title: Ga-DRR1: Gossypium arboreum drought stressed root tissue replicate 1

city: Lahore

first: Muhammad

middle: Bilal

last: Sarwar

state: Punjab

address: 87-west canal bank road, Thokar Niaz baig

department: National Center of Excellence in Molecular Biology

country: Pakistan

institute: University of the Punjab

hyb_protocol: Oligonucleotide printed microarray slides were hybridized with cDNA target according to the protocol established by ArrayIt. 2x HybIT hybridization solution (cat#HHS) by Arrayit was used for hybridization. The microarray slides were inserted into the hybridization cassette chambers and hybridization solution was aliquoted onto the slides with a ratio of 2.0 µl of hybridization solution per cm2 area of each slide. The cassette was submerged in a water bath at a set temperature of 42 °C for 18 hours after which they were washed and scanned subsequently. Separate hybridization was carried out for each sample using single dye

scan_protocol: Slides were scanned with UC4 Scanner at respective wavelength (Genomic Solutions®) and Intensities were observed for each sample

data_processing: GeneSpring GX data analysis software by Agilent was used for data analysis and customized technology was created providing conditions and parameters for our in-house built experimental procedure. Data was uploaded in the form of csv files into software after initial background correction. Normalization was carried out by using Percentile Shift method and Scaling option was also applied to overcome inter array differences. Hierarchical Clustering was performed from normalized intensity values using differentially expressed sequence information keeping fold change cutoff as 1.5 (Dalman et al., 2012),  associated with each sample.

organism: Gossypium arboreum

source_name: drought stressed root tissue

label_protocol: Aminoallyl labelled target cDNA was prepared and coupled with Cy3 dye for every sample.  For this 20ug total RNA was used for cDNA synthesis by using SuperscriptTM III Reverse Transcriptase enzyme (cat#18080093) as per manufacturer recommendation with modified (2:3) in ratio 50X aminoallyl-dNTP mixture.  QIAquick PCR Purification Kit by Qiagen cat # 28106 was used for cDNA purification with some modifications. 20µl 0.1M (pH:9) freshly mads buffer was used to elute the cDNA from column. cDNA quality and quantity parameters was checked by ND-1000. SpeedvacTM concentrator by Thermo Scientific (SAVANT DNA120) was to concentrate the volume up to 5µl for dye coupling.

growth_protocol: plants were grow in green house condition in pots have soil misture with ratio (1:1:1)

extract_protocol: Modified CTAB method was used to extract the RNA from the leaf sample, further purifcation of extracted samples were performend with Ambion RNA extraction kit

treatment_protocol: Stop giving water to treated groups

tag: kingdom

value: Plant

value: Root

tag: Stage

value: 6 week old plants

tag: treatment period

value: 10 Days


title: Ga-CRR2: Gossypium arboreum control root tissue tissue replicate 2

status: Public on Jun 03 2021

type: RNA

molecule: total RNA

source_name: normal root tissue

tag: tissue


title: Ga-CRR1: Gossypium arboreum control root tissue tissue replicate 1


title: Ga-CRR3: Gossypium arboreum control root tissue tissue replicate 3


title: Ga-DRR2: Gossypium arboreum drought stressed root tissue replicate 2


title: Ga-DRR3: Gossypium arboreum drought stressed root tissue replicate 3


title: Ga-LDR2: Gossypium arboreum drought stressed leaf tissue replicate 2

source_name: drought stressed leaf tissue

value: Leaf


title: Ga-LDR1: Gossypium arboreum drought stressed leaf tissue replicate 1


title: Ga-LCR3: Gossypium arboreum control leaf tissue replicate 3

source_name: normal leaf tissue


title: Ga-LCR2: Gossypium arboreum control leaf tissue replicate 2


title: Ga-LDR3: Gossypium arboreum drought stressed leaf tissue replicate 3


title: Gh-LDR1: Gossypium hirsutum leaf drought stressed tissue replicate 1

organism: Gossypium hirsutum


title: Gh-CRR2: Gossypium hirsutum control root tissue replicate 2


title: Gh-LDR3: Gossypium hirsutum leaf drought stressed tissue replicate 3


title: Gh-CRR1: Gossypium hirsutum control root tissue replicate 1


title: Gh-DRR1: Gossypium hirsutum drought stressed root tissue replicate 1


title: Gh-DRR2: Gossypium hirsutum drought stressed root tissue replicate 2


title: Gh-CRR3: Gossypium hirsutum control root tissue replicate 3


title: Gh-LCR2: Gossypium hirsutum leaf control tissue replicate 2


title: Gh-LDR2: Gossypium hirsutum leaf drought stressed tissue replicate 2


title: Ga-LCR1: Gossypium arboreum control leaf tissue replicate 1


title: Gh-DRR3: Gossypium hirsutum drought stressed root tissue replicate 3


title: Gh-LCR1: Gossypium hirsutum leaf control tissue replicate 1


title: si-Thbs1 rep2

type: SRA

city: Shanghai

first: Lijuan

last: Pei

address: CHIFENG ROAD 67

country: China

institute: Tongji University

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rn6 or mm10 whole genome using hisat2 v2.1.0 with parameters -p 8 --dta -x -1 -2 -S
Raw transcripts were assembled using the StringTie (v1.3.4). Counts per million (cpm) were calculated by the edgeR (v3.20.9).
Genome_build: rn6 or mm10
Supplementary_files_format_and_content: gene count

organism: Rattus norvegicus

growth_protocol: Neonatal rat’s hearts were harvested from 1-day old SD rats. Next, the ventricles were separated and cut into pieces (1-3 mm2), then they were dissociated in 0.25% trypsin (Gibco, 15090046) at 4 °C overnight. Then the tissue was transferred to 0.1% collagenase type Ⅱ (Worthington, LS004176) to further digest at 37°C at 145 rpm, and the supernatant was collected into DMEM medium containing 10% FBS every 5 min. The digestion procedure was repeated 3-4 times. When the tissue was completely digested, the supernatant was centrifuged at 1500 rpm for 6 min. Then, the cells were plated in DMEM medium which containing 10% FBS, 100 unit/ml penicillin and 100 mg/ml streptomycin at 15 cm dishes at an atmosphere of 5% CO2 at 37℃ for 90 min, to remove cells that are easier attached the dishes than cardiomyocytes. Finally, the culture supernatant was collected, plated in the plates which were coated with collagen and then incubated 24 h in an atmosphere of 5% CO2 at 37 ℃ with the same medium. After 24 h, the medium was changed to cardiomyocyte medium: DMEM: F12 (1:1) medium containing 0.25% FBS, 3 mM sodium pyruvate, 0.1 mM Vitamin C and 2 mM L-Glu.

extract_protocol:
The total RNA was extracted by TRIzol extraction reagent (Invitrogen, 15596018). Furthermore, the purity and concentration of RNA were examined by measuring the absorbance value at 260 and 280 nm.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: NRVCs were add Reelin vs PBS for 48h ,transfected with 50 nM si-Vldlr or si-Thbs1 and si-control for 60h, transduced with AAV9-cTnT-Vldlr or AAV9-CMV-GFP for 72h.

tag: strain

value: SD rat

tag: genotype/treatment

value: heart

tag: cell type

value: Neoatal Rat Ventricular Cardiomyocytes (NRVC)


title: si-Control_t rep1


title: si-Thbs1 rep1


title: Gh-LCR3: Gossypium hirsutum leaf control tissue replicate 3


title: si-Control_t rep2


title: si-Vldlr rep1

value: si-Vldlr


title: Reelin rep1

value: Reelin


title: Vldlr OE rep2

source_name: NRVC_Vldlr OE

value: Vldlr OE


title: Reelin rep2


title: PBS rep2

value: PBS


title: Vldlr OE rep1


title: Control rep2

value: Control


title: si-Control_v rep2


title: IFNb_TIC_3

city: New York

first: Philip

last: Hasel

address: 435 E 30th St

country: USA

institute: NYU Langone Medical Centre

data_processing:
Sequenced reads were trimmed for adaptor sequences, aligned to the mm10 reference genome using HISAT2 followed by transcript assembly and quantification using StringTie
Differential gene expression was assessed using DESeq2. Expression values are given as FPKM.
Genome_build: mm10
Supplementary_files_format_and_content: processed file includes FPKM, padj (DESeq2) and log 2 fold changes

source_name: P5 rat brain

extract_protocol:
RNA was extracted using the Agilent Absolutely Total RNA Purification Kit
cDNA was generated using the SMART-seq HT kit and libraries were generated using the Nextera XT kit (Takara Bio).

treatment_protocol: Primary immunopanned astrocytes were treated with IFNg (3 ng/ml), IFNb (1000 U/ml), TNFa (30 ng/ml)+IL1a (3 ng/ml) +C1q (40 ng/ml) or combincations thereof for 24h, RNA collected and sequenced on a NovaSeq6000

tag: stimulation

value: IFNb (1000 U/ml)+TIC

value: Primary rat astrocytes


title: si-Vldlr rep2


title: IFNg_TIC_2

value: IFNg (3 ng/ml)+TIC


title: TIC_2

value: TNFa (30 ng/ml)+IL1a (3 ng/ml) +C1q (40 ng/ml)


title: IFNb_TIC_2


title: IFNb_TIC_1


title: IFNb_3

value: IFNb (1000 U/ml)


title: IFNg_TIC_3


title: IFNb_1


title: IFNg_1

value: IFNg (3 ng/ml)


title: IFNg_TIC_1


title: TIC_3


title: Control_3


title: IFNb_2


title: IFNg_3


title: IFNg_2


title: Control_1


title: si-Control_v rep1


title: PBS rep1


title: Neuron Control Day 22 rep3

city: Houston

first: Juan

last: Botas

state: TX

address: 1250 Moursund St.

institute: Texas Children's Neurological Research Institute

data_processing:
Illumina Casava v.1.8.2 software was used for basecalling
Reads were aligned using Bowtie version 0.12.0
Expression was quantified using RSEM version 1.1.19
Differential expression analysis was performed using DESeq2
Genome_build: dm3
Supplementary_files_format_and_content: Normalized counts by gene from RSEM

organism: Drosophila melanogaster

source_name: Head, elav-GAL4/+

growth_protocol: Drosophila expressing the N-terminal construct and corresponding controls were obtained at 7,9, and 11 days post-eclosion for the neuronal driver, and at 5, 7, and 8 days post-eclosion for the glial driver. Drosophila expressing the full-length construct, samples were obtained at 18, 20, and 22 days post-eclosion for both the neuronal and glial driver.

extract_protocol:
At the selected ages, animals were transferred to 1.5ml tubes, flash frozen in liquid nitrogen, vigorously shaken and then sieved to collect 50 heads/genotype/replica (~5mg tissue/replica). Total RNA was extracted using the miRNeasy Mini Kit (Qiagen Cat. # 210074).
Illumina TruSeq Stranded mRNA sample preparation kit (Illumina Cat. #20020595)

treatment_protocol: The neuronal N-terminal, glial N-terminal, and glial FL model Drosophila were raised at 28oC. The neuronal full-length model Drosophila were raised at 29oC. For each genotype at each timepoint, we also collected an equivalent number of control animals (elav-GAL4 or repo-GAL4) that were raised in the same conditions.

value: Neuron

tag: age

tag: cultured temperature

tag: genotype

value: Head


title: WTB Wild-Type replicate 1

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description: GCaMP6 is expressed from AAVS1

data_processing:
RNA-Seq data was aligned to the human hg19 reference genome and transcriptome (Ensembl 72) using the software STAR. To accurately detect diverse alternative splicing events in iPSC-CM RNA-Seq, we adapted a recently developed Percent Spliced In (PSI) splicing method called MultiPath-PSI. MultiPath-PSI is available through AltAnalyze version 2.1.1, requiring aligned BAM files as input and was extensively benchmarked against other local splicing variation approaches (http://altanalyze.readthedocs.io/en/latest/Algorithms/#multipath-psi-splicing-algorithm). For gene expression Quantification Kallisto (https://pachterlab.github.io/kallisto/) was used.
Genome_build: hg19
Supplementary_files_format_and_content: PSI splicing events predicted from MultiPath-PSI

organism: Homo sapiens

source_name: iPS cell-derived cardiomyocytes

growth_protocol: The iPS cell lines were differentiated into iPS-CMs using the method that controls WNT signaling by small molecules 16. Briefly, iPS cells were seeded at 1.25–2.5x10^4 cells/cm2 onto 12-well plates coated with 80 μg/μl growth factor-reduced Matrigel (BD Biosciences) in mTeSR1 supplemented with 10 μM Y-27632 (Selleckchem) for 24 h (day –3). mTeSR1 medium was changed daily for the next 2 days. On day 0, iPS cells were treated with 12 μM CHIR99021 (CHIR) (Tocris) in RPMI supplemented with B-27 (RPMI/B27) without insulin (Life Technologies) for exactly 24 h. On day 1, the culture medium was replaced with fresh RPMI/B27 without insulin and maintained for 48 h. On day 3, cells were treated with 5 μM IWP2 (Tocris) in RPMI/B27 without insulin and maintained for 48 h. On day 5, fresh RPMI/B27 without insulin was added to the cells, and on day 7, the medium was switched to RPMI/B27 with insulin. Afterward, fresh RPMI/B27 with insulin was added to the cells every 3 days. We used a metabolic selection protocol with glucose-free DMEM containing lactate to purify iPS-CMs. Cells were replated on day 15–18 of differentiation, and then on day 20–22 media were replaced with DMEM (without glucose, with sodium pyruvate, Thermo Fisher Scientific) supplemented with Glutamax, non-essential amino acids, and buffered lactate (4 mM). Stock-buffered lactate solution was prepared by dissolving sodium L-lactate powder (Sigma-Aldrich) at 1 M concentration in 1 M HEPES solution. Lactate media were exchanged 2–3 times, with a total exposure of 48 hours for each treatment. After the final lactate treatment (day 24–28), media were changed to RPMI/B27. The purified iPS-CMs at day 30 were harvested for RNA-Seq or cryopreserved for further analyses.

