-177-12_BENIGN

tag: age

value: remission

value: normal

value: prostate tissue


title: 945RTytoInput


title: DNA_METHYLATION_15-008/057_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/057
A10-178-39_TUMOR

tag: gleason score


title: DNA_METHYLATION_15-008/057_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/057
A10-171-47_BUFFYCOAT

tag: race


title: GC071392_TATGCAGT-CCTAAGAC

description: smart-seq2 protocol

tag: initially inactive x allele


title: DNA_METHYLATION_15-008/056_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/056
A10-177-38_BENIGN

tag: pathologic stage

tag: 5-year disease status


title: GC071392_TATGCAGT-CGAGGCTG

description: smart-seq2 protocol


title: GC071392_TATGCAGT-ACTCGCTA

description: smart-seq2 protocol


title: GC071392_TATGCAGT-ACTGAGCG

description: smart-seq2 protocol


title: K104780_RNASeq

description:
transcriptome profile
K104780_RNASeq

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


title: K104782_RNASeq

description:
transcriptome profile
K104782_RNASeq

value: High


title: GC071392_TATGCAGT-AAGAGGCA

description: smart-seq2 protocol


title: K104444_RNASeq

description:
transcriptome profile
K104444_RNASeq

value: Post

value: Average


title: K104335_RNASeq

description:
transcriptome profile
K104335_RNASeq


title: K104531-RNAseq (second donation from K102516)

description:
transcriptome profile
K104531_RNASeq


title: 945LFACSInput

tag: genotype

tag: sort method

value: FACSAria FACS

tag: trap fraction

value: TRAP Input

tag: experiment

value: Sort Comparison

tag: tissue

value: brain


title: DNA_METHYLATION_15-008/056_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/056
A10-177-39_TUMOR

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

tag: race

value: white

tag: age

tag: sample type

value: cancer


title: DNA_METHYLATION_15-008/056_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/056
A10-171-46_BUFFYCOAT

tag: pathologic stage

tag: 5-year disease status

value: remission

value: normal

value: buffy coat


title: K102516_RNASeq

description:
transcriptome profile
K102516_RNASeq

tag: age of menarche

tag: menopausal status

value: Pre

value: No

tag: blood relatives cancer

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)


title: 823LTytoInput

tag: genotype

tag: sort method

value: Tyto FACS

tag: trap fraction

tag: experiment

tag: inhibitors

tag: tissue


title: DNA_METHYLATION_15-008/055_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/055
A10-177-37_TUMOR

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

tag: race

value: unknown

tag: age

value: prostate tissue


title: 945LFACSPos

value: TRAP Pos Fraction


title: 822RTytoPos


title: 823LTytoPos


title: GC071392_TACTCCTT-TGCAGCTA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: K102424_RNASeq

description:
transcriptome profile
K102424_RNASeq

tag: age of menarche

tag: menopausal status

value: Post

tag: blood relatives cancer

value: Yes

value: WHITE

tag: hispanic

tag: bmi

tag: ever pregnant

tag: risk category

value: High


title: K102551_RNASeq

description:
transcriptome profile
K102551_RNASeq

tag: life time risk (tyrer-cuzick score)


title: DNA_METHYLATION_15-008/055_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/055
A10-177-36_BENIGN

tag: disease state

value: prostate cancer

value: male

tag: pathologic stage

tag: 5-year disease status

tag: sample type

tag: tissue


title: DNA_METHYLATION_15-008/053_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/053
A10-177-33_TUMOR

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

tag: race

value: black

value: cancer


title: K109027

description:
whole methylome (Methyl Capture)
K109027_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

tag: age

tag: age of menarche

tag: menopausal status


title: GC071392_TACTCCTT-TACGCTGC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: GC071392_TACTCCTT-TAGGCATG

description: smart-seq2 protocol


title: DNA_METHYLATION_15-008/055_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/055
A10-171-45_BUFFYCOAT

value: remission

value: normal


title: K109019

description:
whole methylome (Methyl Capture)
K109019_MeCap

value: Pre

tag: blood relatives cancer

tag: hispanic

tag: bmi

tag: ever pregnant

tag: risk category


title: GC071392_TACTCCTT-TCCTGAGC

description: smart-seq2 protocol


title: DNA_METHYLATION_15-008/053_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/053
A10-171-44_BUFFYCOAT

tag: disease state

tag: pathologic stage

tag: 5-year disease status

tag: sample type

value: buffy coat


title: 73AMTytoInput

tag: genotype

tag: sort method

value: Cd11b Microglia Microbeads AutoMACS to Tyto FACS

tag: trap fraction

value: TRAP Input

tag: experiment

value: Sort Comparison

tag: inhibitors

tag: tissue

value: brain


title: 822RTytoInput

value: Tyto FACS


title: DNA_METHYLATION_15-008/053_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/053
A10-177-32_BENIGN

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

tag: race

tag: age

value: prostate tissue


title: 73AMPos

value: Cd11b Microglia Microbeads AutoMACS

value: TRAP Pos Fraction


title: 73AMTytoPos


title: GC071392_TACTCCTT-TCGACGTC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: GC071392_TACTCCTT-TAGCGCTC

description: smart-seq2 protocol


title: DNA_METHYLATION_15-008/052_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/052
A10-180-8_TUMOR

tag: disease state

value: prostate cancer

value: white

tag: pathologic stage


title: GC071392_TACTCCTT-TAAGGCGA

description: smart-seq2 protocol


title: K108987

description:
whole methylome (Methyl Capture)
K108987_MeCap

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: Average


title: K108978

description:
whole methylome (Methyl Capture)
K108978_MeCap

value: Pre


title: 73AMInput

tag: genotype

tag: sort method

tag: trap fraction

tag: experiment

tag: inhibitors

tag: tissue


title: GC071392_TACTCCTT-GTAGAGGA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: K109011

description:
whole methylome (Methyl Capture)
K109011_MeCap

tag: age

tag: race

value: High


title: K108994

description:
whole methylome (Methyl Capture)
K108994_MeCap

tag: age of menarche

tag: menopausal status


title: 72AMPos


title: GC071392_TACTCCTT-GGAGCTAC

description: smart-seq2 protocol


title: DNA_METHYLATION_15-008/052_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/052
A10-171-43_BUFFYCOAT

tag: disease state

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type

value: normal

value: buffy coat


title: K108977 (second donation from K106845)

description:
whole methylome (Methyl Capture)
K108977_MeCap

tag: blood relatives cancer

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: GC071392_TACTCCTT-GGACTCCT

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: 69RTytoPos

tag: genotype

tag: sort method

value: Tyto FACS

tag: trap fraction

tag: experiment

value: Sort Comparison

tag: inhibitors

tag: tissue

value: brain


title: 72AMInput

value: Cd11b Microglia Microbeads AutoMACS

value: TRAP Input


title: DNA_METHYLATION_15-008/051_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/051
A10-177-30_TUMOR

