title: Wild-type 1

description:
Samples were processed according to manufacturer instructions.  In brief, RNA sample concentrations were measured on a Qubit 3.0 Fluorometer with a QubitTM RNA HS Assay kit.  70 µL of hybridization buffer was mixed with Immunology Panel Reporter CodeSet solution, and 8 µL of this master mix was mixed in a separate reaction vessel with 100 ng of RNA per tissue sample and RNA-free water up to 13 µL total.  2 µL of Capture ProbeSet was added to each vessel, mixed and placed on a thermocycler at 65ºC for 16-48 hours before being maintained at 4ºC for less than 24 hours.  Nanostring nCounter Prep Station performed automated fluidic sample processing to purify and immobilize hybridized sample to cartridge surface.  Digital barcode reads were analyzed by Nanostring nCounter® Digital Analyzer.
wm44c


title: SERUM3

status: Public on Sep 22 2023

type: SRA

city: Chicago

first: Morgan

last: Zenner

state: IL

address: 909 South Wolcott Ave

department: Pathology

country: USA

institute: University of Illinois at Chicago College of Medicine

description:
7_V1_TTAGGC
Qiagen GeneGlobe Primary Analysis Summary_SERUMEV.xlsx
ev_CPM_tmm_normalizedcounts_no_piR.xlsx
ev_serum_CPM_tmm_normalizedcounts_no_piR.xlsx

library_source: transcriptomic

data_processing:
GeneGlobe data analysis center
Reads were trimmed using cutadapt, which removed the 3' adapters and low-quality bases
MicroRNA sequences with less than 16 bp and UMI sequences less than 10 bp were removed
MicroRNAs were mapped to miRBase using bowtie, which allowed up to two mismatches
Assembly: miRBase version 22
Supplementary files format and content: Excel files (CPM_tmm_normalizedcounts)

molecule: total RNA

organism: Homo sapiens

source_name: Serum

growth_protocol: Patient-derived prostate epithelial cells were maintained in PrEBM media in humidified atmosphere with 5% CO2 at 37C. Patient-derived prostate stromal cells were maintained in MCDB media with 5% FBS and DHT and Fgfb in humidified atmosphere with 5% CO2 at 37C. Patient-derived prostate tissue slices were maintained in PrEBM media in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Primary epithelial cell, stromal cell, and tissue slice RNA was harvested using miRNeasy  Mini kit (Qiagen). Primary epithelial cell EV, stromal cell EV, tissue slice EV, and serum EV RNA was harvested using the Serum/Plasma miRNeasy kit (Qiagen). 100 ng of total RNA was used for the construction of cell and tissue sequencing libraries. 5 uL of RNA was used for  the construction of cell EV, tissue EV, and serum EV sequencing libraries.
microRNA libraries for smallRNA-seq were prepared using the QIAseq miRNA Library Kit following manufacturer's protocols. Libraries were diluted to 10 nM for sequencing.
smallRNA-seq by HiSeq 4000 single read 100 nucleotides

treatment_protocol: Prostate tissue slices, epithelial cells, and stromal cells were grown to 70% confluence and then cultured in EV-free media for two days. Evs were isolated from the cell media by differential ultracentifugation.

tag: tissue

value: Serum

tag: cell type

tag: sample type

value: extracellular vesicles (from serum)

tag: genotype

value: WT

tag: treatment

value: fresh collection


title: SERUM1

description:
1_V1_ATCACG
Qiagen GeneGlobe Primary Analysis Summary_SERUMEV.xlsx
ev_CPM_tmm_normalizedcounts_no_piR.xlsx
ev_serum_CPM_tmm_normalizedcounts_no_piR.xlsx


title: PHH in MPCC treated with FFA followed by reversal

type: RNA

city: Baltimore

first: Karissa

last: Cottier

state: Maryland

address: 1450 S. Rolling Rd.

institute: BioIVT

description: Test (Group4)

data_processing:
Values for triplicate samples for treatment and 6 samples for control group were averaged for the analysis
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://geneglobe.qiagen.com/us/analyze
For the normalization it uses the average of the arithmetic mean of five housekeeping genes: B2M, HPRT1 , RPLP0, GAPDH, ACTB.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Data from triplicate samples (6 samples for control group) were grouped and the web based software determined fold change for each treatment group as compared to the control group
Matrix normalized worksheet reports normalized signal (against housekeeping genes). Web based analysis software perfomed normalization automatically against housekeeping genes.
Fold Change worksheet reports test/control (such as FFA/control) ratios.

label: SYBR green

source_name: Primary Human Hepatocytes  and 3T3-J2 mouse stromal cells in MPCC

label_protocol: PCR assays were performed using the RT2 Profiler PCR Array Human Fatty Liver (Qiagen, Germantown, MD) following the Manufacturer’s instructions. Reverse transcription was performed using the RT2 First Strand Kit (Qiagen, Germantown, MD). Quantitative real-time PCR were performed (Quantstudio5, Applied Biosystems, MA) with 40 cycles at 95 oC for 15 seconds and 60 oC for 60 seconds.

growth_protocol: MPCC (HEPATOPAC) cultures were created using microfabrication processes to generate an organized co-culture containing cryopreserved primary human hepatocytes (PHH) from BioIVT (Baltimore, MD) and 3T3-J2 murine embryonic fibroblasts. Cryopreserved primary human hepatocytes from  donor lot TWJ were thawed at 37°C, counted, and plated on collagen-patterned 96 or 24 well plates. The cells were allowed to adhere until the following day, when 3T3-J2 fibroblasts were introduced to the culture plates. The resulting culture contained multiple hepatocyte islands having a 500 μm diameter spaced 1200 μm apart, center-to-center; with 3T3-J2 murine fibroblasts filling the area surrounding the hepatocyte islands. MPCC cultures were stabilized in serum containing medium for 7 days. At maturity, approximately 3,100 hepatocytes and 15,000 fibroblasts were present/well in a 96 well plate and about 21,000 hepatocytes and 90,000 fibroblasts were present/well in a 24 well plate. Treatment was initiated on day 7 after initiation of culture manufacture.

extract_protocol: RNA was extracted from treated  and control samples using the RNAeasy kit (Qiagen, Germany) as per manufacturer’s instructions. RNA was quantified spectrophotometrically, and all samples were normalized to the lowest concentration in the group. cDNA synthesis was performed using the RT2 First Strand Kit (Qiagen, Germany).

treatment_protocol: Cells were treated with control medium containing 1.0g/L glucose, 1.1 µM,  and 10% bovine serum or steatosis inducing media containing 0.5 mM free fatty acid (FFA) (Palmitate/Oleate 2:1, Sigma), 10g/L glucose and 1.0g/L fructose (HGF), or a combination of FFA and HGF with media exchanges every other day. Cells were treated with steatosis inducers continuously until day 7 of treatment or switched back to control media on day 4 for 3 days, until day 7 of treatment (reversal samples).

value: 0.5 mM FFA with 1:2 ratio of oleate and palmitate

tag: treatment duration

value: 4 days + 3 days in control medium

tag: hepatocyte vendor

value: TWJ

tag: hepatocyte lot

value: BioIVT

tag: group

value: FFA + reversal


title: PHH in MPCC treated with FFA and HGF

description: Test (Group3)

value: 0.5mM FFA and 10.0g/L glucose and 1.0g/L fructose

value: 7 days

value: FFA + HGF treated


title: PHH in MPCC treated with HGF followed by reversal

description: Test (Group5)

value: 10.0g/L glucose and 1.0g/L fructose

value: HGF + reversal


title: PHH in MPCC treated with high glucose and fructose (HGF)

description: Test (Group2)

value: HGF treated


title: HCFs, CDCP1 siRNA, 48 hrs, rep1

city: Rochester

first: Duan

last: Liu

email: liud25@gmail.com, liu.duan@mayo.edu

state: MN

address: 200 1st ST SW

department: MPET

institute: Mayo Clinic

data_processing:
RNA sequencing quality was determined with FastQC.
Sequencing reads were aligned to human genome using STAR.
Raw counts were generated with featureCounts.
Differential expression analysis was conducted with the EdgeR package using R
Assembly: hg38
Supplementary files format and content: tab-delimited text files  which is a matrix table with raw gene counts for every gene and every sample.

source_name: Primary HCF

growth_protocol: Cryopreserved adult human cardiac fibroblasts (HCFs) were purchased from Cell Applications, Inc. (Cat#:306V-05a, San Diego, CA). Cell culture and subculture were performed following the manufacturer’s Instructions for HCF Culture.

extract_protocol:
Total RNA was extracted with TRIzol® Reagent (ThermoFisher) and the miRNAeasy kit (QIAGEN) per the manufacturer’s instructions.
RNA-seq libraries were generated using the Illumina TruSeq RNA Library Prep Kit v2 (Illumina, San Diego, CA) following the manufacturer’s protocol.

tag: cell line

value: Primary HCF

value: cardiac fibroblast


title: PHH in MPCC treated with  FFA

description: Test (Group1)

value: FFA treated


title: P48_39wks_M_RNAseq

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: polyA+ RNA from placenta tissue

data_processing:
The RNA-seq reads were aligned to the hg38 human reference genome using tophat2 .
Mapped reads were sorted and captured in bam files for further downstream analysis of differential gene expression and  bigwig files were generated to for presentation as browser tracks using custom R scripts.
Assembly: hg38
Supplementary files format and content: BigWig

source_name: placenta villous core

growth_protocol: Placenta tissue samples from the villous core (excluding amnionic and chorionic surfaces) were obtained at the time of scheduled cesarean delivery or pregnancy termination in otherwise uncomplicated pregnancies

extract_protocol:
Frozen tissue was pulverized using a liquid nitrogen-chilled hammer mill and then homogenized in Trizol.  Following chloroform-mediated phase separation, the total RNA was purified from the aqueous phase using RNeasy columns (Qiagen, 74104) according to the manufacturer’s protocol.  The RNA concentration was quantified using a NanoDrop and the quality was assessed by RNA ScreenTape (Agilent).  The total RNA was stored at -80°C until processed.
Ten µg of total RNA were used as input for polyA RNA-seq library construction as previously described (Zhong et al., 2011)

tag: gestational age in weeks

tag: Sex

value: M

tag: trimester


title: P49_39wks_F_RNAseq

description: polyA+ RNA from placenta tissue

value: F


title: P47_39wks_F_RNAseq

description: polyA+ RNA from placenta tissue


title: P46_09wks_M_RNAseq

description: polyA+ RNA from placenta tissue


title: RelBdDC SI-LP steady state

city: Neuherberg

first: Caspar

last: Ohnmacht

address: Ingolstädter Landstraße 1

country: Germany

institute: Helmholtz Munich

description: 10X genomics

library_source: transcriptomic single cell

data_processing:
cellranger (version 7.0.1) was used to align the reads to the mouse genome and obtain per-gene read counts. Subsequent data processing was performed in R using Seurat (version 4.1.1) with default parameters
Assembly: MM10 2020 A
Supplementary files format and content: tab separated values files and matrix files

organism: Mus musculus

source_name: small intestinal lamina propria

extract_protocol:
the small intestine was removed, placed in ice-cold DPBS  and Peyer’s patches were removed. Intestines were cut open longitudinally, washed with ice-cold PBS, and cut into 0.5 - 1 cm pieces. For mucus removal, small intestine pieces were incubated in RPMI 1640 (Gibco) containing 25 mM HEPES (Gibco), 5 mM EDTA (Invitrogen), 3% FCS (Sigma Aldrich), and 0.145 mg/ml DTT (Sigma) for 20 min at 37°C, 80 rpm. Thereafter, tissues were washed three times with RPMI1640 containing 25 mM HEPES and 2 mM EDTA and minced with sharp scissors into 1-2 mm pieces. To generate of single cell suspensions, minced pieces were digested for 30 min by shaking at 100 rpm at 37°C in RPMI 1640 containing 25 mM HEPES, 200 iU/ml Collagenase IV (Worthington), and 0.2 mg/ml DNaseI (Sigma). Tissue pieces were then pipetted up and down several times and cell suspensions were collected. One more cycle of digestion with fresh medium was performed and cell suspensions were filtered through a 100 µm cell strainer (Corning). Cell suspension was centrifuged at 450 g, for 5 min at 4°C, cell pellets were resuspended in 40% Percoll (Cytiva) and layered onto an 80% Percoll solution. The Percoll gradient was centrifuged at 1600 g at room temperature for 15 min. The interlayer containing lamina propria cells were used for FACS. Cells were stained with antibodies against CD45, CD64, B220, CD11c and MHCII and before sorting 7AAD was added to label dead cells. They were then sorted for CD45+7AAD-, CD64-, B220-, CD11c+ MHCII+ using the FACS Aria Fusion and collected in PBS with 0.04% BSA. For mesenteric lymph nodes, organ was collected and cut into 1-2 mm pieces. Tissue pieces were digested by incubation in RPMI 1640 containing 25 mM HEPES, 200 iU/ml Collagenase IV (Worthington), and 0.2 mg/ml DNAseI (Sigma) for 30 min at 37°C, shaking at 100 rpm. After washing, cell suspension was stained in a similar manner as SI-LP cells.
Library was prepared according to manufacturers instructions (Chromium Next GEM Single Cell 3' Kit v3.1; 10X Genomics)

treatment_protocol: Control or RelBdDC mice were either isolated from mesenteric lymoh nodes or lamina propria of the small intestine at steady state or 4 days or 14 days after infection with 200 L3 stage larvae of Heligmosomoides polygyrus bakeri.

