title: genomic DNA from meningioma [UT44_RD-20-74]

description:
meningioma sample
UT44_RD-20-74


title: genomic DNA from meningioma [UT34_RD-20-64]

status: Public on Apr 27 2022

type: genomic

city: New York

first: Department of Pathology

last: NYU Langone Health

state: NY

address: 240 East 38th Street

department: Department of Pathology

country: USA

institute: NYU Langone Health Ambulatory Care Center

description:
meningioma sample
UT34_RD-20-64

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

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

data_processing: Bioconductor R package Minfi (version 1.40.0) in Rstudio.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: membranes

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from DNA was extracted from formalin-fixed paraffin-embedded (FFPE) meningioma samples using Maxwell Promega FFPE kit (Promega Inc, WI). DNA methylation profiling was performed in accordance to the Illumina methylation microarray protocol guide. The processed microarrays were then scanned using the Illumina iScan to generate the raw methylation probe intensity values.

value: CHOM

tag: basename

tag: slide

tag: array

tag: gender

value: F

tag: grade

tag: histology

value: CHORDOID MENINGIOMA


title: genomic DNA from meningioma [UT50_RD-20-518]

description:
meningioma sample
UT50_RD-20-518

value: ATM

value: ATYPICAL MENINGIOMA


title: genomic DNA from meningioma [UT33_RD-20-63]

description:
meningioma sample
UT33_RD-20-63


title: genomic DNA from meningioma [UT38_RD-20-68]

description:
meningioma sample
UT38_RD-20-68


title: 9E11_Input_Rep1

type: SRA

city: Chicago

first: Debu

last: Chakravarti

state: IL

address: 303 E Superior St

department: Obstetrics and Gynecology

institute: Northwestern University

library_source: genomic

data_processing:
For single-end reads (ChIP-seq) raw fastq files were aligned with bowtie (v1.2.2, settings: -t --best -m 1) using pre-built genome indexes for both hg38 and mm10, downloaded from source (http://bowtie-bio.sourceforge.net/manual.shtml, NCBI). For paired-end ATAC-seq, reads were aligned with bowtie2 (v2.2.6, settings: --very-sensitive -X 800). For paired-end RNA-seq, reads were aligned to the hg38 reference genome (NCBI, GRCh38.p12) using STAR (43) (v2.7.5, settings: --alignIntronMin 20 --alignIntronMax 500000).
ChIP- and ATAC-seq sequence alignment files were converted to binary format using samtools (version 1.9) and used as input for peaks calling (HOMER, v4.11.1) (settings: -tbp 1, style = factor/histone/dnase).
Using diffBind (v3.12, settings: minMembers = 4 score=DBA_SCORE_TMM_MINUS_FULL) for differential binding analysis, each timepoint (1-, 4-, 8-, 24- and 48-hr) was compared to DMSO and peaks called by HOMER were used to define a consensus peak list
Visualization for ChIP-seq data including bigwigs, heatmaps and read coverage histograms were generated with deeptools bamCoverage (settings: --binSize 1 --normalizeUsing RPGC –effectiveGenomeSize mouse/human --extendReads    120 –ignoreDuplicates), plotHeatmap and plotProfile function (deepTools v3.3.0)
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: ChIP-seq: peak .txt files from HOMER, differential binding table is output from diffBind; RNA-seq: count matrix from featureCounts; ATAC-seq: peak .xls files from macs2

growth_protocol: All cell lines in this study were maintained in RPMI (ThermoFisher, Cat#: 11875093) supplemented with 10% Gibco FBS (REF:26140-079) in a humidified incubator at 37°C with 5% CO2

extract_protocol:
For ChIP-seq, the cell nuclear fraction was clarified from sonicated and histone-DNA complexes were isolated with antibodies. For RNA-seq, total RNA extracts were isolated from MYCi and vehicle control treated cells. For ATAC-seq, nuclei were isolated and inspected before Tn5 tagmentation.
As input for library preparation, < 1 ng – 5 ng of immunoprecipitated DNA was used. ChIPseq library preparation was carried out with KAPA Hyper Prep Kit (Cat#: KK8502). For RNAseq, 500 ng of RNA was used as input with a ribosome depletion library kit (KAPA Biosystems, Cat#: KK8560).
multiplex

treatment_protocol: Cells were isolated 72 hours after plating with a fresh media change 48-hours after plating. Each treatment was given such that isolation 72-hours after plating represents each timepoint.

tag: cell type

value: cancer cell line

tag: treatment


title: genomic DNA from meningioma [UT39_RD-20-69]

description:
meningioma sample
UT39_RD-20-69


title: 22RV1-WDR5-PTG-2017-09-27

tag: antibody

value: WDR5 (Proteintech, Cat#:15544-1-AP


title: 9E11_Input_Rep2


title: 22RV1-WDR5-PTG-2017-09-21


title: genomic DNA from meningioma [UT40_RD-20-70]

description:
meningioma sample
UT40_RD-20-70


title: genomic DNA from meningioma [UT56_RD-20-524]

description:
meningioma sample
UT56_RD-20-524

value: MNG

value: MENINGOTHELIAL MENINGIOMA


title: Muscle, E-selectin/AAV2/2, rep2

type: RNA

city: Miami

first: Zhao-Jun

last: Liu

state: FL

address: 1600 NW 10th Ave, RMSB 1010

department: Surgery

institute: University of Miami Miller School of Medicine

description:
treatment
SAMPLE 3 (E-selectin)

data_processing:
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
Fold Change worksheet reports test/control (i.e., E-selectin/AAV2/2 / LacZ/AAV2/2) ratios.

label: SYBR Green

molecule: total RNA

organism: Mus musculus

source_name: ischemic hindlimb muscle

label_protocol: PCR arrays were performed using the Qiagen RT2 Profiler PCR Array (Angiogenesis, PAMM-024Z) (Germantown, MD), according to manufacturer recommendations.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

treatment_protocol: Hindlimb muscle was treated with intramuscular E-selectin/AAV2/2 (treatment) or LacZ/AAV2/2 (control) prior to induction of ischemia.

tag: strain

value: FVB

tag: stress

value: induction of ischemia

tag: tissue

value: ischemic adductor and gastrocnemius muscles

tag: time

value: 21 days


title: genomic DNA from meningioma [UT42_RD-20-72]

description:
meningioma sample
UT42_RD-20-72


title: Muscle, LacZ/AAV2/2, rep1

description:
control
SAMPLE 2 (LacZ)


title: 22Rv1_48hr_FOXA1_R2

value: FOXA1 (Bethyl Laboratories, A305-249A)

value: 48hr MYCi - 10 µM


title: Muscle, E-selectin/AAV2/2, rep1

description:
treatment
SAMPLE 1 (E-selectin)


title: 22Rv1_48hr_FOXA1_R1


title: 22Rv1_DMSO_FOXA1_R3


title: HepG2 STAT3shRNA1

city: Wuhan

first: Deng

middle: wen

last: sheng

address: Qing ling street

department: School of Life Sciences and Health

country: China

institute: Wuhan University of Science and Technology

library_source: transcriptomic

data_processing: Not provided

source_name: Liver

growth_protocol: HepG2 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol: Not provided

value: Liver

tag: cell line

value: STAT3 shRNA


title: genomic DNA from meningioma [UT25_RD-19-612]

description:
meningioma sample
UT25_RD-19-612

value: ATYPICAL AND INVASIVE MENINGIOMA


title: 22Rv1_DMSO_FOXA1_R2


title: HepG2 CtrlshRNA1

value: Ctrl shRNA


title: genomic DNA from meningioma [UT24_RD-19-611]

description:
meningioma sample
UT24_RD-19-611

value: F


title: Muscle, LacZ/AAV2/2, rep2

description:
control
SAMPLE 4 (LacZ)


title: 22Rv1_DMSO_FOXA1_R1


title: motor neurons, CTRL4-42, b

city: ULM

first: Alberto

last: Catanese

address: Albert-Einstein-Allee 11

country: Germany

institute: Ulm University

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp
Clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were mapped to the reference genome using HISAT2 software
Featurecounts was used to count the read numbers mapped of each gene, including known and novel genes. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Assembly: GRCh38
Supplementary files format and content: FPKM gene count

source_name: iPSC-derived motor neurons

growth_protocol: Motor neurons were chemically differentiated from hiPSC as described in Catanese et al., 2019 (doi: 10.1080/15548627.2019.1589257)

extract_protocol:
Total RNA was extracted using the RNeasy extraction kit from Qiagen (Cat No./ID: 74104), following the protocol provided with the kit. Material from two independent differentiations was pooled after the extraction.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations

tag: patient id

value: iPSC-derived motor neurons

tag: disease state

value: Healthy control

tag: genotype

tag: age

tag: Sex

value: male

tag: developmental stage

value: 42 days in vitro


title: 22Rv1_48hr_AR_R2

value: cancer cell line

value: AR (Abcam, ab108341)


title: motor neurons, CTRL1-42, c

value: female


title: 22Rv1_48hr_AR_R1


title: motor neurons, CTRL4-42, a


title: 22Rv1_DMSO_AR_R3


title: motor neurons, CTRL1-42, b


title: 22Rv1_DMSO_AR_R1


title: 22Rv1_48hr_FOXA1_R3


title: motor neurons, CTRL1-42, a


title: genomic DNA from meningioma [UT19_RD-19-606]

description:
meningioma sample
UT19_RD-19-606

value: ATM

tag: basename

tag: slide

tag: array

tag: gender


title: 48hr_Input_Rep4

tag: cell type

tag: treatment


title: 48hr_Input_Rep3


title: genomic DNA from meningioma [UT32_RD-19-619]

description:
meningioma sample
UT32_RD-19-619

tag: grade

tag: histology

value: ATYPICAL MENINGIOMA


title: motor neurons, C9orf4-42, b

value: ALS

value: C9orf72 mutated


title: genomic DNA from meningioma [Ut15_RD-19-602]

description:
meningioma sample
Ut15_RD-19-602


title: genomic DNA from meningioma [UT27_RD-19-614]

description:
meningioma sample
UT27_RD-19-614


title: 22Rv1_DMSO_AR_R2

tag: antibody


title: 9E11_MYC_Rep1

value: c-MYC (abcam, ab56-9E11),


title: 48hr_Input_Rep2

value: 48hr MYCi - 10 µM


title: genomic DNA from meningioma [UT20_RD-19-607]

description:
meningioma sample
UT20_RD-19-607


title: genomic DNA from meningioma [UT17_RD-19-604]

description:
meningioma sample
UT17_RD-19-604


title: motor neurons, C9orf4-42, a


title: HepG2 CtrlshRNA2

tag: tissue

value: Liver


title: genomic DNA from meningioma [UT23_RD-19-610]

description:
meningioma sample
UT23_RD-19-610


title: genomic DNA from meningioma [UT16_RD-19-603]

description:
meningioma sample
UT16_RD-19-603


title: 48hr_Input_Rep1


title: HepG2 STAT3shRNA2

tag: cell line

value: STAT3 shRNA


title: 48hr_H3K27ac_Rep2

value: H3K27ac (Active Motif, Cat#:39685)


title: motor neurons, CTRL4-21, c

tag: patient id

value: 21 days in vitro


title: 48hr_MAX_Rep4

value: MAX (Proteintech, Cat#:10426-1-AP)


title: 48hr_H3K27ac_Rep1


title: motor neurons, CTRL4-21, b

value: iPSC-derived motor neurons

tag: disease state

value: Healthy control


title: motor neurons, C9orf3-42, c

tag: genotype

value: male

value: 42 days in vitro


title: genomic DNA from meningioma [UT9_RD-19-596]