extract_protocol: Total RNA was purified from iPS-CMs by using TRIzol and PureLink RNA Mini Kit (Thermo Fisher Scientific) according manufactures’ instructions. The RNAseq libraries were prepared from the purified RNA by using TruSeq RNA Library Prep Kit v2 (Illumina). Paired-end 100 bp RNAseq was performed with HiSeq (Illumina). An average of ~90 million reads were obtained from this iPS-cell RNA-Seq data (45-182 million PE reads).

tag: cell line

value: WTB from a healthy female patient

value: iPS cell-derived cardiomyocytes

tag: differentiation

value: WNT modulation method day 26

tag: purification

value: Lactate method (PMID:23168164)

value: Wild-Type


title: WTB RBM20 R636S Het replicate 2

description: GCaMP6 is expressed from AAVS1

value: R636S Het


title: Neuron Control Day 22 rep1


title: WTB Wild-Type replicate 2

description: GCaMP6 is expressed from AAVS1


title: WTB RBM20 R636S Het replicate 1

description: GCaMP6 is expressed from AAVS1


title: Neuron Control Day 20 rep2


title: Neuron Control Day 20 rep1


title: TIC_1


title: Neuron Control Day 18 rep2


title: Neuron Control Day 22 rep2


title: Neuron Control Day 18 rep3


title: Neuron Full-length mHTT Day 11 rep2

source_name: Head, elav-GAL4/+; UAS-HTTFLQ200/+

value: Full-length mHTT


title: Neuron Control Day 18 rep1


title: Neuron Full-length mHTT Day 9 rep2


title: Neuron Full-length mHTT Day 11 rep3


title: Control_2

value: PBS


title: Neuron Full-length mHTT Day 11 rep1


title: Neuron Full-length mHTT Day 7 rep3


title: Neuron Full-length mHTT Day 9 rep1


title: Neuron Full-length mHTT Day 7 rep1


title: Neuron Control Day 11 rep2

value: Control


title: Neuron Full-length mHTT Day 7 rep2


title: Neuron Control Day 11 rep1


title: Neuron Control Day 9 rep3


title: Neuron Control Day 9 rep2


title: Neuron Control Day 20 rep3


title: Neuron Control Day 9 rep1


title: Neuron N-terminal mHTT Day 11 rep3

source_name: Head, elav-GAL4/+; UAS-HTTNT231Q128/+

value: N-terminal mHTT


title: Neuron Control Day 7 rep3


title: Neuron N-terminal mHTT Day 11 rep2


title: Neuron Full-length mHTT Day 9 rep3


title: Neuron N-terminal mHTT Day 9 rep2


title: Neuron N-terminal mHTT Day 9 rep3


title: Neuron N-terminal mHTT Day 9 rep1


title: Neuron N-terminal mHTT Day 7 rep3


title: Glia Control Day 22 rep1

source_name: Head, repo-GAL4/+

value: Glia


title: Glia Control Day 20 rep2


title: Neuron N-terminal mHTT Day 7 rep2


title: Glia Control Day 22 rep3


title: Neuron Control Day 11 rep3


title: Neuron N-terminal mHTT Day 7 rep1


title: Glia Control Day 20 rep1


title: Glial Control Day 20 rep3


title: Glia Control Day 22 rep2


title: Glial Control Day 18 rep3


title: Glia Control Day 18 rep1


title: Glia Full-length mHTT Day 22 rep2

source_name: Head, repo-GAL4/+; UAS-HTTFLQ200/+


title: Glia Full-length mHTT Day 20 rep2


title: Glia Full-length mHTT Day 22 rep3


title: Glia Full-length mHTT Day 22 rep1


title: Glia Control Day 18 rep2


title: Glial Full-length mHTT Day 20 rep3


title: Neuron Control Day 7 rep2


title: Glial Control Day 8 rep3


title: Neuron Control Day 7 rep1


title: Glia Full-length mHTT Day 20 rep1


title: Glial Control Day 7 rep3


title: Glia Control Day 8 rep2


title: Glia Control Day 8 rep1


title: Glia Control Day 5 rep2


title: Glia Control Day 7 rep2


title: Glia Control Day 7 rep1


title: Glia Full-length mHTT Day 18 rep2


title: Neuron N-terminal mHTT Day 11 rep1


title: Glia Control Day 5 rep3


title: Glia N-terminal mHTT Day 5 rep2

source_name: Head, repo-GAL4/+; UAS-HTTNT231Q128/+


title: Glia N-terminal mHTT Day 7 rep3


title: Glial N-terminal mHTT Day 8 rep3


title: Glial N-terminal mHTT Day 5 rep3


title: Glia N-terminal mHTT Day 7 rep2


title: Glia Full-length mHTT Day 18 rep3


title: Glia N-terminal mHTT Day 8 rep1


title: Glia N-terminal mHTT Day 8 rep2


title: Glia Control Day 5 rep1


title: Glia N-terminal mHTT Day 5 rep1


title: Glia Full-length mHTT Day 18 rep1


title: WT_30_MG_18

city: Ithaca

first: Jeffrey

last: Pleiss

state: NY

address: 453 Biotech

institute: Cornell University

description:
Nascent RNA
WT_30_Combined_total_counts_raw.txt
WT_30_Combined_concordant_unspliced_counts_raw.txt
WT_30_Combined_concordant_unspliced_counts_norm.txt

data_processing:
Trimming was performed via Fastp version 0.20.0 with parameters: --disable_trim_poly_g --adapter_sequence CTGTCTCTTATACACATCT --adapter_sequence_r2 CTGTCTCTTATACACATCT
Alignment was performed via STAR (version 2.7.2b) with the following parameters --clip5pNbases 7 0 --peOverlapNbasesMin 5 --peOverlapMMp 0.1 --outFilterMultimapNmax 1 --alignIntronMin 10 --alignIntronMax 1100 --outSAMattributes All --runThreadN 8 --outSAMunmapped Within KeepPairs --alignSJoverhangMin 3 --alignSplicedMateMapLmin 3 --alignMatesGapMax 3000 --alignEndsType EndToEnd6
Target intron isoform counting was performed using custom scripts.
Genome_build: SGD S. cerevisiae reference genome assembly R64-1-124
Supplementary_files_format_and_content: tab deliminated files of feature counts (rows) by sample (columns)

organism: Saccharomyces cerevisiae

source_name: Filter collected cells from culture medium

growth_protocol: Yeast strains were grown in standard synthetic medium (CSM)

extract_protocol:
Total RNA was extracted using standard hot phenol chloroform extraction. A fixed quantity of total RNA plus a fixed quantity of 4-thiouracil labeled total s. pombe RNA were combined for each sample. 4-thiouracil labeled RNA was purified via biotinylation and pull-down with streptavidin beads.
Libraries were constructed via multiplexed primer extension sequencing (MPE-seq)

treatment_protocol: Actively growing cells were treated with 4-thiouracil. Samples were collected in regular intervals in a time course. Sample collection involved filter collection followed by rapid freezing in dry ice.

tag: labeling time (sec)

tag: replicate

tag: rna population

value: Nascent RNA


title: WT_30_MG_16


title: WT_30_MG_19


title: WT_30_MG_17


title: WT_30_MG_20


title: WT_30_MG_14


title: Glia N-terminal mHTT Day 7 rep1


title: WT_30_MG_12


title: WT_30_MG_15


title: WT_30_MG_11


title: WT_30_MG_10


title: WT_30_MG_8


title: WT_30_MG_6


title: WT_30_MG_4


title: WT_30_MG_5


title: WT_30_MG_2


title: WT_30_MG_3


title: WT_30_MG_1


title: WT_30_MG_13


title: WT_30_MG_7


title: WT_30_MG_9


title: prostate_cancer_primary_1148

city: San Diego

first: Elai

last: Davicioni

state: California

address: 9725 Lusk Blvd

institute: Veracyte, Inc

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data was normalized uisng SCAN (SCAN.UPC package from Bioconductor)
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg38.core.mps

label: biotin

source_name: FFPE prostate cancer

label_protocol: RNA was amplified, fragmented and biotinylated using the WT-Ovation FFPE system (NuGen, San Carlos, CA) according to the manufacturer’s recommendations with minor modifications

extract_protocol: After histopathologic review of formalin-fixed, paraffin-embedded (FFPE) tumor blocks from each case by an expert pathologists, the tumor block with the index lesion was selected for specimen processing. The index lesion was identified as the prostatectomy FFPE block with the highest pathologic Gleason grade, regardless of its volume. Two 0.6-mm diameter tissue biopsy punch tool cores were sampled to enrich for tumor cells from the highest Gleason grade in the index lesion and placed in a microfuge tube for RNA extraction.

value: FFPE prostate cancer

tag: primary gleason

tag: secondary gleason

tag: decipher risk group

value: Higher

tag: race

value: White (Non-Hispanic)


title: prostate_cancer_primary_1145

tag: tissue

value: Lower


title: prostate_cancer_primary_1144


title: prostate_cancer_primary_1152


title: prostate_cancer_primary_1149


title: prostate_cancer_primary_1143


title: prostate_cancer_primary_1150

value: Average


title: prostate_cancer_primary_1146


title: prostate_cancer_primary_1140


title: prostate_cancer_primary_1147


title: prostate_cancer_primary_1151


title: prostate_cancer_primary_1142


title: prostate_cancer_primary_1136


title: prostate_cancer_primary_1137


title: prostate_cancer_primary_1138


title: prostate_cancer_primary_1141


title: prostate_cancer_primary_1131


title: prostate_cancer_primary_1133


title: prostate_cancer_primary_1139


title: prostate_cancer_primary_1132


title: prostate_cancer_primary_1130


title: prostate_cancer_primary_1128


title: prostate_cancer_primary_1129


title: prostate_cancer_primary_1135


title: Control rep1

tag: strain

value: SD rat

tag: genotype/treatment

value: heart

value: Neoatal Rat Ventricular Cardiomyocytes (NRVC)