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

tag: race

value: unknown

tag: pathologic stage

tag: age

value: cancer

value: prostate tissue


title: GC071392_TACTCCTT-GCTCATGA

description: smart-seq2 protocol

value: Mus


title: 69RTytoInput


title: DNA_METHYLATION_15-008/052_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/052
A10-177-31_BENIGN

value: white

tag: 5-year disease status

tag: sample type


title: K108959

description:
whole methylome (Methyl Capture)
K108959_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: GC071392_TACTCCTT-GCGTAGTA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: K108928 (second donation from K106620)

description:
whole methylome (Methyl Capture)
K108928_MeCap

value: Pre

value: AFRNAMER


title: GC071392_TACTCCTT-CTCTCTAC

description: smart-seq2 protocol


title: 67AMTytoPos

tag: genotype

tag: sort method

value: Cd11b Microglia Microbeads AutoMACS to Tyto FACS

tag: trap fraction

value: TRAP Pos Fraction

tag: experiment

value: Sort Comparison

tag: inhibitors

tag: tissue


title: 67AMTytoInput

value: TRAP Input

value: brain


title: K108912 (second donation from K106507)

description:
whole methylome (Methyl Capture)
K108912_MeCap

tag: age

tag: race


title: K108919

description:
whole methylome (Methyl Capture)
K108919_MeCap

tag: age of menarche

tag: menopausal status


title: DNA_METHYLATION_15-008/050_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/050
A10-177-28_TUMOR

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

value: unknown

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type


title: DNA_METHYLATION_15-008/051_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/051
A10-177-29_BENIGN

value: normal

value: prostate tissue


title: DNA_METHYLATION_15-008/051_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/051
A10-171-42_BUFFYCOAT

value: buffy coat


title: GC071392_TACTCCTT-CGAGGCTG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: 69LFACSInput

tag: genotype

tag: sort method

value: FACSAria FACS

tag: trap fraction

tag: experiment


title: K108899 (second donation from K106157)

description:
whole methylome (Methyl Capture)
K108899_MeCap

tag: age

value: Post

value: No

tag: blood relatives cancer

value: Don‚Äôt know

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: 69LFACSPos

value: TRAP Pos Fraction

value: Sort Comparison

tag: inhibitors

tag: tissue


title: K108921 (second donation from K106801)

description:
whole methylome (Methyl Capture)
K108921_MeCap

tag: age of menarche

tag: menopausal status


title: DNA_METHYLATION_15-008/050_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/050
A10-177-3_BENIGN

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

tag: pathologic stage

tag: 5-year disease status

tag: sample type


title: GC071392_TACTCCTT-CGTACTAG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: K108890

description:
whole methylome (Methyl Capture)
K108890_MeCap

tag: age

value: Pre

tag: blood relatives cancer

tag: race

tag: hispanic

tag: bmi

tag: ever pregnant


title: 66AMTytoInput

tag: genotype

tag: sort method

value: Cd11b Microglia Microbeads AutoMACS to Tyto FACS

tag: trap fraction

value: TRAP Input

tag: experiment

tag: inhibitors

tag: tissue

value: brain


title: GC071392_TACTCCTT-CGGAGCCT

description: smart-seq2 protocol


title: DNA_METHYLATION_15-008/048_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/048
A10-177-25_BENIGN

tag: disease state

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

value: unknown

tag: pathologic stage

value: recurrence

value: normal

value: prostate tissue


title: K108883

description:
whole methylome (Methyl Capture)
K108883_MeCap

tag: age

tag: age of menarche

tag: menopausal status

value: Post

value: No

tag: blood relatives cancer

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: High


title: 66AMTytoPos

tag: genotype

tag: sort method


title: K108895

description:
whole methylome (Methyl Capture)
K108895_MeCap

value: Yes

tag: race

value: WHITE

tag: hispanic

tag: bmi

tag: ever pregnant


title: GC071392_TACTCCTT-CGATCAGT

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: 67AMPos

value: Cd11b Microglia Microbeads AutoMACS

tag: trap fraction

value: TRAP Pos Fraction

tag: experiment

value: Sort Comparison

tag: inhibitors

tag: tissue


title: GC071392_TACTCCTT-ATGCGCAG

description: smart-seq2 protocol


title: DNA_METHYLATION_15-008/050_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/050
A10-171-41_BUFFYCOAT

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

tag: pathologic stage

tag: age

tag: 5-year disease status

value: remission

tag: sample type

value: buffy coat


title: GC071392_TACTCCTT-CCTAAGAC

description: smart-seq2 protocol


title: GC071392_TACTCCTT-ACTCGCTA

description: smart-seq2 protocol


title: DNA_METHYLATION_15-008/047_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/047
A10-178-38_TUMOR

value: male

tag: race

value: white

value: cancer


title: 67AMInput

tag: genotype

tag: sort method

value: TRAP Input

value: brain


title: 992RFACSInput

value: FACSAria FACS


title: 66AMPos


title: DNA_METHYLATION_15-008/048_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/048
A10-177-26_TUMOR

value: unknown

value: recurrence

value: prostate tissue


title: K108958

description:
whole methylome (Methyl Capture)
K108958_MeCap

tag: age of menarche

tag: menopausal status

value: Pre

value: No

tag: blood relatives cancer

value: Yes

value: AFRNAMER

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: High


title: DNA_METHYLATION_15-008/045_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/045
A10-177-21_BENIGN

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

tag: preoperative psa

value: normal

tag: tissue


title: GC071392_TACTCCTT-AGGCAGAA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: DNA_METHYLATION_15-008/045_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/045
A10-177-22_TUMOR

value: male

tag: gleason score

tag: race

tag: pathologic stage

tag: age

tag: 5-year disease status

value: remission

tag: sample type


title: 991RTytoPos

tag: genotype

tag: sort method

value: Tyto FACS

tag: trap fraction

value: TRAP Pos Fraction

tag: experiment

value: Sort Comparison

tag: inhibitors


title: DNA_METHYLATION_15-008/048_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/048
A10-171-40_BUFFYCOAT

tag: disease state

tag: patientid

value: buffy coat


title: K108885

description:
whole methylome (Methyl Capture)
K108885_MeCap

tag: age of menarche

tag: menopausal status

tag: blood relatives cancer

value: WHITE

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: Average


title: DNA_METHYLATION_15-008/047_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/047
A10-177-10_BENIGN

tag: gender

tag: preoperative psa

tag: gleason score

tag: race

value: white

tag: pathologic stage

tag: age

tag: 5-year disease status

tag: tissue

value: prostate tissue


title: GC071392_TAAGGCTC-TGCAGCTA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: K108879

description:
whole methylome (Methyl Capture)
K108879_MeCap

tag: age of menarche

tag: menopausal status

value: Pre

value: No


title: 66AMInput

tag: genotype

tag: sort method

value: Cd11b Microglia Microbeads AutoMACS

tag: trap fraction

value: TRAP Input

tag: experiment

tag: inhibitors

value: brain


title: DNA_METHYLATION_15-008/045_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/045
A10-171-38_BUFFYCOAT

