title: 35N Normal  lung tissues

description: Normal  lung tissues


title: 35T Adenocarcinoma (AC)

status: Public on Sep 14 2019

type: RNA

city: Shijiazhuang

first: Lingxiao

last: Xing

state: Hebei

address: No.361 East Zhongshan Road

country: China

institute: Hebei Medical University

description: Adenocarcinoma (AC)

hyb_protocol: Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242):

scan_protocol: Agilent Microarray Scanner (Agilent p/n G2565BA)

molecule: total RNA

organism: Homo sapiens

source_name: Fresh frozen tissue

label_protocol: Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442)

extract_protocol: The total RNA was extracted from tissues using TRIzol® Reagent (Invitrogen life technologies)

tag: tissue

value: tumor


title: 32N Normal  lung tissues

description: Normal  lung tissues

data_processing: Agilent Microarray Scanner (Agilent p/n G2565BA)

value: normal


title: 32T Squamous cell carcinoma (SCC)

description: Squamous cell carcinoma (SCC)


title: 29T Adenocarcinoma (AC)

description: Adenocarcinoma (AC)


title: 30N Normal  lung tissues

description: Normal  lung tissues


title: 30T Adenocarcinoma (AC)

description: Adenocarcinoma (AC)


title: 24T Squamous cell carcinoma (SCC)

description: Squamous cell carcinoma (SCC)


title: 2PB

type: SRA

city: Derio

first: MARTA

last: ALONSO-HEARN

state: Bizkaia

address: Berreaga 1

department: Animal Health

country: Spain

institute: NEIKER

library_source: transcriptomic

data_processing:
Data filtering: The raw reads were filtered by their length (minimum size 60 bp long) and percentage of ambiguous base N less than 5 % using Prinseq-lite
Rad alignment: Trimmed reads were subsequently mapped to the Bos Taurus reference genome (Bos_taurus.UMD3.1. version 87) with TopHat mapper. Reads were assigned to a gene if they were not multi-hit reads. The resulting alignment files were provided to Cufflinks to generate a transcriptome assembly for each condition. These assemblies were then merged together using Cuffmerge, which is included in the Cufflinks package.
Abundance measurements: This merged assembly provided a uniform basis for calculating gene and transcript expression levels in each condition. The reads and merged assembly were fed to Cuffdiff which calculates expression levels and tested the statistical significance of each observed change in expression.The fold change (in log2 scale), P-values and false discovery rates (FDR) for each gene were obtained.
Genome_build: Bos_taurus.UMD3.1. version 87
Supplementary_files_format_and_content: files include FPKM values for each Sample

organism: Bos taurus

source_name: Peripheral blood

extract_protocol:
At the time of slaughter, PB samples were collected from the coccygeal vein of all the cows included in the study in PAXgene Blood RNA tubes (2.5 ml) (Qiagen, Hilden, Germany). Total RNA was extracted from the PB samples using the PAXgene blood RNA kit according to the manufacturer´s instructions (Qiagen, Hilden, Germany). For RNA isolation, 150-200 mg of ICV of all the animals were harvested and immediately submerged in 2 ml of RNA later (Sigma, St. Louis, MO). Purification of RNA was performed using the Dynabeads mRNA DIRECT Micro Kit according to the manufacturer’s instructions (Invitrogen, Spain). Residual genomic DNA was removed using DNase digestion with RNase-free DNase I Amplification grade following the recommended protocol (Invitrogen, Spain). Concentration and quality of the total RNAs were measured using an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US). All samples had an RNA integrity value of 7 or greater.
Approximately 250 ng of RNA were used for each RNA-Seq library creation using the Illumina NEBNext® Ultra Directional RNA Library preparation kit following the manufacturer´s instructions (Illumina Inc, CA, US). All RNA-Seq libraries were quantified using a Qubit® Fluorometer and doubled stranded DNA high Sensitivity Assay Kit (Invitrogen). RNA-Seq libraries quality was assessed using an Agilent Bioanalyzer and Agilent high sensitivity DNA chip to confirm that the insert sizes were 200-250 bp for all the individual libraries.

tag: breed

value: Holstein

value: Peripheral blood

tag: agent

value: control

tag: lesion stage

value: no lesion


title: ILC2 Maf fl/fl Il7rCre RNA-seqRep 2

status: Public on Sep 13 2019

city: Durham

first: Maria

last: Ciofani

state: NC

address: 207 Research Drive, 128 Jones Building

department: Integrative Immunobiology

country: USA

institute: Duke University School of Medicine

data_processing:
Sequences for TruSeq Illumina adapters were removed from the raw reads using Trimmomatic v0.32 (Bolger et al., 2014).
Reads were aligned against the latest mouse reference genome (GRCm38) using the aligner STAR v2.4.1a following the proposed 2-pass strategy, removing alignments containing non-canonical splice junctions (--outFilterIntronMotifs RemoveNoncanonical)
Aligned reads were assigned to genes in the GENCODE vM13 comprehensive gene annotation using the featureCounts command in the subread package with default settings (v1.4.6-p4)
Differential expression analysis was performed using DESeq2 (v1.22.0) running on R (v3.5.1). Briefly, raw counts were imported and filtered to remove genes with low or no expression, that is, keeping genes having two or more counts per million (CPMs) in two or more samples.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files with raw gene counts

organism: Mus musculus

source_name: Maf KO ILC2

growth_protocol: Mice were maintained under specific pathogen-free conditions.

extract_protocol:
5,000-15,000 sort purified Nkp46+ ILC3 (CD3-CD19-CD127+CD90hiKLRG1-CCR6-NKp46+) and CCR6+ ILC3 (CD3-CD19-CD127+CD90hiKLRG1-CCR6+NKp46-) and approximately 17,000 ILC2 (CD3-CD19-CD127+KLRG1+) from Maf+/+Il7rCre and Maffl/flIl7rCre SILP were frozen in Trizol. RNA was purified from the aqueous phase using the RNeasy Plus Micro Kit (Qiagen).
Libraries were constructed from RNA using the Clontech SMARTer v3/v4 ultra-low input RNA-Seq kit (Takara Biosciences).

tag: strain background

value: C57Bl/6 (N5 backcross)

tag: genotype/variation

value: Maf KO

tag: age

value: adult

value: small intestine lamina propria

tag: cell type


title: CCR6+ ILC3 Maf fl/fl Il7rCre RNA-seqRep 2

source_name: Maf KO CCR6+ ILC3

value: CCR6+ ILC3


title: ILC2 Maf fl/fl Il7rCre RNA-seq Rep 3


title: NKp46+ ILC3 Maf fl/fl Il7rCre RNA-seq Rep 1

source_name: Maf KO NKp46+ ILC3

value: NKp46+ ILC3


title: NKp46+ ILC3 Maf fl/fl Il7rCre RNA-seqRep 2


title: NKp46+ ILC3 Maf fl/fl Il7rCre RNA-seqRep 3


title: CCR6+ ILC3 Maf fl/fl Il7rCre RNA-seqRep 3


title: ILC2 Maf fl/fl Il7rCre RNA-seq Rep 1


title: CCR6+ ILC3 Maf fl/fl Il7rCre RNA-seq Rep 1


title: ILC2 Maf+/+ Il7rCre RNA-seq Rep 3

source_name: Maf WT ILC2

value: Maf WT


title: CCR6+ ILC3 Maf+/+ Il7rCre RNA-seq Rep 3

source_name: Maf WT CCR6+ ILC3


title: NKp46+ ILC3 Maf+/+ Il7rCre RNA-seq Rep 3

source_name: Maf WT NKp46+ ILC3


title: 29N Normal  lung tissues

description: Normal  lung tissues


title: ILC2 Maf+/+ Il7rCre RNA-seq Rep 2


title: CCR6+ ILC3 Maf+/+ Il7rCre RNA-seq Rep 2


title: CCR6+ ILC3 Maf+/+ Il7rCre RNA-seq Rep 1


title: ILC2 Maf+/+ Il7rCre RNA-seq Rep 1


title: NKp46+ ILC3 Maf+/+ Il7rCre RNA-seq Rep 1


title: NKp46+ ILC3 Maf+/+ Il7rCre RNA-seq Rep 2


title: McSC_TyrTom

city: New York

first: Qi

last: Sun

state: NY

address: 550 1st Avenue, Smilow 410

department: Dermatology

institute: New York University

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software
The Cell Ranger Single-Cell Software Suite (https://support.10xgenomics.com/single-cell-gene- expression/software/pipelines/latest/what-is-cell-ranger) was used to perform sample demultiplexing, barcode processing, and single-cell 3′ gene counting.
The cDNA insert was aligned to the mm10/GRCm38 reference genome.
Only confidently mapped, non-PCR duplicates with valid barcodes and UMIs were used to generate the gene-barcode matrix.
Genome_build: mm10
Supplementary_files_format_and_content: Indexed BAM files containing position-sorted reads aligned to the genome and gene-barcode matrices.

molecule: polyA RNA

source_name: melanocyte stem cells isolated from telogen back skin of Tyr-CreER; R26R-Tomato mice

extract_protocol:
1) Back skin of Tyr-CreER; R26R-Tomato mice were incubated with 0.25% Trypsin at 37 degree for 2 hrs and then stirred in DMEM+10% FBS for 30min to get single cells, which were FACSed to isolated Tomato+ single melanocyte stem cells.  2) Melanoma tumors were chopped and incubated in 0.35% collagenase I for 1hr at 37 degree (100rpm shaking) to get single cells, which were FACSed to get single Tomato+ tumor cells.
Single-cell RNA-Seq libraries were prepared using the following Single Cell 3’ Reagent Kits v2: Chromium™ Single Cell 3’ Library & Gel Bead Kit v2, PN-120237; Single Cell 3’ Chip Kit v2 PN-120236 and i7 Multiplex Kit PN-120262" (10x Genomics) as described in https://www.ncbi.nlm.nih.gov/pubmed/28091601, and following the Single Cell 3’ Reagent Kits v2 User Guide (Manual Part # CG00052 Rev A).

treatment_protocol: 1) 7 week old Tyr-CreER; R26R-Tomato mice were treated with Tamoxifen for 7 days. Melanocyte stem cells were isolated from back skin of mouse at 1 day after last treatment. 2) Melanocyte stem cells were isoalted from 7 week old back skin of  Tyr-CreER; Braf V600E fl/+; Pten fl/fl;R26R-Tomato mice and then transplanted onto immunodeficient nude mice. Nude mice were treated with tamoxifen for 7 days. Tumors harvested for analysis at 47 days after transplantation.

tag: treatment

value: Tamoxifen for 7 days

tag: source

value: mouse back skin

value: mouse melanocyte stem cells

value: 7 weeks old mice


title: 24N Normal  lung tissues

description: Normal  lung tissues


title: VPS00177A1_VPE00010

city: Pittsburgh

first: Anna

middle: J

last: Jasinska

state: PA

address: 3550 Terrace Street

department: School of Medicine

institute: University of Pittsburgh

description: 2008-100; 2015-008

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.17
Aligned to Chlorocebus sabaeus (ChlSab1.1) using STAR spliced read aligner
Count read using HT-seq using ChlSab1.1.87 as reference
Normalization (TMM), quantitation (FPKM).
Genome_build: ChlSab1.1
Supplementary_files_format_and_content: FPKM

molecule: other

organism: Chlorocebus sabaeus

source_name: 2008100, amniotic fluid supernatant, cell free RNA

extract_protocol:
We used a QIAamp Circulating Nucleic Acid Kit (Qiagen) for RNA isolation, and after extraction, for a cleanup after DNase treatment, we purified the RNA using an RNeasy MinElute Cleanup Kit (Qiagen)
We created cDNA libraries from 100 ng of total RNA using an Ovation cDNA synthesis/SPIA amplification kit (Nugen).
HiSeq2500 instrument using RAPID, Version 2

tag: status

value: alive

tag: gender

value: F

tag: biosource

value: amniotic fluid supernatant (AFS)


title: VPS00169A1_VPE00006

description: 2006-020; 2015-011

source_name: 2006020, amniotic fluid supernatant, cell free RNA

value: stillborn

value: M


title: iso_MC_1_ribo

city: Berkeley

first: Jungwoo Wren

last: Kim

state: CA

address: Barker Hall, Room 416

department: Molecular and Cell Biology

institute: UC Berkeley

description:
iso_MC_1
ribosome profiling
iso_hDA_ribo.csv, iso_hDA_TE.csv

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequences were processed and trimmed using Greg Hannon's fastx_toolkit setup and rRNA depleted, aligned following a protocol from Ingolia NT. Nature Protocols (2012).  Tophat (2.1.1) with Bowtie2 (2.3.4.1) were used.
Counted reads were processed by DESeq2 (1.22.2), and translation efficiency was calculated.
Genome_build: hg38
Supplementary_files_format_and_content: comma-separated value files (CSV) with DESeq2 processed expression levels and translation efficiency
Supplementary_files_format_and_content: hDA_mRNA.csv: DESeq2 output, RNA-seq, non-isogenic
Supplementary_files_format_and_content: hDA_ribo.csv: DESeq2 output, ribosome profiling, non-isogenic
Supplementary_files_format_and_content: hDA_TE.csv: DESeq2 output, translation efficiency, non-isogenic
Supplementary_files_format_and_content: iso_hDA_mRNA.csv: DESeq2 output, RNA-seq, isogenic
Supplementary_files_format_and_content: iso_hDA_ribo.csv: DESeq2 output, ribosome profiling, isogenic
Supplementary_files_format_and_content: iso_hDA_TE.csv: DESeq2 output, translation efficiency, isogenic

source_name: human dopamine neurons

extract_protocol:
hDA samples: samples were lysed on the culture plates, incubated in refrigerated rotator and processed.
Libraries were prepared for sequencing using previously published ribosome profiling protocol.
ribosome profiling, RNA-seq

tag: strain

value: mutation-corrected

value: iPSC-differentiated dopamine neurons

value: Differentiation day 60

tag: genotype

value: wild-type


title: iso_MC_2_mRNA

description:
iso_MC_2
iso_hDA_mRNA.csv, iso_hDA_TE.csv


title: HDM15wk_antiIL33 [836125]

city: Tarrytown

first: Wei Keat

last: Lim

address: 777 Old Saw Mill River Rd

institute: Regeneron Pharmaceuticals

data_processing:
Array Studio software (OmicSoft) used for reads mapping.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include read count for each sample

source_name: lung

extract_protocol:
Total RNA was purified using MagMAX™-96 Total RNA Isolation Kit (Ambion by Life Technologies) according to manufacturer’s specifications. Genomic DNA was removed using RNase-Free DNase Set (Qiagen).
Strand-specific RNA-seq libraries were prepared using KAPA stranded mRNA-Seq Kit (KAPA Biosystems).