value: small intestinal lamina propria

value: dendritic cells

value: RelBdDC

value: steady state


title: control mLN steady state

description: 10X genomics

source_name: mesenteric lymph nodes

value: mesenteric lymph nodes

value: control


title: RelBdDC 4d

description: 10X genomics

value: 4d Hpb


title: control mLN 14d

description: 10X genomics

value: 14d Hpb


title: control 4d

description: 10X genomics


title: RelBdDC mLN 14d

description: 10X genomics


title: control SI-LP steady state

description: 10X genomics


title: P50_39wks_M_RNAseq

description: polyA+ RNA from placenta tissue


title: Wild-type Testis 4

city: Madrid

first: Alfonso

last: Gutiérrez-Adán

address: Av. Puerta de Hierro 28

department: Animal Reproduction

country: Spain

institute: INIA

data_processing:
Sequence reads were trimmed for low-quality sequence using Trimmomatic.
Trimmed sequence reads were mapped to GRCm39 using STAR.
Genes were quantified by featureCounts and differential expression was evaluated with DESeq2.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: Adult testis

extract_protocol:
Total RNA was extracted from testes using TRIzol reagent and then treated with Dnase for 1 h.
RNA libraries were prepared using the TruSeq RNA kit from Illumina (NEB, USA) according to the manufacturer’s recommendations.

value: Adult testis

value: WT


title: HCFs, CDCP1 siRNA, 48 hrs, rep2


title: Wild-type Testis 3


title: Wild-type Testis 2


title: P41_10wks_F_RNAseq

description: polyA+ RNA from placenta tissue


title: P42_10wks_M_RNAseq

description: polyA+ RNA from placenta tissue


title: Primary human hepatocytes (PHH) in micropatterned co-culture (MPCC)

description: Control

value: 7 days

value: TWJ

value: BioIVT

value: Control Group


title: Wild-type Testis 1


title: P40_19wks_M_RNAseq

description: polyA+ RNA from placenta tissue


title: Ak9 knockout Testis 4


title: P39_16wks_M_RNAseq

description: polyA+ RNA from placenta tissue


title: Ak9 knockout Testis 3


title: RelBdDC mLN steady state

description: 10X genomics


title: Ak9 knockout Testis 2


title: P38_16wks_M_RNAseq

description: polyA+ RNA from placenta tissue


title: P45_08wks_M_RNAseq

description: polyA+ RNA from placenta tissue


title: P44_19wks_M_RNAseq

description: polyA+ RNA from placenta tissue


title: Ak9 knockout Testis 1


title: P35_22wks_F_RNAseq

description: polyA+ RNA from placenta tissue


title: P43_15wks_M_RNAseq

description: polyA+ RNA from placenta tissue


title: P36_17wks_F_RNAseq

description: polyA+ RNA from placenta tissue


title: P33_08wks_M_RNAseq

description: polyA+ RNA from placenta tissue


title: P30_10wks_F_RNAseq

description: polyA+ RNA from placenta tissue


title: P34_12wks_F_RNAseq

description: polyA+ RNA from placenta tissue


title: P37_20wks_F_RNAseq

description: polyA+ RNA from placenta tissue


title: P29_10wks_M_RNAseq

description: polyA+ RNA from placenta tissue


title: P32_39wks_F_RNAseq

description: polyA+ RNA from placenta tissue


title: P31_12wks_F_RNAseq

description: polyA+ RNA from placenta tissue


title: P27_16wks_F_RNAseq

description: polyA+ RNA from placenta tissue


title: P28_12wks_F_RNAseq

description: polyA+ RNA from placenta tissue


title: P25_09wks_F_RNAseq

description: polyA+ RNA from placenta tissue


title: P24_08wks_F_RNAseq

description: polyA+ RNA from placenta tissue


title: P26_19wks_M_RNAseq

description: polyA+ RNA from placenta tissue


title: P21_39wks_F_RNAseq

description: polyA+ RNA from placenta tissue


title: P22_21wks_F_RNAseq

description: polyA+ RNA from placenta tissue


title: P23_16wks_F_RNAseq

description: polyA+ RNA from placenta tissue


title: P13_39wks_M_RNAseq

description: polyA+ RNA from placenta tissue


title: P11_39wks_M_RNAseq

description: polyA+ RNA from placenta tissue


title: P10_39wks_F_RNAseq

description: polyA+ RNA from placenta tissue


title: P09_39wks_M_RNAseq

description: polyA+ RNA from placenta tissue


title: P08_39wks_F_RNAseq

description: polyA+ RNA from placenta tissue


title: P50_39wks_M_PROseq

description: in vitro transcribed RNA from placenta nuclei

data_processing:
library strategy: PRO-seq
The PRO-seq reads were aligned to the hg38 human reference genome using tophat2 .
Mapped reads were sorted and captured in bam files for further downstream analysis of differential gene expression and  bigwig files were generated to for presentation as browser tracks using custom R scripts.
Assembly: hg38
Supplementary files format and content: BigWig

extract_protocol:
Frozen tissue was pulverized using a liquid nitrogen-chilled hammer mill, homogenized in ice-cold Swelling Buffer (10 mM Tris-HCl pH 8, 2 mM magnesium acetate, 3 mM calcium chloride, 0.25mM DTT, and 1x cOmplete protease inhibitor cocktail (Roche, 11697498001)), and passed through a 40 micron filter.  The nuclei were released from the pulverized tissue in Lysis Buffer   (Swelling Buffer containing 10 mM NaCl, 300 mM sucrose, and 0.5% NP-40), washed three times in Lysis Buffer  , and flash frozen in Nuclei Freezing Buffer (50 mM Tris-HCl pH 8.3, 5 mM magnesium chloride, 0.1 mM EDTA, 40% glycerol) in aliquots of 5 x 106 nuclei.
Nuclear run-on was performed at 37°C for 5 minutes using biotin-labeled CTP.  PRO-seq libraries were constructed following the protocol of Mahat and colleagues (Mahat et al., 2016)

tag: molecule type

value: nascent RNA


title: P49_39wks_F_PROseq


title: P47_39wks_F_PROseq


title: P48_39wks_M_PROseq

value: M


title: P46_09wks_M_PROseq


title: P41_10wks_F_PROseq

value: F


title: P43_15wks_M_PROseq


title: P45_08wks_M_PROseq


title: P42_10wks_M_PROseq


title: P44_19wks_M_PROseq


title: P36_17wks_F_PROseq


title: P39_16wks_M_PROseq


title: P12_39wks_F_RNAseq

description: polyA+ RNA from placenta tissue


title: P34_12wks_F_PROseq


title: P40_19wks_M_PROseq


title: P33_08wks_M_PROseq


title: P35_22wks_F_PROseq


title: P38_16wks_M_PROseq


title: P32_39wks_F_PROseq


title: P30_10wks_F_PROseq


title: P31_12wks_F_PROseq


title: P28_12wks_F_PROseq


title: P29_10wks_M_PROseq


title: P26_19wks_M_PROseq


title: P23_16wks_F_PROseq


title: P21_39wks_F_PROseq


title: P11_39wks_M_PROseq


title: P12_39wks_F_PROseq


title: P13_39wks_M_PROseq


title: P10_39wks_F_PROseq


title: P37_20wks_F_PROseq


title: P09_39wks_M_PROseq


title: prostate cancer patient pre-treatment serum EV, ENACTEV6007

data_processing:
The raw data (raw CT) values were input into GeneGlobe with a CT cutoff value of 33. In the GeneGlobe preprocessing, all CTs greater than 33 were changed to a value of 33 and the CTs were adjusted for the interplate calibrator (UniSp3) according to the miRCURY LNA miRNA PCR Panels & Assays Data Analysis Handbook.
Normalization values for each sample were calculated using the NormFinder method in GeneGlobe. The microRNAs used for normalization of serum samples included: miR-107, miR-24-3p, let-7i-5p, miR-19b-3p, miR-16-5p, miR-320a, miR-23a-3p, miR-21-5p, let-7b-5p, and miR-25-3p. The microRNAs included for normalization of serum EV samples included: included hsa-miR-107, hsa-miR-24-3p, hsa-miR-30c-5p, hsa-miR-93-5p, hsa-let-7i-5p, hsa-miR-222-3p, hsa-miR-27a-3p, hsa-miR-23a-3p, hsa-miR-21-5p, and hsa-miR-27b-3p.
These normalized values were then used to make comparisons between groups (adverse pathology versus not adverse pathology) to determine significantly different microRNAs using p < 0.05
The significant microRNAs were then used to generate random forest models to predict adverse pathology
The Fold Change Template shows the p-values for each microRNA. The microRNAs with p<0.05 were included in the random forest model to predict adverse pathology.

label: SYBR Green

source_name: peripheral venous source

label_protocol: PCR assay were performed using a miRCURY LNA miRNA Custom PCR Panel Catalog#YCA25430 (Qiagen) following the manufacturers instructions. Reverse transcription was performed from 5µ L total RNA using the miRCURY LNA RT Kit (Qiagen). Quantitative real-time PCR were performed (Applied Biosystems ViiA 7) with 40 cycles at 95C for 10 seconds and 56C for 60 seconds.

extract_protocol: Total RNA was extracted with the miRNeasy Serum/Plasma kit (Qiagen).

tag: patient id

tag: disease state

value: prostate cancer

value: serum

value: serum EVs

tag: grade of prostate cancer at biopsy

value: low-grade (0)

tag: capra risk

value: INTERMEDIATE

tag: capra score

tag: fraction

value: microRNA


title: P08_39wks_F_PROseq


title: Fetal_W20_Tissue. Nuclei_rep9

city: Irvine

first: Michael

last: Hicks

state: CA

address: 845 Health Sciences Road, Room 3101

institute: University of California, Irvine

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660009146-A-B07
GeoMx readout mode: NGS

data_processing:
Matrix 1: This is a matrix of Deseq2 counts for hPSC SMPC control, fetal SMPC transplant, fetal tissue, and adult tissue. GeoMx platform analysis was conducted with a 5% target filter, including all flagged ROIs. This input was Q3 normalized before exporting the dataset and uploading into R Studio for Deseq2 analysis to obtain PCA plots.
Matrix 2: This is a matrix of Q3 normalized counts for control and AP1903 treated hPSC SMPC . GeoMx platform analysis was conducted with a 20% target filter, including all flagged ROIs. Then, Q3 normalization was conducted.
Matrix shows total normalized counts of RNA oligos.

growth_protocol: hPSCs were cultured in mTESR media, while hPSC derived SMPCs were cultured in SKGM2 media.

extract_protocol:
Mice tibialis anterior skeletal muscle was flash frozen and sectioned at 10µm onto glass coverslips
Following overnigh hybridization, same day primary and secondary antibody stain: Cyto13 (488), ACTC1 (Rb IgG-555), Lamin AC and Spectrin (Ms IgG2b 594), PAX7 (Ms IgG1-647)
Manufacturer protocol was followed except with modifications: 0.025 µg/mL Proteinase K for 5 minutes .  No antigen retrieval.  No 65C baking step.  Primary and secondy antibody staining performed

treatment_protocol: Experiment 2-3.  Mice were intramuscularly injected with 50µL of 1.2% BaCl2 into the tibilias anterior to induce injury. Endogenous mouse Pax7+ cells were ablated prior to transplantation with 400mg/kg tamoxifen chow for 7 days prior to being fed normal chow during experiments. Experiment 3 only. Mice were injected intraperitoneally with AP1903 (10μM in 100μl saline) or control (0.1% DMSO in saline) every two weeks for 90 days (six total injections).