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

tag: sample type

value: normal


title: 992RFACSPos

value: FACSAria FACS


title: GC071392_TACTCCTT-ACTGAGCG

description: smart-seq2 protocol

value: Mus


title: K108859 (second donation from K106609)

description:
whole methylome (Methyl Capture)
K108859_MeCap

tag: blood relatives cancer

tag: race

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: DNA_METHYLATION_15-008/047_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/047
A10-171-39_BUFFYCOAT

value: male

tag: preoperative psa

tag: gleason score

tag: pathologic stage

tag: age

tag: 5-year disease status

value: remission

tag: tissue


title: DNA_METHYLATION_15-008/043_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/043
A10-177-17_BENIGN

tag: disease state

value: recurrence


title: GC071392_TACTCCTT-ATCTCAGG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: GC071392_TACTCCTT-AAGAGGCA

description: smart-seq2 protocol


title: K108874

description:
whole methylome (Methyl Capture)
K108874_MeCap

tag: age of menarche

tag: menopausal status

value: Post

value: Yes


title: GC071392_TAAGGCTC-TAGGCATG

description: smart-seq2 protocol


title: 4wks-A7988

city: La Jolla

first: Zhibo

last: Ma

state: California

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

data_processing:
The raw sequencing data from each mouse was first processed separately in Cell Ranger 4.0.0 using a customized reference based on refdata-gex-mm10-2020-A-R26 to allow quantification of EGFP expression. The EGFP reporter transgene was added to the refdata-gex-mm10-2020-A-R26 reference and rebuilt by running cellranger mkref with default parameters (10x Genomics).
The filtered gene-by-cell count matrices from 10x cellranger were further QCed and analyzed in R package Seurat (v3.2.3). Each library was processed separately in Seurat with NormalizeData(normalization.method = "LogNormalize") function. The normalized data were further linear transformed by ScaleData() function prior to dimension reduction. Principal components analysis (PCA) was performed on the scaled data by only using the most variable 2000 genes (identified using the default “vst” method). Cell were examined across all clusters to determine the low quality cell threshold that accommodates the variation between celltypes. Low quality cells were removed with the same filtering parameters across libraries (percent.mt <=6 & nCount_RNA >= 1000). QCed dataset were reprocessed as described above and clusters were labeled with cell types based on marker gene expression and previously published scRNAseq derived gene signatures in pancreas. Doublets were marked using the doubetFinder R package (largely consistent with the results from Scrublet package) and removed. Two Small clusters of cells with high percentage of inferred doublets label, high number of UMI counts, and shared expression of marker genes were also removed as doublets. QCed meged dataset is stored in the processed data file (Feature_Barcode_rawCountMatrix_Merged_all-samples_QCed.csv)
The union of the most variable 1500 genes from each sample was used as integration features for fastMNN. The first 45 MNN principal components were used in UMAP embedding and cluster identification. EYFP negative clusters of stromal contamination were removed and the epithelium population was further filtered with EYFP transcript to only keep 13362 EYFP+ cells (detectable EYFP transcripts) for downstream analysis. Raw gene-cell count matrix from this filtered EYFP+ subset is stored in the processed data files (Feature_Barcode_rawCountMatrix_Filtered-YFP+_all-samples_QCed.csv).
Tuft and Enteroendocrine cells were subset from the EYFP+ population. One small population of doublets were evident and was removed from the subsequent analysis for tuft+eec subset. Filtered raw gene-cell count matrix for this tuft+eec subset is stored in the processed data files(Feature_Barcode_rawCountMatrix_Tuft+EEC_all-samples_QCed.csv).
Meta data of cluster labels and celltype labels of this analysis are also included in the processed data files
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts per gene per cell

source_name: Pancreata

growth_protocol: mice were maintained in a specified-pathogen-free barrier facility under a 12-hour light cycle.

extract_protocol:
EYFP+ cells were isolated from lineage-traced populations in the pancreata of caerulein-treated mice. The pancreas was quickly dissected and minced in HBSS. Supernatant and fat were removed and pancreatic tissue was then incubated in 10 ml DMEM supplemented with 1 mg/ml collagenase I (Sigma), 1 mg/ml soybean trypsin inhibitor (Gibco), 0.5-1 mg/ml hyaluronidase (Sigma), and 250 ml of DNAse I, shaking gently at 37°C for a maximum of 30 min.  Digestion was monitored and tissue was further digested mechanically by pipetting. Digested tissue was passed through a 100 mm filter, washed with PBS containing 1 mM EDTA and 0.5% BSA, and incubated with ACK lysing buffer (Gibco) to remove red blood cells. Single cell suspensions were incubated on ice with DAPI (molecular probes, 1:1000), used to exclude dead cells. EYFP+ cells were FACS purified at the Salk Institute’s Flow Cytometry core facility on a BD Biosciences Influx and an Aria Fusion cell sorter (100-µm size nozzle, 1 x PBS sheath buffer with sheath pressure set to 20 PSI). Cells were sorted in 1-drop Single Cell sort mode for counting accuracy.
10x Genomics 3' single cell gene expression: FACS-isolated YFP+ cells were loaded onto a microfluidic chip with barcoded beads according to 10X Chromium Next GEM Single Cell 3’ (v3.1, Catalog # 1000128, 10x Genomics Inc.). Subsequent cell lysis, first strand cDNA synthesis and amplification were carried out according to the 10X v3.1 protocol, with cDNA amplification set for 11 cycles. Following sample indexing and bead-based library purification, the final library size distribution and concentration were measured using TapeStation (Agilent Biosystems) and Qubit (ThermoFisher). The libraries were pooled in equal molar ratio and sequenced on Illumina NovaSeq 6000.

treatment_protocol: Acinar cells were labeled with daily tamoxifen treatment (Sigma, 5 mg/day, 5 days/week for two weeks) delivered in corn oil (Sigma) by oral gavage. followed by inducing pancreatitis with caerulein (Bachem) administered intraperitoneally (IP) at 250 mg/kg, twice a day, for five days a week and then allowed to recover for two days for either two or four weeks .

tag: strain

value: Backcrossed into CD-1

tag: genotype

value: 10 weeks at the time of injury induction

tag: treatment

value: 4 weeks of caerulein treatment

value: pancreas

tag: cell type

value: sorted EYFP+ pancreas cells


title: 4wks-A7933


title: 991RTytoInput

tag: sort method

value: Tyto FACS

tag: trap fraction

tag: experiment

value: Sort Comparison

tag: inhibitors


title: K108587

description:
whole methylome (Methyl Capture)
K108587_MeCap

value: Pre

value: No

tag: blood relatives cancer

value: Don‚Äôt know

tag: race

value: ASIAN

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: Average


title: K108865

description:
whole methylome (Methyl Capture)
K108865_MeCap

tag: age

tag: age of menarche

value: WHITE


title: DNA_METHYLATION_15-008/043_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/043
A10-177-18_TUMOR

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: cancer

tag: tissue

value: prostate tissue


title: DNA_METHYLATION_15-008/043_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/043
A10-171-37_BUFFYCOAT

tag: race

value: recurrence

value: normal

value: buffy coat


title: DNA_METHYLATION_15-008/042_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/042
A10-171-36_BUFFYCOAT

value: remission


title: K108860 (second donation from K105906)

description:
whole methylome (Methyl Capture)
K108860_MeCap

tag: menopausal status

tag: blood relatives cancer

value: Yes

tag: hispanic

value: High


title: GC071392_TAAGGCTC-TAAGGCGA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: GC071392_TAAGGCTC-TCGACGTC

description: smart-seq2 protocol


title: P19 cells-Baf45d siRNA transfection-RA treated-2

city: Hefei

first: Chao

last: Liu

state: Anhui

address: 81 Meishan Road

department: Histology and Embryology

country: China

institute: Anhui Medical University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house per l scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
For DESeq2 with biological replicates, differential expression analysis of two conditions/groups (three biological replicates per condition/groups) was performed using the DESeq2 R package (1.16.1).
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the cluster Profiler R package, in which gene length bias was corrected. GO terms with corrected P-value less than 0.05 were considered significantly enriched by differential expressed genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.
Gene Set Enrichment Analysis (GSEA) is a computational approach to determine if a pre-defined Gene Set can show a significant consistent difference between two biological states. The genes were ranked according to the degree of differential expression in the two samples, and then the predefined Gene Set were tested to see if they were enriched at the top or bottom of the list. Gene set enrichment analysis can include subtle expression changes.
Genome_build: mm9

source_name: P19 cells

growth_protocol: P19 cells were replated at a density of 2.5 × 105 cells/well and cultured overnight in Dulbecco's modified Eagle's medium (DMEM, HyClone) containing 10 % foetal bovine serum (BI) supplemented with 50 units per millilitre penicillin and 50 µg per millilitre streptomycin under 5 % CO2 in a humidified incubator.