title: prostate_cancer_primary_1134


title: prostate_cancer_primary_1124


title: prostate_cancer_primary_1127


title: prostate_cancer_primary_1125


title: prostate_cancer_primary_1126


title: prostate_cancer_primary_1116


title: prostate_cancer_primary_1119


title: prostate_cancer_primary_1122


title: prostate_cancer_primary_1121


title: prostate_cancer_primary_1115


title: prostate_cancer_primary_1112


title: prostate_cancer_primary_1111


title: prostate_cancer_primary_1120


title: prostate_cancer_primary_1114


title: prostate_cancer_primary_1117


title: prostate_cancer_primary_1110


title: prostate_cancer_primary_1109


title: prostate_cancer_primary_1118


title: prostate_cancer_primary_1106


title: prostate_cancer_primary_1123


title: prostate_cancer_primary_1103


title: prostate_cancer_primary_1113


title: prostate_cancer_primary_1099


title: prostate_cancer_primary_1108


title: prostate_cancer_primary_1105


title: prostate_cancer_primary_1101


title: prostate_cancer_primary_1098


title: prostate_cancer_primary_1104


title: prostate_cancer_primary_1094


title: prostate_cancer_primary_1097


title: prostate_cancer_primary_1100


title: prostate_cancer_primary_1095


title: prostate_cancer_primary_1088


title: prostate_cancer_primary_1087


title: prostate_cancer_primary_1093


title: prostate_cancer_primary_1089


title: prostate_cancer_primary_1107


title: prostate_cancer_primary_1092


title: prostate_cancer_primary_1102


title: prostate_cancer_primary_1084


title: prostate_cancer_primary_1080


title: prostate_cancer_primary_1090


title: prostate_cancer_primary_1096


title: prostate_cancer_primary_1091


title: prostate_cancer_primary_1079


title: prostate_cancer_primary_1077


title: prostate_cancer_primary_1076


title: prostate_cancer_primary_1082


title: prostate_cancer_primary_1075


title: prostate_cancer_primary_1086


title: prostate_cancer_primary_1083


title: prostate_cancer_primary_1081


title: prostate_cancer_primary_1072


title: prostate_cancer_primary_1078


title: prostate_cancer_primary_1073


title: prostate_cancer_primary_1085


title: prostate_cancer_primary_1074


title: prostate_cancer_primary_1071


title: prostate_cancer_primary_1062


title: prostate_cancer_primary_1064


title: prostate_cancer_primary_1068


title: prostate_cancer_primary_1070


title: prostate_cancer_primary_1059


title: prostate_cancer_primary_1069


title: prostate_cancer_primary_1065


title: prostate_cancer_primary_1067


title: prostate_cancer_primary_1066


title: prostate_cancer_primary_1061


title: prostate_cancer_primary_1058


title: prostate_cancer_primary_1063


title: prostate_cancer_primary_1055


title: prostate_cancer_primary_1057


title: prostate_cancer_primary_1051


title: prostate_cancer_primary_1056


title: prostate_cancer_primary_1050


title: prostate_cancer_primary_1053


title: prostate_cancer_primary_1046


title: prostate_cancer_primary_1044


title: prostate_cancer_primary_1054


title: prostate_cancer_primary_1052


title: prostate_cancer_primary_1047


title: prostate_cancer_primary_1045


title: prostate_cancer_primary_1049


title: prostate_cancer_primary_1060


title: prostate_cancer_primary_1043


title: prostate_cancer_primary_1048


title: prostate_cancer_primary_1042


title: prostate_cancer_primary_1039


title: prostate_cancer_primary_1037


title: prostate_cancer_primary_1041


title: prostate_cancer_primary_1035


title: prostate_cancer_primary_1034


title: prostate_cancer_primary_1040


title: prostate_cancer_primary_1036


title: prostate_cancer_primary_1033


title: prostate_cancer_primary_1038


title: prostate_cancer_primary_1026


title: prostate_cancer_primary_1030


title: prostate_cancer_primary_1023


title: prostate_cancer_primary_1029


title: prostate_cancer_primary_1028


title: prostate_cancer_primary_1021


title: prostate_cancer_primary_1025


title: prostate_cancer_primary_1018


title: prostate_cancer_primary_1020


title: prostate_cancer_primary_1024


title: prostate_cancer_primary_1027


title: prostate_cancer_primary_1015


title: prostate_cancer_primary_1017


title: prostate_cancer_primary_1016


title: prostate_cancer_primary_1011


title: prostate_cancer_primary_1031


title: prostate_cancer_primary_1013


title: prostate_cancer_primary_1007


title: prostate_cancer_primary_1014


title: prostate_cancer_primary_1004


title: prostate_cancer_primary_1019


title: prostate_cancer_primary_1010


title: prostate_cancer_primary_1008


title: prostate_cancer_primary_1012


title: prostate_cancer_primary_1005


title: prostate_cancer_primary_1006


title: prostate_cancer_primary_1003


title: prostate_cancer_primary_1009


title: prostate_cancer_primary_1002


title: prostate_cancer_primary_996


title: prostate_cancer_primary_997


title: prostate_cancer_primary_994


title: prostate_cancer_primary_1000


title: prostate_cancer_primary_998


title: prostate_cancer_primary_993


title: prostate_cancer_primary_995


title: prostate_cancer_primary_989


title: prostate_cancer_primary_988


title: prostate_cancer_primary_992


title: prostate_cancer_primary_999


title: prostate_cancer_primary_990


title: prostate_cancer_primary_991


title: prostate_cancer_primary_987


title: prostate_cancer_primary_986


title: prostate_cancer_primary_985


title: prostate_cancer_primary_981


title: prostate_cancer_primary_984


title: prostate_cancer_primary_980


title: prostate_cancer_primary_983


title: prostate_cancer_primary_982


title: prostate_cancer_primary_976


title: prostate_cancer_primary_1001


title: prostate_cancer_primary_975


title: prostate_cancer_primary_977


title: prostate_cancer_primary_973


title: prostate_cancer_primary_974


title: prostate_cancer_primary_970


title: prostate_cancer_primary_1022


title: prostate_cancer_primary_978


title: prostate_cancer_primary_967


title: prostate_cancer_primary_966


title: prostate_cancer_primary_969


title: prostate_cancer_primary_971


title: prostate_cancer_primary_965


title: prostate_cancer_primary_968


title: prostate_cancer_primary_958


title: prostate_cancer_primary_964


title: prostate_cancer_primary_961


title: prostate_cancer_primary_960


title: prostate_cancer_primary_962


title: prostate_cancer_primary_957


title: prostate_cancer_primary_963


title: prostate_cancer_primary_959


title: prostate_cancer_primary_956


title: prostate_cancer_primary_949


title: prostate_cancer_primary_952


title: prostate_cancer_primary_955


title: prostate_cancer_primary_950


title: prostate_cancer_primary_954


title: prostate_cancer_primary_948


title: prostate_cancer_primary_951


title: prostate_cancer_primary_947


title: prostate_cancer_primary_953


title: prostate_cancer_primary_945


title: prostate_cancer_primary_943


title: prostate_cancer_primary_946


title: prostate_cancer_primary_942


title: prostate_cancer_primary_940


title: prostate_cancer_primary_941


title: prostate_cancer_primary_944


title: prostate_cancer_primary_935


title: prostate_cancer_primary_932


title: prostate_cancer_primary_936


title: prostate_cancer_primary_933


title: prostate_cancer_primary_930


title: prostate_cancer_primary_931


title: prostate_cancer_primary_938


title: prostate_cancer_primary_929


title: prostate_cancer_primary_934


title: prostate_cancer_primary_937


title: prostate_cancer_primary_921


title: prostate_cancer_primary_1032


title: prostate_cancer_primary_922


title: prostate_cancer_primary_928


title: prostate_cancer_primary_923


title: prostate_cancer_primary_926


title: prostate_cancer_primary_925


title: prostate_cancer_primary_924


title: prostate_cancer_primary_939


title: prostate_cancer_primary_919


title: prostate_cancer_primary_920


title: prostate_cancer_primary_917


title: prostate_cancer_primary_918


title: prostate_cancer_primary_927


title: prostate_cancer_primary_913


title: prostate_cancer_primary_910


title: prostate_cancer_primary_914


title: prostate_cancer_primary_915


title: prostate_cancer_primary_905


title: prostate_cancer_primary_912


title: prostate_cancer_primary_916


title: prostate_cancer_primary_903


title: prostate_cancer_primary_906


title: prostate_cancer_primary_909


title: prostate_cancer_primary_904


title: prostate_cancer_primary_908


title: prostate_cancer_primary_907


title: prostate_cancer_primary_893


title: prostate_cancer_primary_902


title: prostate_cancer_primary_896


title: prostate_cancer_primary_901


title: prostate_cancer_primary_911


title: prostate_cancer_primary_899


title: prostate_cancer_primary_891


title: prostate_cancer_primary_888


title: prostate_cancer_primary_900


title: prostate_cancer_primary_979


title: prostate_cancer_primary_894


title: prostate_cancer_primary_884


title: prostate_cancer_primary_897


title: prostate_cancer_primary_895


title: prostate_cancer_primary_887


title: prostate_cancer_primary_972


title: prostate_cancer_primary_886


title: prostate_cancer_primary_889


title: prostate_cancer_primary_885


title: prostate_cancer_primary_890


title: prostate_cancer_primary_892


title: prostate_cancer_primary_898


title: prostate_cancer_primary_881


title: prostate_cancer_primary_882


title: prostate_cancer_primary_880


title: prostate_cancer_primary_878


title: prostate_cancer_primary_876


title: prostate_cancer_primary_883


title: prostate_cancer_primary_871


title: prostate_cancer_primary_877


title: prostate_cancer_primary_873


title: prostate_cancer_primary_872


title: prostate_cancer_primary_875


title: prostate_cancer_primary_874


title: prostate_cancer_primary_870


title: prostate_cancer_primary_868


title: prostate_cancer_primary_869


title: prostate_cancer_primary_865


title: prostate_cancer_primary_866


title: prostate_cancer_primary_867


title: prostate_cancer_primary_863


title: prostate_cancer_primary_862


title: prostate_cancer_primary_864


title: prostate_cancer_primary_861


title: prostate_cancer_primary_858


title: prostate_cancer_primary_856


title: prostate_cancer_primary_857


title: prostate_cancer_primary_854


title: prostate_cancer_primary_853


title: prostate_cancer_primary_852


title: prostate_cancer_primary_851


title: prostate_cancer_primary_850


title: prostate_cancer_primary_845


title: prostate_cancer_primary_848


title: prostate_cancer_primary_859


title: prostate_cancer_primary_879


title: prostate_cancer_primary_855


title: prostate_cancer_primary_860


title: prostate_cancer_primary_843


title: prostate_cancer_primary_846


title: prostate_cancer_primary_840


title: prostate_cancer_primary_844


title: prostate_cancer_primary_842


title: prostate_cancer_primary_839


title: prostate_cancer_primary_833


title: prostate_cancer_primary_838


title: prostate_cancer_primary_837


title: prostate_cancer_primary_847


title: prostate_cancer_primary_836


title: prostate_cancer_primary_828


title: prostate_cancer_primary_830


title: prostate_cancer_primary_832


title: prostate_cancer_primary_829


title: prostate_cancer_primary_831


title: prostate_cancer_primary_827


title: prostate_cancer_primary_823


title: prostate_cancer_primary_825


title: prostate_cancer_primary_835


title: prostate_cancer_primary_826


title: prostate_cancer_primary_824


title: prostate_cancer_primary_822


title: prostate_cancer_primary_821


title: prostate_cancer_primary_816


title: prostate_cancer_primary_820


title: prostate_cancer_primary_834


title: prostate_cancer_primary_819


title: prostate_cancer_primary_814


title: prostate_cancer_primary_817


title: prostate_cancer_primary_813


title: prostate_cancer_primary_841


title: prostate_cancer_primary_818


title: prostate_cancer_primary_805


title: prostate_cancer_primary_804


title: prostate_cancer_primary_810


title: prostate_cancer_primary_801


title: prostate_cancer_primary_812


title: prostate_cancer_primary_808


title: prostate_cancer_primary_799


title: prostate_cancer_primary_800


title: prostate_cancer_primary_806


title: prostate_cancer_primary_802


title: prostate_cancer_primary_815


title: prostate_cancer_primary_795


title: prostate_cancer_primary_794


title: prostate_cancer_primary_811


title: prostate_cancer_primary_809


title: prostate_cancer_primary_807


title: prostate_cancer_primary_798


title: prostate_cancer_primary_797


title: prostate_cancer_primary_803


title: prostate_cancer_primary_793


title: prostate_cancer_primary_796


title: prostate_cancer_primary_792


title: prostate_cancer_primary_790


title: prostate_cancer_primary_791


title: prostate_cancer_primary_789


title: prostate_cancer_primary_787


title: prostate_cancer_primary_780


title: prostate_cancer_primary_785


title: prostate_cancer_primary_788


title: prostate_cancer_primary_776


title: prostate_cancer_primary_784


title: prostate_cancer_primary_779


title: prostate_cancer_primary_774


title: prostate_cancer_primary_783


title: prostate_cancer_primary_782


title: prostate_cancer_primary_773


title: prostate_cancer_primary_778


title: prostate_cancer_primary_786


title: prostate_cancer_primary_772


title: prostate_cancer_primary_777


title: prostate_cancer_primary_775


title: prostate_cancer_primary_769


title: prostate_cancer_primary_768


title: prostate_cancer_primary_781


title: prostate_cancer_primary_766


title: prostate_cancer_primary_763


title: prostate_cancer_primary_762


title: prostate_cancer_primary_765


title: prostate_cancer_primary_761


title: prostate_cancer_primary_771


title: prostate_cancer_primary_767


title: prostate_cancer_primary_764


title: prostate_cancer_primary_770


title: prostate_cancer_primary_849


title: prostate_cancer_primary_758


title: prostate_cancer_primary_759


title: prostate_cancer_primary_756


title: prostate_cancer_primary_755


title: prostate_cancer_primary_754


title: prostate_cancer_primary_750


title: prostate_cancer_primary_757


title: prostate_cancer_primary_753


title: prostate_cancer_primary_744


title: prostate_cancer_primary_752


title: prostate_cancer_primary_746


title: prostate_cancer_primary_742


title: prostate_cancer_primary_745


title: prostate_cancer_primary_760


title: prostate_cancer_primary_748


title: prostate_cancer_primary_751


title: prostate_cancer_primary_747


title: prostate_cancer_primary_736


title: prostate_cancer_primary_741


title: prostate_cancer_primary_743


title: prostate_cancer_primary_739


title: prostate_cancer_primary_740


title: prostate_cancer_primary_732


title: prostate_cancer_primary_735


title: prostate_cancer_primary_734


title: prostate_cancer_primary_738


title: prostate_cancer_primary_733


title: prostate_cancer_primary_729


title: prostate_cancer_primary_749


title: prostate_cancer_primary_737


title: prostate_cancer_primary_731


title: prostate_cancer_primary_730


title: prostate_cancer_primary_725


title: prostate_cancer_primary_723


title: prostate_cancer_primary_728


title: prostate_cancer_primary_727


title: prostate_cancer_primary_724


title: STING shRNA 2, 2'3'-cGAMP 2

city: Berkeley

first: Shally

middle: Rebecca

last: Margolis

state: CA

address: 415 Life Sciences

department: Molecular and Cell Biology

institute: UC Berkeley

data_processing:
fastq read quality was assessed using FastQC (v0.11.9)
Reads were pseudoaligned to the N. vectensis transcriptome (NCBI: GCF_000209225.1) and quantified using kallisto (v0.46.1)
Normalized read counts were generated using DESeq2
Genome_build: NCBI Nematostella vectensis Annotation Release 100 (Assembly Accesssion  GCF_000209225.1)
Supplementary_files_format_and_content: tab delimited txt files with normalized read counts for each sample and each gene