tag: slide name

tag: segment label

value: Nuclei

tag: cell type

value: Fetal Tissue

value: False

value: True

tag: engraft fetal actc1+

tag: engraft fetal actc1-

tag: hpsc myofiber

tag: tissue myofiber

tag: label microscope_slide


title: Fetal_W20_Tissue. Nonmyogenic_rep4

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660009146-A-B11
GeoMx readout mode: NGS

value: Full ROI

tag: treatment


title: Fetal_W20_Tissue. Myofiber_rep8

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660009146-A-B06
GeoMx readout mode: NGS

value: MyoFiber


title: Fetal_W20_Tissue. Myofiber_rep9

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660009146-A-B08
GeoMx readout mode: NGS


title: Fetal_W20_Tissue. Nonmyogenic_rep2

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660009146-A-B09
GeoMx readout mode: NGS


title: P27_16wks_F_PROseq

tag: gestational age in weeks

tag: Sex

tag: trimester


title: prostate cancer patient pre-treatment serum EV, ENACTEV5031

tag: patient id

tag: disease state

tag: tissue

tag: sample type

value: LOW


title: prostate cancer patient pre-treatment serum EV, ENACTEV5021

tag: grade of prostate cancer at biopsy

tag: capra risk

tag: capra score

tag: fraction


title: Fetal_W20_Tissue. Nuclei_rep8

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660009146-A-B05
GeoMx readout mode: NGS

tag: slide name

tag: segment label

tag: cell type

tag: engraft fetal actc1+


title: P25_09wks_F_PROseq

tag: molecule type


title: P22_21wks_F_PROseq


title: prostate cancer patient pre-treatment serum EV, ENACTEV4014

value: high-grade (1)


title: prostate cancer patient pre-treatment serum EV, ENACTEV4016


title: Fetal_W20_Tissue. Myofiber_rep7

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660009146-A-B04
GeoMx readout mode: NGS

tag: treatment

tag: engraft fetal actc1-

tag: hpsc myofiber

tag: tissue myofiber

tag: label microscope_slide


title: Fetal_W20_Tissue. Nuclei_rep7

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660009146-A-B03
GeoMx readout mode: NGS


title: Fetal_W20_Tissue. Nonmyogenic_rep1

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660009146-A-B02
GeoMx readout mode: NGS


title: prostate cancer patient pre-treatment serum EV, ENACTEV4011

tag: patient id

tag: disease state


title: Fetal_W20_Tissue. Nuclei_rep6

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660009146-A-A12
GeoMx readout mode: NGS


title: Fetal_W20_Tissue. Nonmyogenic_rep3

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660009146-A-B10
GeoMx readout mode: NGS


title: prostate cancer patient pre-treatment serum EV, ENACTEV4013

tag: tissue

tag: sample type


title: Fetal_W20_Tissue. Myofiber_rep6

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660009146-A-B01
GeoMx readout mode: NGS


title: P24_08wks_F_PROseq

tag: gestational age in weeks

tag: Sex

tag: trimester

value: nascent RNA


title: Fetal_W20_Tissue. Myofiber_rep5

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660009146-A-A11
GeoMx readout mode: NGS

tag: slide name


title: prostate cancer patient pre-treatment serum EV, ENACTEV4007

tag: ap

tag: grade of prostate cancer at biopsy

tag: capra risk

tag: capra score

tag: fraction


title: prostate cancer patient pre-treatment serum EV, ENACTEV5034


title: Fetal_W20_Tissue. Nuclei_rep5

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660009146-A-A10
GeoMx readout mode: NGS

tag: segment label

tag: cell type

tag: treatment

tag: engraft fetal actc1+

tag: engraft fetal actc1-


title: prostate cancer patient pre-treatment serum EV, ENACTEV4004

tag: patient id

tag: disease state


title: prostate cancer patient pre-treatment serum EV, ENACTEV4005

tag: tissue

tag: sample type


title: Fetal_W20_Tissue. Myofiber_rep4

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660009146-A-A09
GeoMx readout mode: NGS

tag: hpsc myofiber

tag: tissue myofiber

tag: label microscope_slide


title: Fetal_W20_Tissue. Nuclei_rep4

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660009146-A-A08
GeoMx readout mode: NGS

tag: slide name


title: Fetal_W20_Tissue. Myofiber_rep3

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660009146-A-A07
GeoMx readout mode: NGS


title: Fetal_W20_Tissue. Myofiber_rep2

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660009146-A-A05
GeoMx readout mode: NGS


title: prostate cancer patient pre-treatment serum EV, ENACTEV4003

tag: grade of prostate cancer at biopsy


title: prostate cancer patient pre-treatment serum EV, ENACTEV4002

tag: capra risk


title: prostate cancer patient pre-treatment serum EV, ENACTEV3063

tag: capra score


title: Fetal_W20_Tissue. Nuclei_rep3

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660009146-A-A06
GeoMx readout mode: NGS


title: prostate cancer patient pre-treatment serum EV, ENACTEV3062

tag: fraction


title: prostate cancer patient pre-treatment serum EV, ENACTEV3064


title: Fetal_W20_Tissue. Nuclei_rep2

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660009146-A-A04
GeoMx readout mode: NGS

tag: segment label


title: Fetal_W20_Tissue. Nuclei_rep1

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660009146-A-A02
GeoMx readout mode: NGS

tag: cell type


title: Fetal_W20_Tissue. Myofiber_rep1

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660009146-A-A03
GeoMx readout mode: NGS

tag: treatment


title: prostate cancer patient pre-treatment serum EV, ENACTEV4009


title: prostate cancer patient pre-treatment serum EV, ENACTEV3059


title: prostate cancer patient pre-treatment serum EV, ENACTEV3058


title: prostate cancer patient pre-treatment serum EV, ENACTEV3061


title: prostate cancer patient pre-treatment serum EV, ENACTEV3055


title: prostate cancer patient pre-treatment serum EV, ENACTEV3057


title: Engrafted_hPSC_AP1903. Myofiber_rep8

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-E10
GeoMx readout mode: NGS

value: Day 90 A

value: Segment 2

value: hPSC SMPC

tag: engraft fetal actc1+


title: prostate cancer patient pre-treatment serum EV, ENACTEV3053

value: prostate cancer

value: serum

tag: ap


title: prostate cancer patient pre-treatment serum EV, ENACTEV3052

tag: patient id

value: serum EVs

value: low-grade (0)


title: Engrafted_hPSC_AP1903. PAX7-_rep9

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-E12
GeoMx readout mode: NGS

tag: engraft fetal actc1-


title: Engrafted_hPSC_AP1903. Myofiber_rep7

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-E09
GeoMx readout mode: NGS


title: Engrafted_hPSC_AP1903. PAX7-_rep7

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-E08
GeoMx readout mode: NGS


title: Engrafted_hPSC_AP1903. Myofiber_rep6

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-E07
GeoMx readout mode: NGS


title: prostate cancer patient pre-treatment serum EV, ENACTEV3049

tag: disease state

tag: tissue

value: microRNA


title: Engrafted_hPSC_AP1903. PAX7+_rep3

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-E06
GeoMx readout mode: NGS

value: Segment 1

tag: hpsc myofiber


title: prostate cancer patient pre-treatment serum EV, ENACTEV3050

tag: sample type


title: Engrafted_hPSC_AP1903. PAX7-_rep6

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-E05
GeoMx readout mode: NGS

tag: tissue myofiber

tag: label microscope_slide


title: Engrafted_hPSC_AP1903. Myofiber_rep5

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-E03
GeoMx readout mode: NGS

tag: slide name


title: Engrafted_hPSC_AP1903. PAX7-_rep5

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-E04
GeoMx readout mode: NGS


title: prostate cancer patient pre-treatment serum EV, ENACTEV3047

tag: grade of prostate cancer at biopsy

tag: capra risk


title: prostate cancer patient pre-treatment serum EV, ENACTEV3043

tag: capra score

tag: fraction


title: Engrafted_hPSC_AP1903. PAX7+_rep2

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-D12
GeoMx readout mode: NGS

tag: segment label

tag: cell type


title: Engrafted_hPSC_AP1903. Myofiber_rep3

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-E01
GeoMx readout mode: NGS

tag: treatment

tag: engraft fetal actc1+


title: prostate cancer patient pre-treatment serum EV, ENACTEV3044

tag: patient id


title: prostate cancer patient pre-treatment serum EV, ENACTEV3042


title: Engrafted_hPSC_AP1903. PAX7-_rep8

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-E11
GeoMx readout mode: NGS

tag: engraft fetal actc1-


title: prostate cancer patient pre-treatment serum EV, ENACTEV3041

tag: disease state


title: Engrafted_hPSC_AP1903. PAX7+_rep1

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-D10
GeoMx readout mode: NGS


title: prostate cancer patient pre-treatment serum EV, ENACTEV3040

tag: tissue


title: prostate cancer patient pre-treatment serum EV, ENACTEV3039


title: Engrafted_hPSC_AP1903. Myofiber_rep1

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-D08
GeoMx readout mode: NGS

tag: hpsc myofiber


title: Engrafted_hPSC_AP1903. PAX7-_rep4

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-D09
GeoMx readout mode: NGS


title: prostate cancer patient pre-treatment serum EV, ENACTEV3051

tag: sample type


title: prostate cancer patient pre-treatment serum EV, ENACTEV3032


title: prostate cancer patient pre-treatment serum EV, ENACTEV3029

tag: ap


title: prostate cancer patient pre-treatment serum EV, ENACTEV3048


title: Engrafted_hPSC_AP1903. PAX7-_rep3

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-D07
GeoMx readout mode: NGS

tag: tissue myofiber

tag: label microscope_slide


title: prostate cancer patient pre-treatment serum EV, ENACTEV3033

tag: grade of prostate cancer at biopsy


title: prostate cancer patient pre-treatment serum EV, ENACTEV3038

tag: capra risk


title: Engrafted_hPSC_AP1903. PAX7-_rep2

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-D06
GeoMx readout mode: NGS

tag: slide name


title: prostate cancer patient pre-treatment serum EV, ENACTEV3028

value: INTERMEDIATE

tag: capra score

tag: fraction


title: Engrafted_hPSC_AP1903. Myofiber_rep4

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-E02
GeoMx readout mode: NGS

tag: segment label

tag: cell type

value: False


title: Engrafted_hPSC_Untreated. PAX7-_rep9

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-D04
GeoMx readout mode: NGS

value: Day 90

tag: treatment

value: True

tag: engraft fetal actc1+


title: prostate cancer patient pre-treatment serum EV, ENACTEV3027

tag: patient id


title: prostate cancer patient pre-treatment serum EV, ENACTEV3026

tag: disease state


title: Engrafted_hPSC_AP1903. Myofiber_rep2

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-D11
GeoMx readout mode: NGS

tag: engraft fetal actc1-


title: prostate cancer patient pre-treatment serum EV, ENACTEV3025

tag: tissue


title: Engrafted_hPSC_Untreated. PAX7-_rep7

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-D02
GeoMx readout mode: NGS

tag: hpsc myofiber


title: Engrafted_hPSC_Untreated. PAX7-_rep6

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-D01
GeoMx readout mode: NGS


title: Engrafted_hPSC_Untreated. PAX7-_rep5

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-C12
GeoMx readout mode: NGS


title: prostate cancer patient pre-treatment serum EV, ENACTEV3024

tag: sample type


title: prostate cancer patient pre-treatment serum EV, ENACTEV3021


title: prostate cancer patient pre-treatment serum EV, ENACTEV3023

tag: ap


title: prostate cancer patient pre-treatment serum EV, ENACTEV3020


title: Engrafted_hPSC_Untreated. PAX7-_rep3

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-C10
GeoMx readout mode: NGS

tag: tissue myofiber

tag: label microscope_slide


title: Engrafted_hPSC_Untreated. PAX7-_rep4

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-C11
GeoMx readout mode: NGS