description:
meningioma sample
UT9_RD-19-596

value: F


title: 48hr_MAX_Rep3

value: cancer cell line


title: motor neurons, CTRL4-21, a

tag: age


title: 48hr_MAX_Rep2


title: motor neurons, C9orf3-42, a

tag: Sex


title: 48hr_MYC_Rep4

value: c-MYC (abcam, ab32072-Y69)


title: 48hr_MYC_Rep3


title: 48hr_MAX_Rep1


title: genomic DNA from meningioma [UT46_RD-20-76]

description:
meningioma sample
UT46_RD-20-76

value: ATM

value: ATYPICAL MENINGIOMA


title: motor neurons, CTRL1-21, b

value: female

tag: developmental stage


title: 48hr_MYC_Rep2


title: motor neurons, C9orf4-21, b

value: ALS

value: C9orf72 mutated


title: genomic DNA from meningioma [Ut14_RD-19-601]

description:
meningioma sample
Ut14_RD-19-601

tag: basename

value: ATYPICAL AND INVASIVE MENINGIOMA


title: motor neurons, CTRL1-21, a


title: motor neurons, C9orf4-21, c


title: genomic DNA from meningioma [UT5_RD-19-592]

description:
meningioma sample
UT5_RD-19-592

tag: slide


title: 48hr_MYC_Rep1

value: 48hr MYCi - 10 µM


title: motor neurons, C9orf3-21, c


title: 24hr_Input_Rep4

value: 24hr MYCi - 10 µM


title: motor neurons, C9orf3-21, a

value: 21 days in vitro


title: motor neurons, C9orf3-21, b


title: 24hr_Input_Rep2


title: motor neurons, C9orf4-21, a


title: 24hr_Input_Rep1


title: 24hr_CTCF_Rep2

value: CTCF (Active Motif, Cat#:61932),


title: genomic DNA from meningioma [UT36_RD-20-66]

description:
meningioma sample
UT36_RD-20-66

value: CHOM

tag: array

value: CHORDOID MENINGIOMA


title: g9d2_1

city: San Diego

first: Zhao

last: Chen

state: California

address: 4955 Directors Pl

institute: Sorrento Therapeutics Inc.

data_processing:
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Index of the reference genome (Human GRCh38/hg38) was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Primary T cell

growth_protocol: Healthy donor LeukPak was purchased from Hemocare. Peripheral blood mononuclear cells (PBMCs) were isolated by density gradient centrifugation and frozen in CyroStor CD10 (Sigma-Aldrich). On day 0, T cells were isolated from frozen PBMCs, activated with Dynabeads Human T-expander CD3/CD28 (Thermo Fisher Scientific) and cultured in CTS OpTmizer T cell expansion medium supplemented with 5% human serum, and 300 U/ml of IL-2. On day 3, Dynabeads were magnetically removed and cells were continued to culture for one day.

extract_protocol:
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms and paired-end reads were generated.

treatment_protocol:
Activated T cells on day 4 were washed with PBS and transfected by electroporation of TRAC RNP and donor DNA using the Neon Transfection System (Thermo Fisher).
The GDT or DT transduced cells were stimulated with A549 cells which were seeded one day prior to the coculture. After overnight coculture, T cells were purified using EasySep Dead cell removal kit (STEMCELL Technologies) followed by CD4 and CD8+ T cells enrichment (Miltenyi Biotec).

value: Primary T cell

value: Activated T cell

tag: cell subtype

value: δ-TCRγδ-T cells (g9d2 group)

value: TRAC KO/KI

value: stimulated with A549 cells

tag: time

value: 1 day


title: gamma9_2

tag: cell type

value: γ-TCRγ-T cells (gamma9 group)

tag: treatment


title: gamma9_3


title: g9d2_2


title: g9d2_3


title: 24hr_H3K27ac_Rep1

value: cancer cell line

value: H3K27ac (Active Motif, Cat#:39685)


title: 24hr_MAX_Rep4

value: MAX (Proteintech, Cat#:10426-1-AP)


title: 24hr_MAX_Rep3


title: genomic DNA from meningioma [UT37_RD-20-67]

description:
meningioma sample
UT37_RD-20-67

tag: gender

value: F

tag: grade

tag: histology


title: 24hr_Input_Rep3


title: 24hr_MAX_Rep2

tag: antibody


title: 24hr_MAX_Rep1


title: RNA-SEQ, A12-60-6, PCBN123, prostate tissue

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

description:
Paired-end RNA-seq for prostate tissue sample A12-60-6 from patient PCBN123
processed_counts.txt
processed_TPM.txt
A12-60-6

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.
Assembly: hg19
Supplementary files format and content: tab separated values, gene symbol, description, transcripts-per-million (TPM) or count

source_name: prostate tissue

extract_protocol:
RNA was extracted from OCT prostate tissues using the Qiagen RNeasy 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.
Paired-end

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, embedded in OCT, and frozen.

value: prostate cancer

tag: patient id

value: male

tag: preoperative psa

tag: sample gleason score

tag: % tumor

tag: % tumor-in-normal contamination

tag: patient gleason score

tag: race

value: WHITE

tag: pathologic stage

tag: 5-year disease status

value: recurrence

tag: sample type

value: TUMOR


title: RNA-SEQ, A12-60-2, PCBN123, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-60-2 from patient PCBN123
processed_counts.txt
processed_TPM.txt
A12-60-2

source_name: buffy coat

tag: disease state

tag: age


title: RNA-SEQ, A12-60-5, PCBN122, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-60-5 from patient PCBN122
processed_counts.txt
processed_TPM.txt
A12-60-5

value: remission

value: BENIGN


title: RNA-SEQ, A12-60-7, PCBN123, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-60-7 from patient PCBN123
processed_counts.txt
processed_TPM.txt
A12-60-7


title: 24hr_MYC_Rep4

tag: cell type

value: c-MYC (abcam, ab32072-Y69)

tag: treatment

value: 24hr MYCi - 10 µM


title: 24hr_H3K27ac_Rep2


title: 24hr_CTCF_Rep1

value: CTCF (Active Motif, Cat#:61932),


title: gamma9_1

tag: cell line

value: Primary T cell

value: Activated T cell

tag: cell subtype

tag: genotype

value: TRAC KO/KI

value: stimulated with A549 cells

tag: time


title: RNA-SEQ, A12-60-4, PCBN122, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-60-4 from patient PCBN122
processed_counts.txt
processed_TPM.txt
A12-60-4

tag: patient id

tag: gender

tag: preoperative psa


title: 24hr_MYC_Rep3

value: cancer cell line

tag: antibody


title: 22Rv1_48hr_AR_R3

value: AR (Abcam, ab108341)

value: 48hr MYCi - 10 µM


title: motor neurons, CTRL4-42, c

value: iPSC-derived motor neurons

value: Healthy control

tag: Sex

tag: developmental stage

value: 42 days in vitro


title: 24hr_MYC_Rep2


title: RNA-SEQ, A12-60-1, PCBN122, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-60-1 from patient PCBN122
processed_counts.txt
processed_TPM.txt
A12-60-1

value: prostate cancer

value: male

tag: sample gleason score

tag: % tumor

tag: % tumor-in-normal contamination

tag: patient gleason score

tag: race

value: WHITE

tag: pathologic stage


title: RNA-SEQ, A12-32-17, PCBN121, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-32-17 from patient PCBN121
processed_counts.txt
processed_TPM.txt
A12-32-17

tag: disease state

tag: age

tag: 5-year disease status

value: recurrence

tag: sample type

value: BENIGN


title: 8hr_Input_Rep4

tag: cell type

tag: treatment

value: 8hr MYCi - 10 µM


title: RNA-SEQ, A12-32-18, PCBN121, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-32-18 from patient PCBN121
processed_counts.txt
processed_TPM.txt
A12-32-18

tag: patient id

tag: gender

value: TUMOR


title: 24hr_MYC_Rep1

tag: antibody

value: c-MYC (abcam, ab32072-Y69)

value: 24hr MYCi - 10 µM


title: 8hr_Input_Rep3


title: RNA-SEQ, A12-32-15, PCBN120, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-32-15 from patient PCBN120
processed_counts.txt
processed_TPM.txt
A12-32-15

tag: preoperative psa


title: motor neurons, C9orf4-42, c

value: ALS

tag: genotype

value: C9orf72 mutated

tag: Sex

value: female

tag: developmental stage


title: 8hr_Input_Rep1

value: cancer cell line


title: 8hr_Input_Rep2


title: RNA-SEQ, A12-33-30, PCBN120, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-33-30 from patient PCBN120
processed_counts.txt
processed_TPM.txt
A12-33-30

tag: sample gleason score

tag: % tumor

tag: % tumor-in-normal contamination


title: 8hr_H3K27ac_Rep2

value: H3K27ac (Active Motif, Cat#:39685)


title: RNA-SEQ, A12-32-14, PCBN119, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-32-14 from patient PCBN119
processed_counts.txt
processed_TPM.txt
A12-32-14

tag: patient gleason score

tag: race

tag: pathologic stage

value: remission


title: genomic DNA from meningioma [UT1_RD-19-588]

description:
meningioma sample
UT1_RD-19-588

value: ATM

tag: basename

tag: slide

tag: array

value: F

tag: grade

tag: histology

value: ATYPICAL MENINGIOMA


title: RNA-SEQ, A12-32-11, PCBN118, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-32-11 from patient PCBN118
processed_counts.txt
processed_TPM.txt
A12-32-11

tag: disease state

value: prostate cancer

tag: patient id

tag: gender

value: male

value: ASIAN

tag: age

tag: 5-year disease status

tag: sample type


title: 8hr_H3K27ac_Rep1

tag: cell type

tag: antibody

tag: treatment


title: 8hr_MAX_Rep3

value: MAX (Proteintech, Cat#:10426-1-AP)


title: RNA-SEQ, A12-32-12, PCBN118, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-32-12 from patient PCBN118
processed_counts.txt
processed_TPM.txt
A12-32-12

tag: preoperative psa

tag: sample gleason score

tag: % tumor

tag: % tumor-in-normal contamination

tag: patient gleason score


title: RNA-SEQ, A12-32-13, PCBN119, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-32-13 from patient PCBN119
processed_counts.txt
processed_TPM.txt
A12-32-13

tag: race

value: WHITE

tag: pathologic stage

value: BENIGN


title: RNA-SEQ, A12-33-28, PCBN118, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-33-28 from patient PCBN118
processed_counts.txt
processed_TPM.txt
A12-33-28


title: RNA-SEQ, A12-33-29, PCBN119, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-33-29 from patient PCBN119
processed_counts.txt
processed_TPM.txt
A12-33-29


title: 8hr_MAX_Rep1

value: 8hr MYCi - 10 µM


title: 8hr_MYC_Rep3

value: c-MYC (abcam, ab32072-Y69)


title: 8hr_MAX_Rep2


title: 8hr_MYC_Rep4


title: RNA-SEQ, A12-32-9, PCBN117, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-32-9 from patient PCBN117
processed_counts.txt
processed_TPM.txt
A12-32-9


title: RNA-SEQ, A12-33-27, PCBN117, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-33-27 from patient PCBN117
processed_counts.txt
processed_TPM.txt
A12-33-27


title: RNA-SEQ, A12-33-31, PCBN121, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-33-31 from patient PCBN121
processed_counts.txt
processed_TPM.txt
A12-33-31

value: recurrence


title: RNA-SEQ, A12-32-16, PCBN120, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-32-16 from patient PCBN120
processed_counts.txt
processed_TPM.txt
A12-32-16

value: TUMOR


title: 8hr_MYC_Rep2


title: RNA-SEQ, A12-32-10, PCBN117, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-32-10 from patient PCBN117
processed_counts.txt
processed_TPM.txt
A12-32-10