molecule: polyA RNA

organism: Nematostella vectensis

source_name: whole embryos

growth_protocol: Animals were maintained at room temperature in 1/3x sea water

extract_protocol:
For polyps, total RNA was extracted using Qiagen RNeasy Mini kits according to the manufacturer’s protocol. Embryos were homogenized in Trizol (Thermo Fisher Scientific) and RNA was extracted according to the manufacturer’s protocol
For polyps, libraries were prepared using WaferGen PrepX library prep kits with oligo dT beads for mRNA enrichment according to the manufacturer’s protocol. For embryos, libraries were prepared as follows: oligo dT beads from the KAPA mRNA Capture Kit (KK8581) were used for mRNA enrichment; fragmentation, adapter ligation and cDNA synthesis were performed using the KAPA RNA HyperPrep kit (KK8540); libraries were pooled evenly by molarity and sequenced to generate 25M read pairs per sample

treatment_protocol: Polyps were treated with 500μM CDNs for 24 hours; embryos with treated with 100μM 2'3'-cGAMP for 4 hours.

tag: treatment

tag: shRNA

value: STING 2


title: STING shRNA 2, untreated 2

value: untreated


title: STING shRNA 1, 2'3'-cGAMP 2

value: STING 1


title: prostate_cancer_primary_714


title: prostate_cancer_primary_716


title: prostate_cancer_primary_717


title: prostate_cancer_primary_722


title: STING shRNA 1, untreated 2


title: prostate_cancer_primary_711


title: prostate_cancer_primary_713


title: prostate_cancer_primary_707


title: prostate_cancer_primary_709


title: prostate_cancer_primary_708


title: prostate_cancer_primary_718


title: prostate_cancer_primary_720


title: prostate_cancer_primary_712


title: prostate_cancer_primary_726


title: prostate_cancer_primary_705


title: prostate_cancer_primary_715


title: STING shRNA 2, 2'3'-cGAMP 1


title: GFP shRNA, untreated 2

value: GFP


title: STING shRNA 1, untreated 1


title: prostate_cancer_primary_721


title: GFP shRNA, 2'3'-cGAMP 4


title: STING shRNA 1, 2'3'-cGAMP 1


title: GFP shRNA, 2'3'-cGAMP 3


title: GFP shRNA, untreated 1


title: STING shRNA 2, untreated 1


title: NFkB shRNA 1, 2'3'-cGAMP 2

value: NFkB 1


title: prostate_cancer_primary_704


title: STAT shRNA 1, 2'3'-cGAMP 2

value: STAT 1


title: GFP shRNA, 2'3'-cGAMP 5


title: prostate_cancer_primary_710


title: prostate_cancer_primary_703

value: African American


title: prostate_cancer_primary_701


title: prostate_cancer_primary_702


title: prostate_cancer_primary_700


title: STAT shRNA 2, 2'3'-cGAMP 2

value: STAT 2


title: prostate_cancer_primary_706


title: prostate_cancer_primary_699


title: prostate_cancer_primary_695


title: prostate_cancer_primary_697


title: prostate_cancer_primary_698


title: prostate_cancer_primary_696


title: prostate_cancer_primary_694


title: prostate_cancer_primary_693


title: NFkB shRNA 2, 2'3'-cGAMP 2

value: NFkB 2


title: prostate_cancer_primary_692

value: FFPE prostate cancer


title: STAT shRNA 2, 2'3'-cGAMP 1


title: GFP shRNA, 2'3'-cGAMP 2


title: NFkB shRNA 1, 2'3'-cGAMP 1


title: NFkB shRNA 2, 2'3'-cGAMP 1


title: GFP shRNA, 2'3'-cGAMP 1


title: prostate_cancer_primary_691


title: prostate_cancer_primary_719


title: prostate_cancer_primary_687


title: prostate_cancer_primary_688


title: prostate_cancer_primary_690


title: prostate_cancer_primary_689


title: STAT shRNA 1, 2'3'-cGAMP 1


title: prostate_cancer_primary_685


title: prostate_cancer_primary_684

value: Higher


title: MNase-ChIP-seq_H3-HA_Nrd1-AA_+Rap

city: Geneva

first: Julien

last: Soudet

address: 30 quai Ansermet

department: BICEL

country: Switzerland

institute: Université de Genève

library_source: genomic

data_processing:
RNA-seq:
Single-end reads were aligned to sacCer3 genome assembly using Bowtie2 (Langmead and Salzberg, 2012) with options ‘-k 20–end-to-end–sensitive -X 800’. PCR duplicates were removed from the analysis. BigWig coverage files were generated using Bam2wig function. Differential expression analysis was performed using the R/Bioconductor package DEseq on mRNA annotations Ensembl (Saccharomyces_cerevisiae.EF4.65.gtf). Antisense transcripts with a fold-change of at least 2 and multiple testing adjusted p-value lower than 0.05 were considered differentially expressed and defined as inducible Antisense Genes (iAS). Calculations of fold-changes were subsequently performed using the density files (bigWig files).
ChEC-seq:
Adapters were first removed from the paired-end reads using the Trim Galore! Tool with default options from the Galaxy server (Afgan et al., 2018). Paired-end reads were then aligned to sacCer3 genome assembly using (Langmead and Salzberg, 2012). PCR duplicates were removed from the analysis. DeepTools 2.0 (Ramirez et al., 2016) was then used through the bamCoverage function with size selection of fragments (0-120bp for TBP-ChEC and mainly 120-200bp for Hir2-ChEC) and counting of only the 3bp at the center of fragments.
MNase-seq:
Paired-end reads were aligned to sacCer3 genome assembly using Bowtie2 (Langmead and Salzberg, 2012). PCR duplicates were removed from the analysis. Then, deepTools 2.0 (Ramirez et al., 2016) was used through the bamCoverage function with size selection of fragments (120-200bp to visualize only proper nucleosomes and not “fragile nucleosomes” (Brahma and Henikoff, 2019)), counting only the 3bp at the center of fragments and counts per million (cpm) normalization.
MNase-ChIP-seq:
Paired-end reads were aligned to sacCer3 genome assembly using Bowtie2 (Langmead and Salzberg, 2012). PCR duplicates were removed from the analysis. Then, deepTools 2.0 (Ramirez et al., 2016) was used through the bamCoverage function with size selection of fragments (120-200bp to visualize only proper nucleosomes and not “fragile nucleosomes” (Brahma and Henikoff, 2019)), counting only the 3bp at the center of fragments and counts per million (cpm) normalization.
Genome_build: saccer3
Supplementary_files_format_and_content: NOT PROVIDED: REQUESTED

molecule: genomic DNA

growth_protocol: The Nrd1-AA strain transformed with the pGAL-H3-3xHA-URA3 plasmid (gift from Michel Strubin lab) was grown overnight in SC -URA +2% Raffinose at 30°C. Cells were then diluted to OD600nm0.2 to resume exponential growth until OD600nm 0.4. -factor (20ng/ml final concentration) was added to the culture for 3h at 30°C to synchronize cells in G1-phase. Galactose powder (2% final concentration) was then directly added to the medium to induce H3HA synthesis and the culture was split to add or not rapamycin (1 μg/ml final) for 1h. Cells were then processed for MNase-ChIP-seq as in (Gill et al., 2020). Newly synthesized H3HA was immunoprecipitated with an anti-HA antibody (anti-HA.11, 901502, BioLegend).

extract_protocol:
Cells were processed for MNase-ChIP-seq as in (Gill et al., 2020). Newly synthesized H3HA was immunoprecipitated with an anti-HA antibody (anti-HA.11, 901502, BioLegend).
Libraries were prepared using NEBnext Ultra DNA library prep kit for Illumina (NEB). Samples were paired-end sequenced at the iGE3 genomics platform of the University of Geneva.

treatment_protocol: Anchor-away of Nrd1 was induced by adding 1 μg/ml of rapamycin to the medium for 1 hour.

tag: genotype/variation

value: Plus Rapamycin 1h (1μg/ml)


title: MNase-seq_Nrd1-AA_-Rap

growth_protocol: All the different strains are derived from W303 and HHY anchor away genetic backgrounds (Haruki et al., 2008). Most of the cell cultures were grown in YEPD medium (1% yeast extract, 1% peptone) supplemented with 2% glucose as carbon source with the exception of the induction of newly-synthesized H3HA  grown in SC -URA. All strains were grown at 30°C.

extract_protocol:
The MNase-seq experiments were performed as described in (Gill et al., 2020).
Libraries were prepared using NEBnext Ultra DNA library prep kit for Illumina (NEB). Samples were paired-end sequenced at the iGE3 genomics platform of the University of Geneva.

value: Minus Rapamycin 1h (1μg/ml)


title: MNase-ChIP-seq_H3-HA_Nrd1-AA_-Rap


title: prostate_cancer_primary_676

value: Average


title: prostate_cancer_primary_682


title: prostate_cancer_primary_679

value: Lower


title: prostate_cancer_primary_681


title: prostate_cancer_primary_680


title: prostate_cancer_primary_671


title: prostate_cancer_primary_678


title: prostate_cancer_primary_672


title: ChEC-seq_TBP_MNase_dhir2_30sec

extract_protocol:
The experiment was performed as described in (Gill et al., 2020) except that induction of MNase activity by addition of calcium was performed for 1 min and 5 min for the Hir2-ChEC, 30 sec for the TBP-ChEC and 5 min for the free-MNase control.
Samples were then sequenced using a paired-end approach at the iGE3 genomics sequencing platform of Geneva.

value: Nrd1-AA dhir2 TBP-MNase


title: prostate_cancer_primary_686


title: prostate_cancer_primary_683


title: prostate_cancer_primary_673


title: prostate_cancer_primary_675


title: prostate_cancer_primary_670


title: MNase-seq_Nrd1-AA_dhir2_-Rap

value: Nrd1-AA dhir2


title: ChEC-seq_Hir2_MNase_+Rap_5min

value: Nrd1-AA Hir2-MNase


title: ChEC-seq_Hir2_MNase_+Rap_1min


title: ChEC-seq_TBP_MNase_30sec

value: Nrd1-AA TBP-MNase


title: prostate_cancer_primary_677


title: prostate_cancer_primary_668


title: prostate_cancer_primary_667


title: prostate_cancer_primary_674


title: prostate_cancer_primary_669


title: ChEC-seq_Hir2_MNase_-Rap_5min


title: ChEC-seq_Free-Mnase_-Rap_5min

value: Nrd1-AA Free-MNase


title: ChEC-seq_Hir2_MNase_-Rap_1min


title: prostate_cancer_primary_665


title: RNA-seq_Nrd1-AA_dhir2_+Rap_rep2

extract_protocol:
RNAs were extracted using Glass-beads and TRIzol (Invitrogen). For RT-qPCR experiments, RNAs were reverse-transcribed using SuperScriptII (Invitrogen). Primers used for reverse transcription and PCR are listed in Table S3.
RNA library preparation and single-end stranded sequencing were performed at the iGE3 genomics platform of the University of Geneva. All RNA-seq experiments were performed in duplicates.