value: lung

tag: time point


title: iso_MC_1_mRNA

description:
iso_MC_1
iso_hDA_mRNA.csv, iso_hDA_TE.csv


title: iso_MC_2_ribo

description:
iso_MC_2
ribosome profiling
iso_hDA_ribo.csv, iso_hDA_TE.csv


title: HDM15wk_antiIL33 [836122]


title: iso_GS_2_ribo

description:
iso_GS_2
ribosome profiling
iso_hDA_ribo.csv, iso_hDA_TE.csv

value: patient-derived

value: G2019S LRRK2


title: HDM15wk_antiIL33 [836121]


title: HDM15wk_antiIL33 [836120]


title: iso_GS_2_mRNA

description:
iso_GS_2
iso_hDA_mRNA.csv, iso_hDA_TE.csv


title: HDM15wk_antiIL33 [836119]


title: iso_GS_1_ribo

description:
iso_GS_1
ribosome profiling
iso_hDA_ribo.csv, iso_hDA_TE.csv


title: HDM15wk_Iso [836101]


title: HDM15wk_antiIL33 [836124]


title: HDM4wk [836089]

value: HDM


title: HDM15wk [836092]


title: CD44pos

city: Birmingham

first: Changde

last: Cheng

state: AL

address: 1824 6th Ave S, Wallace Tumor Institute 520A

department: Medicine

institute: University of Alabama at Birmingham

data_processing:
The Cell Ranger 2.0.1 Single-Cell Software Suite (10x Genomics) was implemented to process the raw sequencing data from the Illumina HiSeq run. This pipeline performed de-multiplexing, alignment (GRCh38/STAR), and barcode processing to generate gene-cell matrices used for downstream analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: cell ranger count matrix for single cells in each sample

growth_protocol: The human alveolar rhabdomyosarcoma cell line, Rh41, was cultured in a 5% CO2 incubator in 75cm2 vented flask containing DMEM media supplemented with 10% FBS, and 2X glutamine until the cells reached 75% confluence at approximately 3.6X106 cells.

extract_protocol:
The cells were detached from the flask with 7 mls of 1X citrate saline to which 7mls of DPBS was added followed by centrifugation at 300xG for 7 minutes. The cells pellet was resuspended in 300 ul of blocking buffer (Rat IgG/PBS) and incubated on ice for 30 minutes. 50ul of the cells in blocking buffer were transferred to a separate tube for the isotype control. The cells were washed with1ml of staining buffer (5% BSA/PBS) and centrifuged at 300XG for 5 minutes. The pellet containing approximately 3X10^6 cells was incubated with Rat IgG2B anti-CD44-Alexa 488 antibody (R&D systems) in staining buffer (15ul antibody + 135 ul of staining buffer) for 30 minutes on ice. For the isotype control ~600,000 cells were incubated with 5ul of Rat IgG2B-Alexa488 (R&D systems) + 45ul of staining buffer for 30 minutes on ices. After the incubation both sets of cells were pelleted and washed with 1ml of staining buffer as described above and resuspended in staining buffer, followed by flow cytometric analysis to identify the fraction of CD44 positive and negative populations.
For the single cell experiment Rh41 cells were cultured and harvested and washed in DPBS as described above, and resuspended in PBS/0.2%BSA at a concentration of 1X106 cells per ml. The 10x Genomics single-cell platform performs 3’ gene expression profiling by poly-A selection of mRNA within a single cell, which utilizes a cell barcode and UMIs (unique molecular identifiers) for each transcript. Single-cell suspensions were loaded onto the Chromium Controller according to their respective cell counts to generate approximately 6000 partitioned single-cell GEMs (Gel Bead-In-EMulsions). The library was prepared using the Chromium Single Cell 3’ v2 Library and Gel Bead Kit (10x Genomics) according to the manufacturers protocol. The cDNA content of each sample after cDNA amplification of 12 cycles was quantified and quality checked by High-Sensitivity DNA chip on a 2100 Bioanalyzer (Agilent Technologies) at a dilution of 1:6. This quantification was used to determine final library amplification cycles in the protocol, which calculated out to 12 cycles. After library quantification and quality check by DNA 1000 chip (Agilent Technologies), samples were diluted to 3.5nM for loading onto the HiSeq 4000 (Illumina) with a 2 x 75 Paired-end kit using the following read length: 26 bp Read1 (10x cell barcode and UMI), 8 bp i7 Index (sample index), and 98 bp Read2 (insert). An average of 400,000,000 reads per sample was obtained, which translated to roughly 80,000 mean reads per cell, per sample.

tag: cell line

tag: cell subtype

value: CD44 positive


title: HDM4wk [836090]

tag: tissue


title: HDM15wk [836094]

tag: agent


title: CD44neg

value: The human alveolar rhabdomyosarcoma cell line

value: CD44 negative


title: iso_GS_1_mRNA

description:
iso_GS_1
iso_hDA_mRNA.csv, iso_hDA_TE.csv


title: HDM4wk [836087]


title: Melanoma_Tbpt

source_name: melanoma cells derived from transplant of melanocyte stem cells isolated from Tyr-CreER; Braf V600E fl/+; Pten fl/fl;R26R-Tomato mice

value: Tamoxifen for 7 days

value: transplant of oncogenic mouse melanocyte stem cells

value: mouse melanoma cells

value: 47 days after transplantation


title: HDM4wk [836088]


title: HDM4wk [836086]


title: HDM4wk [836085]


title: VPS00173A1_VPE00008

description: 1999-034; 2203

source_name: 1999034, amniotic fluid supernatant, cell free RNA

value: spontaneous aborton

value: amniotic fluid supernatant (AFS)


title: Saline [836084]

value: Saline


title: Saline [836083]


title: HDM15wk_antiIL33 [836123]


title: HDM15wk_antiIL33 [801673]


title: HDM15wk_Iso [801660]


title: HDM15wk_antiIL33 [801680]


title: HDM15wk_antiIL33 [801675]


title: HDM15wk_antiIL33 [801677]


title: HDM15wk [801647]


title: HDM15wk_antiIL33 [801679]


title: HDM15wk [801645]


title: HDM15wk_Iso [801661]


title: Saline [836082]


title: Saline [836081]


title: Saline [836080]


title: HDM15wk [801646]


title: HDM15wk_Iso [801658]


title: HDM15wk_antiIL33 [801674]


title: Saline [798869]


title: HDM4wk [801640]


title: Saline [801638]


title: HDM15wk_antiIL33 [801676]


title: miR-1a_Input

city: Tianjin

first: Henan

last: XU

address: No.94 Weijin Road

department: immunology

institute: Nankai University

data_processing:
Basecalls performed using Illumia bcl2fastq2.17
Raw reads after quanlity analysis were aligned to the reference genome (mm10) using TopHat (v2.0.14) after removing adapter
RPKM (Reads Per Kilobase per Million mapped reads) were calculated by Cuffnorm
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: peritoneal macrophages

growth_protocol: mouse primary peritoneal macrophage cells were harvest and cultured in DMEM (Gibco) supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Input RNA and modified miRIP RNA productions were extract with Trizol reagents according to the manufacturer’s protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: modified miRIP experiment was performed using biotin-labeled miR-1 as probes, and then co-purified RNAs were analyzed using Illumina HiSeq2000 sequencing.

value: 6 weeks

value: peritoneal macrophages

tag: molecule subtype

value: Input RNA


title: HDM4wk [801639]

value: lung


title: HDM15wk [801649]


title: HDM15wk [801644]


title: miR-1a_Mature

value: Modified miRIP RNA


title: HDM4wk [801642]


title: HDM4wk [801641]


title: A_Nkx25_input

city: Boston

first: Brynn

middle: Nicole-Yoshiko

last: Akerberg

state: MA

address: 300 Longwood Ave

department: Cardiology

institute: Boston Children's Hospital

description: Adult Nkx2.5-fbio input

library_source: genomic

data_processing:
fastq files were aligned to the mm9 genome using Bowtie2
bam files were sorted and blacklisted regions were filtered out from .bam files (samtools)
bigwig files were generated using peakcaller MACS2 and deeptools
Genome_build: mm9

molecule: genomic DNA

source_name: adult ventricle apex (distal 1/3)

extract_protocol:
Tissue was homogenized and crosslinked for 30', RT in 1% formaldehyde/1XPBS, quenched with 500mM glycine 5', RT and washed multiple times with 1XPBS.
KAPA HiFi Hyperprep library construction

value: mixed

value: adult ventricle apex (distal 1/3)

tag: Stage

value: P42 adult

tag: chip antibdoy


title: A_Nkx25_fb1

description: Adult Nkx2.5-fbio ChIPSeq

value: M280 Streptavidin Dynabeads


title: HDM15wk_antiIL33 [801678]


title: F_Nkx25_input

description: Fetal Nkx2.5-fbio input

source_name: dissected E12.5 mouse ventricle

value: dissected E12.5 mouse ventricle

value: embryonic


title: F_Nkx25_fb2

description: Fetal Nkx2.5-fbio ChIPSeq


title: F_Nkx25_fb1

description: Fetal Nkx2.5-fbio ChIPSeq


title: A_Nkx25_fb2

description: Adult Nkx2.5-fbio ChIPSeq


title: NIKs-pLXSN-2_ctrl: Empty pLXSN

city: LYON

first: Alexis

last: Robitaille

state: Rhône-Alpes

address: 150 Cours Albert Thomas

department: Section of Infections

country: France

institute: International Agency for Research on Cancer (IARC)

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Background subtraction, color correction and SSN normalization was performed using the lumi R package

label: biotin

source_name: NIKs cell

label_protocol: Biotinylated cRNA were prepared with the Illumina Total Prep RNA Amplification Kit (Ambion®)

growth_protocol: Naturally immortalized keratinocytes (NIKS) were grown together with NIH3T3 feeder cells in FAD medium, containing Ham’s F-12 (PAA), DMEM (GIBCO), 2% fetal calf serum (PAA), 100 U/ml penicillin and 0.1mg/ml streptomycin (Pen Strep; GIBCO, Invitrogen), adenine (SIGMA), 10 ng/ml human epidermal growth factor (R&D), 5 mg/ml insulin (Sigma-Aldrich), 400 μg/ml hydrocortisone (SIGMA), 10 mg/ml ciprofloxacin hydrochloride (EUROMEDEX) and 20 mg of cholera toxin (List Biological Laboratories). All cells were cultured at 37°C with 5% CO2.

extract_protocol: Total RNA was extracted from NIKs cell expressing early genes of 6 PyVs, by using Absolutely RNA miniprep kit (Stratagene) according to the manufacturer protocol. RNA integrity and quantification were characterized by measuring the 28s/18s rRNA ratio and RIN (RNA Integrity Number) using the Agilent 2100 bioanalyzer instrument and the RNA 6000 Nano kit.

treatment_protocol: Retroviral transduction of keratinocytes with the early genes from PyVs cloned in pLXSN was performed. After viral transduction, keratinocytes were selected in medium containing 1 mg/ml G418 (PAA).

value: Naturally immortalized keratinocytes (NIKs)


title: NIKs-JCV_DUP: JCV sT/LT

description: replicate 2


title: NIKs-MCV_DUP: MCV sT/LT

description: replicate 2


title: NIKs-KIV_DUP: KIV sT/LT

description: replicate 2


title: NIKs-pLXSN_DUP: Empty pLXSN

description: replicate 2


title: NIKs-WUV_DUP: WUV sT/LT

description: replicate 2


title: BTSC395s: brain tumor stem cells-like (BTSCs) 395s

city: Freiburg

first: Maria Stella

last: Carro

address: Breisacherstraße 64

country: Germany

institute: Freiburg University Medical Center

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

source_name: GBM

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: BTSCs were grown as neurospheres in Neurobasal medium (Gibco #10888022) containing B27 supplement (Gibco #12587010), N2 supplement (Gibco #17502048), b-FGF (20 ng/ml), EGF (20 ng/ml), LIF (10 ng/ml, CellGS #GFH200-20), 2 µg/ml Heparin and L-glutamine (2mM).