title: 8hr_MYC_Rep1


title: 4hr_Input_Rep4

value: 4hr MYCi - 10 µM


title: 8hr_MAX_Rep4

value: cancer cell line


title: RNA-SEQ, A12-32-8, PCBN116, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-32-8 from patient PCBN116
processed_counts.txt
processed_TPM.txt
A12-32-8


title: 4hr_Input_Rep2


title: 4hr_Input_Rep3


title: RNA-SEQ, A12-32-5, PCBN115, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-32-5 from patient PCBN115
processed_counts.txt
processed_TPM.txt
A12-32-5


title: motor neurons, C9orf3-42, b

value: iPSC-derived motor neurons

value: ALS

tag: genotype

value: C9orf72 mutated

tag: Sex

tag: developmental stage

value: 42 days in vitro


title: RNA-SEQ, A12-33-25, PCBN115, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-33-25 from patient PCBN115
processed_counts.txt
processed_TPM.txt
A12-33-25

tag: disease state

tag: patient id

tag: gender


title: 4hr_Input_Rep1


title: 4hr_H3K27ac_Rep2

value: H3K27ac (Active Motif, Cat#:39685)


title: RNA-SEQ, A12-32-3, PCBN114, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-32-3 from patient PCBN114
processed_counts.txt
processed_TPM.txt
A12-32-3

value: prostate cancer

tag: age

tag: 5-year disease status

tag: sample type


title: 4hr_MAX_Rep4

tag: cell type

tag: antibody

tag: treatment


title: 4hr_MAX_Rep3


title: RNA-SEQ, A12-32-4, PCBN114, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-32-4 from patient PCBN114
processed_counts.txt
processed_TPM.txt
A12-32-4

value: male

tag: preoperative psa

tag: sample gleason score

tag: % tumor


title: 4hr_MAX_Rep1


title: RNA-SEQ, A12-32-1, PCBN113, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-32-1 from patient PCBN113
processed_counts.txt
processed_TPM.txt
A12-32-1

tag: % tumor-in-normal contamination

tag: patient gleason score

tag: race

value: remission


title: RNA-SEQ, A12-32-2, PCBN113, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-32-2 from patient PCBN113
processed_counts.txt
processed_TPM.txt
A12-32-2

tag: pathologic stage


title: RNA-SEQ, A12-32-7, PCBN116, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-32-7 from patient PCBN116
processed_counts.txt
processed_TPM.txt
A12-32-7


title: 4hr_MYC_Rep4


title: 4hr_MYC_Rep3


title: RNA-SEQ, A12-31-31, PCBN112, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-31-31 from patient PCBN112
processed_counts.txt
processed_TPM.txt
A12-31-31


title: RNA-SEQ, A12-33-23, PCBN113, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-33-23 from patient PCBN113
processed_counts.txt
processed_TPM.txt
A12-33-23


title: 4hr_MYC_Rep2


title: 4hr_MYC_Rep1


title: RNA-SEQ, A12-31-32, PCBN112, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-31-32 from patient PCBN112
processed_counts.txt
processed_TPM.txt
A12-31-32


title: RNA-SEQ, A12-33-26, PCBN116, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-33-26 from patient PCBN116
processed_counts.txt
processed_TPM.txt
A12-33-26


title: RNA-SEQ, A12-31-29, PCBN111, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-31-29 from patient PCBN111
processed_counts.txt
processed_TPM.txt
A12-31-29


title: 1hr_Input_Rep4

value: 1hr MYCi - 10 µM


title: 1hr_Input_Rep3


title: 4hr_H3K27ac_Rep1


title: 1hr_Input_Rep1


title: RNA-SEQ, A12-32-6, PCBN115, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-32-6 from patient PCBN115
processed_counts.txt
processed_TPM.txt
A12-32-6

value: WHITE


title: 1hr_Input_Rep2


title: RNA-SEQ, A12-33-21, PCBN111, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-33-21 from patient PCBN111
processed_counts.txt
processed_TPM.txt
A12-33-21


title: RNA-SEQ, A12-31-27, PCBN110, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-31-27 from patient PCBN110
processed_counts.txt
processed_TPM.txt
A12-31-27

value: BENIGN


title: RNA-SEQ, A12-33-22, PCBN112, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-33-22 from patient PCBN112
processed_counts.txt
processed_TPM.txt
A12-33-22


title: 1hr_H3K27ac_Rep2


title: RNA-SEQ, A12-31-30, PCBN111, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-31-30 from patient PCBN111
processed_counts.txt
processed_TPM.txt
A12-31-30


title: 1hr_H3K27ac_Rep1


title: RNA-SEQ, A12-31-28, PCBN110, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-31-28 from patient PCBN110
processed_counts.txt
processed_TPM.txt
A12-31-28


title: 1hr_MAX_Rep4

value: MAX (Proteintech, Cat#:10426-1-AP)


title: RNA-SEQ, A12-33-24, PCBN114, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-33-24 from patient PCBN114
processed_counts.txt
processed_TPM.txt
A12-33-24


title: 4hr_MAX_Rep2


title: RNA-SEQ, A12-33-20, PCBN110, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-33-20 from patient PCBN110
processed_counts.txt
processed_TPM.txt
A12-33-20


title: RNA-SEQ, A12-31-25, PCBN109, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-31-25 from patient PCBN109
processed_counts.txt
processed_TPM.txt
A12-31-25

value: HISPANIC


title: RNA-SEQ, A12-31-26, PCBN109, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-31-26 from patient PCBN109
processed_counts.txt
processed_TPM.txt
A12-31-26


title: 1hr_MAX_Rep2


title: 1hr_MAX_Rep1


title: 1hr_MAX_Rep3


title: RNA-SEQ, A12-31-23, PCBN108, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-31-23 from patient PCBN108
processed_counts.txt
processed_TPM.txt
A12-31-23

value: recurrence


title: RNA-SEQ, A12-31-24, PCBN108, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-31-24 from patient PCBN108
processed_counts.txt
processed_TPM.txt
A12-31-24

value: TUMOR


title: RNA-SEQ, A12-33-18, PCBN108, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-33-18 from patient PCBN108
processed_counts.txt
processed_TPM.txt
A12-33-18


title: 1hr_MYC_Rep1

value: c-MYC (abcam, ab32072-Y69)


title: 1hr_MYC_Rep2

value: cancer cell line


title: RNA-SEQ, A12-31-21, PCBN107, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-31-21 from patient PCBN107
processed_counts.txt
processed_TPM.txt
A12-31-21


title: RNA-SEQ, A12-31-22, PCBN107, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-31-22 from patient PCBN107
processed_counts.txt
processed_TPM.txt
A12-31-22


title: RNA-SEQ, A12-33-19, PCBN109, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-33-19 from patient PCBN109
processed_counts.txt
processed_TPM.txt
A12-33-19


title: DMSO_Input_Rep3


title: RNA-SEQ, A12-31-19, PCBN106, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-31-19 from patient PCBN106
processed_counts.txt
processed_TPM.txt
A12-31-19


title: DMSO_Input_Rep4


title: motor neurons, CTRL1-21, c

value: iPSC-derived motor neurons

value: Healthy control

tag: genotype

tag: Sex

value: female

tag: developmental stage

value: 21 days in vitro


title: RNA-SEQ, A12-31-20, PCBN106, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-31-20 from patient PCBN106
processed_counts.txt
processed_TPM.txt
A12-31-20

tag: disease state

tag: patient id

tag: gender


title: DMSO_Input_Rep2


title: RNA-SEQ, A12-33-16, PCBN106, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-33-16 from patient PCBN106
processed_counts.txt
processed_TPM.txt
A12-33-16

tag: age

tag: 5-year disease status

tag: sample type


title: DMSO_CTCF_Rep2

tag: cell type

tag: antibody

value: CTCF (Active Motif, Cat#:61932),

tag: treatment


title: DMSO_H3K27ac_Rep2

value: H3K27ac (Active Motif, Cat#:39685)


title: RNA-SEQ, A12-31-18, PCBN105, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-31-18 from patient PCBN105
processed_counts.txt
processed_TPM.txt
A12-31-18

value: prostate cancer

value: male

tag: preoperative psa

tag: sample gleason score

tag: % tumor


title: RNA-SEQ, A12-31-17, PCBN105, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-31-17 from patient PCBN105
processed_counts.txt
processed_TPM.txt
A12-31-17

tag: % tumor-in-normal contamination

tag: patient gleason score

tag: race

value: remission


title: DMSO_CTCF_Rep1


title: RNA-SEQ, A12-33-15, PCBN105, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-33-15 from patient PCBN105
processed_counts.txt
processed_TPM.txt
A12-33-15

value: WHITE

tag: pathologic stage


title: DMSO_H3K27ac_Rep1


title: 1hr_MYC_Rep4

value: 1hr MYCi - 10 µM


title: 1hr_MYC_Rep3


title: DMSO_MAX_Rep4

value: MAX (Proteintech, Cat#:10426-1-AP)


title: RNA-SEQ, A12-31-15, PCBN104, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-31-15 from patient PCBN104
processed_counts.txt
processed_TPM.txt
A12-31-15

value: BENIGN


title: DMSO_MAX_Rep3


title: RNA-SEQ, A12-31-16, PCBN104, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-31-16 from patient PCBN104
processed_counts.txt
processed_TPM.txt
A12-31-16


title: RNA-SEQ, A12-33-17, PCBN107, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-33-17 from patient PCBN107
processed_counts.txt
processed_TPM.txt
A12-33-17

value: recurrence


title: RNA-SEQ, A12-33-14, PCBN104, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-33-14 from patient PCBN104
processed_counts.txt
processed_TPM.txt
A12-33-14


title: DMSO_MAX_Rep2


title: RNA-SEQ, A12-31-13, PCBN103, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-31-13 from patient PCBN103
processed_counts.txt
processed_TPM.txt
A12-31-13


title: DMSO_Input_Rep1


title: RNA-SEQ, A12-31-14, PCBN103, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-31-14 from patient PCBN103
processed_counts.txt
processed_TPM.txt
A12-31-14

value: TUMOR


title: DMSO_MYC_Rep2

value: c-MYC (abcam, ab32072-Y69)


title: RNA-SEQ, A12-33-13, PCBN103, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-33-13 from patient PCBN103
processed_counts.txt
processed_TPM.txt
A12-33-13


title: RNA-SEQ, A12-31-11, PCBN102, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-31-11 from patient PCBN102
processed_counts.txt
processed_TPM.txt
A12-31-11


title: DMSO_MYC_Rep3

value: cancer cell line


title: DMSO_MYC_Rep4


title: DMSO_MYC_Rep1


title: RNA-SEQ, A12-31-9, PCBN101, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-31-9 from patient PCBN101
processed_counts.txt
processed_TPM.txt
A12-31-9


title: RNA-SEQ, A12-33-12, PCBN102, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-33-12 from patient PCBN102
processed_counts.txt
processed_TPM.txt
A12-33-12


title: RNA-SEQ, A12-33-11, PCBN101, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-33-11 from patient PCBN101
processed_counts.txt
processed_TPM.txt
A12-33-11


title: Hela STING deficient untreated 72h-3

city: Freiburg

first: Elham

last: Bavafaye Haghighi

address: Breisacherstr. 153

department: Institut für Medizinische Bioinformatik und Systemmedizin

institute: University Hospital of Freiburg

data_processing:
Dropseq tool v1.12 (Macosko et al., 2015) was used for mapping raw sequencing data to the reference genome with default parameters
Create bam file without alignment
java -jar PATHTOPICARD/picard.jar FastqToSam F1=FORWARDREAD F2=REVERSEREAD O=RUNNAME.bam SM=RUNNAME
Sort bam file according to read ID
java -jar PATHTOPICARD/picard.jar SortSam I=RUNNAME.bam O=RUNNAME_sorted.bam SORT_ORDER=queryname
Start Dropseq tool
PATHTODROPSEQTOOLS/Drop-seq_alignment.sh -g PATHTOSTARINDEX -r PATHTOGENOMEREFERENCE -d PATHTODROPSEQTOOLS -s PATHTOSTARALIGNER -o OUTPUTFOLDER RUNNAME_sorted.bam
Get UMI filtered matix
PATHTODROPSEQTOOLS/DigitalExpression' -m 30g -t I=star_gene_exon_tagged.bam O=DGE_Matrix.txt CELL_BARCODE_TAG=XC MOLECULAR_BARCODE_TAG=XM CELL_BC_FILE=BARCODESUSED
Genome_build: Gencode gene annotations v28 and the human reference genome GRCh38 were derived from the Gencode homepage (EMBL-EBI).
Supplementary_files_format_and_content: Tab-delimited text file includes raw count values for each sample.

source_name: Hela 229  cervical cancer STING deficient cell line

growth_protocol: Hela and MDA cells were routinely cultured in RPMI medium. Splitted every 3 days and culture into 10cm2 or 15cm2 dishes.

extract_protocol:
Total RNA was extracted using the High Pure RNA isolation kit (Roche #11828665001)
Total RNA was isolated from purified Treg cells and Tconv cells with RNAeasy Plus micro kit (QIAGEN). Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer (Agilent Technologies). RNaseq analysis: library preparation for bulk 30-sequencing of poly(A)-RNA was done as described previously (Parekh et al., 2016). Briefly, barcoded cDNA of each sample was generated with a Maxima RT polymerase (Thermo Fisher) using oligo-dT primer containing barcodes, unique molecular identifiers (UMIs) and an adaptor. 50 ends of the cDNAs were extended by a template switch oligo (TSO) and full-length cDNA was amplified with primers binding to the TSO-site and the adaptor. NEB UltraII FS kit was used to fragment cDNA. After end repair and A-tailing a TruSeq adapter was ligated and 3’-end-fragments were finally amplified using primers with Illumina P5 and P7 overhangs. In comparison to Parekh et al. (2016), the P5 and P7 sites were exchanged to allow sequencing of the cDNA in read1 and barcodes and UMIs in read2 to achieve a better cluster recognition. The library was sequenced on a NextSeq 500 (Illumina) with 75 cycles for the cDNA in read1 and 16 cycles for the barcodes and UMIs in read2.
3'-sequencing of polyA-RNA

tag: cell line

value: Hela 229

tag: genotype

value: Hela 229 STING deficient


title: Hela STING deficient untreated 72h-2


title: RNA-SEQ, A12-31-10, PCBN101, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-31-10 from patient PCBN101
processed_counts.txt
processed_TPM.txt
A12-31-10

tag: disease state

tag: patient id


title: Hela STING deficient untreated 72h-1


title: Hela CAD deficient untreated 72h-4

source_name: Hela 229  cervical cancer CAD deficient cell line

value: Hela 229 CAD deficient


title: RNA-SEQ, A12-31-7, PCBN100, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-31-7 from patient PCBN100
processed_counts.txt
processed_TPM.txt
A12-31-7

tag: gender

tag: age


title: Hela CAD deficient untreated 72h-3


title: RNA-SEQ, A12-31-8, PCBN100, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-31-8 from patient PCBN100
processed_counts.txt
processed_TPM.txt
A12-31-8

tag: 5-year disease status

tag: sample type


title: DMSO_MAX_Rep1

tag: cell type

tag: antibody


title: RNA-SEQ, A12-33-10, PCBN100, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-33-10 from patient PCBN100
processed_counts.txt
processed_TPM.txt
A12-33-10

tag: preoperative psa


title: Hela CAD deficient untreated 72h-2


title: RNA-SEQ, A12-31-5, PCBN99, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-31-5 from patient PCBN99
processed_counts.txt
processed_TPM.txt
A12-31-5

tag: sample gleason score


title: RNA-SEQ, A12-31-6, PCBN99, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-31-6 from patient PCBN99
processed_counts.txt
processed_TPM.txt
A12-31-6

tag: % tumor


title: RNA-SEQ, A12-33-9, PCBN99, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-33-9 from patient PCBN99
processed_counts.txt
processed_TPM.txt
A12-33-9

tag: % tumor-in-normal contamination


title: Hela STING deficient untreated 72h-4


title: Hela Ctrl untreated 72h-3

source_name: Hela 229  cervical cancer control cell line

value: Hela 229 control


title: Hela CAD deficient untreated 72h-1


title: RNA-SEQ, A12-31-12, PCBN102, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-31-12 from patient PCBN102
processed_counts.txt
processed_TPM.txt
A12-31-12

tag: patient gleason score


title: RNA-SEQ, A12-31-3, PCBN98, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-31-3 from patient PCBN98
processed_counts.txt
processed_TPM.txt
A12-31-3

tag: race

value: ASIAN


title: RNA-SEQ, A12-31-4, PCBN98, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-31-4 from patient PCBN98
processed_counts.txt
processed_TPM.txt
A12-31-4

tag: pathologic stage


title: RNA-SEQ, A12-33-8, PCBN98, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-33-8 from patient PCBN98
processed_counts.txt
processed_TPM.txt
A12-33-8


title: Hela Ctrl untreated 72h-4

tag: cell line


title: RNA-SEQ, A12-31-1, PCBN97, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-31-1 from patient PCBN97
processed_counts.txt
processed_TPM.txt
A12-31-1


title: Hela Ctrl untreated 72h-1

tag: genotype


title: MDA-MB-231 STING deficient untreated 72h-4

source_name: MDA-MB-231  breast cancer STING deficient cell line

value: MDA-MB-231 STING deficient


title: Hela Ctrl untreated 72h-2


title: MDA-MB-231 STING deficient untreated 72h-2


title: RNA-SEQ, A12-33-7, PCBN97, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-33-7 from patient PCBN97
processed_counts.txt
processed_TPM.txt
A12-33-7

tag: disease state

value: prostate cancer


title: MDA-MB-231 STING deficient untreated 72h-3


title: MDA-MB-231 CAD deficient untreated 72h-3

source_name: MDA-MB-231 breast cancer CAD deficient cell line

value: MDA-MB-231 CAD deficient


title: MDA-MB-231 CAD deficient untreated 72h-2


title: RNA-SEQ, A12-30-31, PCBN96, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-30-31 from patient PCBN96
processed_counts.txt
processed_TPM.txt
A12-30-31

tag: patient id

value: male

value: NATIVE AMERICAN

value: remission


title: MDA-MB-231 STING deficient untreated 72h-1


title: RNA-SEQ, A12-33-6, PCBN96, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-33-6 from patient PCBN96
processed_counts.txt
processed_TPM.txt
A12-33-6

tag: gender


title: MDA-MB-231 Ctrl untreated 72h-4

source_name: MDA-MB-231  breast cancer control cell line

value: MDA-MB-231 control


title: MDA-MB-231 CAD deficient untreated 72h-1


title: MDA-MB-231 Ctrl untreated 72h-3


title: MDA-MB-231 Ctrl untreated 72h-2


title: RNA-SEQ, A12-33-5, PCBN95, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-33-5 from patient PCBN95
processed_counts.txt
processed_TPM.txt
A12-33-5

value: WHITE

value: Unk

tag: age


title: RNA-SEQ, A12-33-4, PCBN94, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-33-4 from patient PCBN94
processed_counts.txt
processed_TPM.txt
A12-33-4

value: BLACK

tag: 5-year disease status


title: RNA-SEQ, A12-30-25, PCBN93, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-30-25 from patient PCBN93
processed_counts.txt
processed_TPM.txt
A12-30-25

tag: sample type

value: BENIGN


title: RNA-SEQ, A12-30-27, PCBN94, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-30-27 from patient PCBN94
processed_counts.txt
processed_TPM.txt
A12-30-27


title: RNA-SEQ, A12-30-24, PCBN92, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-30-24 from patient PCBN92
processed_counts.txt
processed_TPM.txt
A12-30-24

value: recurrence

value: TUMOR


title: RNA-SEQ, A12-30-28, PCBN94, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-30-28 from patient PCBN94
processed_counts.txt
processed_TPM.txt
A12-30-28


title: RNA-SEQ, A12-30-29, PCBN95, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-30-29 from patient PCBN95
processed_counts.txt
processed_TPM.txt
A12-30-29


title: RNA-SEQ, A12-30-26, PCBN93, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-30-26 from patient PCBN93
processed_counts.txt
processed_TPM.txt
A12-30-26


title: RNA-SEQ, A12-33-3, PCBN93, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-33-3 from patient PCBN93
processed_counts.txt
processed_TPM.txt
A12-33-3


title: RNA-SEQ, A12-33-2, PCBN92, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-33-2 from patient PCBN92
processed_counts.txt
processed_TPM.txt
A12-33-2


title: MDA-MB-231 Ctrl untreated 72h-1


title: RNA-SEQ, A12-31-2, PCBN97, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-31-2 from patient PCBN97
processed_counts.txt
processed_TPM.txt
A12-31-2


title: RNA-SEQ, A12-30-21, PCBN91, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-30-21 from patient PCBN91
processed_counts.txt
processed_TPM.txt
A12-30-21


title: Bp tumor 9

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

data_processing:
NextSeq 500 using v3 chemistry. Software: Control v2.0.0.24, RTA 2.4.6. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Reads were quantified using 3’ digital gene expression reads and RSEM version 1.2.15 with alignments prepared using bowtie2 version 2.2.3
Genome_build: Zv10 with an ensembl version 80 annotation
Supplementary_files_format_and_content: aha_120821_Counts.txt.gz is a tab delimited text file of raw count data
Supplementary_files_format_and_content: aha_120821_l2cpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset

organism: Danio rerio

source_name: Bp tumor

extract_protocol:
Trizol extraction (Invitrogen)
3’ Digital gene expression libraries were created by cleaning  RNA samples were cleaned using SPRI beads (1.8X), quantified and quality assessed using an Advanced Analytical Fragment Analyzer. 10ng of total RNA was used for library preparation. 3’DGE-custom primers 3V6NEXT-bmc#1-24 were added to a final concentration of 1 uM. (5'-/5Biosg/ACACTCTTTCCCTACACGACGCTCTTCCGATCT[BC6]N10T30VN-3'  where  5Biosg = 5’  biotin, [BC6] = 6bp barcode specific to each sample/well, N10 = Unique Molecular Identifiers, Integrated DNA technologies), to generate two subpools of 24 samples each. After addition of the oligonucleotides, Maxima H Minus RT was added per manufacturer’s recommendations with Template-Switching oligo 5V6NEXT (10uM, [5V6NEXT : 5’-iCiGiCACACTCTTTCCCTACACGACGCrGrGrG-3’  where  iC: iso-dC, iG: iso-dG, rG: RNA G ])  followed by incubation at 42C for 90’ and inactivation at 80C for 10’. Following the template switching reaction, cDNA from 24 wells containing unique well identifiers were pooled together and cleaned using RNA Ampure beads at 1.0X. cDNA was eluted with 17 ul of water followed by digestion with Exonuclease I at 37C for 30 minutes, and inactivated at 80C for 20 minutes. Second strand synthesis and PCR amplification was done by adding the Advantage 2 Polymerase Mix (Clontech) and the SINGV6 primer (10 pmol, Integrated DNA Technologies 5’-/5Biosg/ACACTCTTTCCCTACACGACGC-3’) directly to the exonuclease reaction. 8 cycles of PCR were performed followed by clean up using regular SPRI beads at 0.6X, and eluted with 20ul of EB. Successful amplification of cDNA was confirmed using the Fragment Analyzer. Illumina libraries were then produced using standard Nextera tagmentation substituting P5NEXTPT5-bmc primer (25μM, Integrated DNA Technologies, (5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCG*A*T*C*T*-3’  where  * = phosphorothioate bonds. ) in place of the normal N500 primer.  Final libraries were cleaned using SPRI beads at 0.7X and quantified using the Fragment Analyzer and qPCR

treatment_protocol: Fish were anesthetized in 0.1% Tricaine for 20 minutes and tumors were manually dissected from the fish and immediately processed in Trizol reagent (invitrogen)

tag: genetic background

value: AB/Tübingen (TAB5/14)

tag: transgene

tag: tissue

value: uveal melanoma tumor


title: RNA-SEQ, A12-30-32, PCBN96, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-30-32 from patient PCBN96
processed_counts.txt
processed_TPM.txt
A12-30-32

tag: preoperative psa

tag: sample gleason score


title: RNA-SEQ, A12-33-1, PCBN91, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-33-1 from patient PCBN91
processed_counts.txt
processed_TPM.txt
A12-33-1

tag: % tumor

tag: % tumor-in-normal contamination


title: Bp tumor 8


title: RNA-SEQ, A12-30-23, PCBN92, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-30-23 from patient PCBN92
processed_counts.txt
processed_TPM.txt
A12-30-23

tag: patient gleason score

tag: race


title: RNA-SEQ, A12-30-22, PCBN91, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-30-22 from patient PCBN91
processed_counts.txt
processed_TPM.txt
A12-30-22

tag: pathologic stage


title: Bp tumor 7

tag: genotype


title: RNA-SEQ, A12-30-19, PCBN90, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-30-19 from patient PCBN90
processed_counts.txt
processed_TPM.txt
A12-30-19

tag: disease state


title: Bp tumor 6


title: Bp tumor 5


title: RNA-SEQ, A12-28-26, PCBN90, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-28-26 from patient PCBN90
processed_counts.txt
processed_TPM.txt
A12-28-26

tag: patient id


title: RNA-SEQ, A12-30-20, PCBN90, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-30-20 from patient PCBN90
processed_counts.txt
processed_TPM.txt
A12-30-20

tag: gender


title: RNA-SEQ, A12-30-30, PCBN95, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-30-30 from patient PCBN95
processed_counts.txt
processed_TPM.txt
A12-30-30

tag: age


title: Bp tumor 4


title: Bp tumor 3


title: RNA-SEQ, A12-30-17, PCBN89, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-30-17 from patient PCBN89
processed_counts.txt
processed_TPM.txt
A12-30-17

tag: 5-year disease status


title: RNA-SEQ, A12-28-25, PCBN89, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-28-25 from patient PCBN89
processed_counts.txt
processed_TPM.txt
A12-28-25

tag: sample type


title: RNA-SEQ, A12-30-16, PCBN88, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-30-16 from patient PCBN88
processed_counts.txt
processed_TPM.txt
A12-30-16


title: Qp_skin tumor 9

source_name: Qp_skin tumor

tag: genetic background

value: cutaneous melanoma tumor


title: Bp tumor 1

tag: transgene


title: Qp_skin tumor 7

tag: tissue


title: Qp_skin tumor 8


title: RNA-SEQ, A12-30-15, PCBN88, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-30-15 from patient PCBN88
processed_counts.txt
processed_TPM.txt
A12-30-15

tag: preoperative psa


title: Qp_skin tumor 6


title: Qp_skin tumor 4


title: Qp_skin tumor 3


title: RNA-SEQ, A12-28-23, PCBN87, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-28-23 from patient PCBN87
processed_counts.txt
processed_TPM.txt
A12-28-23

tag: sample gleason score


title: RNA-SEQ, A12-30-11, PCBN86, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-30-11 from patient PCBN86
processed_counts.txt
processed_TPM.txt
A12-30-11

tag: % tumor


title: RNA-SEQ, A12-30-12, PCBN86, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-30-12 from patient PCBN86
processed_counts.txt
processed_TPM.txt
A12-30-12

tag: % tumor-in-normal contamination


title: Qp_skin tumor 5


title: Qp_skin tumor 1


title: Qp_skin tumor 2


title: RNA-SEQ, A12-30-13, PCBN87, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-30-13 from patient PCBN87
processed_counts.txt
processed_TPM.txt
A12-30-13

tag: patient gleason score


title: Qp_eye tumor 8

source_name: Qp_eye tumor


title: RNA-SEQ, A12-28-22, PCBN86, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-28-22 from patient PCBN86
processed_counts.txt
processed_TPM.txt
A12-28-22

tag: race


title: RNA-SEQ, A12-30-9, PCBN85, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-30-9 from patient PCBN85
processed_counts.txt
processed_TPM.txt
A12-30-9

tag: pathologic stage


title: RNA-SEQ, A12-30-10, PCBN85, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-30-10 from patient PCBN85
processed_counts.txt
processed_TPM.txt
A12-30-10


title: RNA-SEQ, A12-30-18, PCBN89, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-30-18 from patient PCBN89
processed_counts.txt
processed_TPM.txt
A12-30-18


title: RNA-SEQ, A12-28-21, PCBN85, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-28-21 from patient PCBN85
processed_counts.txt
processed_TPM.txt
A12-28-21


title: Qp_eye tumor 7

tag: genotype


title: Qp_eye tumor 6


title: Bp tumor 2


title: RNA-SEQ, A12-30-7, PCBN84, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-30-7 from patient PCBN84
processed_counts.txt
processed_TPM.txt
A12-30-7

tag: disease state


title: Qp_eye tumor 5


title: RNA-SEQ, A12-28-24, PCBN88, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-28-24 from patient PCBN88
processed_counts.txt
processed_TPM.txt
A12-28-24

tag: patient id


title: RNA-SEQ, A12-30-14, PCBN87, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-30-14 from patient PCBN87
processed_counts.txt
processed_TPM.txt
A12-30-14

tag: gender


title: RNA-SEQ, A12-30-8, PCBN84, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-30-8 from patient PCBN84
processed_counts.txt
processed_TPM.txt
A12-30-8

tag: age


title: Qp_eye tumor 3


title: Qp_eye tumor 2


title: RNA-SEQ, A12-28-20, PCBN84, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-28-20 from patient PCBN84
processed_counts.txt
processed_TPM.txt
A12-28-20

tag: 5-year disease status


title: Qp_eye tumor 1


title: RNA-SEQ, A12-30-6, PCBN83, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-30-6 from patient PCBN83
processed_counts.txt
processed_TPM.txt
A12-30-6

tag: sample type


title: Qm tumor 9

source_name: Qm tumor

tag: genetic background

value: mitfa-/-


title: Qm tumor 10

tag: transgene


title: RNA-SEQ, A12-28-19, PCBN83, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-28-19 from patient PCBN83
processed_counts.txt
processed_TPM.txt
A12-28-19


title: Qp_eye tumor 4

tag: tissue


title: Qm tumor 8


title: Qm tumor 7


title: Qm tumor 5


title: RNA-SEQ, A12-30-1, PCBN81, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-30-1 from patient PCBN81
processed_counts.txt
processed_TPM.txt
A12-30-1

tag: preoperative psa


title: RNA-SEQ, A12-30-3, PCBN82, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-30-3 from patient PCBN82
processed_counts.txt
processed_TPM.txt
A12-30-3

tag: sample gleason score


title: RNA-SEQ, A12-30-2, PCBN81, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-30-2 from patient PCBN81
processed_counts.txt
processed_TPM.txt
A12-30-2

tag: % tumor


title: Qm tumor 6


title: RNA-SEQ, A12-29-31, PCBN80, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-29-31 from patient PCBN80
processed_counts.txt
processed_TPM.txt
A12-29-31

tag: % tumor-in-normal contamination


title: RNA-SEQ, A12-30-4, PCBN82, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-30-4 from patient PCBN82
processed_counts.txt
processed_TPM.txt
A12-30-4

tag: patient gleason score


title: Qm tumor 3


title: RNA-SEQ, A12-28-16, PCBN80, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-28-16 from patient PCBN80
processed_counts.txt
processed_TPM.txt
A12-28-16

tag: race


title: RNA-SEQ, A12-30-5, PCBN83, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-30-5 from patient PCBN83
processed_counts.txt
processed_TPM.txt
A12-30-5

tag: pathologic stage


title: Qm tumor 1

tag: genotype


title: RNA-SEQ, A12-28-17, PCBN81, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-28-17 from patient PCBN81
processed_counts.txt
processed_TPM.txt
A12-28-17

tag: disease state


title: RNA-SEQ, A12-29-32, PCBN80, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-29-32 from patient PCBN80
processed_counts.txt
processed_TPM.txt
A12-29-32

tag: patient id


title: Qm tumor 2


title: Qpm tumor 10

source_name: Qpm tumor


title: RNA-SEQ, A12-29-29, PCBN79, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-29-29 from patient PCBN79
processed_counts.txt
processed_TPM.txt
A12-29-29

tag: gender


title: Qpm tumor 9


title: RNA-SEQ, A12-28-18, PCBN82, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-28-18 from patient PCBN82
processed_counts.txt
processed_TPM.txt
A12-28-18

tag: age


title: RNA-SEQ, A12-29-30, PCBN79, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-29-30 from patient PCBN79
processed_counts.txt
processed_TPM.txt
A12-29-30

tag: 5-year disease status


title: RNA-SEQ, A12-28-15, PCBN79, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-28-15 from patient PCBN79
processed_counts.txt
processed_TPM.txt
A12-28-15

tag: sample type


title: RNA-SEQ, A12-29-27, PCBN78, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-29-27 from patient PCBN78
processed_counts.txt
processed_TPM.txt
A12-29-27


title: RNA-SEQ, A12-29-28, PCBN78, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-29-28 from patient PCBN78
processed_counts.txt
processed_TPM.txt
A12-29-28


title: Qpm tumor 7

tag: genetic background


title: RNA-SEQ, A12-28-14, PCBN78, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-28-14 from patient PCBN78
processed_counts.txt
processed_TPM.txt
A12-28-14


title: Qpm tumor 5

tag: transgene


title: Qpm tumor 4

tag: tissue


title: Qm tumor 4


title: RNA-SEQ, A12-29-23, PCBN76, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-29-23 from patient PCBN76
processed_counts.txt
processed_TPM.txt
A12-29-23

tag: preoperative psa


title: Qpm tumor 3


title: Qpm tumor 2


title: Qpm tumor 1


title: RNA-SEQ, A12-29-26, PCBN77, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-29-26 from patient PCBN77
processed_counts.txt
processed_TPM.txt
A12-29-26

tag: sample gleason score


title: RNA-SEQ, A12-28-13, PCBN77, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-28-13 from patient PCBN77
processed_counts.txt
processed_TPM.txt
A12-28-13

tag: % tumor


title: RNA-SEQ, A12-29-24, PCBN76, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-29-24 from patient PCBN76
processed_counts.txt
processed_TPM.txt
A12-29-24

tag: % tumor-in-normal contamination


title: RNA-SEQ, A12-28-12, PCBN76, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-28-12 from patient PCBN76
processed_counts.txt
processed_TPM.txt
A12-28-12

tag: patient gleason score


title: RNA-SEQ, A12-29-19, PCBN74, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-29-19 from patient PCBN74
processed_counts.txt
processed_TPM.txt
A12-29-19

tag: race


title: RNA-SEQ, A12-29-21, PCBN75, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-29-21 from patient PCBN75
processed_counts.txt
processed_TPM.txt
A12-29-21

tag: pathologic stage


title: RNA-SEQ, A12-28-11, PCBN75, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-28-11 from patient PCBN75
processed_counts.txt
processed_TPM.txt
A12-28-11


title: RNA-SEQ, A12-29-22, PCBN75, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-29-22 from patient PCBN75
processed_counts.txt
processed_TPM.txt
A12-29-22


title: RNA-SEQ, A12-29-20, PCBN74, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-29-20 from patient PCBN74
processed_counts.txt
processed_TPM.txt
A12-29-20


title: RNA-SEQ, A12-29-17, PCBN73, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-29-17 from patient PCBN73
processed_counts.txt
processed_TPM.txt
A12-29-17


title: RNA-SEQ, A12-28-10, PCBN74, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-28-10 from patient PCBN74
processed_counts.txt
processed_TPM.txt
A12-28-10


title: Qpm tumor 8

tag: genotype


title: RNA-SEQ, A12-29-18, PCBN73, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-29-18 from patient PCBN73
processed_counts.txt
processed_TPM.txt
A12-29-18

tag: disease state


title: RNA-SEQ, A12-28-9, PCBN73, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-28-9 from patient PCBN73
processed_counts.txt
processed_TPM.txt
A12-28-9

tag: patient id


title: RNA-SEQ, A12-29-15, PCBN72, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-29-15 from patient PCBN72
processed_counts.txt
processed_TPM.txt
A12-29-15

tag: gender


title: RNA-SEQ, A12-29-16, PCBN72, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-29-16 from patient PCBN72
processed_counts.txt
processed_TPM.txt
A12-29-16

tag: age


title: RNA-SEQ, A12-28-8, PCBN72, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-28-8 from patient PCBN72
processed_counts.txt
processed_TPM.txt
A12-28-8

tag: 5-year disease status


title: RNA-SEQ, A12-29-25, PCBN77, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-29-25 from patient PCBN77
processed_counts.txt
processed_TPM.txt
A12-29-25

tag: sample type


title: RNA-SEQ, A12-29-13, PCBN71, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-29-13 from patient PCBN71
processed_counts.txt
processed_TPM.txt
A12-29-13


title: RNA-SEQ, A12-28-7, PCBN71, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-28-7 from patient PCBN71
processed_counts.txt
processed_TPM.txt
A12-28-7


title: RNA-SEQ, A12-29-14, PCBN71, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-29-14 from patient PCBN71
processed_counts.txt
processed_TPM.txt
A12-29-14


title: RNA-SEQ, A12-29-12, PCBN70, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-29-12 from patient PCBN70
processed_counts.txt
processed_TPM.txt
A12-29-12


title: RNA-SEQ, A12-29-11, PCBN70, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-29-11 from patient PCBN70
processed_counts.txt
processed_TPM.txt
A12-29-11


title: RNA-SEQ, A12-28-6, PCBN70, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-28-6 from patient PCBN70
processed_counts.txt
processed_TPM.txt
A12-28-6


title: RNA-SEQ, A12-29-9, PCBN69, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-29-9 from patient PCBN69
processed_counts.txt
processed_TPM.txt
A12-29-9


title: RNA-SEQ, A12-29-7, PCBN68, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-29-7 from patient PCBN68
processed_counts.txt
processed_TPM.txt
A12-29-7


title: RNA-SEQ, A12-29-8, PCBN68, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-29-8 from patient PCBN68
processed_counts.txt
processed_TPM.txt
A12-29-8


title: RNA-SEQ, A12-29-5, PCBN67, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-29-5 from patient PCBN67
processed_counts.txt
processed_TPM.txt
A12-29-5


title: RNA-SEQ, A12-29-10, PCBN69, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-29-10 from patient PCBN69
processed_counts.txt
processed_TPM.txt
A12-29-10


title: RNA-SEQ, A12-60-3, PCBN67, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-60-3 from patient PCBN67
processed_counts.txt
processed_TPM.txt
A12-60-3


title: RNA-SEQ, A12-28-3, PCBN67, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-28-3 from patient PCBN67
processed_counts.txt
processed_TPM.txt
A12-28-3


title: Qpm tumor 6

tag: genetic background


title: RNA-SEQ, A12-28-4, PCBN68, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-28-4 from patient PCBN68
processed_counts.txt
processed_TPM.txt
A12-28-4


title: RNA-SEQ, A12-29-6, PCBN67, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-29-6 from patient PCBN67
processed_counts.txt
processed_TPM.txt
A12-29-6


title: RNA-SEQ, A12-29-3, PCBN66, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-29-3 from patient PCBN66
processed_counts.txt
processed_TPM.txt
A12-29-3

value: UNKNOWN


title: RNA-SEQ, A12-29-4, PCBN66, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-29-4 from patient PCBN66
processed_counts.txt
processed_TPM.txt
A12-29-4

value: prostate cancer


title: CTRPRE027

city: Kanagawa

first: Satoko

last: Takizawa

address: kamakurashi

country: Japan

institute: Toray industries inc

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.).

data_processing: The presence of miRNA was determined based on a corresponding microarray signal of greater than [the mean + 2 × standard deviation] of the negative controls signal, of which the top and bottom ranked ones by signal intensity were removed. Once a miRNA was considered present, the mean signal of the negative controls of which the top and bottom 5% ranked by signal intensity were removed was subtracted from the miRNA signal. When the signal value was negative (or undetEsophageal Cancerted) after background subtraction, the value was replaced by 0.1 on a base 2 logarithm scale.

source_name: Serum

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

tag: Sex

value: F

value: Healthy

tag: treatment

value: serum


title: CTRPRE026

value: M

tag: tissue


title: RNA-SEQ, A12-28-2, PCBN66, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-28-2 from patient PCBN66
processed_counts.txt
processed_TPM.txt
A12-28-2

value: male

tag: preoperative psa

tag: sample gleason score


title: RNA-SEQ, A12-28-5, PCBN69, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-28-5 from patient PCBN69
processed_counts.txt
processed_TPM.txt
A12-28-5

tag: % tumor

tag: % tumor-in-normal contamination

value: WHITE


title: CTRPRE025


title: RNA-SEQ, A12-29-1, PCBN65, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-29-1 from patient PCBN65
processed_counts.txt
processed_TPM.txt
A12-29-1

tag: patient gleason score

tag: race

value: remission


title: RNA-SEQ, A12-29-2, PCBN65, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-29-2 from patient PCBN65
processed_counts.txt
processed_TPM.txt
A12-29-2

tag: pathologic stage


title: CTRPRE023

tag: disease state


title: CTRPRE021


title: CTRPRE022


title: RNA-SEQ, A12-28-1, PCBN65, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-28-1 from patient PCBN65
processed_counts.txt
processed_TPM.txt
A12-28-1

tag: patient id


title: RNA-SEQ, A12-22-7, PCBN64, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-22-7 from patient PCBN64
processed_counts.txt
processed_TPM.txt
A12-22-7

tag: gender


title: RNA-SEQ, A12-22-8, PCBN64, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-22-8 from patient PCBN64
processed_counts.txt
processed_TPM.txt
A12-22-8

tag: age


title: CTRPRE020


title: CTRPRE019


title: RNA-SEQ, A12-19-16, PCBN64, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-19-16 from patient PCBN64
processed_counts.txt
processed_TPM.txt
A12-19-16

tag: 5-year disease status


title: CTRPRE024


title: RNA-SEQ, A12-22-5, PCBN63, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-22-5 from patient PCBN63
processed_counts.txt
processed_TPM.txt
A12-22-5

tag: sample type


title: RNA-SEQ, A12-22-6, PCBN63, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-22-6 from patient PCBN63
processed_counts.txt
processed_TPM.txt
A12-22-6


title: CTRPRE018


title: CTRPRE013


title: CTRPRE014


title: RNA-SEQ, A12-22-3, PCBN62, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-22-3 from patient PCBN62
processed_counts.txt
processed_TPM.txt
A12-22-3

value: NATIVE AMERICAN


title: CTRPRE017


title: RNA-SEQ, A12-19-15, PCBN63, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-19-15 from patient PCBN63
processed_counts.txt
processed_TPM.txt
A12-19-15


title: CTRPRE016


title: CTRPRE012


title: CTRPRE010


title: RNA-SEQ, A12-19-14, PCBN62, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-19-14 from patient PCBN62
processed_counts.txt
processed_TPM.txt
A12-19-14


title: CTRPRE011


title: CTRPRE009


title: RNA-SEQ, A12-22-2, PCBN61, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-22-2 from patient PCBN61
processed_counts.txt
processed_TPM.txt
A12-22-2


title: RNA-SEQ, A12-22-1, PCBN61, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-22-1 from patient PCBN61
processed_counts.txt
processed_TPM.txt
A12-22-1

value: BENIGN


title: RNA-SEQ, A12-19-13, PCBN61, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-19-13 from patient PCBN61
processed_counts.txt
processed_TPM.txt
A12-19-13


title: RNA-SEQ, A12-19-12, PCBN60, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-19-12 from patient PCBN60
processed_counts.txt
processed_TPM.txt
A12-19-12

value: recurrence


title: RNA-SEQ, A12-21-27, PCBN60, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-21-27 from patient PCBN60
processed_counts.txt
processed_TPM.txt
A12-21-27


title: RNA-SEQ, A12-21-28, PCBN60, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-21-28 from patient PCBN60
processed_counts.txt
processed_TPM.txt
A12-21-28

value: TUMOR


title: RNA-SEQ, A12-21-25, PCBN59, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-21-25 from patient PCBN59
processed_counts.txt
processed_TPM.txt
A12-21-25


title: CTRPRE007


title: CTRPRE008


title: CTRPRE015


title: RNA-SEQ, A12-22-4, PCBN62, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-22-4 from patient PCBN62
processed_counts.txt
processed_TPM.txt
A12-22-4


title: CTRPRE006


title: CTRPRE005


title: CTRPRE004


title: RNA-SEQ, A12-21-23, PCBN58, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-21-23 from patient PCBN58
processed_counts.txt
processed_TPM.txt
A12-21-23


title: CTRPRE003


title: CTRPRE001


title: OVRPOST004

value: OS

value: Post


title: CTRPRE002


title: OVRPOST007


title: OVRPOST006


title: OVRPOST005


title: RNA-SEQ, A12-21-24, PCBN58, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-21-24 from patient PCBN58
processed_counts.txt
processed_TPM.txt
A12-21-24


title: RNA-SEQ, A12-21-21, PCBN57, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-21-21 from patient PCBN57
processed_counts.txt
processed_TPM.txt
A12-21-21


title: RNA-SEQ, A12-19-10, PCBN58, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-19-10 from patient PCBN58
processed_counts.txt
processed_TPM.txt
A12-19-10


title: control

city: Shanghai

first: shi

last: song

state: Shanghai

institute: Shanghai OE Biotech Co., Ltd

description: one control jejunum sample from the non infected piglet

data_processing:
The Cell Ranger software pipeline (version 3.1.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

molecule: polyA RNA

organism: Sus scrofa

source_name: piglet jejunum tissue

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: 5 days old


title: RNA-SEQ, A12-19-9, PCBN57, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-19-9 from patient PCBN57
processed_counts.txt
processed_TPM.txt
A12-19-9


title: RNA-SEQ, A12-21-19, PCBN56, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-21-19 from patient PCBN56
processed_counts.txt
processed_TPM.txt
A12-21-19


title: case

description: one case jejunum sample from the PEDV infected piglet


title: OVRPOST003


title: RNA-SEQ, A12-21-20, PCBN56, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-21-20 from patient PCBN56
processed_counts.txt
processed_TPM.txt
A12-21-20


title: unaffected 6

city: Tehran

first: kolsoum

last: InanlooRahatloo

address: velenjak

country: Iran

institute: University of social welfare and rehabilitation sciences

data_processing:
Paired-end fastq sequence reads from each sample were quality and adaptor trimmed using trimmomatic (v0.36).
The trimmed reads were subsequently aligned to the UCSC human reference genome assembly hg19 and the human transcriptome sequences (Ensembl v70) using the ultrafast aligner the Spliced Transcripts Alignment to a Reference software (STAR, v. 2.5.3) with maximum tolerated mismatches set at 10 and the outSAMstrandField intronMotif option enabled8.
The trimmed reads were also assembled to hg19 using the Tophat v2.1.1 (http://tophat.cbcb.umd.edu) with the Illumina-supplied hg19 gene-model annotation file (gtf annotation). The number of reads uniquely mapped to each gene were counted using Python-HTSeq count module (version 0.5.3p9)
Differential expression analysis was performed on the counts data using DESeq2 (version 1.1.0, http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html)10.
Cufflinks (http://cufflinks.cbcb.umd.edu) was used to estimate the gene expression level (FPKM, fragments per kilobase of exon per million fragments mapped).
Briefly, after read counts were retrieved for each gene, differential gene expression was compared using the DESeq2 package in the following four groups: 1) two patients with mutation in CCNT2 gene and all 6 controls, 2) two patients with mutation in CDK9 gene and all 6 controls, 3) two patients with mutation in TAF2 gene and all 6 controls, and 4) all 6 patients and all 6 controls. Read counts for the patients and controls were compared to determine the log2-fold change in abundance of each transcript. In some cases, raw p-values were then adjusted for multiple testing with the Benjamini-Hochberg procedure. For CCNT2 and TAF2 family, genes with p-value of 0.01 or less and for CDK9 family genes with adjusted p-value of 0.05 or less were termed as differentially expressed genes. The analysis was performed using R 2.15 and R 3.1.3.
Genome_build: hg19
Supplementary_files_format_and_content: processed data files are in excel format and contains differentially expressed genes with p value, fold change and q value.

source_name: Blood

extract_protocol:
RNA extraction using QIAamp RNA Blood Kit (Qiagen)
Illumina TruSeq stranded total RNA with ribo-zero globin
Ten micrograms of total RNA was used to generate index-tagged paired-end cDNA libraries. Sample preparation was performed using TruSeq stranded total RNA with ribo-zero globin sample preparation kit (Illumina). Briefly, rRNA and globin RNA was depleted using Globin Removal Mix (Illumina). RNA fragmentation was performed using RNA Fragmentation Reagents (Life Technologies) to obtain 200–300 bp fragments. First strand cDNA was generated using the Superscript II Reverse Transcriptase and random hexamers (Life technologies). Second strand cDNA was synthesized and 3’ ends adenylation was performed (Illumina). Illumina sequencing adapters were ligated to cDNA and PCR amplification was performed on the adapter-ligated cDNA with 2X Phusion DNA polymerase Master Mix (New England Biolabs). Samples were sequenced 100bp (2×100) paired-end on Illumina HiSeq2500

tag: condition

value: unaffected


title: RNA-SEQ, A12-19-8, PCBN56, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-19-8 from patient PCBN56
processed_counts.txt
processed_TPM.txt
A12-19-8


title: RNA-SEQ, A12-19-11, PCBN59, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-19-11 from patient PCBN59
processed_counts.txt
processed_TPM.txt
A12-19-11


title: RNA-SEQ, A12-21-26, PCBN59, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-21-26 from patient PCBN59
processed_counts.txt
processed_TPM.txt
A12-21-26


title: OVRPOST002

tag: Sex


title: unaffected 5


title: OVRPOST001

tag: treatment


title: RNA-SEQ, A12-21-18, PCBN55, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-21-18 from patient PCBN55
processed_counts.txt
processed_TPM.txt
A12-21-18


title: OVRPRE006

value: Pre

tag: tissue


title: OVRPRE005


title: RNA-SEQ, A12-19-7, PCBN55, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-19-7 from patient PCBN55
processed_counts.txt
processed_TPM.txt
A12-19-7

value: prostate cancer

tag: preoperative psa


title: RNA-SEQ, A12-21-22, PCBN57, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-21-22 from patient PCBN57
processed_counts.txt
processed_TPM.txt
A12-21-22

tag: sample gleason score

value: no tumor


title: unaffected 3


title: unaffected 4


title: RNA-SEQ, A12-19-6, PCBN54, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-19-6 from patient PCBN54
processed_counts.txt
processed_TPM.txt
A12-19-6

tag: % tumor


title: unaffected 2


title: RNA-SEQ, A12-21-15, PCBN54, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-21-15 from patient PCBN54
processed_counts.txt
processed_TPM.txt
A12-21-15

tag: % tumor-in-normal contamination


title: RNA-SEQ, A12-21-16, PCBN54, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-21-16 from patient PCBN54
processed_counts.txt
processed_TPM.txt
A12-21-16

tag: patient gleason score


title: RNA-SEQ, A12-21-14, PCBN53, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-21-14 from patient PCBN53
processed_counts.txt
processed_TPM.txt
A12-21-14

tag: race


title: unaffected 1


title: RNA-SEQ, A12-21-13, PCBN53, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-21-13 from patient PCBN53
processed_counts.txt
processed_TPM.txt
A12-21-13

tag: pathologic stage


title: RNA-SEQ, A12-19-5, PCBN53, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-19-5 from patient PCBN53
processed_counts.txt
processed_TPM.txt
A12-19-5

tag: disease state


title: RNA-SEQ, A12-21-17, PCBN55, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-21-17 from patient PCBN55
processed_counts.txt
processed_TPM.txt
A12-21-17

tag: patient id


title: OVRPRE007


title: RNA-SEQ, A12-21-12, PCBN52, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-21-12 from patient PCBN52
processed_counts.txt
processed_TPM.txt
A12-21-12

tag: gender


title: OVRPRE004

value: F

tag: age


title: RNA-SEQ, A12-19-4, PCBN52, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-19-4 from patient PCBN52
processed_counts.txt
processed_TPM.txt
A12-19-4

tag: 5-year disease status


title: OVRPRE003

value: serum


title: RNA-SEQ, A12-21-9, PCBN51, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-21-9 from patient PCBN51
processed_counts.txt
processed_TPM.txt
A12-21-9

tag: sample type


title: affected 2

tag: condition

value: affected


title: affected 1


title: RNA-SEQ, A12-21-10, PCBN51, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-21-10 from patient PCBN51
processed_counts.txt
processed_TPM.txt
A12-21-10

value: male


title: OVRPRE002

tag: Sex


title: OVRPRE001

tag: treatment


title: PBCPOST023

value: PBC

tag: tissue


title: RNA-SEQ, A12-21-7, PCBN50, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-21-7 from patient PCBN50
processed_counts.txt
processed_TPM.txt
A12-21-7

tag: preoperative psa

value: WHITE

value: remission


title: PBCPOST025


title: RNA-SEQ, A12-21-8, PCBN50, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-21-8 from patient PCBN50
processed_counts.txt
processed_TPM.txt
A12-21-8

tag: sample gleason score


title: PDX6

city: Chapel Hill

middle: M.

last: Perou

state: NC

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

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

institute: University of North Carolina at Chapel Hill

description: 190205_UNC17-D00216_0599_ACD1FJANXX_TAAGTGGT-CTTAAGCC_S8_L002

data_processing:
Purity-filtered reads were aligned to the human reference GRCh38/hg38 genome using Spliced Transcripts Aligned to a Reference (STAR) version 2.4.2a1. Transcript (GENCODE v22) abundance estimates were generated by Salmon version 0.6.02 in ‘-quant’ mode, based on the STAR alignments
Raw read counts for all RNAseq samples normalized to fixed upper quartile3
RNAseq normalized gene counts were then log2 transformed (zeros were unchanged) using Cluster 3.0 v1.52
Genes were filtered for those expressed in 70% of samples
Matrix was median centered and column standardized using R studio v1.1.463
Genome_build: hg38
Supplementary_files_format_and_content: txt file. Content: 40n samples logtrans, 70% filtered, median-centered, column standardized

source_name: Patient-derived xenograft - WHIM2

growth_protocol: We obtained 9 flash frozen paired normal and ER+ breast tumor samples, 15 TNBC breast tumor samples, and 7 flash frozen tumor samples from 2 TNBC PDX models (WHIM2 and WHIM30)

extract_protocol:
total RNA extracted using Qiagen Rneasy Mini Kit
mRNAseq libraries were made from total RNA using the Illumina TruSeq mRNA sample preparation kit and sequenced on an Illumina HiSeq 2500 using a 2x50bp configuration

treatment_protocol: Untreated

tag: tumor status

value: PDX

value: Basal

tag: tnbc-high tertiles

value: High

tag: er-high tertiles

value: Low


title: RNA-SEQ, A12-19-2, PCBN50, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-19-2 from patient PCBN50
processed_counts.txt
processed_TPM.txt
A12-19-2

tag: % tumor

tag: % tumor-in-normal contamination

tag: patient gleason score

tag: race


title: RNA-SEQ, A12-21-11, PCBN52, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-21-11 from patient PCBN52
processed_counts.txt
processed_TPM.txt
A12-21-11

source_name: prostate tissue

tag: disease state

tag: patient id

tag: gender

tag: pathologic stage

value: BENIGN


title: RNA-SEQ, A12-21-6, PCBN49, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-21-6 from patient PCBN49
processed_counts.txt
processed_TPM.txt
A12-21-6

tag: age

tag: 5-year disease status

value: recurrence

tag: sample type

value: TUMOR


title: RNA-SEQ, A12-21-5, PCBN49, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-21-5 from patient PCBN49
processed_counts.txt
processed_TPM.txt
A12-21-5


title: PDX5

description: 190205_UNC17-D00216_0599_ACD1FJANXX_CTACGACA-GAGTCCAA_S6_L002


title: PBCPOST021

tag: Sex

value: M

tag: treatment

value: Post

tag: tissue


title: PDX4

description: 190205_UNC17-D00216_0599_ACD1FJANXX_TCGTAGTG-AGACTTGG_S5_L002

source_name: Patient-derived xenograft - WHIM30

tag: tumor status


title: PDX3

description: 190205_UNC17-D00216_0599_ACD1FJANXX_GATTCTGC-GACGAGAG_S4_L001

tag: tnbc-high tertiles


title: PBCPOST020


title: RNA-SEQ, A12-19-1, PCBN49, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-19-1 from patient PCBN49
processed_counts.txt
processed_TPM.txt
A12-19-1

source_name: buffy coat

value: prostate cancer

tag: preoperative psa

tag: sample gleason score


title: RNA-SEQ, A12-21-4, PCBN48, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-21-4 from patient PCBN48
processed_counts.txt
processed_TPM.txt
A12-21-4

tag: % tumor

tag: % tumor-in-normal contamination

value: HISPANIC


title: PDX2

description: 190205_UNC17-D00216_0599_ACD1FJANXX_AGCCTCAT-AGTAGAGA_S3_L001

tag: er-high tertiles


title: PBCPOST019

value: F

tag: disease state

value: serum


title: RNA-SEQ, A12-18-24, PCBN48, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-18-24 from patient PCBN48
processed_counts.txt
processed_TPM.txt
A12-18-24

tag: patient id

value: male

tag: patient gleason score

tag: race


title: RNA-SEQ, A12-21-1, PCBN47, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-21-1 from patient PCBN47
processed_counts.txt
processed_TPM.txt
A12-21-1

tag: gender

value: BLACK

tag: pathologic stage

tag: age


title: RNA-SEQ, A12-21-3, PCBN48, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-21-3 from patient PCBN48
processed_counts.txt
processed_TPM.txt
A12-21-3

tag: 5-year disease status

tag: sample type


title: PDX1

description: 190205_UNC17-D00216_0599_ACD1FJANXX_CGTTAGAA-TTCAGGTC_S2_L001


title: RNA-SEQ, A12-21-2, PCBN47, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-21-2 from patient PCBN47
processed_counts.txt
processed_TPM.txt
A12-21-2


title: PBCPOST018

tag: Sex

value: PBC

tag: treatment

tag: tissue


title: RNA-SEQ, A12-19-3, PCBN51, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-19-3 from patient PCBN51
processed_counts.txt
processed_TPM.txt
A12-19-3

tag: preoperative psa

value: WHITE

value: remission


title: RNA-SEQ, A12-18-22, PCBN46, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-18-22 from patient PCBN46
processed_counts.txt
processed_TPM.txt
A12-18-22

tag: sample gleason score


title: PBCPOST016


title: RNA-SEQ, A12-20-28, PCBN46, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-20-28 from patient PCBN46
processed_counts.txt
processed_TPM.txt
A12-20-28

tag: % tumor


title: TNBC2

description: 190205_UNC17-D00216_0599_ACD1FJANXX_TACCGAGG-CCTGAACT_S1_L001

source_name: Triple negative breast cancer

tag: tumor status

value: TNBC

value: Basal

tag: tnbc-high tertiles

value: Medium


title: RNA-SEQ, A12-20-27, PCBN46, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-20-27 from patient PCBN46
processed_counts.txt
processed_TPM.txt
A12-20-27

tag: disease state

tag: % tumor-in-normal contamination

value: BENIGN


title: RNA-SEQ, A12-20-25, PCBN45, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-20-25 from patient PCBN45
processed_counts.txt
processed_TPM.txt
A12-20-25

tag: patient id

tag: patient gleason score


title: PBCPOST015


title: TNBC15

description: 181205_UNC17-D00216_0591_ACD0YEANXX_GGCATTCT-CTAGCTTG_S31_L008

tag: er-high tertiles


title: RNA-SEQ, A12-18-21, PCBN45, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-18-21 from patient PCBN45
processed_counts.txt
processed_TPM.txt
A12-18-21

tag: gender

tag: race

tag: pathologic stage


title: PBCPOST017

tag: age


title: TNBC4

description: 181205_UNC17-D00216_0591_ACD0YEANXX_CCGTGAAG-CAGTGGAT_S29_L008

value: Normal-like

value: Low

value: High


title: RNA-SEQ, A12-18-23, PCBN47, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-18-23 from patient PCBN47
processed_counts.txt
processed_TPM.txt
A12-18-23

tag: 5-year disease status

tag: sample type


title: RNA-SEQ, A12-18-20, PCBN44, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-18-20 from patient PCBN44
processed_counts.txt
processed_TPM.txt
A12-18-20


title: TNBC7

description: 181205_UNC17-D00216_0591_ACD0YEANXX_TTACAGGA-TGACAAGC_S30_L008


title: RNA-SEQ, A12-20-23, PCBN44, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-20-23 from patient PCBN44
processed_counts.txt
processed_TPM.txt
A12-20-23


title: RNA-SEQ, A12-20-21, PCBN43, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-20-21 from patient PCBN43
processed_counts.txt
processed_TPM.txt
A12-20-21


title: RNA-SEQ, A12-20-24, PCBN44, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-20-24 from patient PCBN44
processed_counts.txt
processed_TPM.txt
A12-20-24

value: TUMOR


title: PBCPOST013

tag: Sex

value: M

tag: treatment

value: Post

tag: tissue


title: PBCPOST012

value: F


title: RNA-SEQ, A12-20-22, PCBN43, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-20-22 from patient PCBN43
processed_counts.txt
processed_TPM.txt
A12-20-22

value: prostate cancer

tag: preoperative psa

tag: sample gleason score

tag: % tumor


title: PBCPOST014

tag: disease state

value: serum


title: RNA-SEQ, A12-18-19, PCBN43, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-18-19 from patient PCBN43
processed_counts.txt
processed_TPM.txt
A12-18-19

value: male

tag: % tumor-in-normal contamination


title: TNBC14

description: 181205_UNC17-D00216_0591_ACD0YEANXX_TCCAACGC-TTGGACTT_S28_L007

tag: tumor status

tag: tnbc-high tertiles


title: PBCPOST011

value: PBC


title: RNA-SEQ, A12-20-19, PCBN42, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-20-19 from patient PCBN42
processed_counts.txt
processed_TPM.txt
A12-20-19

tag: patient id

tag: patient gleason score

value: WHITE


title: PBCPOST010


title: RNA-SEQ, A12-18-18, PCBN42, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-18-18 from patient PCBN42
processed_counts.txt
processed_TPM.txt
A12-18-18

tag: gender

tag: race

value: remission


title: TNBC3

description: 181205_UNC17-D00216_0591_ACD0YEANXX_AATGCCTC-TCGATCCA_S32_L008

value: TNBC

tag: er-high tertiles


title: RNA-SEQ, A12-20-20, PCBN42, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-20-20 from patient PCBN42
processed_counts.txt
processed_TPM.txt
A12-20-20

tag: pathologic stage

tag: age

tag: 5-year disease status


title: TNBC1

description: 181205_UNC17-D00216_0591_ACD0YEANXX_CTTGGTAT-CCAAGTCC_S27_L007

value: LumB


title: RNA-SEQ, A12-20-26, PCBN45, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-20-26 from patient PCBN45
processed_counts.txt
processed_TPM.txt
A12-20-26

tag: sample type


title: TNBC5

description: 181205_UNC17-D00216_0591_ACD0YEANXX_GTCGGAGC-GGTTATAA_S26_L007

value: Basal


title: RNA-SEQ, A12-20-17, PCBN41, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-20-17 from patient PCBN41
processed_counts.txt
processed_TPM.txt
A12-20-17

value: recurrence

value: BENIGN


title: RNA-SEQ, A12-20-18, PCBN41, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-20-18 from patient PCBN41
processed_counts.txt
processed_TPM.txt
A12-20-18


title: RNA-SEQ, A12-20-15, PCBN40, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-20-15 from patient PCBN40
processed_counts.txt
processed_TPM.txt
A12-20-15


title: TNBC6

description: 181205_UNC17-D00216_0591_ACD0YEANXX_ACTAAGAT-AACCGCGG_S25_L007

value: Low


title: PBCPOST008

tag: Sex

tag: treatment

tag: tissue


title: RNA-SEQ, A12-18-17, PCBN41, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-18-17 from patient PCBN41
processed_counts.txt
processed_TPM.txt
A12-18-17

tag: preoperative psa

tag: sample gleason score

tag: % tumor


title: RNA-SEQ, A12-18-16, PCBN40, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-18-16 from patient PCBN40
processed_counts.txt
processed_TPM.txt
A12-18-16

tag: disease state

tag: % tumor-in-normal contamination


title: RNA-SEQ, A12-20-16, PCBN40, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-20-16 from patient PCBN40
processed_counts.txt
processed_TPM.txt
A12-20-16

tag: patient id


title: TNBC9

description: 181205_UNC17-D00216_0591_ACD0YEANXX_ATGAGGCC-GTTAATTG_S24_L006

tag: tumor status

tag: tnbc-high tertiles

value: High


title: RNA-SEQ, A12-18-15, PCBN39, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-18-15 from patient PCBN39
processed_counts.txt
processed_TPM.txt
A12-18-15

tag: gender

tag: patient gleason score

tag: race


title: TNBC12

description: 181205_UNC17-D00216_0591_ACD0YEANXX_GCAGAATT-ACCGGCCA_S21_L006

value: Medium

tag: er-high tertiles


title: RNA-SEQ, A12-20-14, PCBN39, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-20-14 from patient PCBN39
processed_counts.txt
processed_TPM.txt
A12-20-14

tag: pathologic stage

tag: age

tag: 5-year disease status

value: TUMOR


title: PBCPOST005

tag: Sex

tag: treatment

value: Post


title: RNA-SEQ, A12-20-13, PCBN39, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-20-13 from patient PCBN39
processed_counts.txt
processed_TPM.txt
A12-20-13

tag: preoperative psa

tag: sample type


title: PBCPOST006

value: F

tag: tissue


title: RNA-SEQ, A12-18-14, PCBN38, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-18-14 from patient PCBN38
processed_counts.txt
processed_TPM.txt
A12-18-14

tag: disease state

value: prostate cancer

tag: sample gleason score

tag: % tumor


title: TNBC11

description: 181205_UNC17-D00216_0591_ACD0YEANXX_GGTACCTT-AAGACGTC_S23_L006

tag: tumor status


title: PDX7

description: 190205_UNC17-D00216_0599_ACD1FJANXX_CGGACAAC-TCCGGATT_S7_L002

value: PDX

tag: tnbc-high tertiles


title: PBCPOST009

value: M

value: serum


title: RNA-SEQ, A12-20-9, PCBN37, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-20-9 from patient PCBN37
processed_counts.txt
processed_TPM.txt
A12-20-9

tag: patient id

tag: gender

value: male

tag: % tumor-in-normal contamination

value: WHITE


title: PBCPOST004

value: PBC


title: RNA-SEQ, A12-20-12, PCBN38, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-20-12 from patient PCBN38
processed_counts.txt
processed_TPM.txt
A12-20-12

tag: patient gleason score

tag: race

value: remission


title: RNA-SEQ, A12-20-10, PCBN37, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-20-10 from patient PCBN37
processed_counts.txt
processed_TPM.txt
A12-20-10

tag: pathologic stage

tag: age


title: TNBC8

description: 181205_UNC17-D00216_0591_ACD0YEANXX_GCACGGAC-GTCTCGCA_S20_L005

value: TNBC

value: Basal

tag: er-high tertiles


title: PBCPOST003

tag: Sex

tag: treatment


title: TNBC10

description: 181205_UNC17-D00216_0591_ACD0YEANXX_ATGTAAGT-ACTCTATG_S17_L005

value: Normal-like


title: RNA-SEQ, A12-18-13, PCBN37, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-18-13 from patient PCBN37
processed_counts.txt
processed_TPM.txt
A12-18-13

tag: preoperative psa

tag: 5-year disease status

value: recurrence

tag: sample type


title: PBCPOST002

tag: disease state

tag: tissue


title: PBCPOST007


title: RNA-SEQ, A12-20-7, PCBN36, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-20-7 from patient PCBN36
processed_counts.txt
processed_TPM.txt
A12-20-7

tag: sample gleason score

tag: % tumor

value: BENIGN


title: PBCPOST001


title: RNA-SEQ, A12-20-8, PCBN36, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-20-8 from patient PCBN36
processed_counts.txt
processed_TPM.txt
A12-20-8

tag: patient id


title: TNBC13

description: 181205_UNC17-D00216_0591_ACD0YEANXX_AACGTTCC-GGAGTACT_S22_L006

tag: tumor status

tag: tnbc-high tertiles

value: Low

value: Medium


title: RNA-SEQ, A12-18-12, PCBN36, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-18-12 from patient PCBN36
processed_counts.txt
processed_TPM.txt
A12-18-12

tag: gender

tag: % tumor-in-normal contamination

tag: patient gleason score


title: Normal-9

description: 181205_UNC17-D00216_0591_ACD0YEANXX_CGGCGTGA-GCGCCTGT_S18_L005

source_name: Paired Normal Tissue

value: Normal

value: High


title: RNA-SEQ, A12-20-11, PCBN38, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-20-11 from patient PCBN38
processed_counts.txt
processed_TPM.txt
A12-20-11

value: prostate cancer

tag: race

tag: pathologic stage

tag: age


title: RNA-SEQ, A12-20-6, PCBN35, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-20-6 from patient PCBN35
processed_counts.txt
processed_TPM.txt
A12-20-6

value: TUMOR


title: Normal-8

description: 181205_UNC17-D00216_0591_ACD0YEANXX_TAATACAG-ATATTCAC_S19_L005

tag: er-high tertiles