extract_protocol:
RNA of the derived cells were harvested with TRIzol (Invitrogen).
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: P19 cells were replated at a density of 2.5 × 105 cells/well and cultured overnight in Dulbecco's modified Eagle's medium (DMEM, HyClone) containing 10% foetal bovine serum (BI) supplemented with 50 units per millilitre penicillin and 50 µg per millilitre streptomycin under 5% CO2 in a humidified incubator. The next morning, cells were washed with Opti-MEM (Invitrogen) and then transiently transfected with negative control (NC) siRNA, gapdh siRNA and baf45d siRNA (BAF45D) (Genepharma, Shanghai) using Lipofectamine 2000 reagent (Invitrogen) in Opti-MEM without serum. The same volume of alpha-MEM containing 10% foetal bovine serum was added to the culture media 6 h after transfection. The cells were harvested for IB assay at 72 h after transfection or subjected to further analysis. P19 cells from the NC siRNA and BAF45D siRNA groups (three biological replicates per group) were subjected to RA-induced differentiation for 5 days and treated with TRIzol (Invitrogen).

tag: cell lines

tag: chemicals

value: RA(all trans retinoic acid)

tag: sirnas


title: GC071392_TAAGGCTC-GGAGCTAC

description: smart-seq2 protocol


title: GC071392_TAAGGCTC-TCCTGAGC

description: smart-seq2 protocol


title: DNA_METHYLATION_15-008/042_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/042
A10-177-16_TUMOR

tag: disease state

tag: patientid

tag: age


title: 2wks-A7638

tag: strain

value: Backcrossed into CD-1

tag: genotype

value: 10 weeks at the time of injury induction

tag: treatment

value: 2 weeks of caerulein treatment

value: pancreas

tag: cell type

value: sorted EYFP+ pancreas cells


title: P19 cells-NC siRNA transfection-RA treated-3

value: NC(Negative control)


title: GC071392_TAAGGCTC-TAGCGCTC

description: smart-seq2 protocol


title: 2wks-A8324

tag: tissue


title: GC071392_TAAGGCTC-GGACTCCT

description: smart-seq2 protocol


title: DNA_METHYLATION_15-008/040_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/040
A12-3-14_TUMOR

value: prostate cancer

tag: gender

value: male

tag: preoperative psa

tag: gleason score

tag: race

value: black

tag: pathologic stage

tag: 5-year disease status

tag: sample type


title: DNA_METHYLATION_15-008/039_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/039
A10-176-29_TUMOR

value: white

value: cancer

value: prostate tissue


title: K108838

description:
whole methylome (Methyl Capture)
K108838_MeCap

tag: age of menarche

tag: menopausal status

value: Pre

value: No

tag: blood relatives cancer

value: WHITE

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: K108482

description:
whole methylome (Methyl Capture)
K108482_MeCap

tag: age

value: ASIAN

value: Average


title: P19 cells-Baf45d siRNA transfection-RA treated-3

tag: cell lines

tag: chemicals

value: RA(all trans retinoic acid)

tag: sirnas


title: K108518

description:
whole methylome (Methyl Capture)
K108518_MeCap

value: AFRNAMER

value: Yes


title: DNA_METHYLATION_15-008/042_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/042
A10-177-15_BENIGN

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

value: remission

value: normal

tag: tissue


title: GC071392_TAAGGCTC-GCTCATGA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: P19 cells-Baf45d siRNA transfection-RA treated-1


title: GC071392_TAAGGCTC-GTAGAGGA

description: smart-seq2 protocol


title: DNA_METHYLATION_15-008/040_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/040
A10-176-30_BENIGN

value: prostate cancer

tag: race

tag: pathologic stage

tag: 5-year disease status

tag: sample type


title: DNA_METHYLATION_15-008/039_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/039
A10-177-2_BENIGN

value: male


title: DNA_METHYLATION_15-008/040_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/040
A10-171-35_BUFFYCOAT

value: black

value: buffy coat


title: K108194

description:
whole methylome (Methyl Capture)
K108194_MeCap

tag: age of menarche

tag: menopausal status

value: Post

tag: blood relatives cancer

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: K108501 (second donation from K107244)

description:
whole methylome (Methyl Capture)
K108501_MeCap

tag: age


title: K108839

description:
whole methylome (Methyl Capture)
K108839_MeCap


title: P19 cells-NC siRNA transfection-RA treated-1

tag: cell lines

tag: chemicals

tag: sirnas

value: NC(Negative control)


title: GC071392_TAAGGCTC-GCGTAGTA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: K108168

description:
whole methylome (Methyl Capture)
K108168_MeCap

value: Pre

tag: race

value: High


title: VAM1 CMAF 8

city: NEW YORK

first: Hernandez

last: Moura Silva

state: NY

address: 430 E 29th street. 4th floor, Lab 460A

department: Kimmel Center for Biology and Medicine at the Skirball Institute

institute: New York University Langone Medical Center

description: VAM1-CMAF KO 3

data_processing:
Illumina sequencing adapters and reads with Phred quality scores lower than 20 were removed with Trimmomatic. Trimmed reads were mapped to the Mus musculus genome Ensembl annotation release 91 using STAR v2.5.3a with default settings. The number of reads uniquely mapping to each gene feature in the corresponding annotation file was determined using featureCounts. The resulting count tables were passed to R for further analyses.
Differential expression and gene ontology analyses. Consistency between replicates was checked using principal component analysis (PCA) and Euclidean distance-based hierarchical clustering on normalized counts. Weakly expressed genes, defined as having less than 2 Fragment Per Kilobase of transcript per Million mapped reads (FPKM) in at least one group of replicates were removed from differential expression analysis. Counts normalization were performed using the method of Trimmed Mean of M-values (TMM) from edgeR package. Differential expression analyses were performed using limma. Genes were considered significant when the observed log2 fold-change was greater than 1 and the adjusted P value was less than 0.05. The set of significant genes for each contrast of interest was passed to Goseq for functional gene categories enrichment analyses.
Genome_build: mm10
Supplementary_files_format_and_content: xlsx; It contains all normalized read counts for each gene for each subpopulation replicate. The table contains the gene symbol

source_name: epididymal white adipose tissue

extract_protocol:
To isolate leukocytes from adipose tissue mice were anesthetized with a mixture containing 12.5mg/mL ketamine, 2.5mg/mL xylazine, and 25 mg/mL acepromazine and intracardially perfused with PBS with 5 mM EDTA. After dissection, the eWAT was minced and incubated for 35 min at 37oC under gentle agitation (150rpm) in cRPMI (2% BSA FFA-free [Fisher BP9704100], 1mM of Sodium Pyruvate [Gibco, 11360-070], Glutamax 1x [Gibco, 35050-061], MEM non-essential amino acids [Gibco, 11140-050], Hepes [Gibco, 15630-080], Pen Strep [Gibco, 15140-122] and RPMI [Gibco, 21870-076]) containing 1mg/mL of collagenase type VIII (Sigma-Aldrich, C2139) and 100ug/mL of DNase I (Sigma-Aldrich, 10104159001). After digestion, the suspension was washed with ice-cold cRPMI and spun down. The floating fat layer was removed and the leukocyte-enriched pellet was ressuspended in cRPMI and filtered through a 100 μm cell strainer.
Total RNA from sorted target cell populations was isolated using TRIzol LS (Invitrogen; 10296010) followed by DNase I (Qiagen, 79254) treatment and cleanup with RNeasy Plus Micro kit (Qiagen, 74034). RNA quality was assessed using pico bioanalyser chips (Agilent, 5067-1513). Only RNAs displaying a RNA integrity number (RIN) of 9 or higher were used for downstream procedures. RNAseq libraries were prepared using the Nugen Ovation Trio low input RNA Library Systems V2 (Nugen; 0507-08) according to the manufacturer’s instructions by the NYU Genome Technology Center. Pooled libraries were sequenced as 50 nucleotide, paired-end reads on an Illumina NovaSeq6000 using v4 chemistry.