tag: strain background


title: RNA-seq_Nrd1-AA_dhir2_-Rap_rep2


title: RNA-seq_Nrd1-AA_+Rap_rep2


title: RNA-seq_Nrd1-AA_dhir2_+Rap_rep1


title: RNA-seq_Nrd1-AA_+Rap_rep1


title: prostate_cancer_primary_664


title: RNA-seq_Nrd1-AA_-Rap_rep2


title: RNA-seq_Nrd1-AA_-Rap_rep1


title: E80 skeletal muscle Hi-C replicate_3

city: Guangzhou

first: Renqiang

last: Yuan

state: Guangdong

address: No. 135, Xingang Xi Road

institute: SUN YAT-SEN UNIVERSITY

data_processing:
Reads were mapped to the pig genome (Sscrofa 11.1) by BWA (v 0.7.15).
Juicer were used HiC data processing to filter duplication, low-quality alignment read pairs (MAPQ < 30) as well as intra-fragment read pairs.
High-quality reads  normalized with Knight-Ruiz [KR] algorithm and quantile  algorithm to structure contact matrixes at 20 or 100 kb resolution.
Compartments A/B were identified with A-B index as as described by M Jordan Rowley. et al. Mol Cell. 2017 (PMID: 28826674).
Locations of topologically associated domains (TADs) were computed by combining  directionality index (Dixon et al. Nature. 2012 [PMID: 22495300]) and insulation index (Emily Crane et al. Nature. 2017)
Genome_build: Sscrofa11.1

organism: Sus scrofa

source_name: skeletal muscle

extract_protocol:
Hi-C experiment were conducted using DpnII, according to the protocol published by Suhas S P Rao. et al. Cell 2014 (PMID: 25497547) except for using 4% formaldehyde.
DNA libraries were prepared during Hi-C protocol according to experimental procedures described in Suhas S P Rao. et al. Cell 2014 (PMID: 25497547).

tag: breed

value: Luchuan pig

tag: tissue type

value: longissimus dorsi muscle

tag: age

value: embryonic day 80

tag: Sex

value: female

tag: chip antibody

tag: restriction enzyme

value: DpnII (R0543S, NEB)


title: E80 skeletal muscle Hi-C replicate_1


title: E80 skeletal muscle Hi-C replicate_2


title: prostate_cancer_primary_663

tag: primary gleason

value: African American


title: RNA-seq_Nrd1-AA_dhir2_-Rap_rep1


title: E35 skeletal muscle Hi-C replicate_2

value: embryonic day 35


title: E35 skeletal muscle Hi-C replicate_3


title: E35 skeletal muscle Hi-C replicate_1


title: NPCs_LM05_5 [I871T_6]

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

data_processing:
Fastq files were mapped to the hg38 human reference genome with the STAR aligner v2.7 (Dobin et al., 2013).
Differential gene expression and Functional enrichment analyses were performed with DESeq2 (Love et al., 2014) and geneSCF (Subhash et.al. 2016), respectively.
Statistical and downstream bioinformatics analyses were performed within the R environment.
Gene expression heatmaps were produced with GENE-E (Broad Institute).
Genome_build: hg38
Supplementary_files_format_and_content: featureCounts gene counts

source_name: SETBP1 I871T NPCs

extract_protocol:
RNA was isolated with Trizol (Thermo Fisher), and treated with DNase I (NEB) according to manufacturer's instructions.
Library preparation was done with TruSeq RNA Library Prep Kit v2 (Illumina) according to manufacturer's instructions.

tag: cell type

value: iPSC-derived NPCs

tag: sgs model

value: SETBP1 I871T


title: NPCs_LM05_4 [I871T_2]


title: prostate_cancer_primary_657

value: FFPE prostate cancer

tag: secondary gleason

tag: decipher risk group

tag: race


title: prostate_cancer_primary_661

tag: tissue


title: NPCs_LM05_3 [I871T_1]


title: prostate_cancer_primary_659

value: Higher


title: prostate_cancer_primary_653

value: Lower


title: prostate_cancer_primary_655


title: prostate_cancer_primary_658


title: prostate_cancer_primary_652


title: NPCs_MUT5 [D868N_6]

source_name: SETBP1 D868N NPCs

value: SETBP1 D868N


title: prostate_cancer_primary_660

value: Average


title: prostate_cancer_primary_666


title: prostate_cancer_primary_656


title: prostate_cancer_primary_649


title: prostate_cancer_primary_648


title: prostate_cancer_primary_662


title: NPCs_WT6 [D868D_6]

source_name: SETBP1 D868D NPCs

value: SETBP1 D868D


title: prostate_cancer_primary_650


title: prostate_cancer_primary_654


title: prostate_cancer_primary_651


title: prostate_cancer_primary_646


title: prostate_cancer_primary_644


title: NPCs_LM05_2 [D868N_2]


title: prostate_cancer_primary_643


title: prostate_cancer_primary_642


title: prostate_cancer_primary_647


title: prostate_cancer_primary_645


title: prostate_cancer_primary_639


title: DXA1179_262Control

type: genomic

city: Doha

first: Omar

middle: M E

last: Albagha

address: Luqta Street, Education City

department: Health and Life Sciences

country: Qatar

institute: Hamad Bin Khalifa University

description: DNA CpG sites

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing:
The R package RnBeads version 1.10.8 was used for quality control. Samples with low methylated or unmethylated median intensity (<11.0) were excluded (n=35) along with samples with sex mismatch between reported and predicted sex (n=0). Probes with the following criteria were excluded: detection P value >0.05, cross reactive probes, containing a SNP within 3 bp of nucleotide extension site, or those located on sex chromosomes. Additionally, 723 sites were further excluded from the dataset for previously established association with smoking. A total of 56,356 probes were excluded from the initial 485,512 leaving 429,156 CpGs for analysis.
The Enmix method from RnBeads was used for background correction whilst
SWAN from RnBeads was used for between and within array normalization
The M-values, derived using the formulae log2((methylated signal+1)/(unmethylated signal+1)), were used

label: Cy3, Cy5

source_name: white blood cells

label_protocol: standard Illumina protocol

extract_protocol: Genomic DNA was extracted from peripheral blood using standard protocols. Bisulfite conversion was performed on 500µg of DNA using Zymo EZ-96 DNA methylation Kit (Zymo Research, USA). DNA methylation profiling was performed using the Illumina Infinium HumanMethylation 450K array (Illumina, USA) by following the manufacturer’s protocol

tag: mmed

tag: umed

tag: phenotype

value: Control

tag: array

tag: slide

value: white blood cells


title: DXA1047_209Control

description: DNA CpG sites


title: prostate_cancer_primary_641


title: NPCs_WT2 [D868D_2]


title: NPCs_WT1 [D868D_1]


title: H3-2 4 youngest leaves, biological rep1

city: Campinas

first: Michel

middle: George Alberts

last: Vincentz

state: SP

address: Av. Cândido Rondon, 400

department: Biology

country: Brazil

institute: Unicamp

description: Gene Expression data from a pool of the four youngest leaves

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 18 hr at 40° C on GeneChip Arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, scanner serial number 54715780.

data_processing: Robust multi-array average normalization was performed with Expression Console™ (Affymetrix) and statistical data analysis was performed with affylmGUI package (R Development Core Team, 2008). A p-value of <0.05 was used as the cutoff for the selection of differentially expressed genes and expression level between genotypes.

organism: Arabidopsis thaliana

source_name: H3-2 4 youngest leaves

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The plants were grown on a substrate composed of soil (Plantmax HT) and vermiculite (Plantmax) at a 2:1 ratio. Initially seeds were kept in water for 72 h at 4º C in darkness to break dormancy, afterwards were transferred to a growth room maintained at 22º C and 100 μmol.m-2.s-1 of light intensity, under short day (10 h of light/14 h of darkness) for 25 days after germination (DAG) and then the four youngest leaves of five plant per sample were harvested at the end of night.

extract_protocol: RNA for the transcriptome analysis was isolated with the RNeasy Plant Mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions, and quality monitored with the Agilent 2100 (Bioanalyzer, Santa Clara, California, EUA).

treatment_protocol: mutant x wild type plants

value: four youngest leaves of five plants

tag: genotype

value: T-DNA insertion bzip63-2(H3-2, FLAG_610A08)

value: 25 DAG


title: Ws 4 youngest leaves, biological rep2

source_name: Ws 4 youngest leaves

value: wild type Ws

tag: age


title: Ws 4 youngest leaves, biological rep3


title: prostate_cancer_primary_631


title: Ws 4 youngest leaves, biological rep1


title: prostate_cancer_primary_634


title: prostate_cancer_primary_633


title: prostate_cancer_primary_640


title: prostate_cancer_primary_638


title: prostate_cancer_primary_635


title: prostate_cancer_primary_637


title: DXA0870_89Control

description: DNA CpG sites


title: prostate_cancer_primary_632


title: DXA2736_25Control

description: DNA CpG sites


title: PRISM_Control_350Control

description: DNA CpG sites


title: PRISM_Control_459Control

description: DNA CpG sites


title: H3-2 4 youngest leaves, biological rep2


title: H3-2 4 youngest leaves, biological rep3


title: DXA1171_443Control

description: DNA CpG sites


title: DXA2854_150Control

description: DNA CpG sites


title: prostate_cancer_primary_630


title: prostate_cancer_primary_629


title: prostate_cancer_primary_636


title: prostate_cancer_primary_628


title: prostate_cancer_primary_627


title: prostate_cancer_primary_624


title: prostate_cancer_primary_625


title: prostate_cancer_primary_626


title: PRISM_Control_486Control

description: DNA CpG sites


title: DXA1111_394Control

description: DNA CpG sites


title: DXA1295_307Control

description: DNA CpG sites


title: PRISM_Control_219Control

description: DNA CpG sites


title: DXA1735_303Control

description: DNA CpG sites


title: DXA0896_9Control

description: DNA CpG sites


title: DXA1127_177Control

description: DNA CpG sites


title: DXA1369_110Control

description: DNA CpG sites


title: PRISM_Control_305Control

description: DNA CpG sites


title: DXA1227_355Control

description: DNA CpG sites


title: PRISM_Control_91Control

description: DNA CpG sites


title: DXA0970_423Control

description: DNA CpG sites


title: DXA1087_85Control

description: DNA CpG sites


title: prostate_cancer_primary_622


title: DXA1281_45Control

description: DNA CpG sites


title: prostate_cancer_primary_618


title: prostate_cancer_primary_620


title: prostate_cancer_primary_619


title: prostate_cancer_primary_623


title: PRISM_Control_238Control

description: DNA CpG sites


title: prostate_cancer_primary_621


title: prostate_cancer_primary_613


title: prostate_cancer_primary_614


title: DXA1039_306Control

description: DNA CpG sites


title: DXA2689_82Control

description: DNA CpG sites


title: prostate_cancer_primary_617


title: prostate_cancer_primary_612


title: PRISM_Control_340Control

description: DNA CpG sites


title: PRISM_Control_399Control

description: DNA CpG sites


title: DXA1280_372Control

description: DNA CpG sites


title: prostate_cancer_primary_615


title: PRISM_Control_362Control

description: DNA CpG sites


title: prostate_cancer_primary_611


title: PRISM_Control_20Control

description: DNA CpG sites


title: prostate_cancer_primary_616


title: prostate_cancer_primary_610


title: PRISM_Control_478Control

description: DNA CpG sites


title: prostate_cancer_primary_609


title: prostate_cancer_primary_606


title: prostate_cancer_primary_608


title: prostate_cancer_primary_604


title: prostate_cancer_primary_607


title: DXA2659_335Control

description: DNA CpG sites


title: prostate_cancer_primary_603


title: DXA2052_232Control

description: DNA CpG sites


title: DXA2607_137Control

description: DNA CpG sites


title: DXA2028_208Control

description: DNA CpG sites


title: prostate_cancer_primary_605


title: DXA0050_447Control

description: DNA CpG sites


title: PRISM_Control_264Control

description: DNA CpG sites


title: DXA1110_139Control

description: DNA CpG sites


title: prostate_cancer_primary_599


title: DXA0994_223Control

description: DNA CpG sites


title: visit 2 (end of study), group B  2_H8

city: Oslo

first: Stine

middle: Marie

last: Ulven

address: Sognsvannsveien 9

department: Department of Nutrition

country: Norway

institute: University of oslo

description:
visit 2 (end of study), group B
wk 8

hyb_protocol: Illumina HumanHT-12 Expression BeadChips (Illumina Inc., CA, USA)

scan_protocol: Illumina HiScann instrument (Illumina Inc., CA, USA)

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: PBMC, visit 2 (end of study), group B

label_protocol: Illumina Total Prep RNA Amplification Kit (Thermo Fisher Scientific, MA, USA)

extract_protocol: Total RNA was isolated from all PBMC samples using RNeasy Mini kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions.RNA quantity measurements were performed using a Nanodrop ND-1000 Spectrometer (Thermo Fisher Scientific, Gothenburg, Sweden) and RNA integrity number (RIN) value was measured with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) to check the RNA quality.

value: PBMC


title: visit 1 (baseline), group B  2_H9

description:
visit 1 (baseline), group B
wk 0

source_name: PBMC, visit 1 (baseline), group B


title: prostate_cancer_primary_598

value: African American


title: DXA2698_129Control

description: DNA CpG sites


title: prostate_cancer_primary_600


title: DXA2855_463Control

description: DNA CpG sites


title: prostate_cancer_primary_597


title: prostate_cancer_primary_596


title: prostate_cancer_primary_602


title: visit 1 (baseline), group B  2_H7

description:
visit 1 (baseline), group B
wk 0


title: DXA2839_75Control

description: DNA CpG sites


title: prostate_cancer_primary_601


title: prostate_cancer_primary_592


title: prostate_cancer_primary_594


title: visit 2 (end of study), group B  2_H6

description:
visit 2 (end of study), group B
wk 8


title: prostate_cancer_primary_595


title: PRISM_Control_41Control

description: DNA CpG sites


title: prostate_cancer_primary_589


title: prostate_cancer_primary_590


title: prostate_cancer_primary_591


title: visit 1 (baseline), group B  2_H5

description:
visit 1 (baseline), group B
wk 0


title: prostate_cancer_primary_588


title: prostate_cancer_primary_593


title: prostate_cancer_primary_587


title: prostate_cancer_primary_586


title: visit 2 (end of study), group B  2_H4

description:
visit 2 (end of study), group B
wk 8


title: prostate_cancer_primary_585


title: DXA1858_16Control

description: DNA CpG sites


title: DXA1667_159Control

description: DNA CpG sites


title: NPCs_LM05_1 [D868N_1]


title: DXA1246_259Control

description: DNA CpG sites


title: DXA1071_8Control

description: DNA CpG sites


title: prostate_cancer_primary_583


title: PRISM_Control_300Control

description: DNA CpG sites


title: prostate_cancer_primary_584


title: prostate_cancer_primary_582


title: visit 2 (end of study), group B  2_H2

description:
visit 2 (end of study), group B
wk 8


title: PRISM_Control_103Control

description: DNA CpG sites


title: prostate_cancer_primary_581


title: prostate_cancer_primary_580


title: visit 2 (end of study), group B  2_H10

description:
visit 2 (end of study), group B
wk 8


title: prostate_cancer_primary_579


title: DXA1197_427Control

description: DNA CpG sites


title: visit 1 (baseline), group A  2_G9

description:
visit 1 (baseline), group A
wk 0

source_name: PBMC, visit 1 (baseline), group A


title: DXA2029_435Control

description: DNA CpG sites


title: visit 1 (baseline), group B  2_H1

description:
visit 1 (baseline), group B
wk 0


title: prostate_cancer_primary_578


title: visit 2 (end of study), group B  2_G8

description:
visit 2 (end of study), group B
wk 8


title: visit 1 (baseline), group B  2_G7

description:
visit 1 (baseline), group B
wk 0


title: prostate_cancer_primary_575


title: prostate_cancer_primary_576


title: prostate_cancer_primary_574


title: prostate_cancer_primary_572


title: DXA1337_147Control

description: DNA CpG sites


title: prostate_cancer_primary_571


title: prostate_cancer_primary_570


title: visit 1 (baseline), group B  2_H3

description:
visit 1 (baseline), group B
wk 0


title: prostate_cancer_primary_573


title: prostate_cancer_primary_569


title: visit 1 (baseline), group A  2_G5

description:
visit 1 (baseline), group A
wk 0


title: prostate_cancer_primary_577


title: DXA1213_95Control

description: DNA CpG sites


title: PRISM_Control_156Control

description: DNA CpG sites


title: DXA1367_484Control

description: DNA CpG sites


title: prostate_cancer_primary_568


title: visit 2 (end of study), group A  2_G6

description:
visit 2 (end of study), group A
wk 8

source_name: PBMC, visit 2 (end of study), group A


title: DXA1760_4Control

description: DNA CpG sites


title: prostate_cancer_primary_567


title: visit 2 (end of study), group B  2_G4

description:
visit 2 (end of study), group B
wk 8


title: prostate_cancer_primary_564


title: prostate_cancer_primary_565


title: prostate_cancer_primary_566


title: visit 2 (end of study), group A  2_G2

description:
visit 2 (end of study), group A
wk 8


title: prostate_cancer_primary_562


title: visit 2 (end of study), group B  2_G12

description:
visit 2 (end of study), group B
wk 8


title: prostate_cancer_primary_561


title: prostate_cancer_primary_559


title: visit 1 (baseline), group B  2_G11

description:
visit 1 (baseline), group B
wk 0


title: PRISM_Control_354Control

description: DNA CpG sites


title: PRISM_Control_284Control

description: DNA CpG sites


title: prostate_cancer_primary_558


title: visit 1 (baseline), group A  2_G1

description:
visit 1 (baseline), group A
wk 0


title: visit 1 (baseline), group B  2_G3

description:
visit 1 (baseline), group B
wk 0


title: visit 2 (end of study), group A  2_G10

description:
visit 2 (end of study), group A
wk 8


title: prostate_cancer_primary_555


title: prostate_cancer_primary_556


title: prostate_cancer_primary_557


title: prostate_cancer_primary_552


title: prostate_cancer_primary_554


title: prostate_cancer_primary_553


title: prostate_cancer_primary_560


title: visit 2 (end of study), group B  2_F8

description:
visit 2 (end of study), group B
wk 8


title: DXA1698_146Control

description: DNA CpG sites


title: DXA1166_71Control

description: DNA CpG sites


title: DXA2365_363Control

description: DNA CpG sites


title: PRISM_Control_358Control

description: DNA CpG sites


title: prostate_cancer_primary_551


title: DXA1042_235Control

description: DNA CpG sites


title: visit 1 (baseline), group B  2_F7

description:
visit 1 (baseline), group B
wk 0


title: PRISM_Control_403Control

description: DNA CpG sites


title: visit 2 (end of study), group A  2_F6

description:
visit 2 (end of study), group A
wk 8


title: prostate_cancer_primary_548


title: PRISM_Control_98Control

description: DNA CpG sites


title: prostate_cancer_primary_546


title: visit 1 (baseline), group A  2_F5

description:
visit 1 (baseline), group A
wk 0


title: visit 2 (end of study), group B  2_F4

description:
visit 2 (end of study), group B
wk 8


title: prostate_cancer_primary_550


title: prostate_cancer_primary_547


title: prostate_cancer_primary_549


title: prostate_cancer_primary_544


title: prostate_cancer_primary_543


title: PRISM_Control_179Control

description: DNA CpG sites


title: DXA0166_204Control

description: DNA CpG sites


title: visit 1 (baseline), group B  2_F3

description:
visit 1 (baseline), group B
wk 0


title: PRISM_Control_428Control

description: DNA CpG sites


title: visit 2 (end of study), group A  2_F2

description:
visit 2 (end of study), group A
wk 8


title: prostate_cancer_primary_542


title: visit 1 (baseline), group A  2_F1

description:
visit 1 (baseline), group A
wk 0


title: prostate_cancer_primary_541


title: prostate_cancer_primary_540


title: prostate_cancer_primary_545


title: visit 1 (baseline), group A  2_E9

description:
visit 1 (baseline), group A
wk 0


title: prostate_cancer_primary_537


title: prostate_cancer_primary_538


title: prostate_cancer_primary_539


title: PRISM_Control_418Control

description: DNA CpG sites


title: prostate_cancer_primary_536


title: prostate_cancer_primary_535


title: DXA0738_143Control

description: DNA CpG sites


title: DXA0140_215Control

description: DNA CpG sites


title: PRISM_Control_352Control

description: DNA CpG sites


title: visit 2 (end of study), group B  2_E8

description:
visit 2 (end of study), group B
wk 8


title: prostate_cancer_primary_534


title: visit 1 (baseline), group B  2_E7

description:
visit 1 (baseline), group B
wk 0


title: prostate_cancer_primary_532


title: visit 2 (end of study), group A  2_E6

description:
visit 2 (end of study), group A
wk 8


title: prostate_cancer_primary_533


title: prostate_cancer_primary_531


title: visit 1 (baseline), group A  2_E5

description:
visit 1 (baseline), group A
wk 0


title: DXA1927_123Control

description: DNA CpG sites


title: prostate_cancer_primary_530


title: DXA1370_485Control

description: DNA CpG sites


title: PRISM_Control_116Control

description: DNA CpG sites


title: prostate_cancer_primary_529


title: DXA2678_432Control

description: DNA CpG sites


title: prostate_cancer_primary_528


title: visit 2 (end of study), group A  2_E2

description:
visit 2 (end of study), group A
wk 8


title: visit 1 (baseline), group B  2_E3

description:
visit 1 (baseline), group B
wk 0


title: visit 2 (end of study), group B  2_E4

description:
visit 2 (end of study), group B
wk 8


title: prostate_cancer_primary_526


title: prostate_cancer_primary_521


title: prostate_cancer_primary_522


title: prostate_cancer_primary_520


title: prostate_cancer_primary_527


title: prostate_cancer_primary_523


title: prostate_cancer_primary_525


title: visit 1 (baseline), group B  2_E11

description:
visit 1 (baseline), group B
wk 0


title: prostate_cancer_primary_524


title: PRISM_Control_392Control

description: DNA CpG sites


title: PRISM_Control_395Control

description: DNA CpG sites


title: prostate_cancer_primary_518


title: prostate_cancer_primary_517


title: PRISM_Control_33Control

description: DNA CpG sites


title: visit 2 (end of study), group A  2_E10

description:
visit 2 (end of study), group A
wk 8


title: visit 1 (baseline), group A  2_E1

description:
visit 1 (baseline), group A
wk 0


title: prostate_cancer_primary_515


title: prostate_cancer_primary_516


title: prostate_cancer_primary_514


title: visit 2 (end of study), group B  2_E12

description:
visit 2 (end of study), group B
wk 8


title: prostate_cancer_primary_513


title: prostate_cancer_primary_519


title: visit 1 (baseline), group A  2_D9

description:
visit 1 (baseline), group A
wk 0


title: DXA1082_319Control

description: DNA CpG sites


title: PRISM_Control_191Control

description: DNA CpG sites


title: DXA1186_66Control

description: DNA CpG sites


title: prostate_cancer_primary_512


title: visit 2 (end of study), group B  2_D8

description:
visit 2 (end of study), group B
wk 8


title: DXA0973_217Control

description: DNA CpG sites


title: DXA2819_263Control

description: DNA CpG sites


title: visit 2 (end of study), group A  2_D6

description:
visit 2 (end of study), group A
wk 8


title: visit 1 (baseline), group B  2_D7

description:
visit 1 (baseline), group B
wk 0


title: prostate_cancer_primary_509


title: prostate_cancer_primary_508


title: prostate_cancer_primary_507


title: prostate_cancer_primary_503


title: prostate_cancer_primary_506


title: DXA1987_248Control

description: DNA CpG sites


title: prostate_cancer_primary_511


title: PRISM_Control_231Control

description: DNA CpG sites


title: DXA2686_449Control

description: DNA CpG sites


title: prostate_cancer_primary_510


title: prostate_cancer_primary_505


title: visit 2 (end of study), group B  2_D4

description:
visit 2 (end of study), group B
wk 8


title: prostate_cancer_primary_502


title: prostate_cancer_primary_504


title: visit 1 (baseline), group B  2_D3

description:
visit 1 (baseline), group B
wk 0


title: visit 1 (baseline), group A  2_D5

description:
visit 1 (baseline), group A
wk 0


title: prostate_cancer_primary_501


title: DXA1406_99Control

description: DNA CpG sites


title: prostate_cancer_primary_496


title: prostate_cancer_primary_563


title: prostate_cancer_primary_499


title: prostate_cancer_primary_497


title: prostate_cancer_primary_498


title: prostate_cancer_primary_495


title: visit 2 (end of study), group B  2_D12

description:
visit 2 (end of study), group B
wk 8


title: prostate_cancer_primary_500


title: prostate_cancer_primary_494


title: visit 1 (baseline), group B  2_D11

description:
visit 1 (baseline), group B
wk 0


title: visit 2 (end of study), group A  2_D2

description:
visit 2 (end of study), group A
wk 8


title: DXA1919_268Control

description: DNA CpG sites


title: PRISM_Control_322Control

description: DNA CpG sites


title: prostate_cancer_primary_493


title: DXA1282_60Control

description: DNA CpG sites


title: DXA2589_490Control

description: DNA CpG sites


title: visit 1 (baseline), group A  2_D1

description:
visit 1 (baseline), group A
wk 0


title: PRISM_Control_87Control

description: DNA CpG sites


title: PRISM_Control_43Control

description: DNA CpG sites


title: PRISM_Control_302Control

description: DNA CpG sites


title: DXA2578_122Control

description: DNA CpG sites


title: DXA0996_336Control

description: DNA CpG sites


title: visit 1 (baseline), group A  2_C9

description:
visit 1 (baseline), group A
wk 0


title: visit 2 (end of study), group A  2_D10

description:
visit 2 (end of study), group A
wk 8


title: prostate_cancer_primary_488


title: prostate_cancer_primary_489


title: prostate_cancer_primary_486


title: visit 2 (end of study), group B  2_C8

description:
visit 2 (end of study), group B
wk 8


title: prostate_cancer_primary_491


title: visit 2 (end of study), group A  2_C6

description:
visit 2 (end of study), group A
wk 8


title: prostate_cancer_primary_481


title: prostate_cancer_primary_484


title: prostate_cancer_primary_487


title: prostate_cancer_primary_480


title: prostate_cancer_primary_485


title: prostate_cancer_primary_490


title: prostate_cancer_primary_479


title: visit 1 (baseline), group B  2_C7

description:
visit 1 (baseline), group B
wk 0


title: DXA2005_126Control

description: DNA CpG sites


title: prostate_cancer_primary_492


title: prostate_cancer_primary_483


title: prostate_cancer_primary_477


title: prostate_cancer_primary_482


title: visit 1 (baseline), group B  2_C3

description:
visit 1 (baseline), group B
wk 0


title: prostate_cancer_primary_478


title: PRISM_Control_455Control

description: DNA CpG sites


title: visit 1 (baseline), group A  2_C5

description:
visit 1 (baseline), group A
wk 0


title: prostate_cancer_primary_475


title: PRISM_Control_104Control

description: DNA CpG sites


title: prostate_cancer_primary_474


title: DXA1076_270Control

description: DNA CpG sites


title: DXA0247_77Control

description: DNA CpG sites


title: PRISM_Control_439Control

description: DNA CpG sites


title: visit 1 (baseline), group B  2_C11

description:
visit 1 (baseline), group B
wk 0


title: DXA1272_115Control

description: DNA CpG sites


title: prostate_cancer_primary_470


title: visit 2 (end of study), group A  2_C10

description:
visit 2 (end of study), group A
wk 8


title: prostate_cancer_primary_472


title: visit 2 (end of study), group B  2_C12

description:
visit 2 (end of study), group B
wk 8


title: visit 2 (end of study), group B  2_B8

description:
visit 2 (end of study), group B
wk 8


title: prostate_cancer_primary_473


title: PRISM_Control_207Control

description: DNA CpG sites


title: visit 1 (baseline), group B  2_B7

description:
visit 1 (baseline), group B
wk 0


title: prostate_cancer_primary_469


title: DXA1854_37Control

description: DNA CpG sites


title: visit 1 (baseline), group A  2_B9

description:
visit 1 (baseline), group A
wk 0


title: prostate_cancer_primary_467


title: visit 2 (end of study), group A  2_B6

description:
visit 2 (end of study), group A
wk 8


title: visit 1 (baseline), group A  2_B5

description:
visit 1 (baseline), group A
wk 0


title: prostate_cancer_primary_468


title: prostate_cancer_primary_462


title: prostate_cancer_primary_471


title: DXA1657_108Control

description: DNA CpG sites


title: DXA2881_398Control

description: DNA CpG sites


title: prostate_cancer_primary_464


title: prostate_cancer_primary_460


title: prostate_cancer_primary_466


title: prostate_cancer_primary_465


title: prostate_cancer_primary_463


title: visit 2 (end of study), group B  2_B4

description:
visit 2 (end of study), group B
wk 8


title: prostate_cancer_primary_461


title: prostate_cancer_primary_459


title: prostate_cancer_primary_458


title: prostate_cancer_primary_456


title: PRISM_Control_461Control

description: DNA CpG sites


title: visit 2 (end of study), group A  2_B2

description:
visit 2 (end of study), group A
wk 8


title: prostate_cancer_primary_457


title: visit 1 (baseline), group B  2_B3

description:
visit 1 (baseline), group B
wk 0


title: visit 2 (end of study), group B  2_B12

description:
visit 2 (end of study), group B
wk 8


title: PRISM_Control_420Control

description: DNA CpG sites


title: prostate_cancer_primary_452


title: PRISM_Control_444Control

description: DNA CpG sites


title: prostate_cancer_primary_451


title: prostate_cancer_primary_455


title: prostate_cancer_primary_454


title: prostate_cancer_primary_453


title: DXA1045_276Control

description: DNA CpG sites


title: PRISM_Control_121Control

description: DNA CpG sites


title: PRISM_Control_375Control

description: DNA CpG sites


title: visit 2 (end of study), group A  2_B10

description:
visit 2 (end of study), group A
wk 8


title: visit 1 (baseline), group A  2_B1

description:
visit 1 (baseline), group A
wk 0


title: prostate_cancer_primary_450


title: prostate_cancer_primary_447


title: visit 1 (baseline), group B  2_A7

description:
visit 1 (baseline), group B
wk 0


title: visit 2 (end of study), group B  2_C4

description:
visit 2 (end of study), group B
wk 8


title: prostate_cancer_primary_449


title: PRISM_Control_469Control

description: DNA CpG sites


title: PRISM_Control_166Control

description: DNA CpG sites


title: prostate_cancer_primary_448


title: visit 1 (baseline), group B  2_B11

description:
visit 1 (baseline), group B
wk 0


title: prostate_cancer_primary_444


title: prostate_cancer_primary_445


title: prostate_cancer_primary_441


title: prostate_cancer_primary_442


title: visit 2 (end of study), group B  2_A8

description:
visit 2 (end of study), group B
wk 8


title: visit 1 (baseline), group A  2_A9

description:
visit 1 (baseline), group A
wk 0


title: PRISM_Control_487Control

description: DNA CpG sites


title: prostate_cancer_primary_446


title: prostate_cancer_primary_443


title: visit 1 (baseline), group A  2_A5

description:
visit 1 (baseline), group A
wk 0


title: prostate_cancer_primary_438


title: DXA1670_426Control

description: DNA CpG sites


title: prostate_cancer_primary_440


title: prostate_cancer_primary_439


title: visit 2 (end of study), group B  2_A4

description:
visit 2 (end of study), group B
wk 8


title: prostate_cancer_primary_437


title: prostate_cancer_primary_434


title: prostate_cancer_primary_435


title: DXA2814_480Control

description: DNA CpG sites


title: PRISM_Control_106Control

description: DNA CpG sites


title: prostate_cancer_primary_436


title: PRISM_Control_462Control

description: DNA CpG sites


title: DXA2013_107Control

description: DNA CpG sites


title: prostate_cancer_primary_431


title: visit 2 (end of study), group A  2_A2

description:
visit 2 (end of study), group A
wk 8


title: prostate_cancer_primary_432


title: visit 1 (baseline), group B  2_A3

description:
visit 1 (baseline), group B
wk 0


title: prostate_cancer_primary_430


title: visit 2 (end of study), group B  2_A12

description:
visit 2 (end of study), group B
wk 8


title: prostate_cancer_primary_429


title: PRISM_Control_285Control

description: DNA CpG sites


title: PRISM_Control_277Control

description: DNA CpG sites


title: DXA0218_387Control

description: DNA CpG sites


title: prostate_cancer_primary_426


title: prostate_cancer_primary_428


title: prostate_cancer_primary_425


title: prostate_cancer_primary_433


title: visit 2 (end of study), group A  2_A10

description:
visit 2 (end of study), group A
wk 8


title: prostate_cancer_primary_427


title: prostate_cancer_primary_424


title: visit 1 (baseline), group B  2_A11

description:
visit 1 (baseline), group B
wk 0


title: visit 1 (baseline), group A  2_A1

description:
visit 1 (baseline), group A
wk 0


title: PRISM_Control_23Control

description: DNA CpG sites


title: prostate_cancer_primary_423


title: prostate_cancer_primary_422


title: prostate_cancer_primary_476


title: prostate_cancer_primary_418


title: prostate_cancer_primary_419


title: visit 2 (end of study), group B  1_H8

description:
visit 2 (end of study), group B
wk 8


title: visit 1 (baseline), group B  1_H7

description:
visit 1 (baseline), group B
wk 0


title: prostate_cancer_primary_420


title: prostate_cancer_primary_421


title: prostate_cancer_primary_417


title: prostate_cancer_primary_415


title: visit 2 (end of study), group A  1_H6

description:
visit 2 (end of study), group A
wk 8


title: prostate_cancer_primary_414


title: PRISM_Control_35Control

description: DNA CpG sites


title: prostate_cancer_primary_413


title: visit 1 (baseline), group A  1_H9

description:
visit 1 (baseline), group A
wk 0


title: DXA1050_176Control

description: DNA CpG sites


title: PRISM_Control_269Control

description: DNA CpG sites


title: DXA1343_165Control

description: DNA CpG sites


title: PRISM_Control_86Control

description: DNA CpG sites


title: visit 1 (baseline), group A  1_H5

description:
visit 1 (baseline), group A
wk 0


title: prostate_cancer_primary_411


title: prostate_cancer_primary_412


title: prostate_cancer_primary_410


title: prostate_cancer_primary_409


title: visit 1 (baseline), group B  1_H3

description:
visit 1 (baseline), group B
wk 0


title: prostate_cancer_primary_407


title: PRISM_Control_54Control

description: DNA CpG sites


title: prostate_cancer_primary_408


title: PRISM_Control_254Control

description: DNA CpG sites


title: prostate_cancer_primary_406


title: visit 2 (end of study), group A  1_H2

description:
visit 2 (end of study), group A
wk 8


title: PRISM_Control_213Control

description: DNA CpG sites


title: DXA2581_442Control

description: DNA CpG sites


title: PRISM_Control_153Control

description: DNA CpG sites


title: visit 2 (end of study), group B  1_H4

description:
visit 2 (end of study), group B
wk 8


title: visit 2 (end of study), group B  1_H12

description:
visit 2 (end of study), group B
wk 8


title: prostate_cancer_primary_404


title: visit 1 (baseline), group B  1_H11

description:
visit 1 (baseline), group B
wk 0


title: prostate_cancer_primary_405


title: prostate_cancer_primary_403


title: DXA1247_327Control

description: DNA CpG sites


title: prostate_cancer_primary_402


title: visit 1 (baseline), group A  1_H1

description:
visit 1 (baseline), group A
wk 0


title: prostate_cancer_primary_401


title: prostate_cancer_primary_398


title: prostate_cancer_primary_397


title: prostate_cancer_primary_399


title: prostate_cancer_primary_400


title: PRISM_Control_205Control

description: DNA CpG sites


title: prostate_cancer_primary_396


title: PRISM_Control_456Control

description: DNA CpG sites


title: visit 2 (end of study), group A  1_H10

description:
visit 2 (end of study), group A
wk 8


title: visit 1 (baseline), group A  1_G9

description:
visit 1 (baseline), group A
wk 0


title: prostate_cancer_primary_395


title: prostate_cancer_primary_394


title: visit 2 (end of study), group B  1_G8

description:
visit 2 (end of study), group B
wk 8


title: prostate_cancer_primary_393


title: visit 1 (baseline), group B  1_G7

description:
visit 1 (baseline), group B
wk 0


title: prostate_cancer_primary_392


title: PRISM_Control_291Control

description: DNA CpG sites


title: PRISM_Control_275Control

description: DNA CpG sites


title: visit 2 (end of study), group A  1_G6

description:
visit 2 (end of study), group A
wk 8


title: visit 1 (baseline), group A  1_G5

description:
visit 1 (baseline), group A
wk 0


title: PRISM_Control_197Control

description: DNA CpG sites


title: PRISM_Control_464Control

description: DNA CpG sites


title: prostate_cancer_primary_391


title: prostate_cancer_primary_390


title: PRISM_Control_134Control

description: DNA CpG sites


title: DXA0995_377Control

description: DNA CpG sites


title: visit 2 (end of study), group A  2_A6

description:
visit 2 (end of study), group A
wk 8


title: prostate_cancer_primary_389


title: visit 2 (end of study), group B  1_G4

description:
visit 2 (end of study), group B
wk 8


title: prostate_cancer_primary_388


title: prostate_cancer_primary_386


title: visit 1 (baseline), group B  1_G3

description:
visit 1 (baseline), group B
wk 0


title: PRISM_Control_492Control

description: DNA CpG sites


title: prostate_cancer_primary_387


title: prostate_cancer_primary_385


title: prostate_cancer_primary_383


title: prostate_cancer_primary_384


title: DXA1840_163Control

description: DNA CpG sites


title: visit 2 (end of study), group A  1_G2

description:
visit 2 (end of study), group A
wk 8


title: PRISM_Control_404Control

description: DNA CpG sites


title: prostate_cancer_primary_380


title: visit 1 (baseline), group B  1_G11

description:
visit 1 (baseline), group B
wk 0


title: visit 2 (end of study), group B  1_G12

description:
visit 2 (end of study), group B
wk 8


title: prostate_cancer_primary_382


title: prostate_cancer_primary_381


title: visit 2 (end of study), group A  1_G10

description:
visit 2 (end of study), group A
wk 8


title: prostate_cancer_primary_377


title: prostate_cancer_primary_378


title: prostate_cancer_primary_379


title: prostate_cancer_primary_376


title: PRISM_Control_405Control

description: DNA CpG sites


title: prostate_cancer_primary_375


title: prostate_cancer_primary_374


title: visit 1 (baseline), group A  1_G1

description:
visit 1 (baseline), group A
wk 0


title: PRISM_Control_144Control

description: DNA CpG sites


title: prostate_cancer_primary_373


title: DXA2623_413Control

description: DNA CpG sites


title: prostate_cancer_primary_371


title: visit 1 (baseline), group A  1_F9

description:
visit 1 (baseline), group A
wk 0


title: DXA0005_151Control

description: DNA CpG sites


title: DXA1603_164Control

description: DNA CpG sites


title: DXA2671_68Control

description: DNA CpG sites


title: visit 1 (baseline), group B  1_F7

description:
visit 1 (baseline), group B
wk 0


title: DXA1148_100Control

description: DNA CpG sites


title: visit 2 (end of study), group B  1_F8

description:
visit 2 (end of study), group B
wk 8


title: prostate_cancer_primary_368


title: prostate_cancer_primary_369


title: visit 1 (baseline), group A  1_F5

description:
visit 1 (baseline), group A
wk 0


title: prostate_cancer_primary_367


title: visit 2 (end of study), group B  1_F4

description:
visit 2 (end of study), group B
wk 8


title: PRISM_Control_222Control

description: DNA CpG sites


title: prostate_cancer_primary_370


title: prostate_cancer_primary_366


title: prostate_cancer_primary_372


title: prostate_cancer_primary_416


title: visit 1 (baseline), group B  1_F3

description:
visit 1 (baseline), group B
wk 0


title: DXA0144_419Control

description: DNA CpG sites


title: prostate_cancer_primary_363


title: prostate_cancer_primary_360


title: prostate_cancer_primary_361


title: visit 2 (end of study), group A  1_F6

description:
visit 2 (end of study), group A
wk 8


title: prostate_cancer_primary_359


title: prostate_cancer_primary_365


title: prostate_cancer_primary_362


title: prostate_cancer_primary_364


title: prostate_cancer_primary_358


title: PRISM_Control_167Control

description: DNA CpG sites


title: prostate_cancer_primary_357


title: prostate_cancer_primary_356


title: visit 2 (end of study), group B  1_F12

description:
visit 2 (end of study), group B
wk 8


title: PRISM_Control_133Control

description: DNA CpG sites


title: prostate_cancer_primary_354


title: PRISM_Control_408Control

description: DNA CpG sites


title: PRISM_Control_14Control

description: DNA CpG sites


title: visit 1 (baseline), group B  1_F11

description:
visit 1 (baseline), group B
wk 0


title: DXA0950_374Control

description: DNA CpG sites


title: PRISM_Control_482Control

description: DNA CpG sites


title: PRISM_Control_181Control

description: DNA CpG sites


title: visit 2 (end of study), group A  1_F2

description:
visit 2 (end of study), group A
wk 8


title: visit 2 (end of study), group A  1_F10

description:
visit 2 (end of study), group A
wk 8


title: visit 1 (baseline), group A  1_E9

description:
visit 1 (baseline), group A
wk 0


title: prostate_cancer_primary_355


title: prostate_cancer_primary_351


title: prostate_cancer_primary_344


title: prostate_cancer_primary_350


title: prostate_cancer_primary_352


title: prostate_cancer_primary_346


title: prostate_cancer_primary_353


title: DXA1757_373Control

description: DNA CpG sites


title: PRISM_Control_244Control

description: DNA CpG sites


title: prostate_cancer_primary_345


title: visit 2 (end of study), group B  1_E8

description:
visit 2 (end of study), group B
wk 8


title: visit 1 (baseline), group A  1_F1

description:
visit 1 (baseline), group A
wk 0


title: prostate_cancer_primary_349


title: visit 2 (end of study), group A  1_E6

description:
visit 2 (end of study), group A
wk 8


title: prostate_cancer_primary_342


title: prostate_cancer_primary_347


title: prostate_cancer_primary_348


title: prostate_cancer_primary_340


title: visit 2 (end of study), group B  1_E4

description:
visit 2 (end of study), group B
wk 8


title: prostate_cancer_primary_341


title: prostate_cancer_primary_339


title: prostate_cancer_primary_343


title: PRISM_Control_185Control

description: DNA CpG sites


title: visit 1 (baseline), group B  1_E7

description:
visit 1 (baseline), group B
wk 0


title: prostate_cancer_primary_338


title: PRISM_Control_365Control

description: DNA CpG sites


title: DXA1843_281Control

description: DNA CpG sites


title: PRISM_Control_124Control

description: DNA CpG sites


title: visit 1 (baseline), group A  1_E5

description:
visit 1 (baseline), group A
wk 0


title: prostate_cancer_primary_337


title: prostate_cancer_primary_334


title: visit 2 (end of study), group B  1_E12

description:
visit 2 (end of study), group B
wk 8


title: visit 2 (end of study), group A  1_E2

description:
visit 2 (end of study), group A
wk 8


title: visit 1 (baseline), group B  1_E3

description:
visit 1 (baseline), group B
wk 0


title: prostate_cancer_primary_335


title: prostate_cancer_primary_333


title: DXA1413_325Control

description: DNA CpG sites


title: PRISM_Control_161Control

description: DNA CpG sites


title: prostate_cancer_primary_336


title: visit 1 (baseline), group B  1_E11

description:
visit 1 (baseline), group B
wk 0


title: prostate_cancer_primary_332


title: PRISM_Control_410Control

description: DNA CpG sites


title: visit 2 (end of study), group A  1_E10

description:
visit 2 (end of study), group A
wk 8


title: prostate_cancer_primary_327


title: visit 1 (baseline), group A  1_E1

description:
visit 1 (baseline), group A
wk 0


title: prostate_cancer_primary_326


title: prostate_cancer_primary_323


title: prostate_cancer_primary_324


title: prostate_cancer_primary_330


title: prostate_cancer_primary_331


title: prostate_cancer_primary_329


title: DXA1216_28Control

description: DNA CpG sites


title: DXA2804_483Control

description: DNA CpG sites


title: prostate_cancer_primary_325


title: visit 1 (baseline), group A  1_D9

description:
visit 1 (baseline), group A
wk 0


title: visit 2 (end of study), group B  1_D8

description:
visit 2 (end of study), group B
wk 8


title: prostate_cancer_primary_328


title: DXA1352_198Control

description: DNA CpG sites


title: prostate_cancer_primary_322


title: visit 1 (baseline), group B  1_D7

description:
visit 1 (baseline), group B
wk 0


title: prostate_cancer_primary_319


title: visit 2 (end of study), group A  1_D6

description:
visit 2 (end of study), group A
wk 8


title: PRISM_Control_314Control

description: DNA CpG sites


title: PRISM_Control_441Control

description: DNA CpG sites


title: prostate_cancer_primary_320


title: visit 1 (baseline), group A  1_D5

description:
visit 1 (baseline), group A
wk 0


title: DXA2535_400Control

description: DNA CpG sites


title: PRISM_Control_315Control

description: DNA CpG sites


title: prostate_cancer_primary_318


title: visit 2 (end of study), group A  1_D2

description:
visit 2 (end of study), group A
wk 8


title: prostate_cancer_primary_321


title: prostate_cancer_primary_313


title: prostate_cancer_primary_316


title: prostate_cancer_primary_317


title: prostate_cancer_primary_312


title: prostate_cancer_primary_311


title: prostate_cancer_primary_309


title: visit 1 (baseline), group B  1_D3

description:
visit 1 (baseline), group B
wk 0


title: prostate_cancer_primary_315


title: PRISM_Control_142Control

description: DNA CpG sites


title: visit 2 (end of study), group B  1_D4

description:
visit 2 (end of study), group B
wk 8


title: visit 2 (end of study), group B  1_D12

description:
visit 2 (end of study), group B
wk 8


title: prostate_cancer_primary_314


title: DXA1250_192Control

description: DNA CpG sites


title: PRISM_Control_312Control

description: DNA CpG sites


title: prostate_cancer_primary_307


title: visit 1 (baseline), group B  1_D11

description:
visit 1 (baseline), group B
wk 0


title: prostate_cancer_primary_308


title: prostate_cancer_primary_305


title: DXA2869_299Control

description: DNA CpG sites


title: visit 1 (baseline), group A  1_D1

description:
visit 1 (baseline), group A
wk 0


title: prostate_cancer_primary_306


title: 3'3'-cGAMP polyp 2

source_name: whole polyps

tag: treatment


title: prostate_cancer_primary_303


title: PRISM_Control_273Control

description: DNA CpG sites


title: DXA1984_384Control

description: DNA CpG sites


title: PRISM_Control_154Control

description: DNA CpG sites


title: prostate_cancer_primary_302


title: 2'3'-cGAMP polyp 2


title: visit 2 (end of study), group B  1_C8

description:
visit 2 (end of study), group B
wk 8


title: visit 2 (end of study), group A  1_D10

description:
visit 2 (end of study), group A
wk 8


title: visit 1 (baseline), group A  1_C9

description:
visit 1 (baseline), group A
wk 0


title: prostate_cancer_primary_298


title: c-di-GMP polyp 2

value: c-di-GMP


title: prostate_cancer_primary_300


title: prostate_cancer_primary_296


title: prostate_cancer_primary_297


title: c-di-AMP polyp 2

value: c-di-AMP


title: visit 2 (end of study), group A  1_C6

description:
visit 2 (end of study), group A
wk 8


title: prostate_cancer_primary_299


title: PRISM_Control_80Control

description: DNA CpG sites


title: PRISM_Control_97Control

description: DNA CpG sites


title: untreated polyp 2

value: untreated


title: visit 1 (baseline), group A  1_C5

description:
visit 1 (baseline), group A
wk 0


title: prostate_cancer_primary_304

value: FFPE prostate cancer


title: prostate_cancer_primary_295

value: Higher


title: 3'3'-cGAMP polyp 1


title: DXA2549_470Control

description: DNA CpG sites


title: DXA1839_59Control

description: DNA CpG sites


title: visit 1 (baseline), group B  1_C3

description:
visit 1 (baseline), group B
wk 0


title: PRISM_Control_118Control

description: DNA CpG sites


title: DXA1978_397Control

description: DNA CpG sites


title: c-di-GMP polyp 1


title: visit 2 (end of study), group A  1_C2

description:
visit 2 (end of study), group A
wk 8


title: prostate_cancer_primary_292


title: 2'3'-cGAMP polyp 1


title: c-di-AMP polyp 1


title: visit 2 (end of study), group B  1_C4

description:
visit 2 (end of study), group B
wk 8


title: visit 1 (baseline), group B  1_C7

description:
visit 1 (baseline), group B
wk 0


title: untreated polyp 1


title: prostate_cancer_primary_291


title: PRISM_Control_388Control

description: DNA CpG sites


title: prostate_cancer_primary_290


title: PRISM_Control_278Control

description: DNA CpG sites


title: PRISM_Control_239Control

description: DNA CpG sites


title: visit 2 (end of study), group B  1_C12

description:
visit 2 (end of study), group B
wk 8


title: DXA1358_481Control

description: DNA CpG sites


title: visit 2 (end of study), group A  1_C10

description:
visit 2 (end of study), group A
wk 8


title: prostate_cancer_primary_301


title: prostate_cancer_primary_289

value: Lower


title: prostate_cancer_primary_288