title: prostate cancer patient pre-treatment serum EV, ENACTEV3019

tag: grade of prostate cancer at biopsy

tag: capra risk


title: prostate cancer patient pre-treatment serum EV, ENACTEV3016

tag: capra score


title: Engrafted_hPSC_Untreated. PAX7-_rep1

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-C08
GeoMx readout mode: NGS

tag: slide name


title: Engrafted_hPSC_Untreated. PAX7-_rep2

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-C09
GeoMx readout mode: NGS

tag: segment label


title: Engrafted_hPSC_Untreated. Myofiber_rep15

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-C07
GeoMx readout mode: NGS

tag: cell type


title: Engrafted_hPSC_Untreated. PAX7+_rep12

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-C06
GeoMx readout mode: NGS

tag: treatment


title: Engrafted_hPSC_AP1903. PAX7-_rep1

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-D05
GeoMx readout mode: NGS

tag: engraft fetal actc1+


title: Engrafted_hPSC_Untreated. Myofiber_rep14

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-C05
GeoMx readout mode: NGS


title: prostate cancer patient pre-treatment serum EV, ENACTEV3012

tag: patient id

tag: fraction


title: prostate cancer patient pre-treatment serum EV, ENACTEV3010

tag: disease state


title: Engrafted_hPSC_Untreated. PAX7-_rep8

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-D03
GeoMx readout mode: NGS

tag: engraft fetal actc1-


title: Engrafted_hPSC_Untreated. PAX7+_rep11

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-C04
GeoMx readout mode: NGS

tag: hpsc myofiber


title: prostate cancer patient pre-treatment serum EV, ENACTEV3008

tag: tissue

tag: sample type


title: prostate cancer patient pre-treatment serum EV, ENACTEV3007


title: prostate cancer patient pre-treatment serum EV, ENACTEV3006


title: Engrafted_hPSC_Untreated. Myofiber_rep13

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-C03
GeoMx readout mode: NGS

tag: tissue myofiber


title: Engrafted_hPSC_Untreated. PAX7+_rep10

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-B12
GeoMx readout mode: NGS

tag: label microscope_slide


title: Engrafted_hPSC_Untreated. Myofiber_rep12

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-C02
GeoMx readout mode: NGS


title: prostate cancer patient pre-treatment serum EV, ENACTEV3005

tag: grade of prostate cancer at biopsy


title: Engrafted_hPSC_Untreated. Myofiber_rep11

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-B11
GeoMx readout mode: NGS


title: Engrafted_hPSC_Untreated. PAX7+_rep9

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-B10
GeoMx readout mode: NGS


title: prostate cancer patient pre-treatment serum EV, ENACTEV3002

tag: capra risk


title: Engrafted_hPSC_Untreated. Myofiber_rep10

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-B09
GeoMx readout mode: NGS


title: prostate cancer patient pre-treatment serum EV, ENACTEV3015

tag: ap

tag: capra score


title: Engrafted_hPSC_Untreated. Myofiber_rep9

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-B08
GeoMx readout mode: NGS

tag: slide name

tag: segment label


title: prostate cancer patient pre-treatment serum EV, ENACTEV2010


title: Engrafted_hPSC_Untreated. Myofiber_rep8

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-B05
GeoMx readout mode: NGS

tag: cell type

tag: treatment


title: Engrafted_hPSC_Untreated. PAX7+_rep7

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-B04
GeoMx readout mode: NGS

tag: engraft fetal actc1+


title: Engrafted_hPSC_Untreated. Myofiber_rep7

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-B03
GeoMx readout mode: NGS


title: prostate cancer patient pre-treatment serum EV, ENACTEV2008

tag: patient id

tag: fraction


title: prostate cancer patient pre-treatment serum EV, ENACTEV2007

tag: disease state


title: prostate cancer patient pre-treatment serum EV, ENACTEV2009


title: prostate cancer patient pre-treatment serum EV, ENACTEV2006


title: Engrafted_hPSC_Untreated. Myofiber_rep6

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-B01
GeoMx readout mode: NGS

tag: engraft fetal actc1-

tag: hpsc myofiber


title: prostate cancer patient pre-treatment serum EV, ENACTEV2005

tag: tissue

tag: sample type


title: Engrafted_hPSC_Untreated. Myofiber_rep5

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-A11
GeoMx readout mode: NGS

tag: tissue myofiber

tag: label microscope_slide


title: Engrafted_hPSC_Untreated. PAX7+_rep6

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-A12
GeoMx readout mode: NGS


title: prostate cancer patient pre-treatment serum EV, ENACTEV2002

tag: grade of prostate cancer at biopsy

tag: capra risk


title: prostate cancer patient pre-treatment serum EV, ENACTEV2003

tag: ap

tag: capra score


title: Engrafted_hPSC_Untreated. PAX7+_rep5

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-A10
GeoMx readout mode: NGS

tag: slide name

tag: segment label


title: prostate cancer patient pre-treatment serum EV, ENACTEV1023


title: prostate cancer patient pre-treatment serum EV, ENACTEV1022


title: Engrafted_hPSC_Untreated. Myofiber_rep4

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-A09
GeoMx readout mode: NGS

tag: cell type

tag: treatment


title: prostate cancer patient pre-treatment serum EV, ENACTEV3001

tag: patient id


title: Engrafted_hPSC_Untreated. PAX7+_rep4

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-A08
GeoMx readout mode: NGS

tag: engraft fetal actc1+


title: Engrafted_hPSC_Untreated. Myofiber_rep3

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-A07
GeoMx readout mode: NGS


title: Engrafted_hPSC_Untreated. PAX7+_rep8

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-B07
GeoMx readout mode: NGS


title: prostate cancer patient pre-treatment serum EV, ENACTEV1017

tag: disease state

tag: fraction


title: prostate cancer patient pre-treatment serum EV, ENACTEV1020


title: prostate cancer patient pre-treatment serum EV, ENACTEV1021


title: prostate cancer patient pre-treatment serum EV, ENACTEV1015


title: Engrafted_hPSC_Untreated. PAX7+_rep3

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-A06
GeoMx readout mode: NGS

tag: engraft fetal actc1-

tag: hpsc myofiber


title: Engrafted_hPSC_Untreated. Myofiber_rep2

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-A05
GeoMx readout mode: NGS


title: Engrafted_hPSC_Untreated. PAX7+_rep2

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-A04
GeoMx readout mode: NGS


title: Engrafted_hPSC_Untreated. Myofiber_rep1

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-A03
GeoMx readout mode: NGS


title: prostate cancer patient pre-treatment serum EV, ENACTEV1012

tag: tissue

tag: sample type


title: prostate cancer patient pre-treatment serum EV, ENACTEV1014


title: Engrafted_Fetal_Reinjury.  ACTC1+_rep10

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-B10
GeoMx readout mode: NGS

value: Reinjury

value: Fetal SMPC

tag: tissue myofiber

tag: label microscope_slide


title: Engrafted_Fetal_Reinjury.  PAX7+_rep8

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-B09
GeoMx readout mode: NGS


title: Engrafted_hPSC_Untreated. PAX7+_rep1

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008748-H-A02
GeoMx readout mode: NGS


title: Engrafted_Fetal_Reinjury.  ACTC1+_rep9

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-B08
GeoMx readout mode: NGS

value: Full ROI


title: prostate cancer patient pre-treatment serum EV, ENACTEV1009

tag: grade of prostate cancer at biopsy

tag: capra risk

value: LOW


title: prostate cancer patient pre-treatment serum EV, ENACTEV1011

tag: ap

tag: capra score


title: prostate cancer patient pre-treatment serum EV, ENACTEV1005


title: prostate cancer patient pre-treatment serum EV, ENACTEV1008


title: prostate cancer patient pre-treatment serum EV, ENACTEV1006


title: Engrafted_Fetal_Reinjury.  ACTC1-_rep3

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-B07
GeoMx readout mode: NGS

tag: slide name

tag: segment label


title: Engrafted_Fetal_Reinjury.  ACTC1+_rep8

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-B06
GeoMx readout mode: NGS

tag: cell type

tag: treatment


title: prostate cancer patient pre-treatment serum EV, ENACTEV1002

tag: patient id


title: prostate cancer patient pre-treatment serum EV, DODEV60

tag: disease state

value: high-grade (1)

value: HIGH


title: prostate cancer patient pre-treatment serum EV, DODEV61

tag: fraction


title: Engrafted_Fetal_Reinjury.  PAX7+_rep7

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-B04
GeoMx readout mode: NGS

tag: engraft fetal actc1+

tag: engraft fetal actc1-


title: Engrafted_Fetal_Reinjury.  ACTC1+_rep7

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-B02
GeoMx readout mode: NGS

tag: hpsc myofiber


title: Engrafted_Fetal_Reinjury.  ACTC1-_rep2

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-B05
GeoMx readout mode: NGS


title: Engrafted_Fetal_Reinjury.  PAX7+_rep6

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-B03
GeoMx readout mode: NGS


title: prostate cancer patient pre-treatment serum EV, DODEV53

tag: tissue

tag: sample type


title: Engrafted_Fetal_Reinjury.  PAX7+_rep5

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-B01
GeoMx readout mode: NGS

tag: tissue myofiber

tag: label microscope_slide


title: prostate cancer patient pre-treatment serum EV, DODEV52

tag: grade of prostate cancer at biopsy

tag: capra risk


title: prostate cancer patient pre-treatment serum EV, DODEV55

tag: ap

tag: capra score


title: Engrafted_Fetal_Reinjury.  PAX7+_rep4

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-A11
GeoMx readout mode: NGS

tag: slide name

tag: segment label


title: prostate cancer patient pre-treatment serum EV, DODEV51


title: prostate cancer patient pre-treatment serum EV, DODEV49


title: Engrafted_Fetal_Reinjury.  ACTC1-_rep1

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-A10
GeoMx readout mode: NGS

tag: cell type

tag: treatment


title: Engrafted_Fetal_Reinjury.  PAX7+_rep3

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-A09
GeoMx readout mode: NGS


title: prostate cancer patient pre-treatment serum EV, DODEV54

tag: patient id

tag: disease state


title: prostate cancer patient pre-treatment serum EV, DODEV48

tag: fraction


title: Engrafted_Fetal_Reinjury.  ACTC1+_rep5

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-A08
GeoMx readout mode: NGS

tag: engraft fetal actc1+

tag: engraft fetal actc1-


title: Engrafted_Fetal_Reinjury.  PAX7+_rep2

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-A06
GeoMx readout mode: NGS

tag: hpsc myofiber


title: prostate cancer patient pre-treatment serum EV, DODEV47

tag: tissue

tag: sample type


title: prostate cancer patient pre-treatment serum EV, DODEV46


title: Engrafted_Fetal_Reinjury.  ACTC1+_rep4

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-A07
GeoMx readout mode: NGS

tag: tissue myofiber

tag: label microscope_slide


title: Engrafted_Fetal_Reinjury.  ACTC1+_rep2

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-A04
GeoMx readout mode: NGS


title: prostate cancer patient pre-treatment serum EV, DODEV45

tag: grade of prostate cancer at biopsy

tag: capra risk


title: prostate cancer patient pre-treatment serum EV, DODEV44

tag: ap

tag: capra score


title: prostate cancer patient pre-treatment serum EV, DODEV63


title: prostate cancer patient pre-treatment serum EV, DODEV43


title: prostate cancer patient pre-treatment serum EV, DODEV42


title: Engrafted_Fetal_Reinjury.  PAX7+_rep1

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-A02
GeoMx readout mode: NGS

tag: slide name

tag: segment label


title: Engrafted_Fetal_Reinjury.  ACTC1+_rep1

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-A03
GeoMx readout mode: NGS

tag: cell type

tag: treatment


title: Engrafted_Fetal_Reinjury.  ACTC1+_rep6

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-A12
GeoMx readout mode: NGS


title: Engrafted_Fetal_Four-month.  PAX7-_rep3

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-D12
GeoMx readout mode: NGS

value: Four-month

value: human nuclei


title: Engrafted_Fetal_Four-month.  ACTC1-_rep4

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-D11
GeoMx readout mode: NGS


title: Engrafted_Fetal_Four-month.  ACTC1-_rep3

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-D10
GeoMx readout mode: NGS