tag: diet

value: Normal Chow

tag: genotype

value: Lyve1 CRE/+ x CMAF FLOX/FLOX

value: 16 weeks old

tag: strain


title: P19 cells-NC siRNA transfection-RA treated-2

value: RA(all trans retinoic acid)


title: GC071392_TAAGGCTC-TACGCTGC

description: smart-seq2 protocol


title: VAM1 CMAF 5

description: VAM1-CMAF KO 1


title: K108433

description:
whole methylome (Methyl Capture)
K108433_MeCap

tag: age of menarche

tag: menopausal status

value: No

value: WHITE


title: K108206

description:
whole methylome (Methyl Capture)
K108206_MeCap

tag: blood relatives cancer

tag: hispanic

value: Yes

value: Average


title: DNA_METHYLATION_15-008/039_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/039
A10-171-34_BUFFYCOAT

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

value: white

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type

value: normal

tag: tissue


title: GC071392_TAAGGCTC-CGAGGCTG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: K108105

description:
whole methylome (Methyl Capture)
K108105_MeCap

tag: age

tag: race

value: AFRNAMER

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: GC071392_TAAGGCTC-CGATCAGT

description: smart-seq2 protocol


title: K108301

description:
whole methylome (Methyl Capture)
K108301_MeCap

tag: age of menarche

tag: menopausal status

tag: blood relatives cancer

value: AMINALNA

tag: hispanic


title: DNA_METHYLATION_15-008/037_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/037
A10-171-32_BUFFYCOAT

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

value: unknown

value: buffy coat


title: VAM1 WT 7

description:
Littermate controls of samples 4,5,6
VAM1-WT-3

tag: diet

value: Normal Chow

tag: genotype

value: WT x CMAF FLOX/FLOX

tag: strain

value: C57BL/6J (JAX Stock#:0664)


title: K108158

description:
whole methylome (Methyl Capture)
K108158_MeCap

tag: age

value: Post

value: No

tag: race

value: High


title: GC071392_TAAGGCTC-CGGAGCCT

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: DNA_METHYLATION_15-008/038_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/038
A10-171-33_BUFFYCOAT

value: black

tag: pathologic stage

tag: 5-year disease status

tag: sample type

tag: tissue


title: DNA_METHYLATION_15-008/038_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/038
A12-3-13_TUMOR

value: cancer

value: prostate tissue


title: K108059 (second donation from K107241)

description:
whole methylome (Methyl Capture)
K108059_MeCap

tag: age of menarche

tag: menopausal status

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: DNA_METHYLATION_15-008/037_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/037
A10-176-54_TUMOR

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

value: remission


title: VAM1 WT 1

description:
Littermate controls of samples 4,5,6
VAM1-WT-1

tag: diet

tag: genotype

tag: age

value: 16 weeks old

tag: strain


title: K108035

description:
whole methylome (Methyl Capture)
K108035_MeCap

tag: age of menarche

value: Pre

tag: race


title: DNA_METHYLATION_15-008/038_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/038
A12-3-12_BENIGN

value: prostate cancer

value: male

tag: pathologic stage

tag: 5-year disease status

tag: sample type

value: normal

tag: tissue


title: K108129

description:
whole methylome (Methyl Capture)
K108129_MeCap

tag: menopausal status

tag: blood relatives cancer

value: AFRNAMER

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)


title: VAM1 CMAF 6

description: VAM1-CMAF KO 2

value: Normal Chow

value: Lyve1 CRE/+ x CMAF FLOX/FLOX


title: VAM1 WT 2

description:
Littermate controls of samples 4,5,6
VAM1-WT-2

value: WT x CMAF FLOX/FLOX

value: C57BL/6J (JAX Stock#:0664)


title: GC071392_TAAGGCTC-ATCTCAGG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: GC071392_TAAGGCTC-CTCTCTAC

description: smart-seq2 protocol


title: DNA_METHYLATION_15-008/037_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/037
A12-3-11_BENIGN

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

value: unknown


title: GC071392_TAAGGCTC-CGTACTAG

description: smart-seq2 protocol


title: DNA_METHYLATION_15-008/036_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/036
A12-3-9_TUMOR

tag: race

value: white

tag: pathologic stage

tag: age

value: cancer

value: prostate tissue


title: Young scRNAseq

city: Boulder

first: Chi

last: Zhang

state: Colorado

address: 347 UCB

department: MCDB

institute: University of Colorado Boulder

description: single cell RNAseq version 3.0

data_processing:
Fastq files were acquired from illumina sequencing facility
For single cell RNAseq, the reads were processed using cell ranger 3.0.1
Genome_build: mm10
Supplementary_files_format_and_content: barcodes, matrix and feature files

source_name: Epidermal lineages

extract_protocol:
Mice at appropiate age were euthenized. Back skin is dissectd and digested with Collagenase and Trypsin to get single cell suspension. Epidermal cells were sorted based on specific cell surface markers and endogenous fluorescent markers.
For single cell RNAseq, we use 10xgenomics single cell RNAseq vesion 3 protocol.

treatment_protocol: K14Cre mediated Foxc1 Nfatc1 double knockout epidermis, control epidermis and aging epidermis

tag: strain

tag: tissue

value: back skin

value: Post natal day 53


title: GC071392_TAAGGCTC-CCTAAGAC

description: smart-seq2 protocol


title: P38Ctrl

description: single cell RNAseq version 3.0

value: Post natal day 38


title: K108074

description:
whole methylome (Methyl Capture)
K108074_MeCap

tag: age of menarche

tag: menopausal status

value: Post

value: No

tag: blood relatives cancer

value: Yes

tag: risk category

value: Average


title: GC071392_TAAGGCTC-ATGCGCAG

description: smart-seq2 protocol


title: DNA_METHYLATION_15-008/035_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/035
A12-3-8_TUMOR

value: prostate cancer

value: male

tag: 5-year disease status

value: remission

tag: sample type


title: GC071392_TAAGGCTC-AGGCAGAA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: P38_Foxc1/Nfatc1_dKO

description: single cell RNAseq version 3.0


title: DNA_METHYLATION_15-008/035_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/035
A12-3-7_BENIGN

tag: disease state

tag: patientid

value: normal


title: K108078

description:
whole methylome (Methyl Capture)
K108078_MeCap

value: Pre

value: WHITE

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

value: High


title: dCtrl2

data_processing:
Fastq files were acquired from illumina sequencing facility
Sequencing reads were tirmmed for adaptors and test quanlity with fastqc. The trimmed reads were then mapped to mouse genome mm10 using hisat2 with parameters -p 32 --rna-strandness RF
The mapped sam files were then converted to bam files, then sorted and indexed.
The sorted bam files were then counted using htseq-count with parameter -t exon -i gene_id --stranded=reverse -f bam
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited count file

source_name: Back skin hair follicle

extract_protocol:
Mice at appropiate age were euthenized. Back skin is dissectd and digested with Collagenase and Trypsin to get single cell suspension. HFSCs were sorted based on specific cell surface markers and endogenous fluorescent markers.
NEBNext® Ultra™ Directional RNA Library Prep Kit is used for library construction.