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: disease state

value: Glioblastoma (GBM)

value: brain tumor stem cells-like (BTSCs)


title: NIKs-SV40_DUP: SV40 sT/LT

description: replicate 2

tag: cell type


title: BTSC385s: brain tumor stem cells-like (BTSCs) 385s


title: NIKs-MCV2_DUP: MCV sT/LT

description: replicate 4


title: NIKs-MCV2: MCV sT/LT

description: replicate 3


title: NIKs-pLXSN-2_ctrl_DUP: Empty pLXSN

description: replicate 4


title: NIKs-BKV: BKV sT/LT

description: replicate 1


title: Nano oryzanol, hypothalamus, biological repl2

city: Okinawa

first: Chisayo

last: Kozuka

address: 207 Uehara, Nishihara

country: Japan

institute: University of the Ryukyus

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45˚C on GeneChip® Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000.

data_processing: The Affymetrix AGCC system was used to reduce the array images to the intensity values for each probe. These values were then stored in Affymetrix CEL format files and quantified with using the Distribution Free Weighted method (DFW).

source_name: ob/ob mice with γ-oryzanol-encapsulated nanoparticles orally treatment for 4 weeks

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (GeneChip® 3' IVT PLUS Kit, Affymetrix).

growth_protocol: Mice were maintained at chow diet. Liver and hypothalmus were obtained at 4 weeks from treatment start (9 week old).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: ob/ob mice were treated with methylcellurose (as vehicle of γ-oryzanol), γ-oryzanol, water (as vehicle of γ-oryzanol-encapsulated nanoparticles), or γ-oryzanol-encapsulated nanoparticles for 4 weeks.

value: ob/ob

value: male

value: hypothalamus

tag: age

value: 9 week old


title: NIKs-KIV: KIV sT/LT

description: replicate 1


title: NIKs-MCV: MCV sT/LT

description: replicate 1


title: NIKs-BKV_DUP: BKV sT/LT

description: replicate 2


title: BTSC409s: brain tumor stem cells-like (BTSCs) 409s


title: BTSC407s: brain tumor stem cells-like (BTSCs) 407s


title: Nano oryzanol, hypothalamus, biological repl1


title: Nano oryzanol, hypothalamus, biological repl3


title: NIKs-WUV: WUV sT/LT

description: replicate 1


title: BTSC380s: brain tumor stem cells-like (BTSCs) 380s


title: BTSC422s: brain tumor stem cells-like (BTSCs) 422s


title: NIKs-pLXSN: Empty pLXSN

description: replicate 1


title: BTSC349s: brain tumor stem cells-like (BTSCs) 349s


title: NIKs-SV40: SV40 sT/LT

description: replicate 1


title: NIKs-JCV: JCV sT/LT

description: replicate 1


title: Nano vehicle, hypothalamus, biological repl3

source_name: ob/ob mice with vehicle of γ-oryzanol-encapsulated nanoparticles orally treatment for 4 weeks


title: Nano vehicle, hypothalamus, biological repl2


title: BTSC268s: brain tumor stem cells-like (BTSCs) 268s


title: BTSC348s: brain tumor stem cells-like (BTSCs) 348s


title: BTSC205s: brain tumor stem cells-like (BTSCs) 205s


title: BTSC252s: brain tumor stem cells-like (BTSCs) 252s


title: Nano vehicle, hypothalamus, biological repl1


title: BTSC145s: brain tumor stem cells-like (BTSCs) 145s


title: BTSC232s: brain tumor stem cells-like (BTSCs) 232s


title: BTSC168s: brain tumor stem cells-like (BTSCs) 168s


title: Normal vehicle, hypothalamus, biological repl3

source_name: ob/ob mice with vehicle of γ-oryzanol orally treatment for 4 weeks


title: BTSC233s: brain tumor stem cells-like (BTSCs) 233s


title: Normal oryzanol, hypothalamus, biological repl3

source_name: ob/ob mice with γ-oryzanol orally treatment for 4 weeks


title: Normal oryzanol, hypothalamus, biological repl2


title: Nano oryzanol, liver, biological repl3

value: liver


title: JX6: brain tumor stem cells-like (BTSCs) JX6


title: BTSC281s: brain tumor stem cells-like (BTSCs) 281s


title: BTSC217s: brain tumor stem cells-like (BTSCs) 217s


title: BTSC337s: brain tumor stem cells-like (BTSCs) 337s


title: Normal oryzanol, hypothalamus, biological repl1


title: BTSC66s: brain tumor stem cells-like (BTSCs) 66s


title: BTSC23s: brain tumor stem cells-like (BTSCs) 23s


title: Normal vehicle, hypothalamus, biological repl1


title: BTSC71s: brain tumor stem cells-like (BTSCs) 71s


title: BTSC211s: brain tumor stem cells-like (BTSCs) 211s


title: BTSC161s: brain tumor stem cells-like (BTSCs) 161s


title: Nano oryzanol, liver, biological repl2


title: Normal vehicle, hypothalamus, biological repl2


title: Nano oryzanol, liver, biological repl1


title: Control2: Mxer of 75% NOD + 25% BC57BL6/J from germline [Control NOD 75]

type: genomic

city: Montréal

first: Constantin

last: Polychronakos

state: Québec

address: 1001 Décarie

country: Canada

institute: MUHC-RI

description: Technical control  2 out of 3,  75% NOD + 25% BC57BL6/J

hyb_protocol: Scanned on an Agilent scanner done by third party, OGT and Vancouver prostate center.

scan_protocol: Images were quantified using Agilent Feature Extraction Software

data_processing:
Agilent Feature Extraction Workbench Softwareware 7.0-ADM-2, Filtering parameters: Aberration Algorithm: ADM-2
Threshold: 6.0
Centralization: ON
Bin Size: 10
Centralization Threshold: 6.0
Fuzzy Zero: OFF
Combine Replicates (Intra Array): OFF
Combine Replicates (Inter Array): OFF
Genome: NA
Aberration Filters:   minProbes = 3 AND minAvgAbsLogRatio = 0.0 AND maxAberrations = 1000000 AND percentPenetrance = 0
Feature Level Filters: NONE
Array Level Filters: NONE
Expand Non Unique Probes: OFF
Genomic Boundaries: Not Applied

source_name: DNA from tail clip test sample

label_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays.  After hybridization, slides were washed sequential

extract_protocol: DNA extraction using Qiagen Microkit

value: NOD and C57BL/6 mice

tag: mouse status

value: normal

tag: sample source

value: DNA from tail clip Control sample

source_name: DNA from Tail of C57BL/6 mice

value: tail

tag: sample type

value: Refrence sample from the same mouse of test sample


title: Control1: 100% NOD DNA  from germline  [Control NOD 100]

description: Technical control  1 out of 3, 100% NOD DNA sample

value: NOD mouse


title: Control3: Mxer of 25% NOD +  BC57BL6/J from germline [Control NOD 25]

description: Technical control 3 out of 4,  25% NOD + 75% BC57BL6/J


title: Nano vehicle, liver, biological repl3

tag: gender


title: DNA from popliteal LN from BALB/c mice infected with L.major #7 [Leish. BALB/c. 7]

description: Biolohgical control 7 of 7, BALB/c mice, 3 weeks post infection with L. major

source_name: DNA from popliteal LN test samples

tag: strain

value: BALB/c mouse

value: 3 weeks post L. major infection

value: DNA from popliteal LN Control samples

source_name: DNA from Tail of mouse Leish. BALB/c. 7

value: BALB/c


title: DNA from popliteal LN from BALB/c mice infected with L.major #4 [Leish. BALB/c. 4]

description: Biolohgical control 4 of 7, BALB/c mice, 3 weeks post infection with L. major

source_name: DNA from Tail of mouse Leish. BALB/c. 4


title: Nano vehicle, liver, biological repl1


title: Normal oryzanol, liver, biological repl3


title: DNA from popliteal LN from BALB/c mice infected with L.major #5 [Leish. BALB/c. 5]

description: Biolohgical control 5 of 7, BALB/c mice, 3 weeks post infection with L. major

source_name: DNA from Tail of mouse Leish. BALB/c. 5


title: DNA from popliteal LN from BALB/c mice infected with L.major #3 [Leish. BALB/c. 3]

description: Biolohgical control 3 of 7, BALB/c mice, 3 weeks post infection with L. major

source_name: DNA from Tail of mouse Leish. BALB/c. 3


title: DNA from popliteal LN from NOD mice infected with L.major #9 [Leish. NOD 9]

description: Biolohgical control 9 of 10, NOD mice, 3 weeks post infection with L. major

source_name: DNA from Tail of mouse Leish. NOD 9


title: DNA from popliteal LN from BALB/c mice infected with L.major #2 [Leish. BALB/c. 2]

description: Biolohgical control 2 of 7, BALB/c mice, 3 weeks post infection with L. major

source_name: DNA from Tail of mouse Leish. BALB/c. 2


title: Nano vehicle, liver, biological repl2


title: Normal oryzanol, liver, biological repl2


title: Normal oryzanol, liver, biological repl1


title: DNA from popliteal LN from BALB/c mice infected with L.major #1 [Leish. BALB/c. 1]

description: Biolohgical control 1 of 7, BALB/c mice, 3 weeks post infection with L. major

source_name: DNA from Tail of mouse Leish. BALB/c. 1


title: Normal vehicle, liver, biological repl3


title: DNA from popliteal LN from NOD mice infected with L.major #7 [Leish. NOD 7]

description: Biolohgical control 7 of 10, NOD mice, 3 weeks post infection with L. major

source_name: DNA from Tail of mouse Leish. NOD 7


title: DNA from popliteal LN from NOD mice infected with L.major #6 [Leish. NOD 6]

description: Biolohgical control 6 of 10, NOD mice, 3 weeks post infection with L. major

source_name: DNA from Tail of mouse Leish. NOD 6


title: DNA from popliteal LN from NOD mice infected with L.major #10 [Leish. NOD 10]

description: Biolohgical control 10 of 10, NOD mice, 3 weeks post infection with L. major

source_name: DNA from Tail of mouse Leish. NOD 10


title: DNA from popliteal LN from BALB/c mice infected with L.major #6 [Leish. BALB/c. 6]

description: Biolohgical control 6 of 7, BALB/c mice, 3 weeks post infection with L. major

source_name: DNA from Tail of mouse Leish. BALB/c. 6


title: DNA from popliteal LN from NOD mice infected with L.major #8 [Leish. NOD 8]

description: Biolohgical control 8 of 10, NOD mice, 3 weeks post infection with L. major

source_name: DNA from Tail of mouse Leish. NOD 8


title: DNA from popliteal LN from NOD mice infected with L.major #4 [Leish. NOD 4]

description: Biolohgical control 4 of 10, NOD mice, 3 weeks post infection with L. major

source_name: DNA from Tail of mouse Leish. NOD 4


title: DNA from popliteal LN from NOD mice infected with L.major #5 [Leish. NOD 5]

description: Biolohgical control 5 of 10, NOD mice, 3 weeks post infection with L. major

source_name: DNA from Tail of mouse Leish. NOD 5


title: NOMe-seq in RWPE1

city: Los Angeles

first: Suhn

middle: K

last: Rhie

address: 1450 Biggy Street NRT 3504

department: Biochemistry and Molecular Medicine

institute: University of Southern California

data_processing:
library strategy: Nucleosome Occupancy and Methylome Sequencing (NOMe-seq).
The quality of each in situ Hi-C library was checked with FastQC and HIC-Pro version 2.8.0. Raw fastq files were processed through the HiC-Pro version 2.8.0 to make the raw contact count matrices for multiple resolutions. The matrices were normalized using the iterative correction method (iced python library). To increase the sequencing depth, replicates were pooled and processed as above described.
Each ChIP-seq experiment was performed in duplicate and ChIP-seq libraries were sequenced on an Illumina Hiseq machine. All ChIP-seq data were mapped to hg19 and peaks were called using MACS245 after preprocessing data with the ENCODE3 ChIP-seq pipeline (https://www.encodeproject.org/chip-seq/). To call reproducible peaks from two replicates, the naïve overlap tool for histone mark datasets was used, as suggested in the ENCODE3 ChIP-seq standards document (https://www.encodeproject.org/pages/pipelines/) and previously described.
For RNA-seq, reads were mapped to hg19 GENCODE version 19 using STAR 2.4.1d49 and aligned reads were quantified at the gene level using Partek® Flow® software Quantify to annotation model  (Partek Inc., St. Louis, MO, USA). The RPKM normalization method was used and log2 transformed. Differentially expressed genes between normal and cancer cells were selected by using the Gene Specific Algorithm from Partek® Flow® software using the upper quartile normalization method (Partek Inc., St. Louis, MO, USA) (FDR <0.05).
For NOMe-seq, the fastq files were aligned to a bisulfite-converted genome using the BSMAP, and the Bis-SNP was used to call methylation sites. NDR was called using the findNDRs function from the aaRon R package (https://github.com/astatham/aaRon) (P-value cutoff, 1e-8).
Genome_build: GRCh37
Supplementary_files_format_and_content:
For in situ Hi-C, text files include contact count matrices at 10kb and 40kb, respectively
For ChIP-seq, tab-delimited text files include location of peaks
For RNA-seq, tab-delimited text files include log2(RPKM+1) for each gene.
For NOMe-seq, tab-delimited text files include location of nucleosome depleted regions

source_name: NOMe-seq in RWPE1

growth_protocol: The human prostate cancer C42B cells were obtained from ViroMed Laboratories (Minneapolis, MN, USA) whereas the human prostate cancer 22Rv1 (ATCC # CRL-2505) and normal prostate RWPE1 (ATCC # CRL-11609) cells were obtained from ATCC (https://www.atcc.org/). Cells were grown at 37ºC in 5% CO2; the corresponding culture medium for each cell line (RPMI 1640 for C42B and 22Rv1 and Keratinocyte Serum Free Medium for RWPE-1) was supplemented with 10% fetal bovine serum (Gibco by Thermo Fisher Scientific, Waltham, MA, USA) and 1% penicillin and streptomycin. All cell stocks were authenticated at the USC Norris Cancer Center cell culture facility by comparison to the ATCC and/or published genomic criteria for that specific cell line; all cells were documented as free of mycoplasma.