title: prostate cancer patient pre-treatment serum EV, DODEV41

tag: patient id

tag: disease state

value: prostate cancer

value: serum


title: prostate cancer patient pre-treatment serum EV, DODEV38

value: serum EVs

tag: fraction


title: Engrafted_Fetal_Four-month.  PAX7-_rep2

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-D09
GeoMx readout mode: NGS

tag: engraft fetal actc1+

tag: engraft fetal actc1-


title: prostate cancer patient pre-treatment serum EV, DODEV36

tag: tissue

value: low-grade (0)

value: microRNA


title: prostate cancer patient pre-treatment serum EV, DODEV40

tag: sample type


title: Engrafted_Fetal_Four-month.  ACTC1+_rep1

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-D04
GeoMx readout mode: NGS

tag: hpsc myofiber

tag: tissue myofiber


title: Engrafted_Fetal_Reinjury.  ACTC1+_rep3

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-A05
GeoMx readout mode: NGS

tag: label microscope_slide


title: Engrafted_Fetal_Four-month.  ACTC1-_rep2

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-D05
GeoMx readout mode: NGS


title: Engrafted_Fetal_Four-month.  PAX7-_rep1

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-D02
GeoMx readout mode: NGS


title: prostate cancer patient pre-treatment serum EV, DODEV35

tag: grade of prostate cancer at biopsy

tag: capra risk

value: INTERMEDIATE


title: Engrafted_Fetal_Four-month.  PAX7+_rep2

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-D01
GeoMx readout mode: NGS

value: False


title: Engrafted_Fetal_Four-month.  PAX7+_rep3

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-D03
GeoMx readout mode: NGS


title: prostate cancer patient pre-treatment serum EV, DODEV33

tag: ap

tag: capra score


title: prostate cancer patient pre-treatment serum EV, DODEV34


title: Engrafted_Fetal_Four-month.  ACTC1-_rep1

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-C12
GeoMx readout mode: NGS

tag: slide name

tag: segment label


title: prostate cancer patient pre-treatment serum EV, DODEV39


title: Engrafted_Fetal_Four-month.  PAX7+_rep1

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-C11
GeoMx readout mode: NGS

tag: cell type

tag: treatment


title: Engrafted_Fetal_Two-month.  PAX7-_rep1

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-C10
GeoMx readout mode: NGS

value: Two-month


title: prostate cancer patient pre-treatment serum EV, DODEV32

tag: patient id

tag: disease state


title: prostate cancer patient pre-treatment serum EV, DODEV29

tag: fraction


title: prostate cancer patient pre-treatment serum EV, DODEV31


title: prostate cancer patient pre-treatment serum EV, DODEV28


title: Engrafted_Fetal_Two-month.  ACTC1+_rep5

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-C08
GeoMx readout mode: NGS

tag: engraft fetal actc1+

value: True

tag: engraft fetal actc1-


title: prostate cancer patient pre-treatment serum EV, DODEV21

tag: tissue

tag: sample type


title: prostate cancer patient pre-treatment serum EV, DODEV25


title: Engrafted_Fetal_Two-month.  ACTC1-_rep5

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-C09
GeoMx readout mode: NGS

tag: hpsc myofiber

tag: tissue myofiber


title: prostate cancer patient pre-treatment serum EV, DODEV37

tag: grade of prostate cancer at biopsy


title: Engrafted_Fetal_Two-month.  ACTC1+_rep4

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-C07
GeoMx readout mode: NGS

tag: label microscope_slide


title: prostate cancer patient pre-treatment serum EV, DODEV15

tag: ap

tag: capra risk


title: Engrafted_Fetal_Two-month.  ACTC1-_rep3

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-C05
GeoMx readout mode: NGS

tag: slide name


title: Engrafted_Fetal_Two-month.  ACTC1+_rep3

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-C04
GeoMx readout mode: NGS

tag: segment label


title: Engrafted_Fetal_Two-month.  ACTC1-_rep2

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-C03
GeoMx readout mode: NGS

tag: cell type


title: Engrafted_Fetal_Two-month.  ACTC1-_rep4

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-C06
GeoMx readout mode: NGS

tag: treatment


title: prostate cancer patient pre-treatment serum EV, DODEV5

tag: patient id

tag: capra score


title: prostate cancer patient pre-treatment serum EV, DODEV4

tag: disease state

tag: fraction


title: prostate cancer patient pre-treatment serum EV, DODEV12


title: Engrafted_Fetal_Two-month.  ACTC1+_rep2

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-C02
GeoMx readout mode: NGS

tag: engraft fetal actc1+

tag: engraft fetal actc1-


title: Engrafted_Fetal_Two-month.  ACTC1-_rep1

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-C01
GeoMx readout mode: NGS


title: prostate cancer patient pre-treatment serum EV, DODEV27

tag: tissue

tag: sample type


title: prostate cancer patient pre-treatment serum, ENACT6008


title: Engrafted_Fetal_Two-month.  PAX7+_rep1

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-B11
GeoMx readout mode: NGS

tag: hpsc myofiber

tag: tissue myofiber


title: prostate cancer patient pre-treatment serum EV, DODEV17

tag: grade of prostate cancer at biopsy


title: prostate cancer patient pre-treatment serum EV, DODEV3


title: prostate cancer patient pre-treatment serum, ENACT6004

tag: ap


title: prostate cancer patient pre-treatment serum, ENACT6005

tag: capra risk


title: prostate cancer patient pre-treatment serum, ENACT6007


title: prostate cancer patient pre-treatment serum, ENACT6001


title: prostate cancer patient pre-treatment serum, ENACT6000


title: prostate cancer patient pre-treatment serum, ENACT5056


title: FOSL2CTRL_3

city: Nijmegen

first: Jo Huiqing

last: Zhou

address: Geert Grooteplein 26/28

country: Netherlands

institute: Radboud University

data_processing:
Preprocessing of reads was done automatically with workflow tool seq2science v0.7.1
Paired-end reads were trimmed with fastp v0.20.1 with default options. Genome assembly GRCh38.p13 was downloaded with genomepy 0.11.1. The effective genome size was estimated per sample by khmer v2.0 by calculating the number of unique kmers with k being the average read length per sample. Reads of RNAseq samples were aligned with STAR v2.7.6a with default options. Afterwards, duplicate reads were marked with Picard MarkDuplicates v2.23.8. General alignment statistics were collected by samtools stats v1.14. Mapped reads were removed if they did not have a minimum mapping quality of 30, were a (secondary) multimapper or aligned inside the ENCODE blacklist. RNAseq sample counting and summarizing to gene-level was performed on filtered bam using HTSeq-count v0.12. Sample sequencing strandedness was inferred using RSeQC v4.0.0 order to improve quantification accuracy.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include gene count values for each Sample

growth_protocol: Primary human limbal epithelial stem cells were isolated from healthy donors and cultivated in 6 well plates in KSFM medium (Cat. Nr. 17005042, Thermo Fisher, Gibco, Life Technologies, Paisley, UK) supplemented with 500 ng Epidermal growth factor (EGF), 12.5 mg Bovin pituitary extract (BPE) (Cat. Nr. 37000015, Thermo Fisher, Gibco, Life Technologies, Paisley, UK) and 0.1% P/S.

extract_protocol:
Total RNA was isolated using the Quick–RNA MicroPrep kit, according to the manufacturer’s protocol. RNA concentrations were measured using the the DeNovix DS-11FX spectrometer.
500 ng of RNA was was prepared for sequencing using the KAPA RNA HyperPrep Kit with. Libraries were sequenced on the Illumina NextSeq 500, generating an average of 15–20 million reads per sample.

treatment_protocol:
siRNA treatment protocol
After reaching 70-80 % confluence, cells were transfected using Lipofectamin 2000 transfection reagent. For this purpose, 5 l Lipofectamin was added to 250 l Optimem and incubated for 5 minutes, at room  temperature. In a separate tube, siRNA of interest was diluted in 250 l Optimem. The Lipofectamin  was added to the siRNA mixture and incubated for 20 minutes, RT. After the incubation time, transfection mixture was added dropwise to the cells. The cells were incubated at 37°C and 5% CO2 and medium were changed after 24h. Cells were collected 48 hours after transfection for further analysis. FOSL2 siRNA 100 ng Sense: CGAACCUCGUCUUCACCUAtt Antisense: UAGGUGAAGACGAGGUUCGag Ambion. Ctrl siRNA for FOSL2 100 ng Catalog No. 4404021 Ambion. PAX6 siRNA 5 ng combination of two different siRNAs: 5′CCUGGCUAGCGAAAAGCAAUU 5′UGGGCGGAGUUAUGAUACCUU MWG Eurofins. Ctrl siRNA for PAX6 5 ng 5′AGGUAGUGUAAUCGCCUUGUU MWG Eurofins

tag: cell line

value: Limbal stem cells

tag: genotype

value: WT


title: FOSL2KD_4

tag: cell type


title: FOSL2CTRL_4


title: FOSL2KD_3


title: LSC_Aniridia_scRNAseq_2

description:
LSC_Aniridia_scRNAseq_2
scRNA_barcodes_384.tab

data_processing:
For the matrix files, preprocessing of reads was done automatically with workflow tool seq2science v0.9.2 using the scrna-seq workflow, Single-end reads were trimmed with fastp v0.20.1 with default options. Genome assembly GRCh38.p13 was downloaded with genomepy 0.12.0. The genome and gene annotations was extended with custom regions. Reads were aligned and transformed to bus format with kb-python v0.26.4, a python wrapper for kallisto and bustools.
For generating the psuedobulk table, data was prepocessed using the cellseq2 pipeline. Briefly, reads were aligned using star to the GRCh38.p13 genome. After which cells were quality controlled using Seurat, filtering cells on ERCC reads, genes measured and transcripts per cell. After vizualization of the lack of heterogeneity by Umap, pseudo Bulk count data was generated by summing all the cells their UMI counts.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include gene count values for each plate, for each sample a .mtx matrix file with the reads, a .genes.txt file with the genes corresponding the the matrix file, and a .barcodes.txt file containing the barcodes linked to the matrix file

molecule: polyA RNA

source_name: Limbal stem cells

growth_protocol: LSC were cultured in KSFM supplemented with 25 μg/ml Bovine Pituitary Extract, 0.2 ng/ml Epidermal Growth Factor, 0.4 mM CaCl2, 2 mM Glutamine and 100 U/ml Penicillin/Streptomicin. Medium was refreshed every other day untill the cells were 90% confluent.

extract_protocol:
A single-cell suspension was made using trypsin. After which cells were filtered using a 40uM filter to remove cell clumps. Cells were stained with 7-AAD.
Live cells were selected for and FACs-sorted onto 384-well plates containing primers with unique molecular identifiers, according to the SORT-Seq protocol.  Plates were spun down (1200 × g, 1 min, 4 °C) and ERCC spike‐in mix (1:50,000) was dispensed by a Nanodrop into each well. 150 nl of the Reverse Transcription (RT) mix was similarly dispensed into each well. Thermal cycling conditions were set at 4 °C 5 min; 25 °C 10 min; 42 °C 1 h; 70 °C 10 min. Each plate their library was pooled together and the cDNA was purified using AmpureXP beads. Overnight In vitro transcription was carried out at 16 °C, with the lid set at 70 °C. An exonuclease digestion step was performed thereafter for 20 min at 37 °C, followed by fragmentation of the RNA samples. After a beads cleanup, the samples were subjected to library RT and amplification to tag the RNA molecules with specific and unique sample indexes, followed by a final beads cleanup (1:0.8, reaction mix: beads), and the sample cDNA libraries were eluted with DNAse free water. Libraries were quantified using the KAPPA quantification kit following manufacturers protocol after which the plates were sequenced on the Illumina NextSeq 500 for 25 million reads per plate.