treatment_protocol: For K15CrePR samples, mice were treated with tamoxifen for 6 days from P22 till P28 and then collect samples at P30.

tag: age

value: Post natal day 30


title: K108029

description:
whole methylome (Methyl Capture)
K108029_MeCap

tag: race


title: K108015

description:
whole methylome (Methyl Capture)
K108015_MeCap


title: dCtrl1

tag: strain

tag: tissue


title: dKO2


title: GC071392_TAAGGCTC-AAGAGGCA

description: smart-seq2 protocol

value: Mus


title: GC071392_CTTAATAG-TGCAGCTA

description: smart-seq2 protocol


title: DNA_METHYLATION_15-008/036_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/036
A10-171-31_BUFFYCOAT

tag: gender

tag: preoperative psa

tag: gleason score

value: white

tag: pathologic stage

value: buffy coat


title: Old_scRNAseq

description: single cell RNAseq version 3.0

value: back skin

value: 24month old


title: GC071392_TAAGGCTC-ACTGAGCG

description: smart-seq2 protocol


title: dKO1


title: GC071392_TAAGGCTC-ACTCGCTA

description: smart-seq2 protocol


title: DNA_METHYLATION_15-008/035_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/035
A10-171-30_BUFFYCOAT

tag: 5-year disease status

tag: sample type


title: K107962

description:
whole methylome (Methyl Capture)
K107962_MeCap

tag: age of menarche

tag: menopausal status

tag: blood relatives cancer

tag: risk category


title: K107980

description:
whole methylome (Methyl Capture)
K107980_MeCap

value: ASIAN

tag: hispanic

tag: bmi


title: K107981

description:
whole methylome (Methyl Capture)
K107981_MeCap

value: No

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)


title: DNA_METHYLATION_15-008/036_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/036
A12-3-10_BENIGN

tag: disease state

tag: patientid

tag: race

tag: age

value: prostate tissue


title: K107964

description:
whole methylome (Methyl Capture)
K107964_MeCap

value: Post

value: Yes

value: Average


title: Nfatc1 Ctrl2

tag: strain

tag: tissue


title: DNA_METHYLATION_15-008/033_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/033
A12-3-6_TUMOR

value: prostate cancer

tag: gender

value: male

tag: preoperative psa

tag: gleason score

tag: pathologic stage

value: remission

value: cancer


title: GC071392_CTTAATAG-TCCTGAGC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: GC071392_CTTAATAG-TCGACGTC

description: smart-seq2 protocol


title: DNA_METHYLATION_15-008/033_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/033
A12-3-5_BENIGN

tag: 5-year disease status

tag: sample type

value: normal


title: K107928

description:
whole methylome (Methyl Capture)
K107928_MeCap

tag: age of menarche

tag: menopausal status

value: Pre

tag: blood relatives cancer

value: WHITE

tag: hispanic

tag: bmi

tag: risk category

value: High


title: Nfatc1 Ctrl1

tag: age

value: Post natal day 30


title: Nfatc1 cKO2

tag: strain

value: back skin


title: DNA_METHYLATION_15-008/033_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/033
A10-171-29_BUFFYCOAT

tag: disease state

tag: patientid

tag: race

value: white

tag: tissue

value: buffy coat


title: GC071392_CTTAATAG-TAGGCATG

description: smart-seq2 protocol

value: Mus


title: K107731

description:
whole methylome (Methyl Capture)
K107731_MeCap

value: No

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)


title: GC071392_CTTAATAG-TACGCTGC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: GC071392_CTTAATAG-GTAGAGGA

description: smart-seq2 protocol


title: K107661

description:
whole methylome (Methyl Capture)
K107661_MeCap


title: DNA_METHYLATION_15-008/032_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/032
A10-171-28_BUFFYCOAT

tag: gender

tag: preoperative psa

tag: gleason score

tag: pathologic stage

tag: 5-year disease status

tag: sample type


title: DNA_METHYLATION_15-008/032_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/032
A10-176-22_BENIGN

value: prostate tissue


title: K107842 (second donation from K107545)

description:
whole methylome (Methyl Capture)
K107842_MeCap

tag: age of menarche

tag: menopausal status

value: Post

tag: blood relatives cancer

value: AFRNAMER

tag: hispanic

tag: bmi

value: Yes

tag: risk category


title: K107863 (second donation from K105898)

description:
whole methylome (Methyl Capture)
K107863_MeCap

tag: age

tag: race

value: Average


title: dKO_scATAC

description: ATAC

data_processing:
Fastq files were acquired from illumina sequencing facility
For bulk ATACseq, the reads were mapped to mouse genome using bowtie2 with paratmeters -p 18 -q --local. Then we remove the mitochondrial DNA. The sam files were then converted to bamfiles. After we remove duplicates from sorted and indexed bamfiles, peak calling was done by macs2 with parameters -f BAM -g mm --nomodel -q 1e-5.
For single cell ATACseq, the reads were processed using cell ranger atac mm10 1.0.1
Genome_build: mm10
Supplementary_files_format_and_content: Peak file and fragment file

extract_protocol:
Mice at appropiate age were euthenized. Back skin is dissectd and digested with Collagenase and Trypsin to get single cell suspension. HFSCs were sorted based on specific cell surface markers and endogenous fluorescent markers.
For bulk HFSC ATACseq, we were following Nextera DNA Sample Preparation Kit, Illumina. For single cell ATACseq, we use 10xgenomics single cell ATACseq protocol.

treatment_protocol: K14Cre mediated Foxc1 Nfatc1 double knockout and control epidermal cells

tag: strain

tag: tissue

value: Post natal day 28


title: Ctrl_scATAC

description: ATAC


title: K107894 (second donation from K107266)

description:
whole methylome (Methyl Capture)
K107894_MeCap

value: Don‚Äôt know

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)


title: Bulk_HFSC1

description: ATAC

source_name: HFSC


title: Nfatc1 cKO1


title: DNA_METHYLATION_15-008/032_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/032
A10-176-50_TUMOR

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

value: remission

value: cancer


title: GC071392_CTTAATAG-TAGCGCTC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: GC071392_CTTAATAG-TAAGGCGA

description: smart-seq2 protocol


title: DNA_METHYLATION_15-008/030_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/030
A10-171-27_BUFFYCOAT

tag: gleason score

tag: pathologic stage

tag: 5-year disease status

tag: sample type

value: normal


title: Bulk_HFSC2

description: ATAC

value: back skin

value: Post natal day 30


title: DNA_METHYLATION_15-008/030_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/030
A12-3-4_TUMOR

value: white


title: K107659

description:
whole methylome (Methyl Capture)
K107659_MeCap

tag: age of menarche

tag: menopausal status

tag: blood relatives cancer

tag: hispanic

tag: bmi

tag: risk category


title: DNA_METHYLATION_15-008/030_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/030
A10-176-20_BENIGN

tag: race

tag: age

tag: tissue


title: K107713

description:
whole methylome (Methyl Capture)
K107713_MeCap

value: Pre

value: WHITE

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

value: High


title: GC071392_CTTAATAG-GGAGCTAC

description: smart-seq2 protocol

tag: timepoint

value: Mus


title: DNA_METHYLATION_15-008/029_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/029
A10-180-5_TUMOR