extract_protocol:
In situ Hi-C experiments were performed following the original protocol by Rao et al with minor modifications. In situ Hi-C was performed in duplicate and 5 x 106 cells were used for each experiment. 100U of MboI restriction enzyme (NEB, R0147) was used to digest chromatin. For ligation, 2000U T4 DNA Ligase (NEB, M0202) was added and incubated at room temperature for 4 hours with slow rotation. Hi-C material was sheared to a size of 300-500bp using a Covaris instrument (Covaris S2, Woburn, MA). Biotin-tagged DNA was pulled down using Dynabeads MyOne Streptavidin C1 beads (Life technologies, 65002) with 2X Binding Buffer (2X BB: 10mM Tris-HCl (pH 7.5), 1nM EDTA, 2M NaCl).
ChIP assays were performed in C42B, 22Rv1 and RWPE1 cells using H3K9me3 (Cat# 13969 Lot# 1, Cell Signaling and Technology, Inc.), H3K27me3 (Cat# 9733 Lot# 8, Cell Signaling and Technology, Inc.), and H3K36me3 (Cat# 2901 Lot# 3, Cell Signaling and Technology, Inc.) antibodies, according to ENCODE standards (https://www.encodeproject.org/data-standards/).
RNA-seq was performed in triplicate for RWPE1, C42B, and 22Rv1 cells.  RNA was extracted using Trizol reagent (Cat # 15596-018, Thermo Fisher Scientific, NY, USA) and the quality of RNA was assessed using a 2100 Bioanalyzer instrument (Cat # G2939AA, Agilent technologies), as described previously.
For NOMe-seq, after isolating nuclei from the cells, M.CviPI was treated to methylate accessible GpCs. After purifying M.CvPI-treated DNA, sonication was performed. Bisulfite treatment of M.CviPI-methylated DNA resulted to convert all unmethylated Cs to Ts.
In situ Hi-C ibraries were prepared using Kapa Hyper prep kit (Kapa #KK8503) according to the provided protocol. Library was amplified with PCR using Illumina primers.
ChIP-seq: Libraries were barcoded (NEXTflex™ DNA Barcodes) (Bio Scientific, Austin, TX).
RNA-seq libraries were made using KAPA Stranded mRNA-Seq Kit with KAPA mRNA Capture Beads (KK8420) (Kapa Biosystems, Woburn, MA).
NOMe-seq: Libraries were generated using the Accel-NGS Methyl-Seq DNA Library Kit for Illumina Platforms.

value: Human prostate cancer cell line


title: DNA from popliteal LN from NOD mice infected with L.major #3 [Leish. NOD 3]

description: Biolohgical control 3 of 10, NOD mice, 3 weeks post infection with L. major

source_name: DNA from Tail of mouse Leish. NOD 3


title: DNA from popliteal LN from NOD mice infected with L.major #1 [Leish. NOD 1]

description: Biolohgical control 1 of 10, NOD mice, 3 weeks post infection with L. major

source_name: DNA from popliteal LN test samples

source_name: DNA from Tail of mouse Leish. NOD 1


title: in situ Hi-C in C42B rep2

data_processing:
The quality of each in situ Hi-C library was checked with FastQC and HIC-Pro version 2.8.0. Raw fastq files were processed through the HiC-Pro version 2.8.0 to make the raw contact count matrices for multiple resolutions. The matrices were normalized using the iterative correction method (iced python library). To increase the sequencing depth, replicates were pooled and processed as above described.
Each ChIP-seq experiment was performed in duplicate and ChIP-seq libraries were sequenced on an Illumina Hiseq machine. All ChIP-seq data were mapped to hg19 and peaks were called using MACS245 after preprocessing data with the ENCODE3 ChIP-seq pipeline (https://www.encodeproject.org/chip-seq/). To call reproducible peaks from two replicates, the naïve overlap tool for histone mark datasets was used, as suggested in the ENCODE3 ChIP-seq standards document (https://www.encodeproject.org/pages/pipelines/) and previously described.
For RNA-seq, reads were mapped to hg19 GENCODE version 19 using STAR 2.4.1d49 and aligned reads were quantified at the gene level using Partek® Flow® software Quantify to annotation model  (Partek Inc., St. Louis, MO, USA). The RPKM normalization method was used and log2 transformed. Differentially expressed genes between normal and cancer cells were selected by using the Gene Specific Algorithm from Partek® Flow® software using the upper quartile normalization method (Partek Inc., St. Louis, MO, USA) (FDR <0.05).
For NOMe-seq, the fastq files were aligned to a bisulfite-converted genome using the BSMAP, and the Bis-SNP was used to call methylation sites. NDR was called using the findNDRs function from the aaRon R package (https://github.com/astatham/aaRon) (P-value cutoff, 1e-8).
Genome_build: GRCh37
Supplementary_files_format_and_content:
For in situ Hi-C, text files include contact count matrices at 10kb and 40kb, respectively
For ChIP-seq, tab-delimited text files include location of peaks
For RNA-seq, tab-delimited text files include log2(RPKM+1) for each gene.
For NOMe-seq, tab-delimited text files include location of nucleosome depleted regions

source_name: in situ Hi-C in C42B


title: in situ Hi-C in C42B rep3


title: in situ Hi-C in RWPE1 rep2

source_name: in situ Hi-C in RWPE1

value: Human normal prostate cell line


title: Normal vehicle, liver, biological repl2

source_name: ob/ob mice with vehicle of γ-oryzanol orally treatment for 4 weeks

value: ob/ob


title: in situ Hi-C in C42B rep1


title: in situ Hi-C in 22Rv1 rep2

data_processing:
The quality of each Hi-C library was checked with FastQC and HICUP version 0.5.8. Raw fastq files were processed through the HiC-Pro version 2.8.0 to make the raw contact count matrices for multiple resolutions. The matrices were normalized using the iterative correction method (iced python library). Intra-chromosomal significant loops (50kb-10Mb range) were selected with the 5kb resolution contact count matrices using the Fit-Hi-C (false discovery rate (FDR) < 0.05). To increase the sequencing depth, two replicates were pooled and processed as above described.
Genome_build: GRCh37
Supplementary_files_format_and_content: *raw.matrix.txt files contain 3 columns of data: column 1 = region 1, column2 = region 2, column3  = contact frequency. *bed files include chromosome coordinates for each region. Count matrices are provided for 10kb or 40kb windows.

source_name: Human prostate cancer cell line 22Rv1

growth_protocol: 22Rv1 cells (CRL-2505) were obtained from ATCC. Cells were cultured according to the suggested protocols at 37ºC with 5% CO2. The media RPMI 1640 supplemented with 10% fetal bovine serum (Gibco by Thermo Fisher, #10437036) plus 1% penicillin and 1% streptomycin was used to culture cells.

extract_protocol:
In situ Hi-C experiments were performed in 22Rv1 cells following the original protocol by Rao et al with minor modifications. Hi-C was performed in duplicate and 5 x 106 cells were used for each experiment. 100U of MboI restriction enzyme (NEB, R0147) was used to digest chromatin. For ligation, 2000U T4 DNA Ligase (NEB, M0202) was added and incubated at room temperature for 4 hours with slow rotation. Hi-C material was sheared to a size of 300-500bp using a Covaris instrument (Covaris S2, Woburn, MA). Biotin-tagged DNA was pulled down using Dynabeads MyOne Streptavidin C1 beads (Life technologies, 65002) with 2X Binding Buffer (2X BB: 10mM Tris-HCl (pH 7.5), 1nM EDTA, 2M NaCl).
Libraries were prepared using Kapa Hyper prep kit (Kapa #KK8503) according to the provided protocol. HiC library was amplified with 14 cycles of PCR using Illumina primers. Each library was sequenced with 75bp paired-end for ~500M read pairs using Illumina HiSeq 2000.

tag: genotype

value: wild type


title: in situ Hi-C in RWPE1 rep1


title: Normal vehicle, liver, biological repl1

value: male


title: in situ Hi-C in 22Rv1 rep1


title: DNA from PLN of Diabetic mouse 23 [M23]

description: Biological replicate 23 of 25. DNA from diabetic mice, untreated

source_name: DNA from PLN test samples

value: hyperglycemia

value: DNA from PLN test samples

source_name: DNA from Tail of mouse 23


title: DNA from PLN of Diabetic mouse 20 [M20]

description: Biological replicate 20 of 25. DNA from diabetic mice, untreated

source_name: DNA from PLN test sample

value: DNA from PLN test sample

source_name: DNA from Tail of mouse 20


title: DNA from PLN of Diabetic mouse 25 [M25]

description: Biological replicate 25 of 25. DNA from diabetic mice, untreated

source_name: DNA from Tail of mouse 25


title: DNA from peripheral lymph nodes  of Diabetic mouse 20 [M20.L]

description: Control from sample 20, DNA from diabetic mice, untreated

source_name: DNA from peripheral lymph nodes  test samples

source_name: DNA from Tail of mouse 20L


title: DNA from PLN of Diabetic mouse 21 [M21]

description: Biological replicate 21 of 25. DNA from diabetic mice, untreated

source_name: DNA from Tail of mouse 21


title: DNA from PLN of C57BL/6   [M26]

description: Technical control 1out 1, same sample as test and refrence.

source_name: DNA from popliteal LN

value: C57BL/6 mouse

value: normal

value: DNA from popliteal LN

source_name: DNA from Tail of mouse 26


title: DNA from PLN of Diabetic mouse 18 [M18]

description: Biological replicate 18 of 25. DNA from diabetic mice, untreated

source_name: DNA from Tail of mouse 18

value: tail

value: Refrence sample from the same mouse of test sample


title: DNA from PLN of Diabetic mouse 24 [M24]

description: Biological replicate 24 of 25. DNA from diabetic mice, untreated

value: NOD mouse

source_name: DNA from Tail of mouse 24


title: DNA from peripheral lymph nodes  of Diabetic mouse 21 [M21.L]

description: Control from sample 21, DNA from diabetic mice, untreated

source_name: DNA from peripheral lymph nodes test samples

source_name: DNA from Tail of mouse 21L


title: DNA from peripheral lymph nodes  of Diabetic mouse 17 [M17.L]

description: Control from sample 17, DNA from diabetic mice, untreated

source_name: DNA from peripheral lymph nodes  test sample

source_name: DNA from Tail of mouse 17


title: DNA from PLN of Diabetic mouse 17 [M17]

description: Biological replicate 17 of 25. DNA from diabetic mice, untreated


title: DNA from PLN of Diabetic mouse 22 [M22]

description: Biological replicate 22 of 25. DNA from diabetic mice, untreated

source_name: DNA from Tail of mouse 22


title: Control4: 100% BALB/c DNA vrs. C57BL/6 from germline [BALB/c vrs. C57BL/6  ]

description: Technical control 100, BALB/c vrs C57BL/6

source_name: DNA from tail clip test sample

value: BALB/c mouse

value: DNA from tail clip Control sample

source_name: DNA from Tail of C57BL/6 mouse


title: Adipocyte D-allulose added high-fat diet, rep9

city: Daegu

first: Youngji

last: Han

address: Daehakro 80

country: South Korea

institute: Kyungpook National University

data_processing:
Trimmomatic-0.36 software used for filtering
fastQC v0.11.4 software used for data quality check
HISAT2 v2.0.5 software used for alignment
featureCounts software used to quantify gene expression (gene-based)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab deliminated text file containing each gene expression (in raw count) for the sample in the file name

source_name: Mouse Epididymal adipose tissue

growth_protocol: 27 male C57BL/6J mice were obtained from the Jackson Laboratory (Bar Harbor, ME) at 4 weeks of age. All the mice were individually housed under a constant temperature (24°C) and 12-hour light/dark cycle, fed the AIN-76 semi-purified diet for a one-week acclimation period after arrival

extract_protocol:
Total RNA was extracted from the adipose tissue and liver using TRIZOL reagent (Invitrogen Life Technologies, NY) according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyser.
TruSeqStranded mRNA Sample Preparation Protocol

treatment_protocol: The mice were fed a normal diet (ND, n=9), high-fat diet consisting of 20% fat and 1% cholesterol (HFD, n=9) or HFD with 5% (w/w) D-allulose (Sigma Chemical, MO) (ALL, n=9) for 16 weeks.

tag: treatment period

value: 16 weeks

value: Adipocyte

tag: diet

value: D-allulose added high-fat


title: DNA from PLN of Diabetic mouse 19 [M19]

description: Biological replicate 19 of 25. DNA from diabetic mice, untreated

source_name: DNA from PLN test sample

source_name: DNA from Tail of mouse 19


title: replicated sample of M9 [M9B]

description: Control replicated sample of M9

source_name: DNA from PLN test samples

source_name: DNA from Tail of mouse 9


title: Adipocyte D-allulose added high-fat diet, rep7


title: Adipocyte D-allulose added high-fat diet, rep8


title: Adipocyte D-allulose added high-fat diet, rep6


title: Adipocyte D-allulose added high-fat diet, rep5


title: DNA from PLN of Diabetic mouse 16 [M16]

description: Biological replicate 16 of 25. DNA from diabetic mice, untreated

source_name: DNA from Tail of mouse 16


title: Adipocyte D-allulose added high-fat diet, rep4


title: Adipocyte D-allulose added high-fat diet, rep3


title: DNA from PLN of Diabetic mouse 14 [M14]

description: Biological replicate 14 of 25. DNA from diabetic mice, untreated

source_name: DNA from Tail of mouse 14


title: DNA from PLN of Diabetic mouse 11 [M11]

description: Biological replicate 11 of 25. DNA from diabetic mice, untreated

source_name: DNA from Tail of mouse 11


title: Sample 4_Reduced 2

city: Bengaluru

first: Amit

last: Singh

state: KARNATAKA

address: Sir CV Raman Road

department: Microbiology and Cell Biology

country: India

institute: Indian Institute of Science

data_processing:
Illumina HiSeq-2500 for sequencing
BWA (0.7.12-r1039) was used for indexing the reference genome and aligning the reads (q >= 20)
SAMTOOLS (0.1.19-96b5f2294a) was used to filter out multiply mapped reads
BEDTOOLS(2.25.0) was used to calculate the read counts per gene
Normalisation and differential gene expression analysis was done using DESeq2 (genes with atleast 5 reads were selected for each comparative analysis)
Genome_build: Mycobacterium tuberculosis H37Rv, accession number : NC_000962.3
Supplementary_files_format_and_content: raw_data_counts.txt: raw reads count
Supplementary_files_format_and_content: reduced_vs_control.txt: differential gene expression comparison between Reduced (Sample 3,4) and Extra-cellular control (Sample 1,2)
Supplementary_files_format_and_content: basal_vs_control.txt: differential gene expression comparison between Basal (Sample 5,6) and Extra-cellular control (Sample 1,2)
Supplementary_files_format_and_content: reduced_vs_basal.txt: differential gene expression comparison between Reduced (Sample 3,4) and Basal (Sample 5,6)

organism: Mycobacterium tuberculosis H37Rv

source_name: bacteria isolated from THP-1 macrophages

growth_protocol: Mycobacterium tuberculosis H37Rv expressing the biosensor Mrx1-roGFP2 was grown in 7H9-ADS till log phase at 37 degrees Celcius at 180 rpm.

extract_protocol:
Total RNA was extracted from bacteria and subjected to purification and removal of genomic DNA contamination. Ribosomal RNA was depleted to obtain enriched mRNA for library preparation.
Fragmentation and random priming of samples was done for 15 nanograms of mRNA for each sample. First and second strand cDNA synthesis was carried out using NEBNextUltra Dirctional RNA library prep kit for Illumina according to manufacturer’s protocol. Equimolar quantities of all libraries were pooled and sequenced in a highthroughput run on the Illumina HiSeq 2500 sequencer using 1X50 bp single-end reads and a 1% PhiX spike-in control.

treatment_protocol: PMA differentiated THP1 monocytes were infected with log phase culture of Mycobacterium tuberculosis H37Rv expressing biosensor Mrx1-roGFP2 at M.O.I. 10. After 4 hours, extracellular bacteria were removed by treatment with 0.2 microgram/mL of amikacin and washing thrice with pre-warmed PBS. Infected cells were incubated for 24 hours at 37 degrees Celcius in 5% CO2. At 24 hours post-infection, infected macrophages were flow sorted using BD FACS Aria into two bins (based on the Mrx1-roGFP2 excitation ratio read-out) viz. EMSH-reduced (mycothiol redox potential around -300 mV) and EMSH-basal (mycothiol redox potential around -275 mV). For extracellular control, equal number of bacteria (as used for M.O.I. 10 infection of THP1 macrophages) of log phase culture of Mycobacterium tuberculosis H37Rv expressing the Mrx1-roGFP2 biosensor were transferred from 7H9 broth to complete RPMI-1640 media and maintained for 24 hours under the same conditions as infected THP1 macrophages described earlier. This served as the control bacteria lacking exposure to the intra-macrophage environment.

value: log phase bacteria grown in 7H9 media used for infecting THP1 macrophages for 24 hrs

tag: population

value: Isolated intra macrophage Mtb from EMSH – reduced subpopulation


title: DNA from peripheral lymph nodes  of Diabetic mouse 16 [M16.L]

description: Control from sample 16, DNA from diabetic mice, untreated

value: DNA from peripheral lymph nodes  test sample

tag: tissue


title: Sample 6_Basal 2

value: Isolated intra macrophage Mtb from EMSH – basal subpopulation


title: DNA from PLN of Diabetic mouse 8 [M8]

description: Biological replicate 8 of 25. DNA from diabetic mice, untreated

value: hyperglycemia

source_name: DNA from Tail of mouse 8


title: DNA from PLN of Diabetic mouse 13 [M13]

description: Biological replicate 13 of 25. DNA from diabetic mice, untreated

value: DNA from PLN test sample

source_name: DNA from Tail of mouse 13


title: DNA from PLN of Diabetic mouse 12 [M12]

description: Biological replicate 12 of 25. DNA from diabetic mice, untreated

source_name: DNA from Tail of mouse 12


title: Sample 3_Reduced 1


title: Adipocyte D-allulose added high-fat diet, rep2


title: Adipocyte D-allulose added high-fat diet, rep1


title: DNA from PLN of Diabetic mouse 6 [M6]

description: Biological replicate 6 of 25. DNA from diabetic mice, untreated

source_name: DNA from Tail of mouse 6


title: DNA from PLN of Diabetic mouse 7 [M7]

description: Biological replicate 7 of 25. DNA from diabetic mice, untreated

source_name: DNA from Tail of mouse 7


title: DNA from PLN of Diabetic mouse 9 [M9]

description: Biological replicate 9 of 25. DNA from diabetic mice, untreated


title: DNA from PLN of Diabetic mouse 15 [M15]

description: Biological replicate 15 of 25. DNA from diabetic mice, untreated

source_name: DNA from Tail of mouse 15


title: Sample 1_Extra-cellular control 1

source_name: bacteria grown extracellularly

value: log phase bacteria grown in 7H9 media resuspended in complete RPMI-1640 for 24 hrs

value: Homogeneously basal EMSH (mycothiol redox potential)


title: Sample 2_Extra-cellular control 1


title: DNA from PLN of Diabetic mouse 5 [M5]

description: Biological replicate 5 of 25. DNA from diabetic mice, untreated

source_name: DNA from Tail of mouse 5


title: DNA from PLN of Diabetic mouse 10 [M10]

description: Biological replicate 10 of 25. DNA from diabetic mice, untreated

source_name: DNA from Tail of mouse 10


title: Adipocyte High-fat diet, rep8

source_name: Mouse Epididymal adipose tissue

value: high-fat


title: Adipocyte High-fat diet, rep7


title: Adipocyte High-fat diet, rep9


title: gDNA_rep103_Carcinoma

city: Koto-ku

first: Osamu

last: Gotoh

state: Tokyo

address: Ariake 3-8-31

institute: Japanese Foundation For Cancer Research

description:
sample name:
EN679TTRN1

hyb_protocol: Standard Illumina Protocol

scan_protocol: Arrays were imaged using iScan System using standard recommended Illumina scanner setting.

data_processing:
The minfi package in R/Bioconductor
Normalized data matrix (GA_illumina_methylation_EEA_v1_processed.txt) includes Normalized Average Beta (background subtraction and control normalization).

label: Cy5 and Cy3

source_name: Carcinoma

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using the QIAamp DNA Micro Kit (Qiagen), according to the manufacturer’s instructions.

tag: patient diagnosis

value: endometrial endometrioid adenocarcinoma

value: Carcinoma

value: Female

tag: anatomical site

value: Uterus


title: gDNA_rep102_Carcinoma

description:
sample name:
EN678TTRN1


title: gDNA_rep101_Carcinoma

description:
sample name:
EN667TTRN1


title: DNA from PLN of Diabetic mouse 3 [M3]

description: Biological replicate 3 of 25. DNA from diabetic mice, untreated

source_name: DNA from PLN test sample

value: NOD mouse

source_name: DNA from Tail of mouse 3

value: tail

value: Refrence sample from the same mouse of test sample


title: gDNA_rep98_Carcinoma

description:
sample name:
EN634TTRN1


title: gDNA_rep100_Carcinoma

description:
sample name:
EN660TTRN1


title: gDNA_rep97_Hyperplasia

description:
sample name:
EN634TURN1

source_name: Hyperplasia

value: Hyperplasia


title: gDNA_rep99_Carcinoma

description:
sample name:
EN655TTRN1


title: Adipocyte High-fat diet, rep6

value: 16 weeks

value: Adipocyte


title: Adipocyte High-fat diet, rep4


title: gDNA_rep96_Carcinoma

description:
sample name:
EN628TTRN1


title: Adipocyte High-fat diet, rep5


title: gDNA_rep93_Hyperplasia

description:
sample name:
EN611TURN1


title: gDNA_rep94_Carcinoma

description:
sample name:
EN611TTRN1


title: DNA from PLN of Diabetic mouse 4 [M4]

description: Biological replicate 4 of 25. DNA from diabetic mice, untreated

source_name: DNA from Tail of mouse 4


title: gDNA_rep91_Carcinoma

description:
sample name:
EN602TTRN1


title: Adipocyte High-fat diet, rep3


title: gDNA_rep90_Carcinoma

description:
sample name:
EN598TTRN1


title: gDNA_rep89_Hyperplasia

description:
sample name:
EN598TURN1


title: DNA from popliteal LN from NOD mice infected with L.major #2 [Leish. NOD 2]

description: Biolohgical control 2 of 10, NOD mice, 3 weeks post infection with L. major

source_name: DNA from popliteal LN test samples

value: 3 weeks post L. major infection

value: DNA from popliteal LN Control samples

source_name: DNA from Tail of mouse Leish. NOD 2


title: DNA from PLN of Diabetic mouse 1 [M1]

description: Biological replicate 1 of 25. DNA from diabetic mice, untreated

value: hyperglycemia

source_name: DNA from Tail of mouse 1


title: gDNA_rep87_Carcinoma

description:
sample name:
EN593TTRN1


title: gDNA_rep85_Carcinoma

description:
sample name:
EN587TTRN1


title: gDNA_rep95_Hyperplasia

description:
sample name:
EN628TURN1


title: gDNA_rep84_Hyperplasia

description:
sample name:
EN587TURN1


title: gDNA_rep83_Carcinoma

description:
sample name:
EN586TTRN1


title: gDNA_rep82_Hyperplasia

description:
sample name:
EN586TURN1


title: gDNA_rep81_Carcinoma

description:
sample name:
EN573TTRN1


title: Adipocyte Normal diet, rep 7

value: normal


title: Adipocyte Normal diet, rep 8


title: gDNA_rep79_Hyperplasia

description:
sample name:
EN572TURN1


title: Adipocyte Normal diet, rep 6


title: Adipocyte Normal diet, rep 9


title: gDNA_rep80_Carcinoma

description:
sample name:
EN572TTRN1


title: gDNA_rep92_Carcinoma

description:
sample name:
EN603TTRN1


title: Adipocyte Normal diet, rep 5


title: gDNA_rep88_Carcinoma

description:
sample name:
EN594TTRN1


title: gDNA_rep78_Carcinoma

description:
sample name:
EN568TTRN1


title: gDNA_rep74_Carcinoma

description:
sample name:
EN506TTRN1


title: Adipocyte High-fat diet, rep1


title: gDNA_rep75_Hyperplasia

description:
sample name:
EN554TURN1


title: gDNA_rep76_Carcinoma

description:
sample name:
EN554TTRN1


title: gDNA_rep77_Hyperplasia

description:
sample name:
EN568TURN1


title: Adipocyte Normal diet, rep 4


title: Adipocyte Normal diet, rep 3


title: gDNA_rep73_Carcinoma

description:
sample name:
EN503TTRN1


title: Adipocyte Normal diet, rep 2


title: gDNA_rep86_Hyperplasia

description:
sample name:
EN593TURN1


title: gDNA_rep72_Carcinoma

description:
sample name:
EN499TTRN1


title: DNA from PLN of Diabetic mouse 2 [M2]

description: Biological replicate 2 of 25. DNA from diabetic mice, untreated

value: DNA from PLN test sample

source_name: DNA from Tail of mouse 2


title: Sample 5_Basal 1

source_name: bacteria isolated from THP-1 macrophages

value: log phase bacteria grown in 7H9 media used for infecting THP1 macrophages for 24 hrs

value: Isolated intra macrophage Mtb from EMSH – basal subpopulation


title: gDNA_rep71_Hyperplasia

description:
sample name:
EN499TURN1

value: endometrial endometrioid adenocarcinoma


title: Adipocyte Normal diet, rep 1


title: gDNA_rep70_Carcinoma

description:
sample name:
EN497TTRN1

value: Carcinoma


title: gDNA_rep67_Hyperplasia

description:
sample name:
EN491TURN1

value: Female


title: gDNA_rep69_Hyperplasia

description:
sample name:
EN497TURN1

value: Uterus


title: gDNA_rep68_Carcinoma

description:
sample name:
EN491TTRN1


title: gDNA_rep64_Hyperplasia

description:
sample name:
EN438TURN1


title: Liver D-allulose added high-fat diet, rep8

source_name: Mouse Liver

value: Liver

value: D-allulose added high-fat


title: Liver D-allulose added high-fat diet, rep7


title: Adipocyte High-fat diet, rep2

value: high-fat


title: gDNA_rep65_Carcinoma

description:
sample name:
EN438TTRN1


title: Liver D-allulose added high-fat diet, rep9


title: Liver D-allulose added high-fat diet, rep6


title: gDNA_rep66_Carcinoma

description:
sample name:
EN458TTRN1


title: gDNA_rep62_Carcinoma

description:
sample name:
EN430TTRN1


title: gDNA_rep61_Hyperplasia

description:
sample name:
EN430TURN1

value: Hyperplasia


title: gDNA_rep63_Carcinoma

description:
sample name:
EN431TTRN1


title: gDNA_rep59_Carcinoma

description:
sample name:
EN418TTRN1


title: Liver D-allulose added high-fat diet, rep4

value: 16 weeks


title: gDNA_rep60_Carcinoma

description:
sample name:
EN424TTRN1


title: Liver D-allulose added high-fat diet, rep3


title: gDNA_rep56_Hyperplasia

description:
sample name:
EN413TURN1


title: gDNA_rep57_Carcinoma

description:
sample name:
EN413TTRN1


title: Liver D-allulose added high-fat diet, rep2


title: gDNA_rep55_Carcinoma

description:
sample name:
EN402TTRN1


title: gDNA_rep53_Hyperplasia

description:
sample name:
EN394TURN1


title: gDNA_rep54_Carcinoma

description:
sample name:
EN394TTRN1


title: Liver D-allulose added high-fat diet, rep1


title: Liver High-fat diet, rep9


title: Liver High-fat diet, rep8


title: gDNA_rep50_Carcinoma

description:
sample name:
EN378TTRN1


title: Liver High-fat diet, rep7


title: gDNA_rep47_Carcinoma

description:
sample name:
EN356TTRN1


title: gDNA_rep51_Carcinoma

description:
sample name:
EN390TTRN1


title: gDNA_rep58_Hyperplasia

description:
sample name:
EN418TURN1


title: gDNA_rep49_Hyperplasia

description:
sample name:
EN378TURN1


title: gDNA_rep48_Carcinoma

description:
sample name:
EN358TTRN1


title: Liver High-fat diet, rep6


title: Liver D-allulose added high-fat diet, rep5


title: gDNA_rep42_Carcinoma

description:
sample name:
CU120TTRN1


title: gDNA_rep43_Carcinoma

description:
sample name:
CU121TTRN1


title: gDNA_rep41_Hyperplasia

description:
sample name:
CU120TURN1


title: gDNA_rep45_Hyperplasia

description:
sample name:
EN354TURN1


title: gDNA_rep38_Carcinoma

description:
sample name:
CU113TTRN1


title: gDNA_rep39_Hyperplasia

description:
sample name:
CU114TURN1


title: Liver High-fat diet, rep5


title: gDNA_rep36_Carcinoma

description:
sample name:
CU110TTRN1


title: gDNA_rep35_Carcinoma

description:
sample name:
CU108TTRN1


title: gDNA_rep52_Carcinoma

description:
sample name:
EN392TTRN1


title: Liver High-fat diet, rep4


title: Liver High-fat diet, rep2


title: gDNA_rep33_Carcinoma

description:
sample name:
CU106TTRN1


title: gDNA_rep46_Carcinoma

description:
sample name:
EN354TTRN1


title: Liver High-fat diet, rep1


title: Liver Normal diet, rep 9


title: gDNA_rep32_Carcinoma

description:
sample name:
CU105TTRN1


title: gDNA_rep40_Carcinoma

description:
sample name:
CU114TTRN1


title: gDNA_rep28_Carcinoma

description:
sample name:
CU101TTRN1


title: gDNA_rep30_Hyperplasia

description:
sample name:
CU104TURN1


title: gDNA_rep29_Carcinoma

description:
sample name:
CU103TTRN1


title: gDNA_rep24_Hyperplasia

description:
sample name:
CU098TURN1


title: gDNA_rep37_Hyperplasia

description:
sample name:
CU113TURN1


title: gDNA_rep25_Carcinoma

description:
sample name:
CU098TTRN1


title: Liver High-fat diet, rep3


title: gDNA_rep26_Carcinoma

description:
sample name:
CU099TTRN1


title: gDNA_rep22_Hyperplasia

description:
sample name:
CU096TURN1


title: gDNA_rep19_Carcinoma

description:
sample name:
CU092TTRN1


title: gDNA_rep20_Carcinoma

description:
sample name:
CU093TTRN1


title: Liver Normal diet, rep 5


title: Liver Normal diet, rep 4


title: Liver Normal diet, rep 6


title: Liver Normal diet, rep 3


title: Liver Normal diet, rep 7


title: gDNA_rep34_Carcinoma

description:
sample name:
CU107TTRN1


title: gDNA_rep27_Hyperplasia

description:
sample name:
CU101TURN1


title: Liver Normal diet, rep 2


title: gDNA_rep21_Carcinoma

description:
sample name:
CU095TTRN1


title: gDNA_rep12_Carcinoma

description:
sample name:
CU081TTRN1


title: Liver Normal diet, rep 1


title: gDNA_rep17_Hyperplasia

description:
sample name:
CU086TURN1


title: gDNA_rep23_Carcinoma

description:
sample name:
CU096TTRN1


title: gDNA_rep15_Carcinoma

description:
sample name:
CU083TTRN1


title: H3K27me3 NKp46+ ILC3 Maf fl/fl Il7rCre Rep 2

description: Nkp46_ILC3.cutandrun.H3K27me3.Maf_KO.rep2

data_processing:
library strategy: CUT&RUN
Sequences for TruSeq Illumina adapters were removed from the raw reads using Trimmomatic v0.32 (Bolger et al., 2014).
Paired-end reads were mapped using Bowtie2 (v2.3.4.3 PMID: 22388286) against both Saccharomyces Cerevisiae (sacCer3) and Mouse (mm10) genomes in --very-sensitive-local mode, allowing for fragments of up to 700bp and discarding all but paired concordant alignments (parameters for bowtie2: -I 10 -X 700 --local --very-sensitive-local --no-discordant --no-mixed --no-unal --phred33).
Duplicates were removed using Picard MarkDuplicates v1.130
Signal files were generated with deeptools bamCoverage (v3.0.1 PMID:24799436) ignoring duplicates, extending reads to match the fragment size defined by paired mates and scaling the values by 1e6 divided by the total number of reads mapping against sacCer3 (parameters: --extendReads --ignoreDuplicates –scaleFactor 1e6/sacCer3_TOTAL_NREADS)
To quantify histone signal over specific genomic regions, featureCounts was used assigning fully aligned fragment counts toregions (parameters -p -B).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig signal in RPMs

source_name: H3K27me3 Maf KO

extract_protocol:
Approximately 13 thousand NKp46+ ILC3s (CD3-CD19-CD127+CD90hiKLRG1-CCR6-NKp46+) were sort purified from the small intestine lamina propria of pooled adult Maf+/+ Il7rCre and Maf fl/fl Il7rCre. The CUT&RUN protocol was performed as previously described (Skene et al., 2018).
As described in Skene et al., 2018 using the KAPA HyperPrep Kit.

tag: strain background

value: C57Bl/6 (N5 backcross)

tag: genotype/variation

value: Maf fl/fl Il7r-Cre

value: adult

value: small intestine lamina propria

value: NKp46+ ILC3


title: gDNA_rep16_Carcinoma

description:
sample name:
CU085TTRN1


title: gDNA_rep13_Carcinoma

description:
sample name:
CU082TTRN1


title: H3K27ac NKp46+ ILC3 Maf fl/fl Il7rCre Rep 2

description: Nkp46_ILC3.cutandrun.H3K27ac.Maf_KO.rep2

source_name: H3K27ac Maf KO


title: Liver Normal diet, rep 8

value: normal


title: gDNA_rep11_Hyperplasia

description:
sample name:
CU081TURN1


title: IgG NKp46+ ILC3 Maf fl/fl Il7rCre Rep 2

source_name: IgG Maf KO

value: Maf+/+ Il7r-Cre


title: gDNA_rep9_Hyperplasia

description:
sample name:
CU080TURN1


title: gDNA_rep18_Carcinoma

description:
sample name:
CU086TTRN1


title: gDNA_rep8_Carcinoma

description:
sample name:
CU079TTRN1


title: gDNA_rep7_Carcinoma

description:
sample name:
CU076TTRN1


title: gDNA_rep4_Carcinoma

description:
sample name:
CU072TTRN1


title: gDNA_rep3_Hyperplasia

description:
sample name:
CU072TURN1


title: gDNA_rep5_Carcinoma

description:
sample name:
CU075TTRN1


title: gDNA_rep14_Hyperplasia

description:
sample name:
CU083TURN1


title: gDNA_rep6_Hyperplasia

description:
sample name:
CU076TURN1


title: H3K27ac NKp46+ ILC3 Maf+/+ Il7rCre Rep 2

description: Nkp46_ILC3.cutandrun.H3K27ac.Maf_WT.rep2

source_name: H3K27ac Maf WT


title: gDNA_rep2_Carcinoma

description:
sample name:
CU071TTRN1


title: gDNA_rep1_Hyperplasia

description:
sample name:
CU071TURN1


title: H3K27me3 NKp46+ ILC3 Maf fl/fl Il7rCre Rep 1

description: Nkp46_ILC3.cutandrun.H3K27me3.Maf_KO.rep1


title: gDNA_rep31_Carcinoma

description:
sample name:
CU104TTRN1


title: H3K27me3 NKp46+ ILC3 Maf+/+ Il7rCre Rep 1

description: Nkp46_ILC3.cutandrun.H3K27me3.Maf_WT.rep1

source_name: H3K27me3 Maf WT


title: IgG NKp46+ ILC3 Maf fl/fl Il7rCre Rep 1


title: H3K27ac NKp46+ ILC3 Maf+/+ Il7rCre Rep 1

description: Nkp46_ILC3.cutandrun.H3K27ac.Maf_WT.rep1


title: IgG NKp46+ ILC3 Maf+/+ Il7rCre Rep 1

source_name: IgG Maf WT


title: Nkp46+ILC3 C57Bl/6 ATAC Rep 2

data_processing:
Sequences for TruSeq Illumina adapters were removed from the raw reads using Trimmomatic v0.32 (Bolger et al., 2014).
Reads were aligned using Bowtie v1.0.0 (Langmead et al., 2009), reporting the best alignment with up to 2 mismatches (parameters --best --strata -v 2).
Duplicates were removed using Picard MarkDuplicates v1.130
Low mappability or blacklisted regions identified by the ENCODE project (Consortium, 2012) were filtered out from the final BAM files
Peaks were called using only the first mate in single-end mode ‘--extsize 200 -f BED --nomodel -q 0.1 --shift -100‘.
For the differential binding analysis, first, a union peakset was computed merging individual peak calls using bedtools2 v2.25.0 (Quinlan and Hall, 2010). Then, reads in peaks were estimated using featureCounts and the difference in binding was assessed with DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: peaks in narrowPeak format; RPM signal in bigWig formal

source_name: WT NKp46+ ILC3

extract_protocol:
NKp46+ ILC3 (CD3-CD19-CD127+CD90hiKLRG1-CCR6-NKp46+) and CCR6+ ILC3 (CD3-CD19-CD127+CD90hiKLRG1-CCR6+NKp46-) were sort purified from the small intestine lamina propria of pooled adult Maf+/+ Il7rCre and Maf fl/fl Il7rCre. For the ATAC-seq transitions  DN ILC3s (CD3-CD19-NK1.1-/CD45loCD90.2hi/KLRG1-/NKp46-CCR6-) and NKp46+ ILC3s (CD3-CD19-NK1.1-/CD45loCD90.2hi/KLRG1-/NKp46+CCR6-) were sort purified from C57Bl/6 mice. Additionally, NKp46+ ILC3s (CD3-CD19-/CD45+CD127+ NKp46+RORgthi), NKp46+ RORgtlo (CD3-CD19-/CD45+CD127+ NKp46+RORgtlo), and ILC1s (CD3-CD19-/CD45+CD127+NKp46+RORgt-) were purified from Rorc(t) GFP/+ mice. Cells from 3-7 mice were pooled prior to sorting.  The Omni-ATAC protocol was performed according to Corces et al (Nature Methods, 2017). Nuclei were subjected to Tn5 transposition (Illumina) and transposed DNA was purified using a Qiagen MinElute Kit prior to library amplification.
Transposed DNA fragments were amplified with Nextera PCR primers for a total of 10-12 cycles using NEBNext High-Fidelity Polymerase (NEB).

value: WT


title: H3K27ac NKp46+ ILC3 Maf fl/fl Il7rCre Rep 1

description: Nkp46_ILC3.cutandrun.H3K27ac.Maf_KO.rep1


title: DN ILC3 C57Bl/6 ATAC Rep 2

source_name: WT DN ILC3

value: DN ILC3


title: Nkp46+ILC3 C57Bl/6 ATAC Rep 1


title: DN ILC3 C57Bl/6 ATAC Rep 1


title: Nkp46+ILC3 Rorc(t)-GFP/+ ATAC Rep 2

source_name: Rorc Het NKp46+ ILC3

value: Rorc(t) GFP/+


title: Nkp46+RORgtlo Rorc(t)-GFP/+ ATAC Rep 2

source_name: Rorc Het Nkp46+RORgtlo


title: H3K27me3 NKp46+ ILC3 Maf+/+ Il7rCre Rep 2

description: Nkp46_ILC3.cutandrun.H3K27me3.Maf_WT.rep2


title: Nkp46+ILC3 Rorc(t)-GFP/+ ATAC Rep 1


title: ILC1 Rorc(t)-GFP/+ ATAC Rep 2

source_name: Rorc Het ILC1


title: S1263-00426_CB1F9

city: Kansas City

first: Priyanka

last: Sharma

address: 3901 Rainbow Boulevard

institute: University of Kansas Medical Center

hyb_protocol: Labelled cDNA was combined with dimethyl sulfoxide, hybridization buffer and nuclease free water and hybridised onto an Almac Xcel Array for 18hrs at 40oC.  Following hybridization, all arrays were washed using buffers of varying salt concentrations and stained with streptavidin-phycoerythrin conjugate (SAPE) .    All reaction components are contained within the hybridization, wash and stain kit (ThermoFisher).

scan_protocol: The arrays were scanned on the GeneChip scanner system (Thermofisher) using an epiflourescent, confocal microscope.  A solid-state laser contained within the GeneChip system was used to excite fluorophores bound to the hybridized cDNA molecules. The fluorescent values were firstly converted into an electronic signal and then to a numerical value representing the fluorescent intensity.

data_processing: CEL file intensities have been normalised to probeset level using Robust Multichip Average (RMA) consisting background adjustment, quantile normalisation and summarisation pre-processing (Bolstad et al, 2003).

label: Biotin

source_name: Breast Cell Line

label_protocol: 3.5 µg of cDNA was first enzymatically fragmented by DNase at 37oC for 30min followed by labelling with a terminal deoxynucleotidyl transferase (TdT) and biotin at 37oC for 60min.  All reaction components are contained within the  Encore Biotin Module (NuGEN Inc).

extract_protocol: RNA was extracted from FFPE breast tissue sections using the Roche HighPure RNA Paraffin Extraction Kit.

tag: treatment group

tag: nodal status

tag: tumour size


title: S1263-00426_F6


title: S1263-00426_CB1F8


title: S1263-00426_CB1F7


title: S1263-00426_F3


title: S1263-00422

source_name: Triple Negative Breast Cancer

value: Sequential AC

value: Positive

value: greater than 2 cm and less than or equal to 5 cm


title: S1263-00423

value: Combined AC

value: Negative


title: Nkp46+RORgtlo Rorc(t)-GFP/+ ATAC Rep 1

city: Durham

first: Maria

last: Ciofani

address: 207 Research Drive, 128 Jones Building

institute: Duke University School of Medicine

tag: age

tag: cell type


title: S1263-00425

value: less than or equal to 2 cm


title: S1263-00419


title: S1263-00426_F4


title: S1263-00426_F5


title: S1263-00426_CB1F10


title: S1263-00418


title: S1263-00426_CB1F12


title: S1263-00426_CB1F11


title: S1263-00426_CB1F13


title: gDNA_rep44_Carcinoma

description:
sample name:
EN351TTRN1

source_name: Carcinoma

value: endometrial endometrioid adenocarcinoma

value: Carcinoma

value: Female

value: Uterus


title: S1263-00426_CB1F1


title: S1263-00416_F1


title: S1263-00413

value: greater than 5 cm


title: ILC1 Rorc(t)-GFP/+ ATAC Rep 1

value: adult

value: small intestine lamina propria


title: S1263-00417


title: S1263-00415


title: S1263-00421_F1


title: S1263-00426_CB1F2


title: S1263-00412_F1


title: CCR6+ ILC3 Maf+/+ Il7rCre Rep 2

source_name: Maf WT CCR6+ ILC3

value: C57Bl/6 (N5 backcross)

value: Maf WT

value: CCR6+ ILC3


title: S1263-00414


title: CCR6+ ILC3 Maf fl/fl Il7rCre Rep 1

source_name: Maf KO CCR6+ ILC3

value: Maf KO


title: S1263-00411_F1


title: NKp46+ ILC3 Maf fl/fl Il7rCre Rep 2

source_name: Maf KO NKp46+ ILC3

value: NKp46+ ILC3


title: CCR6+ ILC3 Maf+/+ Il7rCre Rep 1


title: S1263-00410_F1

value: Sequential AC

value: Positive


title: S1263-00409

value: greater than 2 cm and less than or equal to 5 cm


title: S1263-00406

value: Combined AC

value: Negative


title: S1263-00402

value: less than or equal to 2 cm


title: S1263-00401


title: Adult (P42) CM-specific RNASeq rep3

description: rRNA-depleted RNA

data_processing:
fastq files were aligned to mm9 genome using STAR aligner
gene count lists were obtained from STAR aligner
mm9
.txt files containing gene names for each sample and counts

source_name: heart

extract_protocol: RNA was purified using the Purelink RNA mini kit (Life Technologies). Ribosomal RNA was depleted using Ribo-Zero rRNA removal kits (MRZH11124, Epicentre). RNA-seq libraries were prepared using ScriptSeq v2 library kit (SSV21124, Epicentre).

treatment_protocol: For normal fetal and adult cardiomyocyte expression data, isolated, purified cardiomyocytes were used with 3 biological replicates per group. Adult CMs were dissociated and purified from 6 week old hearts by Langendorf collagenase perfusion followed by differential sedimentation as described16. Fetal hearts were dissociated using the Neonatal mouse cardiomyocyte isolation kit (nc-6031, Cellutron Life Technologies) and purified using the mouse neonatal cardiomyocyte isolation kit (130-100-825, Miltenyi). CM preparations were over 90% pure by fluorescence microscopy.

value: mixed mouse strain

tag: Stage

tag: replicate

value: rep 3


title: S1263-00408_F1


title: Adult (P42) CM-specific RNASeq rep2

description: rRNA-depleted RNA

tag: strain

value: rep 2


title: S1263-00407_F1


title: S1263-00403


title: NKp46+ ILC3 Maf fl/fl Il7rCre Rep 1


title: S1263-00404


title: Adult (P42) CM-specific RNASeq rep1

description: rRNA-depleted RNA

value: rep 1


title: S1263-00405


title: S1263-00400_F1


title: S1263-00396


title: S1263-00398_F1


title: S1263-00392


title: S1263-00394_F1


title: S1263-00393


title: gDNA_rep10_Carcinoma

description:
sample name:
CU080TTRN1

value: endometrial endometrioid adenocarcinoma

value: Carcinoma

tag: gender

value: Female

value: Uterus


title: S1263-00397

value: greater than 5 cm


title: S1263-00399_F1


title: S1263-00390_F1


title: S1263-00395


title: A_Tead1_fb2

description: Adult Tead1-fbio ChIPSeq

source_name: adult ventricle apex (distal 1/3)

value: mixed

value: adult ventricle apex (distal 1/3)

value: P42 adult

tag: chip antibdoy

value: M280 Streptavidin Dynabeads


title: S1263-00387

value: Sequential AC

value: greater than 2 cm and less than or equal to 5 cm


title: A_Tead1_input1

description: Adult Tead1-fbio input


title: A_Tead1_fb1

description: Adult Tead1-fbio ChIPSeq


title: S1263-00379

value: Combined AC

value: Negative


title: S1263-00383

value: Positive


title: A_Tbx5_input

description: Adult Tbx5-fbio input


title: S1263-00372


title: S1263-00373_F1


title: S1263-00378


title: S1263-00386


title: S1263-00375_F1

value: less than or equal to 2 cm


title: S1263-00371


title: S1263-00374


title: S1263-00380_F1


title: CCR6+ ILC3 Maf fl/fl Il7rCre Rep 2

value: C57Bl/6 (N5 backcross)

value: Maf KO

value: adult

value: small intestine lamina propria

value: CCR6+ ILC3


title: S1263-00381


title: S1263-00377


title: A_Tbx5_fb2

description: Adult Tbx5-fbio ChIPSeq


title: S1263-00385


title: S1263-00368


title: S1263-00376


title: S1263-00369


title: S1263-00367


title: S1263-00366


title: S1263-00384


title: A_Tbx5_fb1

description: Adult Tbx5-fbio ChIPSeq


title: A_Srf_input

description: Adult Srf-fbio input


title: S1263-00370


title: S1263-00365


title: A_Srf_fb2

description: Adult Srf-fbio ChIPSeq


title: A_Mef2a_input

description: Adult Mef2a-fbio input


title: A_Srf_fb1

description: Adult Srf-fbio ChIPSeq


title: S1263-00364


title: S1263-00363


title: S1263-00362


title: A_Mef2a_fb2

description: Adult Mef2a-fbio ChIPSeq


title: S1263-00354


title: S1263-00356_F1


title: S1263-00353


title: S1263-00360


title: S1263-00351


title: S1263-00355


title: A_Mef2a_fb1

description: Adult Mef2a-fbio ChIPSeq

source_name: dissected E12.5 mouse ventricle

value: dissected E12.5 mouse ventricle


title: S1263-00357


title: mRNA_rep98_Carcinoma

city: Koto

first: Akihisa

last: Takahara

hyb_protocol: After fragmentation, RNA was hybridized with Affymetrix Hybridization, Wash, and Stain Kit on Affymetrix HG-U133 plus2.0 Array following manufactuer's instruction.

scan_protocol: GeneChip was scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data was processed with RMA-dabg using Affymetrix Expression Console software.

label_protocol: Biotinylated cRNA was prepared with Affymetrix GeneChip 3'IVT Plus kit according to the manufactuer's instruction.

extract_protocol: Total RNA was extracted using QIAGEN RNeasy Micro Kit following manufacturer's instruction.

tag: Sex

value: F


title: S1263-00352


title: F_Tead1_input2

description: Fetal Tead1-fbio input

value: mixed

value: embryonic


title: S1263-00350


title: F_Tead1_fb2

description: Fetal Tead1-fbio ChIPSeq


title: mRNA_rep99_Carcinoma


title: F_Tead1_input1

description: Fetal Tead1-fbio input


title: S1263-00361


title: mRNA_rep95_Carcinoma


title: F_Tead1_fb1

description: Fetal Tead1-fbio ChIPSeq


title: mRNA_rep94_Hyperplasia

source_name: Hyperplasia


title: S1263-00389


title: S1263-00348


title: S1263-00345


title: S1263-00346


title: mRNA_rep97_Carcinoma


title: S1263-00349_F1


title: mRNA_rep96_Carcinoma


title: S1263-00347


title: F_Tbx5_input2

description: Fetal Tbx5-fbio input


title: A_Tead1_input2

description: Adult Tead1-fbio input

value: adult ventricle apex (distal 1/3)

value: P42 adult


title: S1263-00344


title: F_Tbx5_fb2

description: Fetal Tbx5-fbio ChIPSeq

value: M280 Streptavidin Dynabeads


title: S1263-00341_F1

value: Sequential AC


title: mRNA_rep93_Carcinoma


title: F_Tbx5_input1

description: Fetal Tbx5-fbio input


title: S1263-00343

value: Combined AC

value: greater than 2 cm and less than or equal to 5 cm


title: S1263-00342

value: Negative


title: S1263-00340


title: mRNA_rep92_Hyperplasia


title: S1263-00337_F1

value: Positive

value: less than or equal to 2 cm


title: S1263-00339_F1


title: NKp46+ ILC3 Maf+/+ Il7rCre Rep 2

source_name: Maf WT NKp46+ ILC3

value: C57Bl/6 (N5 backcross)

value: Maf WT

value: NKp46+ ILC3


title: F_Srf_fb2

description: Fetal Srf-fbio ChIPSeq


title: NKp46+ ILC3 Maf+/+ Il7rCre Rep 1

value: adult

value: small intestine lamina propria


title: F_Tbx5_fb1

description: Fetal Tbx5-fbio ChIPSeq

value: dissected E12.5 mouse ventricle


title: F_Srf_input2

description: Fetal Srf-fbio input

value: mixed


title: F_Srf_input1

description: Fetal Srf-fbio input

value: embryonic


title: F_Mef2c_input

description: Fetal Mef2c-fbio input


title: S1263-00336


title: F_Mef2c_fb2

description: Fetal Mef2c-fbio ChIPSeq


title: F_Srf_fb1

description: Fetal Srf-fbio ChIPSeq


title: S1263-00335_F1

value: greater than 5 cm


title: S1263-00334


title: mRNA_rep91_Carcinoma

value: F


title: mRNA_rep87_Hyperplasia


title: mRNA_rep86_Carcinoma


title: mRNA_rep90_Hyperplasia


title: S1263-00330


title: S1263-00325


title: S1263-00324


title: mRNA_rep85_Carcinoma


title: mRNA_rep88_Carcinoma


title: mRNA_rep84_Hyperplasia


title: mRNA_rep82_Hyperplasia


title: S1263-00322


title: mRNA_rep81_Carcinoma


title: S1263-00317_F1


title: mRNA_rep83_Carcinoma


title: S1263-00321_F1


title: F_Mef2a_input

description: Fetal Mef2a-fbio input


title: S1263-00331


title: S1263-00327


title: S1263-00332


title: S1263-00319


title: mRNA_rep89_Carcinoma


title: S1263-00323_F1


title: S1263-00318


title: S1263-00316


title: S1263-00320_F1


title: S1263-00326_F1


title: S1263-00328


title: F_Mef2a_fb2

description: Fetal Mef2a-fbio ChIPSeq

value: M280 Streptavidin Dynabeads


title: S1263-00315

value: Sequential AC


title: Venous blood sample MM0013_3

city: Riga

first: Monta

last: Brīvība

address: Ratsupites 1

country: Latvia

institute: Latvian Biomedical Research and Study Centre

description: Ion Torrent, Ion Proton System

data_processing:
The reads were trimmed with Trimmomatic 0.36 using window size 5 and quality threshold 10.
Sequencing reads were mapped against human reference genome GRCh38 release 90 and read counts were calculated with STAR 2.5.3a.
Genome_build: GRCh38
Supplementary_files_format_and_content: Text file containing RNA-Seq read counts per gene for all samples claculated with STAR 2.5.3a.

source_name: Venous blood sample

extract_protocol:
Total RNA isolation was performed with PerfectPure RNA Blood Kit (5Prime GmbH, Germany), according to the manufacturer's instructions.
Ribosomal RNA depletion was done with Low Input RiboMinus™ Eukaryote System v2 (Thermo Fisher Scientific, USA) by processing 500ng of total RNA from each sample. For cDNA library preparation we used Ion Total RNA-Seq Kit v2 (Thermo Fisher Scientific, USA), sequencing was done on Ion Proton™ System and Ion PI™ Chip (Thermo Fisher Scientific, USA), following the manufacturer’s instructions.

treatment_protocol: Venous blood samples were collected in Tempus™ Blood RNA Tubes (ThermoFisher Scientific), containing Stabilizing Reagent.

value: Venous blood sample

tag: time point of blood collcetion regarding metformin intervention

value: after 7 days long metformin course

tag: time point of blood collection regarding

value: morning, fasting state

tag: intervention

value: 850mg dose of metformin hydrochloride (Metforal 850mg, Berlin‑Chemie AG)


title: F_Mef2a_fb1

description: Fetal Mef2a-fbio ChIPSeq

data_processing:
fastq files were aligned to the mm9 genome using Bowtie2
bam files were sorted and blacklisted regions were filtered out from .bam files (samtools)
bigwig files were generated using peakcaller MACS2 and deeptools
Genome_build: mm9

tag: tissue


title: Venous blood sample MM0013_2

description: Ion Torrent, Ion Proton System

value: 10 hours after the first metformin intake

value: evening


title: Venous blood sample MM0013_1

description: Ion Torrent, Ion Proton System

value: before administration of metformin


title: Venous blood sample MF0020_3

description: Ion Torrent, Ion Proton System


title: S1263-00314

value: Negative

value: less than or equal to 2 cm


title: Venous blood sample MF0020_2

description: Ion Torrent, Ion Proton System


title: mRNA_rep79_Carcinoma


title: mRNA_rep78_Hyperplasia


title: S1263-00313

value: Combined AC


title: S1263-00306


title: S1263-00333

value: Positive

value: greater than 2 cm and less than or equal to 5 cm


title: S1263-00309


title: S1263-00312


title: S1263-00305


title: S1263-00311


title: S1263-00310


title: mRNA_rep74_Carcinoma


title: Venous blood sample MF0020_1

description: Ion Torrent, Ion Proton System


title: S1263-00303_F1


title: S1263-00302_F1


title: mRNA_rep77_Hyperplasia


title: mRNA_rep76_Carcinoma


title: Venous blood sample MF0014_3

description: Ion Torrent, Ion Proton System


title: S1263-00307


title: S1263-00301


title: S1263-00299


title: S1263-00304


title: Venous blood sample MF0014_2

description: Ion Torrent, Ion Proton System


title: S1263-00300_F1


title: mRNA_rep73_Hyperplasia


title: Venous blood sample MF0014_1

description: Ion Torrent, Ion Proton System


title: S1263-00298_F1


title: Venous blood sample MM0011_3

description: Ion Torrent, Ion Proton System


title: S1263-00297


title: mRNA_rep75_Carcinoma


title: S1263-00296


title: S1263-00295


title: Venous blood sample MM0011_2

description: Ion Torrent, Ion Proton System


title: mRNA_rep72_Carcinoma


title: S1263-00294_F1


title: mRNA_rep71_Hyperplasia


title: Venous blood sample MM0011_1

description: Ion Torrent, Ion Proton System


title: S1263-00291


title: Venous blood sample MF0016_3

description: Ion Torrent, Ion Proton System


title: mRNA_rep69_Hyperplasia


title: mRNA_rep70_Carcinoma


title: S1263-00290


title: Venous blood sample MF0016_2

description: Ion Torrent, Ion Proton System


title: S1263-00293_F1


title: S1263-00292


title: mRNA_rep67_Carcinoma


title: S1263-00289


title: S1263-00288


title: mRNA_rep68_Carcinoma


title: S1263-00287_F1


title: S1263-00285


title: Venous blood sample MF0016_1

description: Ion Torrent, Ion Proton System


title: S1263-00286


title: Venous blood sample MF0017_3

description: Ion Torrent, Ion Proton System


title: mRNA_rep66_Hyperplasia


title: mRNA_rep65_Carcinoma


title: S1263-00283


title: Venous blood sample MF0017_1

description: Ion Torrent, Ion Proton System


title: Venous blood sample MF0006_3

description: Ion Torrent, Ion Proton System


title: S1263-00284


title: S1263-00281


title: Venous blood sample MF0017_2

description: Ion Torrent, Ion Proton System


title: mRNA_rep64_Carcinoma


title: S1263-00280


title: mRNA_rep63_Hyperplasia


title: mRNA_rep80_Hyperplasia


title: S1263-00282_F1


title: S1263-00278_F1


title: mRNA_rep61_Carcinoma


title: S1263-00279


title: Venous blood sample MF0006_1

description: Ion Torrent, Ion Proton System


title: S1263-00275


title: S1263-00276


title: S1263-00273


title: mRNA_rep59_Carcinoma


title: mRNA_rep62_Carcinoma


title: mRNA_rep60_Hyperplasia


title: S1263-00274


title: Venous blood sample MF0006_2

description: Ion Torrent, Ion Proton System


title: S1263-00271


title: Venous blood sample MF0015_3

description: Ion Torrent, Ion Proton System


title: S1263-00277_F1


title: Venous blood sample MF0015_2

description: Ion Torrent, Ion Proton System


title: S1263-00270


title: S1263-00269


title: S1263-00268


title: S1263-00267


title: Venous blood sample MF0012_3

description: Ion Torrent, Ion Proton System


title: Venous blood sample MF0015_1

description: Ion Torrent, Ion Proton System


title: Venous blood sample MF0012_2

description: Ion Torrent, Ion Proton System


title: mRNA_rep58_Hyperplasia


title: Venous blood sample MF0012_1

description: Ion Torrent, Ion Proton System


title: S1263-00265


title: mRNA_rep57_Carcinoma


title: mRNA_rep56_Carcinoma


title: mRNA_rep55_Hyperplasia


title: Venous blood sample MF0008_3

description: Ion Torrent, Ion Proton System


title: mRNA_rep53_Carcinoma


title: S1263-00264_F1


title: S1263-00263


title: S1263-00262


title: S1263-00272


title: Venous blood sample MF0008_2

description: Ion Torrent, Ion Proton System


title: S1263-00252_F1


title: mRNA_rep54_Carcinoma


title: mRNA_rep51_Hyperplasia


title: Venous blood sample MF0008_1

description: Ion Torrent, Ion Proton System


title: S1263-00250


title: S1263-00258_F1


title: mRNA_rep49_Carcinoma


title: S1263-00256


title: S1263-00257_F1


title: mRNA_rep50_Carcinoma


title: S1263-00254


title: S1263-00251


title: S1263-00249


title: S1263-00266_F1


title: S1263-00245


title: S1263-00247


title: S1263-00242


title: Venous blood sample MF0007_1

description: Ion Torrent, Ion Proton System


title: S1263-00241_F1


title: S1263-00244_F1


title: mRNA_rep52_Carcinoma


title: S1263-00259


title: S1263-00240_F1


title: Venous blood sample MF0018_1

description: Ion Torrent, Ion Proton System


title: Venous blood sample MF0018_3

description: Ion Torrent, Ion Proton System


title: Venous blood sample MF0018_2

description: Ion Torrent, Ion Proton System


title: Venous blood sample MM0029_3

description: Ion Torrent, Ion Proton System


title: S1263-00248


title: mRNA_rep46_Carcinoma


title: mRNA_rep47_Carcinoma


title: S1263-00239


title: S1263-00236


title: S1263-00234


title: Venous blood sample MM0029_1

description: Ion Torrent, Ion Proton System


title: mRNA_rep48_Hyperplasia


title: mRNA_rep43_Hyperplasia


title: mRNA_rep45_Hyperplasia


title: Venous blood sample MM0020_3

description: Ion Torrent, Ion Proton System


title: S1263-00232_F1


title: S1263-00231


title: S1263-00237_F1


title: mRNA_rep42_Carcinoma


title: mRNA_rep44_Hyperplasia


title: Venous blood sample MM0029_2

description: Ion Torrent, Ion Proton System


title: S1263-00238_F1


title: S1263-00228


title: S1263-00235


title: Venous blood sample MM0020_2

description: Ion Torrent, Ion Proton System


title: S1263-00230


title: Venous blood sample MM0020_1

description: Ion Torrent, Ion Proton System


title: Venous blood sample MM0031_3

description: Ion Torrent, Ion Proton System


title: S1263-00227


title: mRNA_rep40_Hyperplasia


title: S1263-00224


title: S1263-00225


title: S1263-00223


title: mRNA_rep39_Hyperplasia


title: mRNA_rep41_Hyperplasia


title: mRNA_rep38_Hyperplasia


title: S1263-00222_F1


title: Venous blood sample MM0031_1

description: Ion Torrent, Ion Proton System


title: S1263-00220


title: S1263-00221


title: mRNA_rep36_Hyperplasia


title: S1263-00219


title: Venous blood sample MM0030_3

description: Ion Torrent, Ion Proton System


title: S1263-00217


title: S1263-00218_F1


title: Venous blood sample MM0031_2

description: Ion Torrent, Ion Proton System


title: Venous blood sample MM0030_2

description: Ion Torrent, Ion Proton System


title: Venous blood sample MM0030_1

description: Ion Torrent, Ion Proton System


title: S1263-00214_F1


title: mRNA_rep34_Hyperplasia


title: mRNA_rep35_Hyperplasia


title: S1263-00213


title: Venous blood sample MM0028_3

description: Ion Torrent, Ion Proton System


title: Venous blood sample MF0007_2

description: Ion Torrent, Ion Proton System


title: S1263-00212


title: mRNA_rep37_Hyperplasia


title: S1263-00211


title: Venous blood sample MM0028_1

description: Ion Torrent, Ion Proton System


title: S1263-00229


title: S1263-00205_F1


title: S1263-00207


title: S1263-00210


title: S1263-00209


title: mRNA_rep31_Hyperplasia


title: mRNA_rep33_Hyperplasia


title: Venous blood sample MM0028_2

description: Ion Torrent, Ion Proton System


title: mRNA_rep32_Hyperplasia


title: S1263-00204


title: Venous blood sample MM0026_3

description: Ion Torrent, Ion Proton System


title: mRNA_endometrialCancer_rep30

source_name: endometrial Cancer tissue.

value: endometrial cancer


title: S1263-00203


title: S1263-00200_F1


title: mRNA_endometrialCancer_rep29


title: S1263-00202


title: mRNA_endometrialCancer_rep27


title: Venous blood sample MM0026_2

description: Ion Torrent, Ion Proton System


title: mRNA_endometrialCancer_rep26


title: S1263-00215_F1


title: Venous blood sample MM0025_3

description: Ion Torrent, Ion Proton System


title: Venous blood sample MM0025_2

description: Ion Torrent, Ion Proton System


title: S1263-00199


title: S1263-00201


title: S1263-00196


title: S1263-00198


title: S1263-00197


title: S1263-00195

value: greater than 5 cm


title: Venous blood sample MM0026_1

description: Ion Torrent, Ion Proton System


title: mRNA_endometrialCancer_rep24

value: F


title: S1263-00226


title: Venous blood sample MM0025_1

description: Ion Torrent, Ion Proton System


title: Venous blood sample MM0023_3

description: Ion Torrent, Ion Proton System


title: S1263-00206_F1


title: mRNA_endometrialCancer_rep23


title: Venous blood sample MM0023_2

description: Ion Torrent, Ion Proton System


title: S1263-00193_F1


title: S1263-00190_F1


title: S1263-00189_F1


title: S1263-00191


title: S1263-00187_F1


title: Venous blood sample MM0022_3

description: Ion Torrent, Ion Proton System


title: S1263-00194


title: mRNA_endometrialCancer_rep22


title: mRNA_endometrialCancer_rep19


title: mRNA_endometrialCancer_rep25


title: mRNA_endometrialCancer_rep21


title: S1263-00188


title: mRNA_endometrialCancer_rep20


title: S1263-00184


title: mRNA_endometrialCancer_rep17


title: Venous blood sample MM0022_2

description: Ion Torrent, Ion Proton System


title: S1263-00186


title: S1263-00181


title: Venous blood sample MM0023_1

description: Ion Torrent, Ion Proton System


title: S1263-00183_F1


title: Venous blood sample MM0022_1

description: Ion Torrent, Ion Proton System


title: S1263-00185


title: S1263-00178


title: S1263-00182


title: S1263-00177_F1


title: S1263-00180_F1


title: S1263-00179_F1


title: Venous blood sample MM0021_3

description: Ion Torrent, Ion Proton System


title: mRNA_endometrialCancer_rep15


title: Venous blood sample MM0021_2

description: Ion Torrent, Ion Proton System


title: mRNA_endometrialCancer_rep18


title: mRNA_endometrialCancer_rep14


title: Venous blood sample MM0021_1

description: Ion Torrent, Ion Proton System


title: Venous blood sample MM0019_3

description: Ion Torrent, Ion Proton System


title: S1263-00176


title: S1263-00174_F1


title: S1263-00175


title: Venous blood sample MM0019_2

description: Ion Torrent, Ion Proton System


title: mRNA_endometrialCancer_rep13


title: Venous blood sample MM0019_1

description: Ion Torrent, Ion Proton System


title: S1263-00172


title: mRNA_endometrialCancer_rep12


title: mRNA_endometrialCancer_rep10


title: Venous blood sample MM0018_3

description: Ion Torrent, Ion Proton System


title: S1263-00170


title: S1263-00168


title: S1263-00167_F1


title: mRNA_endometrialCancer_rep11


title: S1263-00173


title: S1263-00164


title: S1263-00166


title: S1263-00171


title: Venous blood sample MM0018_1

description: Ion Torrent, Ion Proton System


title: S1263-00169


title: mRNA_endometrialCancer_rep8


title: S1263-00163_F1


title: S1263-00165


title: S1263-00160


title: S1263-00162