title: FOSL2KD_2


title: FOSL2KD_1


title: FOSL2CTRL_2


title: PAX6CTRL_3


title: PAX6KD_3


title: prostate cancer patient pre-treatment serum, ENACT5032


title: Engrafted_Fetal_Two-month.  ACTC1+_rep1

description:
(v1.0) Human NGS Whole Transcriptome Atlas RNA
DSP-1001660008749-G-B12
GeoMx readout mode: NGS

tag: slide name

tag: segment label

value: Fetal SMPC

tag: treatment

tag: label microscope_slide


title: prostate cancer patient pre-treatment serum, ENACT5031

tag: patient id

tag: disease state

value: LOW

tag: capra score

tag: fraction


title: LSC_Aniridia_scRNAseq_1

description:
LSC_Aniridia_scRNAseq_1
scRNA_barcodes_384.tab


title: prostate cancer patient pre-treatment serum, ENACT6003

tag: tissue

tag: sample type

value: high-grade (1)


title: prostate cancer patient pre-treatment serum, ENACT5034


title: PAX6CTRL_2


title: prostate cancer patient pre-treatment serum, ENACT6006


title: PAX6KD_2


title: prostate cancer patient pre-treatment serum, ENACT5030


title: prostate cancer patient pre-treatment serum, ENACT5033


title: PAX6CTRL_1


title: prostate cancer patient pre-treatment serum, ENACT5029


title: prostate cancer patient pre-treatment serum, ENACT5028


title: FOSL2CTRL_1


title: PAX6KD_1


title: prostate cancer patient pre-treatment serum, ENACT5039


title: LSC_FOSL2_CNR_input

library_source: genomic

data_processing:
Preprocessing of reads was done automatically with workflow tool seq2science v0.7.1
Paired-end reads were trimmed with fastp v0.20.1 with default options. Genome assembly GRCh38.p13 was downloaded with genomepy 0.11.1. Reads of ChIP-seq were aligned with bwa-mem v0.7.17(Li, 2013)with options '-M'. ChiP sample peaks were called with macs2 v2.2.7(Zhang et al., 2008) with optionsthe options ‘--keep-dup 1 --buffer-size 10000 -q 0.1' in BAM mode for narrow peaks datasets ATAC, H3K4me3, TP63. While for broad peaks datasets H3K27me3 and H3K27ac the options: ‘--keep-dup 1 –broad’ were used. The effective genome size was estimated by taking the number of unique kmers in the assembly of the same length as the average read length for each sample.
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

molecule: genomic DNA

growth_protocol: LSC were cultured in KSFM supplemented with 25 μg/ml Bovine Pituitary Extract, 0.2 ng/ml Epidermal Growth Factor and 100 U/ml Penicillin/Streptomicin. Medium was refreshed every other day untill the cells were 90% confluent.

extract_protocol: CUT&RUN


title: LSC_FOSL2_CNR_1

tag: chip antibody

value: Santa Cruz #H129, 1 ug, recognizing the C-terminal alpha tail of p63


title: LSC_FOSL2_CNR_2

value: Diagenode #C15410003


title: prostate cancer patient pre-treatment serum, ENACT5027

tag: grade of prostate cancer at biopsy


title: prostate cancer patient pre-treatment serum, ENACT5026


title: prostate cancer patient pre-treatment serum, ENACT5024


title: prostate cancer patient pre-treatment serum, ENACT5023


title: NTF_PDX_surfaceome_I922_I925

city: Montreal

first: Sonia

last: Cellot

state: Quebec

address: 3175 Côte-Sainte-Catherine

country: Canada

institute: Centre Hospitalier Universitaire (CHU) Sainte-Justine Research Center

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the index.
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.5.1b
Readcounts were computed by STAR during sequence alignment based on gene annotations from Gencode version 26 (based on Ensembl 88)
Expression values were also computed using RSEM version 1.2.28 based on Gencode version 26 transcript annotations
Assembly: GRCh38
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary files format and content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column)

source_name: PDX model spleen cells

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
cDNA libraries were prepared from total RNA using a PolyA selection and the KAPA RNA Hyperprep Kit and were further amplified for sequencing.

tag: leukemia subtype

value: AMKL

tag: gene fusion


title: prostate cancer patient pre-treatment serum, ENACT5022

value: prostate cancer

tag: capra risk


title: Pool_CD34_surf_J4

source_name: Normal umbilical cord blood cells


title: M07e

source_name: Cell line


title: Surf-Pool-NTF


title: Surf-Pool-N5A

source_name: Xenograft model spleen cells


title: CHRF288-11


title: prostate cancer patient pre-treatment serum, ENACT5016

value: serum


title: Surf-Pool-I749


title: L693


title: Surf-Pool-I732


title: prostate cancer patient pre-treatment serum, ENACT5012


title: L691


title: prostate cancer patient pre-treatment serum, ENACT5013


title: N15-BM

source_name: Xenograft model bone marrow cells


title: L619_spleen


title: I747-BM


title: prostate cancer patient pre-treatment serum, ENACT5015

tag: ap


title: prostate cancer patient pre-treatment serum, ENACT5010


title: prostate cancer patient pre-treatment serum, ENACT5018


title: prostate cancer patient pre-treatment serum, ENACT5019


title: prostate cancer patient pre-treatment serum, ENACT5021


title: I750-BM


title: prostate cancer patient pre-treatment serum, ENACT5005


title: prostate cancer patient pre-treatment serum, ENACT5006


title: prostate cancer patient pre-treatment serum, ENACT5007


title: prostate cancer patient pre-treatment serum, ENACT5004


title: prostate cancer patient pre-treatment serum, ENACT5020


title: I749-BM


title: prostate cancer patient pre-treatment serum, ENACT5003


title: I731-BM


title: I732-BM


title: Cell_line-Well_5-D84

source_name: In vitro model


title: prostate cancer patient pre-treatment serum, ENACT5002


title: prostate cancer patient pre-treatment serum, ENACT5000


title: prostate cancer patient pre-treatment serum, ENACT4016


title: prostate cancer patient pre-treatment serum, ENACT5009


title: LSC_scRNAseq_4

growth_protocol: primary KCs  were cultured in Keratinocyte Basal Medium supplemented with 100 U/mL Penicillin/Streptomycin, 0.1 mM ethanolamine, 0.1 mM O-phosphoethanolamine, 0.4% bovine pituitary extract, 0.5 μg/mL hydrocortisone, 5 μg/mL insulin and 10 ng/mL epidermal growth factor. Medium was refreshed every other day until the cells were 90% confluent.  LSC were cultured in KSFM supplemented with 25 μg/ml Bovine Pituitary Extract, 0.2 ng/ml Epidermal Growth Factor, 0.4 mM CaCl2, 2 mM Glutamine and 100 U/ml Penicillin/Streptomicin. Medium was refreshed every other day untill the cells were 90% confluent.

tag: cell type


title: I749-Spleen


title: KC_scRNAseq_1

source_name: Epidermal keratinocytes

value: Epidermal keratinocytes


title: KC_bulkRNAseq_2

tag: cell line

tag: genotype


title: prostate cancer patient pre-treatment serum, ENACT4014


title: LSC_scRNAseq_3


title: LSC_scRNAseq_2


title: prostate cancer patient pre-treatment serum, ENACT4011

value: low-grade (0)


title: prostate cancer patient pre-treatment serum, ENACT4009

value: microRNA


title: prostate cancer patient pre-treatment serum, ENACT4007

value: INTERMEDIATE


title: LSC_scRNAseq_1


title: LSC_bulkRNAseq_2


title: prostate cancer patient pre-treatment serum, ENACT4013


title: LSC_bulkRNAseq_1


title: LSC_chip_input

extract_protocol:
Chromatin was incubated overnight at 4 °C in 1× incubation buffer (0.15% SDS, 1% Triton X-100, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, and 20 mM HEPES) supplemented with protease inhibitors and 0.1% BSA. A 50:50 mix of Protein A and G Dynabeads (Invitrogen) were added. Antibodies against H3K4me3 (Diagenode, C15410003, 1 μg), TP63 (Santa Cruz #H129, 1 μg, recognizing the C-terminal α tail of p63), H3K27ac (Diagenode #C15410174, 1.2 μg) and H3K27me3 (Diagenode #C15410069, 1.5 μg) were used in each ChIP assay. The beads were washed twice with wash buffer 1 (0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, and 20 mM HEPES), once with wash buffer 2 (wash buffer 1 with 500 mM NaCl), once with wash buffer 3 (250 mM LiCl, 0.5% sodium deoxycholate, 0.5% NP-50, 1 mM EDTA, 0.5 mM EGTA, and 20 mM HEPES), and twice with wash buffer 4 (1 mM EDTA, 0.5 mM EGTA, and 20 mM HEPES). After the washing steps, beads were rotated for 20 min at room temperature in elution buffer (1% SDS and 0.1 M NaHCO3). The supernatant was de-cross-linked with 200 mM NaCl and 100 μg/mL proteinase K for 4 h at 65 °C. De-cross-linked DNA was purified with MinElute PCR Purification columns (Qiagen). DNA amounts were determined with Qubit fluorometric quantification (ThermoFisher Scientific).
The pulled down DNA fragments were proceeded on with library construction using KAPA Hyper Prep Kit (Kapa Biosystems #KK8504) according to the standard protocol. The prepared libraries were then sequenced using the NextSeq 500 (Illumina) according to standard Illumina protocols.


title: prostate cancer patient pre-treatment serum, ENACT4006


title: prostate cancer patient pre-treatment serum, ENACT4005


title: prostate cancer patient pre-treatment serum, ENACT4010


title: prostate cancer patient pre-treatment serum, ENACT4004


title: prostate cancer patient pre-treatment serum, ENACT4003


title: LSC_H3K27me3_1


title: prostate cancer patient pre-treatment serum, ENACT4002


title: KC_H3K27me3_1


title: LSC_H3K27ac_1


title: prostate cancer patient pre-treatment serum, ENACT4000


title: prostate cancer patient pre-treatment serum, ENACT4015


title: KC_H3K27ac_1


title: LSC_H3K4me3_1


title: KC_p63_1

value: Santa Cruz #H129, 1 μg, recognizing the C-terminal α tail of p63


title: LSC_p63_2


title: KC_bulkRNAseq_1


title: LSC_ATAC_4

data_processing:
Preprocessing of reads was done automatically with workflow tool seq2science v0.7.1
Paired-end reads were trimmed with fastp v0.20.1 with default options. Genome assembly GRCh38.p13 was downloaded with genomepy 0.11.1. Reads of ATACseq were aligned with bwa-mem v0.7.17(Li, 2013)with options '-M'. ATAC samples were tn5 bias shifted by seq2science. ChiP and ATAC sample peaks were called with macs2 v2.2.7(Zhang et al., 2008) with options '--shift -100 --extsize 200 --nomodel --keep-dup 1 --buffer-size 10000' in BAM mode. The effective genome size was estimated by taking the number of unique kmers in the assembly of the same length as the average read length for each sample.
Assembly: GRCh38.p13
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
A single-cell suspension was made using trypsin. After which cells were filtered using a 40uM filter to remove cell clumps.
50.000 cells were tagmented in bulk in 45 ul of tagmentation mix (20mM Tris pH 7.6, 10mM magnesium Chloride 20% Dimethylformamide), 5ul of tagmentation protein and 0.25 ul of Digitonin. Cells were tagmented for 30min at 37 °C  and 800 rpm. Tagmentation was stopped by adding 50 ul of tagmentation stop buffer (10mM Tris-HCL PH 7.8 and 20 mM EDTA). Cells were stained with DAPI and DAPI positive cells were FACs sorted in 384-well plates containing nextera primers with unique molecular identifiers, NACL ProteinaseK and SDS page. Plates were spun down (1200 × g, 1 min, 4 °C) and were incubated for 15min at 65 °C. 4ul of Tween20 was added. 2ul of H20 was added and finally 10 ul of NEBNext High-Fidelity 2X PCR Master Mix was added to each well. Thermal cycling conditions were set at 72 °C 5 min; 98 °C 5 min;  and then 20 repeats of 98°C for 10s, 63°C for 30s, 72°C for 20s. Plate libraries were pooled and purified using a qiagen PCR purification kit with adjusted buffer volumes. After the column cleanup a final beads cleanup was performed using AmpureXP beads and the sample cDNA libraries were eluted with DNAse free water. Libraries were quantified using the KAPPA quantification kit following manufacturers protocol after which the plates were sequenced on the Illumina NextSeq 500 for 30 million reads per plate. All reads from each plate were aggregated in bulk fastq files.


title: LSC_p63_1


title: prostate cancer patient pre-treatment serum, ENACT3060


title: LSC_ATAC_2


title: prostate cancer patient pre-treatment serum, ENACT3062


title: prostate cancer patient pre-treatment serum, ENACT3058


title: prostate cancer patient pre-treatment serum, ENACT3059


title: LSC_ATAC_3


title: LSC_ATAC_1


title: prostate cancer patient pre-treatment serum, ENACT3061


title: prostate cancer patient pre-treatment serum, ENACT3057


title: KC_ATAC_5


title: KC_ATAC_6


title: prostate cancer patient pre-treatment serum, ENACT3055


title: prostate cancer patient pre-treatment serum, ENACT3054


title: prostate cancer patient pre-treatment serum, ENACT3053


title: prostate cancer patient pre-treatment serum, ENACT3052


title: KC_ATAC_4


title: prostate cancer patient pre-treatment serum, ENACT3064


title: KC_ATAC_2


title: prostate cancer patient pre-treatment serum, ENACT3063


title: prostate cancer patient pre-treatment serum, ENACT3051


title: KC_ATAC_1


title: prostate cancer patient pre-treatment serum, ENACT3049


title: 396NegBSms

city: Oklahoma City

first: Kyla

last: Tooley

state: OK

address: 825 NE 13th St

department: Genes and Human Disease

institute: Oklahoma Medical Research Foundation

data_processing:
Sequencing reads were trimmed using trimmomatic 0.35 with the follwing settings: ILLUMINACLIP: TruSeq3-PE-2.fa:2:30:10 SLIDINGWINDOW:5:30 LEADING:25 TRAILING:25 HEADCROP:4 MINLEN:25 AVGQUAL:25
mm10 genome was prepared with in silico bisulfite conversion using Bismark 0.16.3-intel-2016a "bismark_genome_preparation" with Bowtie2/2.3.41-foss-2017b
Paired, trimmed fastqs were aligned to mm10 using Bismark 0.16.3-intel-2016a with the following settings: -p 6 -N 1 --bowtie2 --non_bs_mm --un
Bams were deduplicated using Bismark 0.16.3-intel-2016a "deduplicate_bam" function
Deduplicated BAM files were run through methylKit 1.10.0 to generate context-specific (CpG/CHG/CHH) coverage text files
Assembly: mm10
Supplementary files format and content: Tab-delimited text files containing CpG/CHG/CHH methylation

source_name: Hippocampus

extract_protocol:
The purification of viable, neuronal-specific nuclei from brain tissue of Tam-induced Camk2a-cre/ERT2+; NuTRAP+ mice was achieved by the INTACT isolation method. For each mouse, the hippocampus from one hemisphere was minced into small pieces and homogenized in 1 ml ice-cold nuclei EZ lysis buffer (#NUC-101, Millipore Sigma) supplemented with 1X HaltTM protease inhibitor cocktail (ThermoFisher Scientific) using a glass dounce tissue grinder set (#D9063; Millipore Sigma: 20 times with pestle A and 15 times with pestle B). Undissociated tissue (largely composed of blood vessels) was removed by centrifugation at 200 x g for 1.5 min at 4°C, and the supernatant containing the nuclear material filtered through a 30 µm strainer and centrifuged at 500 x g for 5 min at 4°C. The resulting nuclear pellet was resuspended in nuclei lysis EZ buffer, incubated on ice for 5 min, washed by centrifugation, and resuspended in 200 µl nuclei EZ storage buffer by gentle trituration with a micropipette. From the total resuspended pellet volume, 10% was reserved as input nuclei fraction and the rest was diluted with 1.6 ml nuclei purification buffer (NPB: 20 mM HEPES, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 1X HaltTM protease inhibitor cocktail), and subjected to the INTACT protocol. Briefly, 30 µl of resuspended M-280 Streptavidin Dynabeads (#11205, ThermoFisher Scientific) were added into a fresh 2 ml microcentrifuge tube and washed with 1ml of NPB using a DynaMag-2 magnet (#12321; ThermoFisher Scientific) for a total of three washes (1 min incubation/each). The washed beads were reconstituted to their initial volume (30 µl) with NPB and gently mixed with the nuclear suspension. The mixture of nuclei and magnetic beads was incubated at 4°C for 40 min under gentle rotation settings to allow the affinity binding of streptavidin beads to the neuronal-specific, biotinylated nuclei. After incubation, the streptavidin-bound nuclei were magnetically separated with the DynaMag-2 magnet for a period of 3 min and the unbound nuclei collected in a fresh 2 ml microcentrifuge tube, centrifuged at 4°C (1,000 x g, 3 min), resuspended in 100 µl of NPB and reserved as the negative nuclei fraction. The nuclei bound to the beads were washed in the magnet for three washes (1 min/each), resuspended in 30 µl of NPB, and reserved as the positive nuclei fraction. From each nuclear fraction (input, negative, and positive), a 3 µl aliquot was mixed with equal volume of DAPI counterstain and used for confocal microscopy visualization and calculation of purity percentage. The AllPrep DNA/RNA kit Micro (#80284, Qiagen, Germantown, MD) was used to extract gDNA from each sample. gDNA was quantified with a Nanodrop 2000c spectrophotometer (Thermofisher Scientific) and its quality assessed by genomic DNA D1000 (#5067-5582) with a 2200 Tapestation analyzer (Agilent Technologies, Santa Clara, CA).
For each input, negative, and positive INTACT-isolated sample 400ng of gDNA was brought up to 50 µl volume with 1X low-EDTA TE buffer and sheared with a Covaris E220 sonicator (Covaris, Inc., Woburn, MA) to an average 200 base pair size using the following settings: intensity of 5, duty cycle of 10%, 200 cycles per burst, 2 cycles of 60 seconds, at 7 °C. The size of sheared products was confirmed by capillary electrophoresis (DNA D1000, Agilent).  gDNA fragments were cleaned by an Agencourt bead-based purification protocol, after which gDNA was quantified (QubitTM dsDNA, Thermofisher Scientific). Two aliquots of 200 ng gDNA fragments were prepared in a 12 µl volume to which 1µl of spike-in control DNA (0.08 ng/ul) with known levels of specific mC, hmC, and fC at individual sites was added. Whole genome oxidative bisulfite (WGoxBS) libraries were constructed with NuGen Ovation Ultra-low Methyl Seq Library System with True-Methyl OXBS module.

value: Hippocampus

value: Neuron

value: Negative

tag: library prep_kit

value: Nugen Ovation Ultra-Low Methyl Seq with True-Methyl OxBS module


title: 396InputBSms

value: Input


title: 396PosBSms

value: Positive


title: 396NegoxBSms


title: prostate cancer patient pre-treatment serum, ENACT3046

value: LOW


title: 396PosoxBSms


title: prostate cancer patient pre-treatment serum, ENACT3047


title: 392PosoxBSms


title: KC_ATAC_3


title: prostate cancer patient pre-treatment serum, ENACT3041


title: prostate cancer patient pre-treatment serum, ENACT3044


title: prostate cancer patient pre-treatment serum, ENACT3043


title: 396InputoxBSms


title: prostate cancer patient pre-treatment serum, ENACT3042


title: prostate cancer patient pre-treatment serum, ENACT3050


title: 392PosBSms


title: 392NegBSms


title: 392InputoxBSms


title: prostate cancer patient pre-treatment serum, ENACT3038


title: 392InputBSms


title: prostate cancer patient pre-treatment serum, ENACT3034


title: 391PosoxBSms


title: prostate cancer patient pre-treatment serum, ENACT3033


title: prostate cancer patient pre-treatment serum, ENACT3048


title: prostate cancer patient pre-treatment serum, ENACT3032


title: prostate cancer patient pre-treatment serum, ENACT3030


title: 392NegoxBSms


title: prostate cancer patient pre-treatment serum, ENACT3040


title: prostate cancer patient pre-treatment serum, ENACT3039


title: 391PosBSms


title: 391InputoxBSms


title: prostate cancer patient pre-treatment serum, ENACT5035


title: prostate cancer patient pre-treatment serum, ENACT3028


title: prostate cancer patient pre-treatment serum, ENACT3027


title: prostate cancer patient pre-treatment serum, ENACT3029


title: 391InputBSms


title: prostate cancer patient pre-treatment serum, ENACT3026


title: 391NegBSms


title: N2_Star_mRNA_R3

city: Tel Aviv

first: Hila

last: Gingold

address: 30 Haim Levanon Street

country: Israel

institute: Tel-Aviv University

data_processing:
Adapter trimming - cutadapt
Quality examination - fastQC
Alignment - Shortstack (small RNA), Bowtie2 (mRNA)
Counting - HTseq_count
Comparisons - DESeq2
Assembly: WS235/ce11

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: 20C fed on E.coli OP-50 bacteria

extract_protocol:
TRIzol®
NEBNext® Small RNA Library Prep Set for Illumina®

value: Whole worm

tag: isolate

value: mRNA


title: N2_mRNA_R2


title: N2_mRNA_R3


title: MY16_Star_mRNA_R3


title: 389PosoxBSms


title: N2_Star_mRNA_R1


title: prostate cancer patient pre-treatment serum, ENACT3024

tag: patient id


title: N2_mRNA_R1


title: N2_Star_mRNA_R2


title: prostate cancer patient pre-treatment serum, ENACT3025

tag: disease state


title: MY16_Star_mRNA_R2


title: 389PosBSms


title: 389NegoxBSms


title: MY16_mRNA_R3


title: 391NegoxBSms


title: MY16_mRNA_R2


title: prostate cancer patient pre-treatment serum, ENACT3023

tag: capra score


title: MY16_Star_mRNA_R1

tag: fraction


title: 389NegBSms

tag: tissue


title: MY16_mRNA_R1


title: N2_Star_sRNA_R2

value: small RNA


title: N2_sRNA_R2


title: N2_Star_sRNA_R1


title: 389InputoxBSms


title: prostate cancer patient pre-treatment serum, ENACT3021

value: prostate cancer

tag: sample type


title: N2_sRNA_R1


title: 389InputBSms


title: prostate cancer patient pre-treatment serum, ENACT3022

value: serum


title: MY16_Star_sRNA_R3


title: P50_39wks_M_Input

description: Genomic DNA from placenta tissue

data_processing:
The ChIP-seq reads were aligned to the hg38 human reference genome using the Bowtie software package (Langmead et al, 2009) .
Mapped reads were further converted to “bed” files for later Metagene and read-density analyses by using the BEDTools software package  (Quinlan et al, 2010).
Assembly: hg38
Supplementary files format and content: peaks.txt

extract_protocol:
Frozen tissue was pulverized using a liquid nitrogen-chilled hammer mill, crosslinked with 1% formaldehyde in a volume of 10mL, quenched by addition of 5mL 2.5 M   glycine for 5 min at 4°C, washed generously in ice-cold PBS, and homogenized in Farnham Lysis Buffer [5 mM PIPES pH 8, 85 mM KCl, 0.5% NP-40, 1 mM DTT, 1x cOmplete protease inhibitor cocktail (Roche, 11697498001)], as described (Murakami et al., 2017).  The nuclei were collected by brief centrifugation and resuspended in SDS Lysis Buffer (50 mM Tris-HCl pH 7.9, 1% SDS, 10 mM EDTA, 1 mM DTT, 1x cOmplete protease inhibitor cocktail) by pipetting and incubating on ice for 10 min.
The chromatin was sheared to ~200 bp DNA fragments by sonication using a Bioruptor sonicator (Diagenode) for 24-28 cycles of 30 sec on and 30 sec off.  Fragment size was verified by agarose gel electrophoresis before quantification of protein concentrations using a BCA protein assay kit (Pierce, 23225). 100 µg of soluble chromatin was precleared with Protein A Dynabeads (Invitrogen, 10001D) before incubation overnight with 2.5 g of antibody: H3K4me1 (Abcam, ab8895) or H3K27ac (Abcam, ab4729).  ChIP-seq libraries were constructed as described previously (Franco et al., 2015)

tag: gestational age in weeks

tag: Sex

value: M

tag: trimester


title: prostate cancer patient pre-treatment serum, ENACT3019

tag: grade of prostate cancer at biopsy

value: low-grade (0)


title: prostate cancer patient pre-treatment serum, ENACT3016

tag: capra risk

value: microRNA


title: MY16_sRNA_R3


title: P50_39wks_M_H3K4me1

description: H3K4me1 ChIP-enriched DNA from placenta tissue


title: MY16_sRNA_R2


title: MY16_Star_sRNA_R2


title: MY16_Star_sRNA_R1


title: prostate cancer patient pre-treatment serum, ENACT3015

tag: ap


title: prostate cancer patient pre-treatment serum, ENACT3014


title: P48_39wks_M_Input

description: Genomic DNA from placenta tissue


title: MY16_sRNA_R1


title: P48_39wks_M_H3K4me1


title: N2_sRNA_R3


title: P50_39wks_M_H3K27ac

description: H3K27 ChIP-enriched DNA from placenta tissue


title: prostate cancer patient pre-treatment serum, ENACT3013

value: INTERMEDIATE


title: prostate cancer patient pre-treatment serum, ENACT3020


title: P44_19wks_M_Input

description: Genomic DNA from placenta tissue


title: scRNA-Seq PBMC_WTA_Tag01-04

city: Menlo Park

first: Mahyar

last: Salek

address: 4025 Bohannon Dr.

institute: Deepcell, Inc

description:
PBMC_WTA_Tag01-04
BD Rhapsody mRNA WTA with sample tag

data_processing:
The sequencing data were processed using the WTA Rhapsody Analysis Pipeline (Version 1.9.1) for DTC samples and WTA Multiplex Rhapsody Analysis Pipeline (Version 1.9.1) for PBMC samples. Data were analyzed and visualized using the BD DataView v1.2.2 software (BD Biosciences, CA) software.
Assembly: GRCh38
Supplementary files format and content: RSEC_MolsPerCell.csv: Data table containing molecules per gene per cell based on RSEC error correction
Supplementary files format and content: Sample_Tag_Calls.csv: Assigned Sample Tag for each putative cell in PBMCs
Supplementary files format and content: .mat: Data with the cell-level gene expression and cell annotation information that can be directly loaded to BD DataView to navigate

source_name: peripheral blood mononuclear cells

extract_protocol:
Total RNA was extracted from live cells using the RNeasy Mini Kit (Qiagen). cDNA synthesis, amplification and library preparation were performed with the Quantseq 3’m RNA-Seq Library Prep Kit (Lexogen) according to the manufacturer’s protocol.
Live DTCs and PBMCs were used in scRNA-Seq experiments. Cells were either directly loaded or retrieved from the positive wells of the microfluidic cartridge following sorting on COSMOS. DTCs and sample-tagged PBMCs were loaded on a BD Rhapsody single cell analysis system following mRNA Whole Transcriptome Analysis (WTA) protocol.
The library was sequenced on Illumina MiniSeq with 76 read cycles.

tag: cell type

value: peripheral blood mononuclear cells

tag: condition

value: fresh cells


title: prostate cancer patient pre-treatment serum, ENACT3012


title: prostate cancer patient pre-treatment serum, ENACT3011


title: scRNA-Seq DTC1sorted

description:
DTC1sorted
BD Rhapsody mRNA whole transcriptome analysis (WTA) system

source_name: Lung

value: Lung

value: dissociated tumor cells

value: Lung Cancer, Adenocarcinoma


title: scRNA-Seq DTC1

description:
DTC1
BD Rhapsody mRNA whole transcriptome analysis (WTA) system


title: scRNA-Seq DTC2

description:
DTC2
BD Rhapsody mRNA whole transcriptome analysis (WTA) system


title: targetd RNA-Seq PBMC_IR-ST_Tag01-04

description: Targeted (human immune response) with sample tag

data_processing:
The sequencing data were processed using the BD Targeted Rhapsody Analysis Pipeline (Version 1.9.1) using BD Rhapsody immune response panel as reference. Data were analyzed and visualized using the BD DataView v1.2.2 software (BD Biosciences, CA) software.
Assembly: BD_Rhapsody_Immune_Response_Panel_Hs_FASTA.fasta
Supplementary files format and content: RSEC_MolsPerCell.csv: Data table containing molecules per gene per cell based on RSEC error correction
Supplementary files format and content: DBEC_MolsPerCell.csv: Data table containing molecules per gene per cell based on DBEC error correction
Supplementary files format and content: Sample_Tag_Calls.csv: Assigned Sample Tag for each putative cell
Supplementary files format and content: .mat: Data with the cell-level gene expression and cell annotation information that can be directly loaded to BD DataView to navigate

extract_protocol:
Total RNA was extracted from live cells using the RNeasy Mini Kit (Qiagen). cDNA synthesis, amplification and library preparation were performed with the Quantseq 3’m RNA-Seq Library Prep Kit (Lexogen) according to the manufacturer’s protocol.
Peripheral blood mononuclear cells (PBMCs) were used in BD targeted mRNA sequencing (human immune response panel). Cells were either directly loaded or retrieved from the positive wells of the microfluidic cartridge following sorting on COSMOS and then were processed following BD Rhapsody single cell analysis system following targeted RNA sequencing (human immune response panel) with sample tag library preparation protocol.
The library was sequenced on Illumina MiniSeq with 76 read cycles.

tag: treatment


title: bulk RNA-Seq FACSsort_rep1

description:
FACSsort_rep1
Lexogen Quantseq3

data_processing:
Read QC, trimming, alignment and counting were performed with the Lexogen Quantseq analysis pipeline. Differential expression analysis was done using DESeq2 and iDEP (http://bioinformatics.sdstate.edu/idep/)
Assembly: GRCh38
Supplementary files format and content: Neutrophil_counts_combined.csv: matrix table containing raw counts for all samples

source_name: neutrophils

extract_protocol:
Total RNA was extracted from live cells using the RNeasy Mini Kit (Qiagen). cDNA synthesis, amplification and library preparation were performed with the Quantseq 3’m RNA-Seq Library Prep Kit (Lexogen) according to the manufacturer’s protocol.
Lexogen QuantSeq 3' mRNA-seq library prep is used
The library was sequenced on Illumina MiniSeq with 151 read cycles

value: neutrophils

value: FACS sorted cells


title: scRNA-Seq DTC3

description:
DTC3
BD Rhapsody mRNA whole transcriptome analysis (WTA) system


title: bulk RNA-Seq DCsort_rep1

description:
DCsort_rep1
Lexogen Quantseq3

value: unstained, Deepcell sorted cells


title: P44_19wks_M_H3K4me1

source_name: placenta villous core


title: bulk RNA-Seq DCsort_rep2

description:
DCsort_rep2
Lexogen Quantseq3


title: P44_19wks_M_H3K27ac


title: prostate cancer patient pre-treatment serum, ENACT3008

value: LOW


title: P43_15wks_M_Input

description: Genomic DNA from placenta tissue


title: prostate cancer patient pre-treatment serum, ENACT3010


title: bulk RNA-Seq fresh_rep1

description:
fresh_rep1
Lexogen Quantseq3

value: freshly isolated cells


title: bulk RNA-Seq fresh_rep2

description:
fresh_rep2
Lexogen Quantseq3


title: P43_15wks_M_H3K4me1


title: PAX5-TSS-b WT, viewpoint 2, rep 2

city: New York

first: Uttiya

last: Basu

address: 701 West 168 Street

institute: Columbia University

data_processing:
Adapter sequences and low-quality ends were trimmed using Cutadapt (version 3.3). Paired-end reads were mapped to viewpoint sequences to identify the valid capture sequences which were aligned to human reference genome (hg38) using Bowtie 2 (version 2.2.9) with default parameter to determine the interacting loci. RPM (reads per million)-normalized bedgraph files were then generated for visualization in IGV and circles plot based on the mapping of captured sequences.
Assembly: hg38
Supplementary files format and content: bedgraph files containing RPM normalized count of captured reads
Library strategy: 4C-Seq

source_name: Lymph node

growth_protocol: All PAX5-TSS2 point mutation clones, deletion clones or wild type clones of SU-DHL-10 were cultured in RPMI, 10 % fetal bovine serum, 1x NEAA, 1mM Sodium Pyruvate, 2mM glutamine, 10mM HEPES, 1x penicillin/streptomycin. Cells were cultured at 37℃ at 5% CO2.

extract_protocol:
Cells were fixed with 4% formaldehyde for 10 minutes. After quenching and cell lysis, cross-linked genomic DNA was digested with HindIII followed by ligation with T4 ligase. After reversion of cross-linking, second digestion with DpnII was performed, then ligate the DNA with T4 ligase to generate circulated DNA.
NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1) and NEBNext® Ultra™ II Q5® Master Mix were used to add index for Illumina sequencing after PCR with different viewpoint primer sets and circulated DNA.

value: Lymph node

tag: cell line

value: B lymphocyte

tag: genotype

value: WT

tag: bait


title: prostate cancer patient pre-treatment serum, ENACT3007

tag: patient id

tag: disease state

value: prostate cancer

value: serum


title: PAX5-TSS-b WT, viewpoint 2, rep 1


title: PAX5-TSS-b del, viewpoint 2, rep 2


title: P48_39wks_M_H3K27ac

value: M


title: prostate cancer patient pre-treatment serum, ENACT3006

value: low-grade (0)

tag: capra score

tag: fraction

value: microRNA


title: P43_15wks_M_H3K27ac


title: PAX5-TSS-b WT, viewpoint 1, rep 4

tag: tissue


title: PAX5-TSS-b del, viewpoint 2, rep 1


title: P42_10wks_M_Input

description: Genomic DNA from placenta tissue

tag: gestational age in weeks


title: prostate cancer patient pre-treatment serum, ENACT3005

tag: sample type


title: PAX5-TSS-b WT, viewpoint 1, rep 3


title: P42_10wks_M_H3K4me1

tag: Sex

tag: trimester


title: PAX5-TSS-b WT, viewpoint 1, rep 2


title: Mit_ESRRB_rep2

city: Memphis

first: Xiaolong

last: Chen

state: TN

address: 262 Danny Thomas Pl

institute: St Jude Children's Research Hospital

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were aligned to mouse genome assembly mm10 by BWA(0.7.17） by internal automatically mapping pipeline.
Uniquely mapped reads for ChIP-seq were obtained using samtools (V1,10), with parameter “-q 10 -F1024".
Stringent peaks for each replicate were called by MACS2 (V 2.1.1.20160309, with default parameters using Input (for ChIP-seq) as control and filtered with fold enrichment cutoff: 5 and p-value threshold: 1e-9.
RPM was applied to the normalized read counts to generatebigwigtracks
Assembly: mm10
Supplementary files format and content: bigwig files of normalized read counts.
Supplementary files format and content: narrowPeak from MACS2

source_name: embryonic stem cells

growth_protocol: mESCs were cultured in Knockout DMEM supplemented with 15% ES-qualified FBS, 1% NEAA, 1% GlutaMAX, 0.5 mM beta-mercaptoethanol, and 10 ng/ml mLIF on 0.1% gelatin-coated tissue culture dishes.

extract_protocol:
truChIP® Chromatin Shearing Kit (https://www.covaris.com/products-services/kits-reagents/truchip)
KAPA Hyper Prep Kit (KK8504)

treatment_protocol: For mitotic synchronization, mESCs were treated with 100 ng/ml nocodazole for 6 hours, and then mitotic cells were collected by gently shake-off.

value: mouse embryonic stem cells

tag: strain

value: nocodazole synchronization

tag: antibody

value: Rabbit (DA1E) mAb IgG XP® Isotype Control (CST#3900S)


title: prostate cancer patient pre-treatment serum, ENACT3004

source_name: peripheral venous source

tag: grade of prostate cancer at biopsy

tag: capra risk


title: Mit_ESRRB_rep3

tag: cell type

tag: treatment


title: Mit_ESRRB_rep1


title: prostate cancer patient pre-treatment serum, ENACT3003

tag: ap


title: PAX5-TSS-b WT, viewpoint 1, rep 1

tag: cell line

tag: genotype

tag: bait


title: Asyn_ESRRB_rep3

value: untreatment


title: prostate cancer patient pre-treatment serum, ENACT3002

tag: patient id

tag: disease state

tag: capra score


title: P41_10wks_F_Input

description: Genomic DNA from placenta tissue

tag: gestational age in weeks

value: F


title: prostate cancer patient pre-treatment serum, ENACT3001

tag: tissue

tag: sample type

tag: fraction


title: PAX5-TSS-b del, viewpoint 1, rep 4


title: PAX5-TSS-b del, viewpoint 1, rep 3


title: P41_10wks_F_H3K4me1

tag: Sex

tag: trimester


title: P41_10wks_F_H3K27ac


title: Asyn_ESRRB_rep1

tag: strain

tag: antibody


title: PAX5-TSS-b del, viewpoint 1, rep 2

tag: cell type


title: prostate cancer patient pre-treatment serum, ENACT2010

tag: grade of prostate cancer at biopsy

value: high-grade (1)

tag: capra risk