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

value: prostate tissue


title: GC071392_CTTAATAG-GGACTCCT

description: smart-seq2 protocol

tag: initially inactive x allele


title: Eosinophils #1

city: Suita

first: Kazuyo

last: Moro

state: Osaka

address: 2-2 Yamada-oka

department: Department of Microbiology and Immunology

country: Japan

institute: Osaka University

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

source_name: Eosinophils

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

tag: strain

value: spleen

tag: cell type

value: CD11b-hi, F4/80+, Gr-1-lo, MHC class II-, Siglec-F+, CD11c- eosinophils

tag: genotype

value: wild-type

tag: treatment


title: macrophages #1

source_name: macrophages

value: CD11b-hi, F4/80+, Gr-1-lo, MHC class II-, Siglec-F-, CD11c- macrophages


title: Dendritic cells #1

source_name: Dendritic cells

value: CD11b-hi, F4/80+, Gr-1-,MHC class II-hi, Siglec-F-,CD11c-hi dendritic cells


title: K107628 (second donation from K106641)

description:
whole methylome (Methyl Capture)
K107628_MeCap

tag: age of menarche

tag: menopausal status

value: No

tag: blood relatives cancer

value: AFRNAMER

tag: hispanic

tag: bmi


title: K107572

description:
whole methylome (Methyl Capture)
K107572_MeCap

tag: age

value: Yes

tag: race

tag: ever pregnant

tag: risk category


title: K107658

description:
whole methylome (Methyl Capture)
K107658_MeCap

value: Post

tag: life time risk (tyrer-cuzick score)


title: DNA_METHYLATION_15-008/029_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/029
A10-171-26_BUFFYCOAT

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: gleason score

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type

value: normal

tag: tissue

value: buffy coat


title: K107545

description:
whole methylome (Methyl Capture)
K107545_MeCap

tag: age of menarche

tag: menopausal status

value: Average


title: GC071392_CTTAATAG-CGGAGCCT

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: LTi cells #2

source_name: LTi cells

tag: strain

value: fetal liver

tag: cell type

value: CD19-, Thy1.2+, CD45+ LTi cells

tag: genotype

tag: treatment

value: LTi cells as CD19- Thy1.2+ CD45+ were sorted from α4β7hi c-Kit+ CD127+ 456 progenitors in fetal livers (E13) cultured with 5 ng/mL rmIL-7 and TSt4/N cells for 16 days


title: DNA_METHYLATION_15-008/028_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/028
A10-171-25_BUFFYCOAT

tag: preoperative psa

tag: race

value: unknown

tag: age


title: Mast cells #1

source_name: Mast cells

value: bone marrow

value: c-Kit+, Fc[Epsilon]RI[alpha]+, CD49b- mast cells

value: wild-type

value: Mast cells were induced from the bone marrow cells of C57BL/6N mice by culturing with 10 ng/mL rmIL-3 for 4 weeks


title: GC071392_CTTAATAG-CGTACTAG

description: smart-seq2 protocol


title: GC071392_CTTAATAG-CGATCAGT

description: smart-seq2 protocol


title: Mast cells #2


title: DNA_METHYLATION_15-008/028_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/028
A10-176-48_TUMOR

tag: disease state

tag: patientid

tag: gender

value: cancer

value: prostate tissue


title: K107540

description:
whole methylome (Methyl Capture)
K107540_MeCap

value: Pre

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


title: GC071392_CTTAATAG-GCTCATGA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: K107509

description:
whole methylome (Methyl Capture)
K107509_MeCap

tag: age of menarche

tag: menopausal status

value: Post


title: LTi cells #1

tag: strain

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: DNA_METHYLATION_15-008/029_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/029
A10-176-19_BENIGN

tag: disease state

value: prostate cancer

tag: patientid

value: male

tag: preoperative psa

tag: gleason score

tag: race

value: white

tag: pathologic stage

tag: age

tag: 5-year disease status

value: remission

tag: sample type

value: normal


title: DNA_METHYLATION_15-008/028_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/028
A10-176-18_BENIGN

tag: gender

value: unknown


title: GC071392_CTTAATAG-GCGTAGTA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: Th17 cells #2

source_name: Th17 cells

tag: strain

value: spleen

value: induced Th17 cells

value: Th17 cells (cultured with 1 ug/mL anti-CD28, 30 ng/mL rmIL-6, 3 ng/mL rmTGFβ) were induced from CD4+ CD62L+ T cells for 7 days on a 5 ug/mL anti-CD3ε coated plate.


title: GC071392_CTTAATAG-CTCTCTAC

description: smart-seq2 protocol


title: K107467

description:
whole methylome (Methyl Capture)
K107467_MeCap

tag: age of menarche

tag: menopausal status

tag: blood relatives cancer

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: Average


title: DNA_METHYLATION_15-008/015_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/015
A10-176-9_BENIGN

tag: disease state

tag: patientid

tag: preoperative psa

tag: gleason score

tag: race

value: recurrence

tag: tissue

value: prostate tissue


title: DNA_METHYLATION_15-008/015_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/015
A12-3-3_TUMOR

tag: gender

tag: pathologic stage

tag: age

tag: 5-year disease status

tag: sample type

value: cancer


title: GC071392_CTTAATAG-CCTAAGAC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: K107456

description:
whole methylome (Methyl Capture)
K107456_MeCap

tag: age of menarche

tag: menopausal status

value: Pre

value: No

tag: blood relatives cancer

value: WHITE

tag: hispanic

tag: bmi


title: Th2 cells #2

source_name: Th2 cells

tag: strain

tag: cell type

value: induced Th2 cells

tag: genotype

value: wild-type

tag: treatment

value: Th2 cells (cultured with 1 ug/mL anti-CD28, 10 ng/mL anti-IL-12, 10 ng/mL anti-IFNγ, 10 ng/mL rmIL-4) were induced from CD4+ CD62L+ T cells for 7 days on a 5 ug/mL anti-CD3ε coated plate.


title: K107480

description:
whole methylome (Methyl Capture)
K107480_MeCap

value: Post

tag: race

tag: ever pregnant

value: Yes

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: DNA_METHYLATION_15-008/014_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/014
A12-3-1_BENIGN

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

value: white

tag: pathologic stage

tag: age

tag: 5-year disease status

value: remission

value: normal

tag: tissue


title: GC071392_CTTAATAG-ATCTCAGG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: DNA_METHYLATION_15-008/015_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/015
A10-172-14_BUFFYCOAT

value: recurrence

tag: sample type

value: buffy coat


title: K107448 (second donation from K106629)

description:
whole methylome (Methyl Capture)
K107448_MeCap

tag: age of menarche

tag: menopausal status

tag: blood relatives cancer

tag: hispanic

tag: bmi

value: Average


title: GC071392_CTTAATAG-ATGCGCAG

description: smart-seq2 protocol


title: DNA_METHYLATION_15-008/014_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/014
A10-172-13_BUFFYCOAT

tag: disease state

tag: race


title: GC071392_CTTAATAG-ACTGAGCG

description: smart-seq2 protocol


title: K107454

description:
whole methylome (Methyl Capture)
K107454_MeCap

value: Pre

value: ASIAN

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: GC071392_CTTAATAG-AAGAGGCA

description: smart-seq2 protocol


title: Th17 cells #1

tag: strain

value: spleen

tag: cell type

value: induced Th17 cells

tag: genotype

tag: treatment

value: Th17 cells (cultured with 1 ug/mL anti-CD28, 30 ng/mL rmIL-6, 3 ng/mL rmTGFβ) were induced from CD4+ CD62L+ T cells for 7 days on a 5 ug/mL anti-CD3ε coated plate.


title: Th2 cells #1

tag: tissue

value: induced Th2 cells

value: wild-type

value: Th2 cells (cultured with 1 ug/mL anti-CD28, 10 ng/mL anti-IL-12, 10 ng/mL anti-IFNγ, 10 ng/mL rmIL-4) were induced from CD4+ CD62L+ T cells for 7 days on a 5 ug/mL anti-CD3ε coated plate.


title: CD19+/CD20+ B cells 1, scVDJ-seq

city: Stanford

first: Aaron

middle: M

last: Newman

state: CA

address: 265 Campus Drive

department: Department of Biomedical Data Science

institute: Stanford University

data_processing:
Library strategy: VDJ-seq
The resulting scVDJ-seq data were mapped to reference “refdata-cellranger-vdj-GRCh38-altsensembl-4.0.0”.
The final clonotypes were downloaded from the Loupe VDJ browser versions 3.0.0 and 4.0.0 (10x Genomics).
Genome_build: hg38
Supplementary_files_format_and_content: Text file containing the following columns: cell barcode, BCR chain, CDR3 amino-acid sequence, CDR3 nucloeotide sequence, clonotype ID, flag indicating whether the clone is dominant or not.

source_name: Diffuse large B cell lymphoma

extract_protocol:
Sample was prepared using the Chromium Single Cell V(D)J Enrichment Kit, Human B Cell, and sequenced using NovaSeq
Chromium Single Cell V(D)J Enrichment Kit, Human B Cell, following manufacturer's protocol
Chromium Single Cell 5' Library Construction Kit, following manufacturer's protocol
Chromium Single Cell 5' Feature Barcode Library Kit, Chromium Single Cell A Chip Kit, Chromium i7 Multiplex Kit, following manufacturer's protocol

tag: patient

value: DLBCL

tag: diagnosis

value: ABC DLBCL

tag: coo

value: ABC

tag: Sex

value: F

tag: age


title: GC071392_CTTAATAG-ACTCGCTA

description: smart-seq2 protocol

source_name: MEF to iPSC reprogramming timecourse

tag: timepoint

tag: initially inactive x allele


title: DNA_METHYLATION_15-008/014_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/014
A12-3-2_TUMOR

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

value: prostate tissue


title: GC071392_CTTAATAG-AGGCAGAA

description: smart-seq2 protocol

value: Mus


title: K107435

description:
whole methylome (Methyl Capture)
K107435_MeCap

source_name: Breast

tag: age of menarche

tag: menopausal status

value: Pre

value: No

tag: blood relatives cancer

value: Yes

tag: race

value: WHITE

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: High


title: NK cells #2

source_name: NK cells

tag: strain

tag: tissue

value: spleen

tag: cell type

value: NK1.1+,Thy1.2- NK cells

tag: genotype

value: wild-type

tag: treatment


title: K107439

description:
whole methylome (Methyl Capture)
K107439_MeCap

tag: age

value: Average


title: K107389

description:
whole methylome (Methyl Capture)
K107389_MeCap

value: Post


title: GC071392_CTTAATAG-CGAGGCTG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: Th1 cells #2

source_name: Th1 cells

value: induced Th1 cells

value: Th1 cells (cultured with 1 ug/mL anti-CD28, 10 ng/mL anti-IL-4, 10 ng/mL rmIL-12) were induced from CD4+ CD62L+ T cells for 7 days on a 5 ug/mL anti-CD3ε coated plate.


title: Th1 cells #1


title: CD19+/CD20+ B cells 3, scVDJ-seq

tag: patient

value: DLBCL

tag: diagnosis

value: ABC DLBCL

tag: coo

value: ABC

tag: Sex

value: M


title: NK cells #1


title: GC071392_CTCCTTAC-TGCAGCTA

description: smart-seq2 protocol

value: Mus


title: K107359

description:
whole methylome (Methyl Capture)
K107359_MeCap

tag: age of menarche

tag: menopausal status

tag: blood relatives cancer

tag: race

tag: hispanic


title: B cells #2

source_name: B cells

tag: strain

value: CD19+ B cells


title: RNA-SEQ_A12-2-22_15-492/006_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A12-2-22
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

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.

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

value: prostate tissue


title: GC071392_CTCCTTAC-TCGACGTC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: K107341

description:
whole methylome (Methyl Capture)
K107341_MeCap

tag: age

tag: age of menarche

value: Pre

value: No

value: ASIAN

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: RNA-SEQ_A10-172-10_15-492/006_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-172-10
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: race

value: normal

value: buffy coat


title: K107339

description:
whole methylome (Methyl Capture)
K107339_MeCap

tag: menopausal status

tag: blood relatives cancer

value: Yes

value: WHITE

tag: hispanic

value: High


title: GC071392_CTCCTTAC-TCCTGAGC

description: smart-seq2 protocol


title: B cells #1

tag: strain

value: spleen

tag: cell type

tag: genotype

value: wild-type

tag: treatment


title: RNA-SEQ_A12-2-18_15-492/004_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A12-2-18
processed_counts.txt
processed_TPM.txt

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

tag: pathologic stage

tag: 5-year disease status

tag: sample type

tag: tissue


title: GC071392_CTCCTTAC-TAGCGCTC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: CD4T cells #1

source_name: CD4T cells

value: CD4+ T cells


title: K107299

description:
whole methylome (Methyl Capture)
K107299_MeCap

tag: age

tag: age of menarche

tag: menopausal status

tag: race

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: GC071392_CTCCTTAC-TACGCTGC

description: smart-seq2 protocol


title: CD8T cells #2

source_name: CD8T cells

tag: strain

tag: cell type

value: CD8+ T cells

tag: genotype

tag: treatment


title: IL-33 ILC2s #2

source_name: IL-33 ILC2s

value: mesentery

value: IL-33 stimulated ILC2s

value: ILC2s were cultured with IL-33 (10ng/ml) for 48hrs.


title: CD4T cells #2


title: IL-33 ILC2s #1


title: RNA-SEQ_A12-2-20_15-492/005_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A12-2-20
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: recurrence

value: cancer

value: prostate tissue


title: RNA-SEQ_A10-172-8_15-492/004_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-172-8
processed_counts.txt
processed_TPM.txt

tag: age

value: remission

tag: sample type

value: normal

tag: tissue

value: buffy coat


title: Naïve ILC2s #2

source_name: Naïve ILC2s

value: Naive ILC2s


title: GC071392_CTCCTTAC-TAGGCATG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: K107264

description:
whole methylome (Methyl Capture)
K107264_MeCap

tag: age of menarche

tag: menopausal status

value: Pre

value: No

tag: blood relatives cancer

value: Yes

tag: race

value: AFRNAMER

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: High


title: K107325

description:
whole methylome (Methyl Capture)
K107325_MeCap

value: WHITE


title: RNA-SEQ_A10-172-9_15-492/005_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-172-9
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score


title: RNA-SEQ_A12-2-16_15-492/003_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A12-2-16
processed_counts.txt
processed_TPM.txt

value: black

tag: pathologic stage

tag: age

tag: 5-year disease status

tag: sample type

tag: tissue


title: K107266

description:
whole methylome (Methyl Capture)
K107266_MeCap

tag: age of menarche

tag: menopausal status

tag: blood relatives cancer

value: Don‚Äôt know

value: Average


title: GC071392_CTCCTTAC-GTAGAGGA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus