title: ATAC-Seq colon_sigmoid_SM-AZPYO

extract_protocol:
Nuclei were extracted from flash frozen tissue either by manual pulverization via mortar and pestle while submerged in liquid nitrogen, or homogenization in a gentleMACS M-tube (Miltenyi) on a gentleMACS Octo Dissociator (Miltenyi) using the “Protein_01_01” protocol in MACS buffer (5 mM CaCl2, 2 mM EDTA, 1X protease inhibitor (Roche, 05-892-970-001), 300 mM MgAc, 10 mM Tris-HCL pH 8, 0.6 mM DTT) and pelleted with a swinging bucket centrifuge (500 x g, 5 min, 4°C; 5920R, Eppendorf).
Extracted nuclei were permeabilized either in 1 mL Nuclear Permeabilization Buffer (1X PBS, 5% Bovine Serum Albumin, 0.2% IGEPAL CA-630 (Sigma), 1 mM DTT, 1X Protease inhibitor), or 1 mL OMNI Buffer (10mM Tris-HCL (pH 7.5), 10mM NaCl, 3mM MgCl2, 0.1% Tween-20 (Sigma), 0.1% IGEPAL-CA630 (Sigma) and 0.01% Digitonin (Promega) in water). After resuspension in permeabilization buffer, nuclei were rotated at 4 ˚C for 5 minutes before being pelleted with a swinging bucket centrifuge (500 x g, 5 min, 4°C; 5920R, Eppendorf). After centrifugation, permeabilized nuclei were resuspended in 500 μL high salt tagmentation buffer (36.3 mM Tris-acetate (pH = 7.8), 72.6 mM potassium-acetate, 11 mM Mg-acetate, 17.6% DMF) and counted using a hemocytometer. Concentration was adjusted to 2,000 nuclei/9 μl, and 2,000 nuclei were dispensed into each well of a 96-well plate per sample (96 tagmentation wells/sample, samples were processed in batches of 2-4 samples). For tagmentation, 1 μL barcoded Tn5 transposomes were added using a BenchSmart™ 96 (Mettler Toledo), mixed five times, and incubated for 60 min at 37 °C with shaking (500 rpm). To inhibit the Tn5 reaction, 10 µL of 40 mM EDTA (final 20mM) were added to each well with a BenchSmart™ 96 (Mettler Toledo) and the plate was incubated at 37 °C for 15 min with shaking (500 rpm). Next, 20 µL of 2x sort buffer (2 % BSA, 2 mM EDTA in PBS) were added using a BenchSmart™ 96 (Mettler Toledo). All wells were combined into a separate FACS tube for each sample, and stained with Draq7 at 1:150 dilution (Cell Signaling). Using a SH800 (Sony), 20 nuclei per sample were sorted per well into eight 96-well plates (total of 768 wells) containing 10.5 µL EB (25 pmol primer i7, 25 pmol primer i5, 200 ng BSA (Sigma)). Preparation of sort plates and all downstream pipetting steps were performed on a Biomek i7 Automated Workstation (Beckman Coulter). After addition of 1 µL 0.2% SDS, samples were incubated at 55 °C for 7 min with shaking (500 rpm). 1 µL 12.5% Triton-X was added to each well to quench the SDS. Next, 12.5 µL NEBNext High-Fidelity 2× PCR Master Mix (NEB) were added and samples were PCR-amplified (72 °C 5 min, 98 °C 30 s, (98 °C 10 s, 63 °C 30 s, 72°C 60 s) × 12 cycles, held at 12 °C). After PCR, all wells were combined. Libraries were purified according to the MinElute PCR Purification Kit manual (Qiagen) using a vacuum manifold (QIAvac 24 plus, Qiagen) and size selection was performed with SPRISelect reagent (Beckmann Coulter, 0.55x and 1.5x). Libraries were purified one more time with SPRISelect reagent (Beckman Coulter, 1.5x). Libraries were quantified using a Qubit fluorimeter (Life technologies) and a nucleosomal pattern of fragment size distribution was verified using a Tapestation (High Sensitivity D1000, Agilent). Libraries were sequenced on a NextSeq500 or HiSeq4000 sequencer (Illumina) using custom sequencing primers with following read lengths: 50 + 10 + 12 + 50 (Read1 + Index1 + Index2 + Read2).
OTHER: single cell ATAC-seq

value: normal

value: flash-frozen tissue

value: female


title: 24h-RSV1

status: Public on Sep 22 2021

type: SRA

city: Athens

first: Ralph

middle: A

last: Tripp

state: GA

address: 113B, Animal Health Research Center

department: Department of Infectious Diseases

country: USA

institute: University of Georgia

library_source: transcriptomic

data_processing:
Reads were trimmed to remove adaptor sequences and then analyzed for miRNA differential expression using Chimira (Vitsios and Enright, 2015) and OASIS 2.0 (Rahman et al., 2018a). Read counts were normalized to a total number of reads per sample and then differential expression was calculated using DESeq2 (Love et al., 2014).
Genome_build: hg38
Supplementary_files_format_and_content: Read counts

molecule: total RNA

organism: Homo sapiens

source_name: neuronal cells

growth_protocol: Human SHSY5Y (SHS) neuroblastoma cells (ATCC CRL 2266) were grown in DMEM (Sigma, St. Louis, MO) containing 10% FBS (Atlanta Biologicals, Atlanta, GA). SHS cells were maintained at 37°C, 5% CO2.

extract_protocol:
Total RNA from mock-treated or virus-infected SHS cells was isolated using RNAzol RT (MRC, Cincinnati, OH) per the manufacturer’s instructions and divided into small and large RNA fractions, and quantified using a Qubit fluorimeter-based RNA assay (Invitrogen Life Tech, Carlsbad, CA).
Illumina next-generation sequencing (NGS) libraries were constructed using a TruSeq® small RNA library (Illumina, San Diego, CA). Briefly, small RNA from mock-treated SHS cells (n=2/group), or RSV- or MeV-infected SHS cells (n=3/group) was isolated at 12 hpi or 24 hpi and ligated with 3’ and 5’ RNA adaptors using T4 RNA ligase 2 (Epicenter Biotechnologies, Madison, WI) at 28°C for 60 min.  Ligated RNA was reverse transcribed using proprietary reverse primers and the first-strand cDNA was amplified with a combination of a proprietary forward primer and reverse primers containing unique index bar codes per the manufacturer’s instructions.  Amplicons were run on a Tapestation 2200 (Agilent, Santa Clara, CA) high-sensitivity DNA chip to visualize products. Indexed samples were pooled per the manufacturer’s protocol and electrophoresed on a 6% TBE-urea PAGE gel. Bands corresponding to 147bp and 157bp corresponding to adaptor-ligated mature miRNA and other non-coding RNAs were cut-out and cDNAs were precipitated. Libraries were validated on a Tapestation 2200 (Agilent) using a high-sensitivity DNA chip.  Libraries were denatured for 5 min using 5M NaOH and loaded onto a MiSeq (Agilent) for sequencing by synthesis.

treatment_protocol: RSV strain A2 (ATCC CCL 81) was propagated in Vero cells  (Oshansky et al., 2009; Dahiya and Atreya, 2014). Briefly, 80% confluent Vero cells were infected (MOI = 1.0) for 1 h at 37°C, 5% CO2. After infection, 2% FBS was added to the DMEM, and the cells were incubated for 3 days until syncytia were evident. On the day of harvest, the cells were removed and centrifuged at 500 xg for 15 min at 4°C.  The WT MV strain Dublin-3267 of MeV was grown in Vero cells expressing human CD150 (SLAM),  a high-affinity receptor for MeV (Tatsuo et al., 2000).

tag: cell line

tag: agent

value: Respiratory Syncytial Virus

tag: time point


title: 12h-RSV3


title: 24h-RSV2


title: 12h-RSV1


title: ATAC-Seq artery_tibial_SM-CHLWW

city: San Diego

first: Bing

last: Ren

state: California

address: 9500 Gilman Dr

institute: University of California San Diego

library_source: genomic

data_processing:
For each sequenced single nucleus ATAC-Seq library, we obtained four FASTQ files, two for paired end DNA reads and two for the combinatorial indexes for i5 and T7 (768 and 364 indices, respectively). We selected all reads with up to 2 mismatches per i5 and T7 index (Hamming distance between each pair of indices is 4) and integrated the concatenated barcode at the beginning of the read name in the demultiplexed FASTQ files.
snATAC-seq reads were aligned to the GRCh38 genome assembly using BWA version 0.7.17-r1188 with the following parameters: "mem -M -k 32 -t 8".
Aligned reads were name sorted and filtered using Samtools version 1.9 with the following parameters: "-f 2 -F 0x70c -q 30".
Duplicated paired-end fragments were removed for each nucleic and nucleic were filtered based on stringent quality control criteria including an enrichment of reads at transcription start sites (TSS enrichment; TSSe) greater than 7-fold, and a minimum of > 1,000 mapped paired-end fragments per nucleus.
Nuclei were further filtered for potential doublets using a version of Scrublet modified for single cell ATAC-seq.
For each sample, we generated a cell by bin (5kb) count matrix and used it for the initial clustering analysis.
Nuclei from all samples were pooled and subjected to clustering analysis using the Taiji pipeline (https://taiji-pipeline.github.io/).
Genome_build: GRCh38
Supplementary_files_format_and_content: bigwig files were generated using bedGraphToBigWig. Score represents RPKM.
Supplementary_files_format_and_content: Fragment files were generated using the Taiji pipeline (https://taiji-pipeline.github.io/). Column 1: chromosome; Column 2: adjusted start position; Column 3: adjusted end position. Column 4: cell barcode; Column 5: the total number of read pairs associated with this fragment (including unique and all duplicate read pairs).
Supplementary_files_format_and_content: metadata.tsv.gz: tab-delimited text files containing final clustering result and metadata of nucleic from all samples

molecule: genomic DNA

source_name: tibial artery

tag: sample type

tag: biosample

tag: donor age (years)

tag: donor sex

value: male

tag: race

value: white

tag: case of death

value: anoxia


title: ATAC-Seq artery_aorta_SM-JF1NU

source_name: aorta

value: asian

value: cerebral vascular accident


title: ATAC-Seq artery_aorta_SM-C1MLC


title: SVGAs-V1-96hpi SVGAs, JCPyV-infected, rep1

city: Orono

first: Melissa

last: Maginnis

state: Maine

address: 5735 Hitchner Hall Room 320

department: Department of Molecular and Biomedical Sciences

institute: University of Maine

description: SVGAs, JCPyV-infected, rep1

data_processing:
Sequenced reads were trimmed for adaptor sequence using Trimmomatic (version 0.39)
Trimmed reads were aligned to the GRCh38 using HISAT2
Read counts per gene were generated using Ensembl GTF file (version X) and HTSeq (version 0.13.5)
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: SVG-A cells

growth_protocol: Primary astrocytes were cultured in astrocyte growth medium and supplemented with SingleQuots supplements (LONZA) and 1% penicillin-streptomycin. SVGAs were cultured in complete minimum essential medium, with 10% fetal bovine serum, 1% penicillin-streptomycin and 0.1% Plasmocin prophylactic.

extract_protocol:
Cells were suspended in TRIzol reagent and placed in the -20°C for storage. Following the last timepoint, total RNA was extracted from each sample with the Direct-zol RNA kits according to the manufacturer’s protocol (Zymo Research).
cDNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Primary astrocytes and SVGAs were plated to 70% confluence in a 24-well plate. Medium was removed and cells were infected with purified JCPyV (MOI = 0.1 FFU/cell) in 200 μl or mock-infected with an empty cell lysate preparation control performed in trip-licate wells for each treatment.

value: transformed with SV40 T Antigen

tag: treatment

value: JCPyV-infected (MOI = 0.1 FFU/cell)

tag: time post infection


title: SVGAs-V2-96hpi SVGAs, JCPyV-infected, rep2

description: SVGAs, JCPyV-infected, rep2


title: SVGAs-V3-96hpi SVGAs, JCPyV-infected, rep3

description: SVGAs, JCPyV-infected, rep3


title: ATAC-Seq artery_aorta_SM-C1PX3


title: ATAC-Seq artery_aorta_SM-CR89M


title: SVGAs-C3-96hpi SVGAs, mock-infected, rep3

description: SVGAs, mock-infected, rep3

value: mock-infected with empty cell lysate preparation control


title: ATAC-Seq adrenal_gland_SM-A8WNO

source_name: adrenal gland


title: ATAC-Seq adipose_omentum_SM-IOBHJ

source_name: adipose omentum


title: NHAs-V3-96hpi NHAs, JCPyV-infected, rep3

description: NHAs, JCPyV-infected, rep3

source_name: Normal Human Astrocytes

value: primary


title: SVGAs-C2-96hpi SVGAs, mock-infected, rep2

description: SVGAs, mock-infected, rep2


title: FK228

city: Hefei

first: haoran

last: wei

state: Anhui

address: University of Science & Technology of China, 443 Huangshan Road, Hefei, Anhui

country: China

institute: ustc

data_processing:
RNA-seq data, raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Clean reads were aligned to the reference genome using TopHat2 v2.1.0.
Cuffdiff v2.2.1 was used to count the reads numbers mapped to each gene.
Genome_build: hg19
Supplementary_files_format_and_content: bed

source_name: Human breast cancer MDA-MB-231 cells

growth_protocol: MDA-MB-231 cells were obtained from the American Type Culture Collection (ATCC; Manassas, VA, USA) and cultured in Dulbecco's Modified Eagle Medium (DMEM; Gibco, Grand Island, NY, USA) supplemented with 10% fetal bovine serum (FBS; BI, Kibbutz Beit-Haemek, Israel) and 1% penicillin/streptomycin (P/S; Invitrogen, Carlsbad, CA, USA). Cells were kept at 37°C in a humidified incubator with 5% CO2 in air.

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen-Life Technologies, Waltham, Massachusetts, USA) following the manufacturer’s instructions. The following sequencing and data analysis work using these RNA samples were performed by BGI-Shenzhen (Shenzhen, Guangdong, China). Briefly, total RNA was qualified and quantified using a NanoDrop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, Waltham, MA, USA).
Oligo(dT)-attached magnetic beads were used to purify mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at the appropriate temperature. Then, first-strand cDNA was generated using random hexamer-primed reverse transcription, followed by second-strand cDNA synthesis. Afterwards, A-Tailing Mix and RNA Index Adapters were added via incubation for end repair. The cDNA fragments obtained from the previous step were amplified by PCR, and the products were purified by Ampure XP Beads (BECKMAN, Brea, CA, USA) and then dissolved in EB solution. The product was validated on an Agilent Technologies 2100 bioanalyzer (Agilent, Santa Clara, CA, USA) for quality control. The double-stranded PCR products from the previous step were heated, denatured, and circularized by the splint oligo sequence to obtain the final library. Single-stranded circular DNA (ssCir DNA) was formatted as the final library.

treatment_protocol: MDA-MB-231 cells were treated separately with three HDAC inhibitors TSA, TDPA, FK228 for 48 hours.

value: FK228(10 nM) for 48 hours.


title: Para_rubber_tree_sapling_mock_treated_48hr_rep3

type: RNA

city: Tsukuba

first: Nobutaka

last: Mitsuda

state: Ibaraki

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

hyb_protocol: Hybridized using Gene Expression Hybridization kit (Agilent) and washed by Gene Expression wash pack (Agilent).

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Agilent Feature Extraction Software (v 9.1.3.1) was used for background subtraction. After that, signal of each probe was divided by median value of filter-passed probes.

organism: Hevea brasiliensis

source_name: Para rubber tree (Hevea brasiliensis) clone PB260 6-week-old sapling treated with water for 48 hours

label_protocol: 200 ng of total RNA was used for labeling procedure using Low Input Qick Amp Labeling kit (One-color) (Agilent).

growth_protocol: All plants were grown on soil in greenhouse at BPPT, Indonesia.

extract_protocol: The ground sample was homogenized in cetyltrimethylammonium bromide (CTAB) reagent containing 2% (w/v) CTAB, 2.5% (w/v) PVP-40, 100 mM Tris-HCl (pH 7.5), 25 mM EDTA (pH 8.0), 2 M NaCl, and 2% 2-mercaptoethanol, then treated with chloroform:isoamyl alcohol (24:1, v/v). The aqueous phase was incubated with 3 M LiCl at 4°C overnight, then RNA was precipitated and the solution was centrifuged at 13 000 rpm for 20 min at 4°C. The pellet was purified with the Plant RNeasy Mini Kit (QIAGEN) following the manufacturer’s instructions. To degrade genomic DNA, the RNA was treated with recombinant DNase I (TAKARA Bio).

treatment_protocol: Stem region 2–5 cm below the shoot apex was swabbed with either 2.5% Ethrel (containing 24% ethephon; Bayer CropScience, Inc.) or distilled water (mock control) using small brushes at around 09:00 in the greenhouse.

tag: genotype

value: Wild type clone PB260

value: water (mock)

tag: treatment duration

value: 48 hours


title: Para_rubber_tree_sapling_mock_treated_48hr_rep2


title: Para_rubber_tree_sapling_mock_treated_48hr_rep1


title: Para_rubber_tree_sapling_mock_treated_24hr_rep3

source_name: Para rubber tree (Hevea brasiliensis) clone PB260 6-week-old sapling treated with water for 24 hours

value: 24 hours


title: TDPA

value: TDPA(10 nM) for 48 hours.


title: ATAC-Seq adipose_omentum_SM-CSSD4

value: normal

value: flash-frozen tissue


title: SVGAs-C1-96hpi SVGAs, mock-infected, rep1

description: SVGAs, mock-infected, rep1


title: ATAC-Seq adipose_omentum_SM-CHZRM

value: male


title: MQL: PBMC PD 3

city: Shanghai

first: Yi

last: Zhang

address: Ruijin er road

institute: Ruijin hospital

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human lncRNA Arrays (4x44K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The lncRNAs that at least 7 out of 14 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed lncRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. The lncRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed lncRNAs were annotated  in detail with the lncRNA/miRNA interaction information. The lncRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed lncRNAs were annotated  in detail with the lncRNA/miRNA interaction information.

source_name: Peripheral blood mononuclear cell

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

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

tag: cell type

value: Peripheral blood mononuclear cell

tag: disease state

value: Parkinson's Disease (PD)


title: Para_rubber_tree_sapling_mock_treated_6hr_rep2

source_name: Para rubber tree (Hevea brasiliensis) clone PB260 6-week-old sapling treated with water for 6 hours

value: 6 hours


title: WJZ: PBMC PD 4


title: XQS: PBMC PD 5


title: GJP: PBMC PD 2


title: NHAs-V1-96hpi NHAs, JCPyV-infected, rep1

description: NHAs, JCPyV-infected, rep1


title: NHAs-V2-96hpi NHAs, JCPyV-infected, rep2

description: NHAs, JCPyV-infected, rep2


title: Para_rubber_tree_sapling_mock_treated_6hr_rep3


title: Para_rubber_tree_sapling_mock_treated_24hr_rep1


title: Para_rubber_tree_sapling_mock_treated_24hr_rep2


title: FLJ: PBMC PD 1


title: Para_rubber_tree_sapling_mock_treated_6hr_rep1


title: NHAs-C3-96hpi NHAs, mock-infected, rep3

description: NHAs, mock-infected, rep3


title: CJ: PBMC normal 4

value: healthy control


title: DMSO

value: DMSO for 48 hours.


title: sh2_rep2

city: Guangzhou

first: Yan

last: Li

state: Guangdong

address: Industrial Road No.253, Guangzhou, Guangdong, 510282, China

department: Department of Neurosurgery

institute: Zhujiang Hospital

data_processing:
BGISEQ-500 software used for basecalling with PE100 strategy.
Raw reads were filtered using SOAPnuke v1.5.2 with parameter -l 15 -q 0.2 -n 0.05.
Sequenced reads were mapped to hg19 using Bowtie2 v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200, and aligned reads were counted using RSEM v1.2.12 with parameters default.
Differential expression analysis using DESeq
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: polyA RNA

source_name: U251 cell line

growth_protocol: U251 cells were maintained at 37°C under 5% CO2 in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum (Gibco) and penicillin/streptomycin.

extract_protocol:
Total RNA was isolated from cultured cell lines.
The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification.We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library.

treatment_protocol: U251 cells were transfected with sh-circGLIS3 or sh-NC lentivirus for 24h with polybrene, and then treated with puromycin for 7 days.

value: glioma cell line

tag: tissue

value: brain

value: transfected with sh-circGLIS3-2 lentivirus


title: NHAs-C1-96hpi NHAs, mock-infected, rep1

description: NHAs, mock-infected, rep1

value: primary

value: mock-infected with empty cell lysate preparation control


title: siFTO IFN rep2

city: DURHAM

first: Stacy

middle: M

last: Horner

state: NC

address: 213 Research Drive CARL 0049

department: Molecular Genetics & Microbiology

institute: Duke University

data_processing:
Trimmed reads aligned to hg19 using Salmon
Differential gene expression analyzed using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Excel spreadsheet files include log2FC

source_name: Huh7 cells

growth_protocol: Huh7 cells were grown at 37C with 5% CO2 in DMEM supplemented with 10% FBS, 1X minimum essential medium non-essential amino acids, and 25 mM HEPES

extract_protocol:
Cells were harvested in TRIzol and RNA was extracted by manufacturer protocol, after which TURBO DNase treatment was performed and RNA was phenol-chloform precipitated.
Libraries were prepared using the KAPA Stranded mRNA-Seq Kit.

treatment_protocol: siRNAs were transfected for 36 hours using Lipofectamine RNAiMax, after which cells were treated with IFN-β at 50 units/mL or mock treatment

tag: sirna

value: FTO

value: IFN-b


title: siFTO IFN rep3


title: SVGAs-V3-48hpi SVGAs, JCPyV-infected, rep3

description: SVGAs, JCPyV-infected, rep3

tag: cell line

value: transformed with SV40 T Antigen

value: JCPyV-infected (MOI = 0.1 FFU/cell)


title: siFTO IFN rep1


title: sh1_rep2

value: transfected with sh-circGLIS3-1 lentivirus


title: TSA

value: TSA(10uM) for 48 hours.


title: SVGAs-V2-48hpi SVGAs, JCPyV-infected, rep2

description: SVGAs, JCPyV-infected, rep2


title: NHAs-C2-96hpi NHAs, mock-infected, rep2

description: NHAs, mock-infected, rep2


title: SVGAs-V1-48hpi SVGAs, JCPyV-infected, rep1

description: SVGAs, JCPyV-infected, rep1


title: siFTO Mock rep3

value: Mock


title: sh1_rep1


title: Control_rep2

value: transfected with sh-NC lentivirus


title: siFTO Mock rep2


title: Control_rep1


title: siFTO Mock rep1


title: SVGAs-C2-48hpi SVGAs, mock-infected, rep2

description: SVGAs, mock-infected, rep2


title: SVGAs-C3-48hpi SVGAs, mock-infected, rep3

description: SVGAs, mock-infected, rep3


title: sh2_rep1


title: TGG: PBMC normal 2

value: Peripheral blood mononuclear cell


title: wild type rat with no tumor fed with spinach, WSN1_miRNA

city: Houston

first: Jia

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

description: Pirc-Spinach-miRNA-exp.csv

data_processing:
Low quality reads from raw fastq data was dicarded and the adpator sequence was trimmed. Bowtie2 was used to map reads to rnt6 genome. Htseqcount was used to count the reads number for each genes and miRNAs. DESeq2 was used to identify significantly differential expressed genes and miRNAs.
Genome_build: rnt6
Supplementary_files_format_and_content: Pirc-Spinach-RNAseq-RPKM.xlsx, Pirc-Spinach-miRNA-exp.csv

organism: Rattus norvegicus

source_name: colon

extract_protocol:
The colonic tissues were snap frozen with liquid nitrogen after the rat necropsy and each tissue sample was lysed in 700 ul Qiazol lysis reagent with tissue homogenizer. Total RNA was isolated from up to 50mg colonic tissue using Qiagen miRNeasy mini kit, according to manufacture's insturctions to cover both mRNA and miRNA. The isolated RNA concentration was measured by a Qubit 4 Fluorometer with the Qubit™ RNA HS Assay Kit  (Thermo Fisher Scientific).
For RNA library preparation, NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB, E7490) and NEBNext® UltraTM Directional RNA Library Prep Kit (NEB, E7420) were performed with 3 mg RNA input as the starting material. For small RNA library preparation, NEBNext® Small RNA Library Prep Set for Illumina® (NEB, E7300) were performed with 1 mg RNA input as the starting material. The RNA went through 3’ ligation, primer hybridization, 5’ ligation, first strand synthesis, PCR amplification and size selection (MinElute Gel Extraction Kit, Qiagen). During library construction, each sample was tagged with a specific index at the PCR amplification step. The library concentration was measured by Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and the size of the library was assessed by 2% agarose gel with 2 ng library material. Samples were diluted to 1 pmol for further library pooling. Before loading the pooled library into the NextSeq 550/500 system (Illumina), 1 nM library was denatured and diluted according to NextSeq  System Denature and Dilute Libraries Guide (Illumina). Stranded RNA sequencing was conducted by paired-end sequencing with 75-bp read length and small RNA sequencing was conducted by single-end sequencing with 50 bp read length following the manufacturer’s protocols.

value: colon

value: wild type

value: with no tumor

tag: diet

value: fed with spinach


title: wild type rat with no tumor not fed with spinach, WCN2_miRNA

description: Pirc-Spinach-miRNA-exp.csv

value: not fed with spinach


title: wild type rat with no tumor fed with spinach, WSN3_miRNA

description: Pirc-Spinach-miRNA-exp.csv


title: wild type rat with no tumor not fed with spinach, WCN3_miRNA

description: Pirc-Spinach-miRNA-exp.csv


title: WGS_TT2

city: HONG KONG

first: Danny

last: Leung

state: HONG KONG

address: Clear Water Bay

institute: HONG KONG UNIV OF SCIENCE & TECHNOLOGY

data_processing:
Bowtie 2 was used to align paired-end reads to each reference and only uniquely aligned reads were included in downstream analysis.
The output SAM files were then converted into BAM files and sorted according to genomic coordinate using SAMtools
The resulting BAM file was subsequently converted into BED file by BEDTools
The BED file was then converted into BedGraph and BigWig files for visualization with the UCSC genome browser
Genome_build: mm10
Supplementary_files_format_and_content: WGS: BigWig files were generated by UCSC utilites; Scores represent raw reads number.
Supplementary_files_format_and_content: Tri-4C: BigWig files were generated by UCSC utilites; Scores represent RPKM in 500bp bins.

organism: Mus musculus

source_name: Embryonic stem cell

growth_protocol: mESCs were grown on 0.1% gelatinized plate supplemented with 15% certified FBS (Life Technologies), 20mM HEPES, 0.1mM non-essential amino acids, 0.1mM 2-mercaptoethanol, 100U/ml penicillin, 0.05mM streptomycin, 1U/ul Leukemia-inhibitory factor(LIF) and 2mM glutamine. Cells were passage at 80% confluency.

extract_protocol:
Genomic DNA of cells was isolated with Bradley’s protocol. The purified DNA was fragmented by sonication.
The fragmented DNA was subjected to next generation sequencing on the MGISEQ-2000-RS platform(BGI).

tag: strain background

value: Embryonic stem cell


title: CSD: PBMC normal 1

value: healthy control


title: siCTRL IFN rep3

value: non-targeting control


title: ZJT: PBMC normal 3


title: SVGAs-C1-48hpi SVGAs, mock-infected, rep1

description: SVGAs, mock-infected, rep1

value: mock-infected with empty cell lysate preparation control


title: wild type rat with no tumor fed with spinach, WSN2_miRNA

description: Pirc-Spinach-miRNA-exp.csv


title: wild type rat with no tumor not fed with spinach, WCN1_miRNA

description: Pirc-Spinach-miRNA-exp.csv


title: ATAC-Seq adipose_omentum_SM-ADYHB

tag: sample type

value: normal

value: flash-frozen tissue

value: female

value: asian

value: cerebral vascular accident


title: siCTRL IFN rep2

value: IFN-b


title: WGS_J1


title: NHAs-V3-48hpi NHAs, JCPyV-infected, rep3

description: NHAs, JCPyV-infected, rep3

value: primary

value: JCPyV-infected (MOI = 0.1 FFU/cell)


title: Pirc rat with tumor fed with spinach, PST3_miRNA

description: Pirc-Spinach-miRNA-exp.csv

value: colon

value: Pirc

value: with tumor


title: siCTRL IFN rep1


title: siCTRL Mock rep3

value: Mock


title: NHAs-V1-48hpi NHAs, JCPyV-infected, rep1

description: NHAs, JCPyV-infected, rep1


title: mLN DKO (HTO)

city: Zwijnaarde

first: Jordy

last: De Coninck

address: Technologiepark 71

department: Department of Biomedical Molecular Biology

country: Belgium

institute: University Gent

data_processing:
Raw data BCL files were demultiplexed using bcl2fastq2 v2.20
Demultiplexed data was then processed using the Cell Ranger v6.0.0 count pipeline. Cell Ranger merges both cDNA and HTO libraries and generates a multimodal .h5 file.
Genome_build: GRCm38.99 (mm10)
Supplementary_files_format_and_content: h5 files including raw counts (output CellRanger Count) for each sample

source_name: Mesenteric lymph nodes

extract_protocol:
Single-cell RNA sequencing was performed on mesenteric lymph nodes (mLN), small intestinal intra-epithelial lymphocytes (SI-IEL), SI lamina propria lymphocytes (SI-LPL), colonic IELs and colonic LPLs isolated from Casp3/7Villin-Cre mice and Casp3/7FL/FL littermates. Single cells were isolated from the tissues by enzymatic digestion and live cells were sorted by fluorescence-activated cell sorting (FACS).
The scRNA libraries were prepared using the GemCode NextGEM Single Cell 3’ Gel Bead and Library kit, version 3.1 (10x Genomics, Cat. PN-1000121) according to the manufacturer’s instructions. The cDNA content of pre-fragmentation and post-sample index PCR samples was analyzed using the 2100 BioAnalyzer (Agilent). Sequencing libraries were loaded on an Illumina NovaSeq flow cell at VIB Nucleomics core with sequencing settings according to the recommendations of 10x Genomics, pooled in a 90:10 ratio for the gene expression and hashtag antibody-derived libraries, respectively.
Single-cell RNA sequencing

tag: number of cells

tag: platform

value: 10X Genomics - v3


title: siCTRL Mock rep2


title: Pirc rat with tumor fed with spinach, PST1_miRNA

description: Pirc-Spinach-miRNA-exp.csv

value: fed with spinach


title: mLN WT (HTO)


title: mLN DKO (cDNA)


title: siCTRL Mock rep1


title: Pirc rat with no tumor fed with spinach, PSN3_miRNA

description: Pirc-Spinach-miRNA-exp.csv

value: with no tumor


title: mLN WT (cDNA)


title: Colon IEL+LPL DKO (cDNA)

source_name: Colon

value: Intra Epithelial Layer (25% CD45+ 25% CD45-) + Lamina Propria (50% CD45+)


title: FOX_2

city: Montreal

first: Jerry

last: Pelletier

state: Qc

address: 3655 Promenade Sir William Olser

country: Canada

institute: McGill University

description:
Infected with pLX_TRC317_FOXP3_v5_PuroR at MOI <= 0.3 then selected with puromycin (2 ug/mL) for 2.5 days
rRNA-depleted stranded RNA

data_processing:
The high quality of sequence reads was confirmed using FastQC tool.
Low-quality bases were trimmed from read extremities using Trimmomatic v.0.33.
Trimmed reads were then mapped to the mouse UCSC hg38 reference assembly using TopHat v2.0.9 in conjunction with Bowtie 1.0.0 algorithms.
Gene expression was quantified by counting the number of uniquely mapped reads with featureCounts using default parameters.
We retained genes that had an expression level of minimum 5 counts per million reads (CPM) in at least 3 of the samples, and performed quantile normalization with the preprocessCore package. TMM normalization and differential gene expression analyses were conducted using the edgeR Bioconductor package (R version 3.6.0).
Pairwise comparisons were performed between samples of the two groups and genes with changes in expression ≥ |2| folds and Benjamini-Hochberg adjusted p values ≤ 0.05 were considered significant.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with CPM values after quantile normalization
Supplementary_files_format_and_content: Tab-delimited text with raw gene counts for every gene in each sample as generated by featureCounts (gene annotation: UCSC hg38)

growth_protocol: Hap1 cells were obtained from Horizon Discovery and maintained in Iscove’s Modified Dulbecco’s Medium supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin antibiotics (Pen-Strep), and 2mM L-glutamine at 37°C and 5% CO2

extract_protocol:
Cells were washed with PBS, and RNA was harvested using the Qiagen RNeasy Mini Kit with on-column DNase I digestion.
Samples were sent to the Institut de Recherches Cliniques de Montréal (IRCM) for library preparation and deep sequencing. RNA integrity was first assessed on Bioanalyzer RNA Pico chips (Agilent), then strand-specific, barcoded libraries were prepared via cDNA production, PCR, and ribosomal RNA (rRNA) depletion . Deep sequencing was performed using the Illumina HiSeq 4000 platform with paired-end 50 reads at approximately 50 million reads per sample.

treatment_protocol: No treatment was performed

value: Near-haploid

tag: origin

value: Derived from male chronic myeloneous leukemia (CML) cell line KBM-7


title: NHAs-C2-48hpi NHAs, mock-infected, rep2

description: NHAs, mock-infected, rep2

value: mock-infected with empty cell lysate preparation control


title: NHAs-C1-48hpi NHAs, mock-infected, rep1

description: NHAs, mock-infected, rep1


title: Colon IEL+LPL DKO (HTO)


title: Pirc rat with no tumor fed with spinach, PSN1_miRNA

description: Pirc-Spinach-miRNA-exp.csv


title: Colon IEL+LPL WT (HTO)


title: SVGAs-V2-24hpi SVGAs, JCPyV-infected, rep2

description: SVGAs, JCPyV-infected, rep2

value: transformed with SV40 T Antigen


title: Pirc rat with no tumor fed with spinach, PSN2_miRNA

description: Pirc-Spinach-miRNA-exp.csv


title: FOX_1


title: Pirc rat with tumor not fed with spinach, PCT2_miRNA

description: Pirc-Spinach-miRNA-exp.csv

value: not fed with spinach


title: Pirc rat with tumor fed with spinach, PST2_miRNA

description: Pirc-Spinach-miRNA-exp.csv


title: Pirc rat with tumor not fed with spinach, PCT3_miRNA

description: Pirc-Spinach-miRNA-exp.csv


title: NHAs-V2-48hpi NHAs, JCPyV-infected, rep2

description: NHAs, JCPyV-infected, rep2


title: GFP_3

description:
Infected with pLX_TRC317_GFP_v5_PuroR at MOI <= 0.3 then selected with puromycin (2 ug/mL) for 2.5 days
rRNA-depleted stranded RNA


title: SVGAs-V3-24hpi SVGAs, JCPyV-infected, rep3

description: SVGAs, JCPyV-infected, rep3


title: ATAC-Seq artery_tibial_SM-IOBHK

source_name: tibial artery

value: normal

tag: biosample

value: flash-frozen tissue

tag: donor age (years)

tag: donor sex

value: female

tag: race

value: asian

value: cerebral vascular accident


title: SVGAs-V1-24hpi SVGAs, JCPyV-infected, rep1

description: SVGAs, JCPyV-infected, rep1

tag: treatment

value: JCPyV-infected (MOI = 0.1 FFU/cell)

tag: time post infection


title: Colon IEL+LPL WT (cDNA)

tag: genotype

tag: cell type


title: GFP_2


title: Pirc rat with tumor not fed with spinach, PCT1_miRNA

description: Pirc-Spinach-miRNA-exp.csv

tag: tissue

value: colon

value: Pirc

tag: disease state

value: with tumor


title: SI LPL DKO (HTO)

source_name: Small Intestine

value: Lamina Propria (100% CD45+)

value: 10X Genomics - v3


title: NHAs-C3-48hpi NHAs, mock-infected, rep3

description: NHAs, mock-infected, rep3

tag: cell line

value: primary


title: SVGAs-C3-24hpi SVGAs, mock-infected, rep3

description: SVGAs, mock-infected, rep3

source_name: SVG-A cells


title: FOX_3

value: Near-haploid


title: GFP_1

value: Derived from male chronic myeloneous leukemia (CML) cell line KBM-7


title: SI LPL DKO (cDNA)


title: SVGAs-C2-24hpi SVGAs, mock-infected, rep2

description: SVGAs, mock-infected, rep2

value: mock-infected with empty cell lysate preparation control


title: Pirc rat with no tumor not fed with spinach, PCN2_miRNA

description: Pirc-Spinach-miRNA-exp.csv

value: with no tumor

tag: diet


title: Cluster5 Child1 Positive Interval5

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Reads were mapped to the reference genome using STAR 2.4 with --outFilterMultimapNmax 1.
Raw count measurements were obtained with featureCounts 1.4.6 keeping only unambiguous reads.
Genome_build: GRCh38.96
Supplementary_files_format_and_content: Raw_counts.txt: Tab-delimited text file includes raw counts measurements.

source_name: whole blood

extract_protocol:
RNA extraction was performed automatically via the PAXgene Blood miRNA Kit and the QIAcube instrument (Qiagen) following the manufacturer’s protocol. RNA concentration and quality were assessed by using the Qubit instrument (Invitrogen) and the Agilent 2100 Bioanalyzer, respectively.
The Stranded Total RNA Ribo-Zero Plus kit from Illumina was used for the library preparation with 100 ng of total RNA as input. Library molarity and quality were assessed with the Qubit and Tapestation using a DNA High sensitivity chip (Agilent Technologies). Libraries were pooled at 2 nM for clustering and sequenced on an Illumina HiSeq 4000 sequencer for a minimum of 30 million single-end 100 reads per sample.

value: whole blood

tag: sars-cov-2 infection

value: Positive

tag: age (years)

tag: time point

value: POS interval 5


title: Pirc rat with no tumor not fed with spinach, PCN1_miRNA

description: Pirc-Spinach-miRNA-exp.csv

value: not fed with spinach


title: SVGAs-C1-24hpi SVGAs, mock-infected, rep1

description: SVGAs, mock-infected, rep1

value: transformed with SV40 T Antigen


title: Cluster5 Child1 Positive Interval4

value: POS interval 4


title: Cluster5 Child1 Positive Interval2

value: POS interval 2


title: SI LPL WT (cDNA)

tag: number of cells

tag: platform


title: NHAs-V3-24hpi NHAs, JCPyV-infected, rep3

description: NHAs, JCPyV-infected, rep3

value: JCPyV-infected (MOI = 0.1 FFU/cell)


title: SI IEL DKO (HTO)

value: Intra Epithelial Layer (50% CD45+ 50% CD45-)


title: wild type rat with no tumor fed with spinach, WSN3_RNAseq

description: Pirc-Spinach-RNAseq-RPKM.xlsx

value: colon

value: wild type

value: fed with spinach


title: wild type rat with no tumor fed with spinach, WSN2_RNAseq

description: Pirc-Spinach-RNAseq-RPKM.xlsx


title: Cluster5 Child1 Positive Interval1

value: POS interval 1


title: SI IEL DKO (cDNA)

value: 10X Genomics - v3


title: NHAs-V1-24hpi NHAs, JCPyV-infected, rep1

description: NHAs, JCPyV-infected, rep1

value: primary


title: wild type rat with no tumor fed with spinach, WSN1_RNAseq

description: Pirc-Spinach-RNAseq-RPKM.xlsx


title: SI IEL WT (HTO)


title: wild type rat with no tumor not fed with spinach, WCN3_RNAseq

description: Pirc-Spinach-RNAseq-RPKM.xlsx


title: NHAs-C3-24hpi NHAs, mock-infected, rep3

description: NHAs, mock-infected, rep3

value: mock-infected with empty cell lysate preparation control


title: SI IEL WT (cDNA)


title: Cluster5 Adult2 Positive Interval5


title: Pirc rat with no tumor not fed with spinach, PCN3_miRNA

description: Pirc-Spinach-miRNA-exp.csv

value: Pirc

value: with no tumor


title: NHAs-C2-24hpi NHAs, mock-infected, rep2

description: NHAs, mock-infected, rep2


title: Cluster5 Adult2 Positive Interval3

value: whole blood

value: Positive

value: POS interval 3


title: wild type rat with no tumor not fed with spinach, WCN2_RNAseq

description: Pirc-Spinach-RNAseq-RPKM.xlsx

value: not fed with spinach


title: SI LPL WT (HTO)

value: Lamina Propria (100% CD45+)


title: Set B: propylthiouracil + propranolol 3

city: San Jose

first: Alexander

middle: Y

last: Payumo

address: One Washington Square

department: Biological Sciences

institute: San Jose State University

data_processing:
RNA-seq reads were first trimmed adapter with cutadapt (v1.9), then discard reads with length less than 15 and quality less than 20. Filtered reads were aligned to mouse Ensembl reference with STAR (v2.5.2b) with parameters of --outFilterMismatchNoverLmax 0.04.
.
Genome_build: mm10
Supplementary_files_format_and_content: TXT: Genomic features at gene level were generated with featureCounts (v1.5.1).

source_name: heart

growth_protocol: Newborn pups are fed by their nursing mothers

extract_protocol:
Hearts were harvested at postnatal day 14, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent.
Illumina Tru-seq RNA Library Prep Kit v2

treatment_protocol: Thyroid hormone was inhibited by treating pregnant female mice with chow containing propylthiouracil (thyroid hormone inhibitor; 0.15% in iodine deficient diet) starting at E13.5 and then maintained thereafter. Newborn pups were injected subcutaneously with phenoxybenzamine (alpha-adrenergic inhibitor; 10 ug/g/day) and/or propranolol (beta-adrenergic inhibitor; 20 ug/g/day) daily from P1 to P14.

tag: strain

value: whole heart

tag: age

value: postnatal day 14

value: propylthiouracil (0.15% in iodine-deficient chow) + propranolol (20 ug/g/day)

tag: sequencing set

value: B


title: NHAs-C1-24hpi NHAs, mock-infected, rep1

description: NHAs, mock-infected, rep1

source_name: Normal Human Astrocytes


title: wild type rat with no tumor not fed with spinach, WCN1_RNAseq

description: Pirc-Spinach-RNAseq-RPKM.xlsx

value: colon

value: wild type


title: Cluster5 Adult2 Positive Interval2

value: POS interval 2


title: Pirc rat with tumor fed with spinach, PST3_RNAseq

description: Pirc-Spinach-RNAseq-RPKM.xlsx

value: with tumor

value: fed with spinach


title: Set B: propylthiouracil + propranolol 2


title: NHAs-V2-24hpi NHAs, JCPyV-infected, rep2

description: NHAs, JCPyV-infected, rep2

value: primary

value: JCPyV-infected (MOI = 0.1 FFU/cell)


title: Cluster5 Adult2 Positive Interval1

value: POS interval 1


title: Cluster5 Adult1 Positive Interval5

value: whole blood

value: POS interval 5


title: Cluster5 Adult1 Positive Interval4

value: Positive

value: POS interval 4


title: CD_C13

city: Aurora

first: Kibrom

middle: Meles

last: Alula

state: CO

department: Pediatrics

institute: University of Colorado Anschutz Medical Campus

data_processing:
Mapping to a reference by STAR v2.5
Quantification by HTSeq v0.6.1
Differential Analysis by DESeq2 (v1.14.1) and EdgeR (v3.16.5) for samples with bio-replicates, and samples without bio-replicate, respectively
Enrichment Analysis by ClusterProfiler v2.4.3 for GO, DO, KEGG, and Reactome enrichment analysis
Protein-Protein Interaction Analysis by NCBI BLAST v2.2.28
Alternative splicing using rMATS v3.2.5
Fusion gene using Star-fusion v1.5.0
SNP/InDel Analysis by GATK (V4.1) and ANNOVAR (v2.4) for SNP/InDel calling, and SNP/InDel Annotation, respectively
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: Intestinal epithelium

extract_protocol:
RNA was extracted and harvested using Qiagen AllPrep DNA/RNA kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Terminal ileal mucosal biopsies from active sites of Crohn's disease or non-IBD control patients were placed in 300 ml DMEM culture media in the endoscopy suite and placed on ice. Within 30 minutes, the biopsies were transported to the lab, dabbed to remove excess culture media, and weighed. Biopsies were then incubated in 300 ml DMEM culture media containing 40 mg/L penicillin, 90 mg/L streptomycin, and 0.5 mg/g tissue Mito-Tempo or vehicle; two biopsies from each patient were used, one biopsy treated with Mito-Tempo and one with vehicle. Biopsies were cultured in a humidified environment at 37°C and 5% CO2 for 2 hr then moved from the culture media and incubated in RNAlater (Qiagen). Total RNA was isolated from patient biopsies using AllPrep DNA/RNA kit (Qiagen).

value: CD

value: Mucosal

value: MitoTempo


title: CD_C12


title: Set B: propylthiouracil + propranolol 1

value: whole heart

value: postnatal day 14

value: propylthiouracil (0.15% in iodine-deficient chow) + propranolol (20 ug/g/day)


title: CD_C11


title: Cluster5 Adult2 Positive Interval4


title: Set B: propylthiouracil 2

value: propylthiouracil (0.15% in iodine-deficient chow)

value: B


title: Pirc rat with tumor fed with spinach, PST1_RNAseq

description: Pirc-Spinach-RNAseq-RPKM.xlsx

value: colon

value: Pirc

value: with tumor


title: Pirc rat with no tumor fed with spinach, PSN3_RNAseq

description: Pirc-Spinach-RNAseq-RPKM.xlsx

value: with no tumor

value: fed with spinach


title: Cluster5 Adult1 Positive Interval3

value: whole blood

value: POS interval 3


title: Pirc rat with no tumor fed with spinach, PSN2_RNAseq

description: Pirc-Spinach-RNAseq-RPKM.xlsx


title: Set B: propranolol 3

value: propranolol (20 ug/g/day)


title: Set B: propylthiouracil 1


title: Pirc rat with no tumor fed with spinach, PSN1_RNAseq

description: Pirc-Spinach-RNAseq-RPKM.xlsx


title: CD_C8


title: Cluster5 Adult1 Positive Interval2

value: Positive

value: POS interval 2


title: CD_C10

value: CD

value: Mucosal


title: Cluster5 Adult1 Positive Interval1

value: POS interval 1


title: CD_C7

value: MitoTempo


title: Cluster4 Child3 Positive Interval1


title: Set B: propranolol 2

value: whole heart

value: postnatal day 14


title: Pirc rat with tumor fed with spinach, PST2_RNAseq

description: Pirc-Spinach-RNAseq-RPKM.xlsx


title: Pirc rat with tumor not fed with spinach, PCT2_RNAseq

description: Pirc-Spinach-RNAseq-RPKM.xlsx

value: not fed with spinach


title: Pirc rat with tumor not fed with spinach, PCT3_RNAseq

description: Pirc-Spinach-RNAseq-RPKM.xlsx

value: colon


title: Set B: propylthiouracil 3

value: propylthiouracil (0.15% in iodine-deficient chow)

value: B


title: CD_C6


title: Set B: propranolol 1


title: Cluster4 Child2 Positive Interval4

value: POS interval 4


title: Set B: saline 3

value: saline


title: Pirc rat with tumor not fed with spinach, PCT1_RNAseq

description: Pirc-Spinach-RNAseq-RPKM.xlsx

value: Pirc

value: with tumor


title: Set B: saline 2


title: CD_C5


title: Set B: saline 1


title: CD_C9


title: Pirc rat with no tumor not fed with spinach, PCN3_RNAseq

description: Pirc-Spinach-RNAseq-RPKM.xlsx

value: with no tumor


title: CD_C4


title: Cluster4 Child2 Positive Interval1

value: whole blood

value: Positive


title: Cluster4 Child2 Positive Interval2

value: POS interval 2


title: Pirc rat with no tumor not fed with spinach, PCN2_RNAseq

description: Pirc-Spinach-RNAseq-RPKM.xlsx


title: CD_C3

value: CD

value: Mucosal


title: CD_C2

value: MitoTempo


title: Cluster4 Child1 Positive Interval2


title: Set A: propylthiouracil + phenoxybenzamine + propranolol 3

value: whole heart

value: propylthiouracil (0.15% in iodine-deficient chow) + phenoxybenzamine (10 ug/g/day) + propranolol (20 ug/g/day)

value: A


title: Pirc rat with no tumor not fed with spinach, PCN1_RNAseq

description: Pirc-Spinach-RNAseq-RPKM.xlsx

value: colon

value: not fed with spinach


title: CD_C1


title: Cluster4 Child1 Positive Interval4


title: Set A: propylthiouracil + phenoxybenzamine + propranolol 2

value: postnatal day 14


title: R_zn_3

city: Wuhan

first: Liu

last: Chen

state: Hubei

address: No.1 Shizishan Street, Hongshan District, Wuhan, Hubei Province, China

department: College of Life Science and Technology

institute: Huazhong Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Mycobacterium_tuberculosis_variant_bovis_BCG_Pasteur_1173P2 whole genome using bowtie2 v2-2.0.5
Fragments per kilobase of exon per million fragments mapped(FPKM). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Mycobacterium tuberculosis variant bovis BCG Pasteur 1173P2
Supplementary_files_format_and_content: gene_fpkm.xls file includes FPKM values for each Sample ...

source_name: CmtR-deleted strain zinc treatment rep3

extract_protocol: Total RNA was isolated using RNAprep Pure Cell/Bacteria Kit (Qiagen, Germany) according to the manufacturers instructions.

treatment_protocol: Wild-type or cmtR-deleted strains of Mycobacterium bovis BCG were cultured in 7H9 medium with shaking at 160 rpm at 37 ? until the mid-logarithmic phase. Then, the cells were treated with 0 mM and 0.5 mM Zinc for 24 h, respectively, and harvested from each sample (each strain in three biological replicates).

value: CmtR-deleted


title: R_zn_2

organism: Mycobacterium tuberculosis variant bovis BCG

source_name: CmtR-deleted strain zinc treatment rep2


title: Cluster4 Adult1 Positive Interval5

value: POS interval 5


title: Cluster4 Child1 Positive Interval1

value: POS interval 1


title: Non-IBD_N12

value: Non-IBD

value: Vehicle


title: R_zn_1

source_name: CmtR-deleted strain zinc treatment rep1


title: Set A: propylthiouracil + phenoxybenzamine + propranolol 1


title: Set A: propylthiouracil + phenoxybenzamine 3

value: propylthiouracil (0.15% in iodine-deficient chow) + phenoxybenzamine (10 ug/g/day)


title: Set A: propylthiouracil + phenoxybenzamine 2


title: Non-IBD_N11


title: R_N_3

source_name: CmtR-deleted strain without zinc treatment  rep3


title: Cluster4 Adult1 Positive Interval2

value: whole blood

value: Positive


title: Set A: propylthiouracil + phenoxybenzamine 1


title: Cluster3 Child1 Positive Interval5


title: R_N_2

source_name: CmtR-deleted strain without zinc treatment  rep2


title: Set A: phenoxybenzamine + propranolol 3

value: phenoxybenzamine (10 ug/g/day) + propranolol (20 ug/g/day)


title: R_N_1

source_name: CmtR-deleted strain without zinc treatment  rep1


title: Non-IBD_N9

value: Mucosal


title: Non-IBD_N8


title: Cluster2 Child1 Positive Interval4

value: POS interval 4


title: Set A: phenoxybenzamine + propranolol 1

value: whole heart


title: Cluster3 Child1 Positive Interval2

value: POS interval 2


title: wt_zn_3

source_name: Wild-type strain zinc treatment rep3

value: wildtype


title: Cluster2 Child1 Positive Interval3

value: POS interval 3


title: wt_zn_2

source_name: Wild-type strain zinc treatment rep2


title: Non-IBD_N13


title: Set A: phenoxybenzamine 3

value: phenoxybenzamine (10 ug/g/day)

value: A


title: Non-IBD_N7


title: Non-IBD_N6


title: Cluster2 Child1 Positive Interval2


title: wt_N_3

source_name: Wild-type strain without zinc treatment  rep3


title: wt_zn_1

source_name: Wild-type strain zinc treatment rep1


title: Set A: phenoxybenzamine 1

value: postnatal day 14


title: Cluster4 Adult1 Positive Interval3


title: Set A: phenoxybenzamine 2


title: Non-IBD_N10


title: Non-IBD_N5


title: Non-IBD_N4


title: Set A: saline 3

value: saline


title: Non-IBD_N3


title: Set A: phenoxybenzamine + propranolol 2


title: Cluster2 Child1 Positive Interval1

value: POS interval 1


title: wt_N_2

source_name: Wild-type strain without zinc treatment  rep2


title: Cluster2 Adult2 Negative Visit5

value: Negative

value: Negative visit 5


title: Cluster2 Adult2 Negative Visit3

value: Negative visit 3


title: wt_N_1

source_name: Wild-type strain without zinc treatment  rep1


title: Set A: saline 2


title: Non-IBD_N1

value: Non-IBD

value: Vehicle


title: Cluster2 Adult2 Negative Visit2

value: whole blood

value: Negative visit 2


title: Cluster2 Adult2 Negative Visit1

value: Negative visit 1


title: Non-IBD_N2

value: Mucosal


title: D3839 EBd7 CD71+ Rhbdf1 and Mpg Captures sample 3 (CTCFDKO_A82_5Promoters)

city: Oxford

first: Mira

middle: Tony

last: Kassouf

state: England

address: John Radcliffe Hospital, Headly way

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description: sequences enriched from a 3C library for their interaction with the Capture point in the Alpha Globin locus as detailed in the sample name

data_processing:
Library strategy: Capture-C-seq
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
In silico restriction enzyme digestion of FASTQ file (dpnIIPE.pl)
Alignment to the genome (Bowtie) maintaining strict read order
Removal of PCR duplicates; Parsing of informative reads and mapping to restriction enzyme fragments (CCanalyser2.pl)
Combining data from multiple replicates (custom scripts)
Removal of ploidy regions and off target capture (custom scripts)
Analysis in R to normalise between tracks using the total number of informative interactions
Genome_build: mm9
Supplementary_files_format_and_content: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.)

source_name: Chromatin from purified CD71+ erythroid cells derived from differentiated D3839 mES cells, Rhbdf1 and Mpg promoters as Capture point, sample 3

extract_protocol:
To produce CD71+ erythroid cells in vitro from differentiated mESCs (WT or mutant D3839 which is a mouse ESC line where mouse alpha globon HS38 and HS39.5 indicating CTCF sites/5' boundary elements have been deleted): 24h prior to differentiation, mESCs were induced by passaging into IMDM base media, trypsinised and plated in differentiation media (IMDM suplemented serum and other reagents and growth factors) in either triple vent petri dishes (Thermo Fisher) or flat-bottom 96-well plates (Thermo Fisher) at 3x104 cells in 10 cm dishes or 250 cells per well of a 96-well plate for up to seven days without disruption. EBs were harvested and disaggregated in 0.25% trypsin for 3 minutes at 37°C. CD71-positive cells were isolated by magnetic column separation (LS Column, Miltenyi), according to the manufacturer’s instructions. Briefly, cells (from disaggregated EBs) were labelled with anti-mouse CD71-FITC (eBioscience 11-0711-85; 1:200) in staining buffer (PBS with 10% FCS; 500 ul per 10^7 cells) for 20 minutes at 4°C, washed, then incubated with MACS anti-FITC separation microbeads (Miltenyi; 10 ul  per 10^7 cells, following the manufacturer’s instructions) and bead-labelled cells were retained by LS columns. Cells were then processed for Capture-C as in Davies J et al, Nature Methods.
The protocol used for generation of the 3C libraries was similar to previous methods with minor modifications. Briefly, cells were crosslinked with 2% formaldehyde (10 minutes, room temperature); quenched with cold glycine; washed in phosphate buffered saline; resuspended in cold lysis buffer (tris 10mM, NaCl 10mM, NP40 0.2%, complete proteinase inhibitor (Roche)) and snap frozen to -80.  Cells were thawed on ice, washed in milliq dH2O and Dounce homogenised on ice (x 40 strokes). Cells were then resuspended with 0.25% SDS and restriction enzyme buffer and incubated at 37C for 1h at 1400rpm on a Comfort Thermomixer (Eppendorf) followed by a further incubation of 1h following the addition of triton X100 (final concentration 1.67%). An overnight digestion was performed using Dpn II (500U /ml (NEB) at 37C / 1400 rpm). The digested chromatin was ligated overnight (Fermentas HC Ligase final concentration 10U/ml) at 16 degrees at 1400 rpm on the Thermomixer.  The samples were then decrosslinked overnight at 65C with Proteinase K (Roche) followed by a 30 min incubation at 37C with RNAse (Roche). Phenol/Chloroform extraction was then performed followed by an Ethanol precipitation and a wash with 70% Ethanol. Digestion efficiencys were assessed by gel electrophoresis (1% agarose) and RT-PCR (Taqman), which showed digestion efficiencies in excess of 80%.  DNA content of the Dpn II 3C libraries were quantitated using a Qubit fluorometer (Life technologies) and 5-10ug of each library was sheared using a Covaris S2 in milliq dH2O. Covaris settings used were: duty cycle 10%, Intensity 5, Cycles/burst 200, Time 6 cycles of 60seconds, Set Mode Frequency sweeping Temperature 4 to 7 degrees. Following shearing DNA was purified using AMPureXP beads (Agencourt) and DNA quality assessed on a Bioanalyser 2100 using a DNA High Sensitivity Chip (Agilent). DNA end repair and adapter ligation was performed using the NEB Next or NEB Ultra II DNA sample preparation reagent kits, depending on the amount of DNA available, using the standard protocol.  Biotinylated capture oligonucleotides were designed to the ends of the viewpoint fragments.  Where possible 1-2ug of each adapter ligated library were hybridized with the biotinylated capture oligonucleotides, using  the Nimblegen SeqCap reagents and an adapted protocol.  The quality of the resultant captured library was assessed by Agilent tapestation or bioanalyser (D1000). The resulting libraries were sequenced using Illumina Next-Seq.
The experimental strategy was to generate very high complexity randomly sonicated 3C libraries with ligated Illumina sequencing adaptors (ideally with several hundred thousand fold coverage).  Oligonucleotide capture technology was then used to pull down the restricion fragments containing the viewpoints of interest and their interacting partners, which were subsequently idendified by high throughput sequencing.  The power of the technique is that multiple samples and genes can be analysed simultaneously by using differently indexed samples.

value: E14TG2a.IV mES derived Erythroid cells

tag: analysis

value: Alpha Globin Locus


title: Cluster2 Adult1 Positive Interval5

source_name: whole blood

value: Positive

value: POS interval 5


title: D3839 EBd7 CD71+ Rhbdf1 and Mpg Captures sample 2 (CTCFDKO_A81_5Promoters)

source_name: Chromatin from purified CD71+ erythroid cells derived from differentiated D3839 mES cells, Rhbdf1 and Mpg promoters as Capture point, sample 2


title: CS1AN_VA UV_24 h Chromatin

first: Yuming

last: Wang

address: Room 512, Anatomy Building

department: School of Basic Medical Science

institute: Guangzhou medical university

data_processing:
Raw data of fastq format were firstly processed through in-house perl scripts to obtain clean reads by removing reads containing adapter, poly-N and low quality reads.
Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with FPKM for every transcript in all samples.

source_name: Skin fibroblast cells

growth_protocol: MRC5_VA cells were routinely maintained in DMEM supplemented with 10% FBS at 37°C in a 5% CO2 water-saturated environment.

extract_protocol:
Total RNA for each cellular fraction was isolated by Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit (Cat#E7530L) was used with 1 μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with 10 J/m2 UV-C light and recovered for the indicated time in the study.

value: skin fibroblast cells derived from Cockayne syndrome patient

tag: treatment

value: treated with 10 J/m2 UV-C irradiation and recovered for 24 hours


title: CS1AN_VA UV_3 h Chromatin

value: treated with 10 J/m2 UV-C irradiation and recovered for 3 hours


title: CS1AN_VA UV_24 h Cytoplasm


title: CS1AN_VA UV_3 h Cytoplasm


title: Cluster2 Adult1 Positive Interval4

value: POS interval 4


title: D3839 EBd7 CD71+ Rhbdf1 and Mpg Captures sample 1 (CTCFDKO_A3_5Promoters)

source_name: Chromatin from purified CD71+ erythroid cells derived from differentiated D3839 mES cells, Rhbdf1 and Mpg promoters as Capture point, sample 1


title: Cluster2 Adult1 Positive Interval3

value: POS interval 3


title: CTX_WT_Female_04 [RNA-Seq]

city: St. Louis

first: Joseph

last: Dougherty

state: MO

address: Couch Biomedical Research Bldg 06316

department: Genetics

institute: Washington University of St. Louis

data_processing:
Adapator trimming using Trimmomatic
Reads alignment using Bowtie2 and STAR
Peak calling using MASC2
Reads counts using HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: Peak, Reads counts

source_name: Cortex

extract_protocol:
Zymo RNA extraction kit
SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech)
ATAC-seq: Corces et al., 2017, Nature Methods

value: WT

tag: Sex

value: f


title: CTX_WT_Female_09 [RNA-Seq]

tag: genotype


title: CS1AN_VA UV_30 min Chromatin

tag: cell type

value: treated with 10 J/m2 UV-C irradiation and recovered for 30 minutes


title: CTX_Het_Male_01 [RNA-Seq]

value: Het

value: m


title: Cluster2 Adult1 Positive Interval2

tag: tissue

value: whole blood

value: POS interval 2


title: CS1AN_VA UV_30 min Cytoplasm


title: Set A: saline 1

source_name: heart

value: whole heart

value: postnatal day 14

value: saline

value: A


title: CTX_Het_Female_07 [RNA-Seq]


title: D3839 EBd7 CD71+ R1 Capture sample 3 (CTCFDKO_A82_Enhancers)

source_name: Chromatin from purified CD71+ erythroid cells derived from differentiated D3839 mES cells, alpha globin enhancer sequence R1 as Capture point, sample 3

value: E14TG2a.IV mES derived Erythroid cells

value: Alpha Globin Locus


title: D3839 EBd7 CD71+ R1 Capture sample 2 (CTCFDKO_A81_Enhancers)

source_name: Chromatin from purified CD71+ erythroid cells derived from differentiated D3839 mES cells, alpha globin enhancer sequence R1 as Capture point, sample 2


title: Cluster2 Adult1 Positive Interval1

value: Positive

value: POS interval 1


title: CS1AN_VA no UV Chromatin

value: skin fibroblast cells derived from Cockayne syndrome patient

value: untreated


title: CS1AN_VA no UV Cytoplasm


title: D3839 EBd7 CD71+ R1 Capture sample 1 (CTCFDKO_A3_Enhancers)

source_name: Chromatin from purified CD71+ erythroid cells derived from differentiated D3839 mES cells, alpha globin enhancer sequence R1 as Capture point, sample 1


title: Cluster1 Child4 Negative Visit5

value: Negative

value: Negative visit 5


title: CTX_Het_Male_07 [RNA-Seq]


title: WT EBd7 CD71+ Rhbdf1 and Mpg Captures  sample 3 (WT_EB11_5Promoters)

source_name: Chromatin from purified CD71+ erythroid cells derived from differentiated WT mES cells, Rhbdf1 and Mpg promoters as Capture point, sample 3


title: MRC5_VA UV_24 h Chromatin (re-analysis)

source_name: Lung fibroblast cells

value: normal lung tissue-derived fibroblast cells

value: treated with 10 J/m2 UV-C irradiation and recovered for 24 hours


title: CTX_Hom_Female_09 [RNA-Seq]

value: Hom

value: f


title: CTX_WT_Female_06 [RNA-Seq]

value: WT


title: Cluster1 Child4 Negative Visit3

value: whole blood

value: Negative visit 3


title: WT EBd7 CD71+ Rhbdf1 and Mpg Captures  sample 2 (WT_EB9_5Promoters)

source_name: Chromatin from purified CD71+ erythroid cells derived from differentiated WT mES cells, Rhbdf1 and Mpg promoters as Capture point, sample 2


title: MRC5_VA UV_3 h Chromatin (re-analysis)

value: treated with 10 J/m2 UV-C irradiation and recovered for 3 hours


title: Cluster1 Child4 Negative Visit1

value: Negative visit 1


title: CTX_Hom_Male_02 [RNA-Seq]

value: m


title: MRC5_VA UV_24 h Cytoplasm (re-analysis)


title: CTX_WT_Female_05 [RNA-Seq]


title: Cluster1 Child3 Positive Interval5

value: POS interval 5


title: Cluster1 Child3 Positive Interval4

value: Positive

value: POS interval 4


title: CTX_WT_Male_03 [RNA-Seq]


title: WT EBd7 CD71+ Rhbdf1 and Mpg Captures  sample 1(WT_EB8_5Promoters)

source_name: Chromatin from purified CD71+ erythroid cells derived from differentiated WT mES cells, Rhbdf1 and Mpg promoters as Capture point, sample 1

value: E14TG2a.IV mES derived Erythroid cells

value: Alpha Globin Locus


title: CTX_Hom_Female_04 [RNA-Seq]


title: MRC5_VA UV_3 h Cytoplasm (re-analysis)


title: Cluster1 Child3 Positive Interval3

value: POS interval 3


title: MRC5_VA UV_30 min Chromatin (re-analysis)

value: treated with 10 J/m2 UV-C irradiation and recovered for 30 minutes


title: CTX_WT_Female_12 [RNA-Seq]


title: Cluster1 Child3 Positive Interval2

value: POS interval 2


title: CTX_Het_Female_02 [RNA-Seq]

value: Het


title: ATAC-Seq muscle_SM-C1MKW

city: San Diego

first: Bing

last: Ren

address: 9500 Gilman Dr

institute: University of California San Diego

data_processing:
For each sequenced single nucleus ATAC-Seq library, we obtained four FASTQ files, two for paired end DNA reads and two for the combinatorial indexes for i5 and T7 (768 and 364 indices, respectively). We selected all reads with up to 2 mismatches per i5 and T7 index (Hamming distance between each pair of indices is 4) and integrated the concatenated barcode at the beginning of the read name in the demultiplexed FASTQ files.
snATAC-seq reads were aligned to the GRCh38 genome assembly using BWA version 0.7.17-r1188 with the following parameters: "mem -M -k 32 -t 8".
Aligned reads were name sorted and filtered using Samtools version 1.9 with the following parameters: "-f 2 -F 0x70c -q 30".
Duplicated paired-end fragments were removed for each nucleic and nucleic were filtered based on stringent quality control criteria including an enrichment of reads at transcription start sites (TSS enrichment; TSSe) greater than 7-fold, and a minimum of > 1,000 mapped paired-end fragments per nucleus.
Nuclei were further filtered for potential doublets using a version of Scrublet modified for single cell ATAC-seq.
For each sample, we generated a cell by bin (5kb) count matrix and used it for the initial clustering analysis.
Nuclei from all samples were pooled and subjected to clustering analysis using the Taiji pipeline (https://taiji-pipeline.github.io/).
Genome_build: GRCh38
Supplementary_files_format_and_content: bigwig files were generated using bedGraphToBigWig. Score represents RPKM.
Supplementary_files_format_and_content: Fragment files were generated using the Taiji pipeline (https://taiji-pipeline.github.io/). Column 1: chromosome; Column 2: adjusted start position; Column 3: adjusted end position. Column 4: cell barcode; Column 5: the total number of read pairs associated with this fragment (including unique and all duplicate read pairs).
Supplementary_files_format_and_content: metadata.tsv.gz: tab-delimited text files containing final clustering result and metadata of nucleic from all samples

source_name: gastrocnemius muscle

extract_protocol:
Nuclei were extracted from flash frozen tissue either by manual pulverization via mortar and pestle while submerged in liquid nitrogen, or homogenization in a gentleMACS M-tube (Miltenyi) on a gentleMACS Octo Dissociator (Miltenyi) using the “Protein_01_01” protocol in MACS buffer (5 mM CaCl2, 2 mM EDTA, 1X protease inhibitor (Roche, 05-892-970-001), 300 mM MgAc, 10 mM Tris-HCL pH 8, 0.6 mM DTT) and pelleted with a swinging bucket centrifuge (500 x g, 5 min, 4°C; 5920R, Eppendorf).
Extracted nuclei were permeabilized either in 1 mL Nuclear Permeabilization Buffer (1X PBS, 5% Bovine Serum Albumin, 0.2% IGEPAL CA-630 (Sigma), 1 mM DTT, 1X Protease inhibitor), or 1 mL OMNI Buffer (10mM Tris-HCL (pH 7.5), 10mM NaCl, 3mM MgCl2, 0.1% Tween-20 (Sigma), 0.1% IGEPAL-CA630 (Sigma) and 0.01% Digitonin (Promega) in water). After resuspension in permeabilization buffer, nuclei were rotated at 4 ˚C for 5 minutes before being pelleted with a swinging bucket centrifuge (500 x g, 5 min, 4°C; 5920R, Eppendorf). After centrifugation, permeabilized nuclei were resuspended in 500 μL high salt tagmentation buffer (36.3 mM Tris-acetate (pH = 7.8), 72.6 mM potassium-acetate, 11 mM Mg-acetate, 17.6% DMF) and counted using a hemocytometer. Concentration was adjusted to 2,000 nuclei/9 μl, and 2,000 nuclei were dispensed into each well of a 96-well plate per sample (96 tagmentation wells/sample, samples were processed in batches of 2-4 samples). For tagmentation, 1 μL barcoded Tn5 transposomes were added using a BenchSmart™ 96 (Mettler Toledo), mixed five times, and incubated for 60 min at 37 °C with shaking (500 rpm). To inhibit the Tn5 reaction, 10 µL of 40 mM EDTA (final 20mM) were added to each well with a BenchSmart™ 96 (Mettler Toledo) and the plate was incubated at 37 °C for 15 min with shaking (500 rpm). Next, 20 µL of 2x sort buffer (2 % BSA, 2 mM EDTA in PBS) were added using a BenchSmart™ 96 (Mettler Toledo). All wells were combined into a separate FACS tube for each sample, and stained with Draq7 at 1:150 dilution (Cell Signaling). Using a SH800 (Sony), 20 nuclei per sample were sorted per well into eight 96-well plates (total of 768 wells) containing 10.5 µL EB (25 pmol primer i7, 25 pmol primer i5, 200 ng BSA (Sigma)). Preparation of sort plates and all downstream pipetting steps were performed on a Biomek i7 Automated Workstation (Beckman Coulter). After addition of 1 µL 0.2% SDS, samples were incubated at 55 °C for 7 min with shaking (500 rpm). 1 µL 12.5% Triton-X was added to each well to quench the SDS. Next, 12.5 µL NEBNext High-Fidelity 2× PCR Master Mix (NEB) were added and samples were PCR-amplified (72 °C 5 min, 98 °C 30 s, (98 °C 10 s, 63 °C 30 s, 72°C 60 s) × 12 cycles, held at 12 °C). After PCR, all wells were combined. Libraries were purified according to the MinElute PCR Purification Kit manual (Qiagen) using a vacuum manifold (QIAvac 24 plus, Qiagen) and size selection was performed with SPRISelect reagent (Beckmann Coulter, 0.55x and 1.5x). Libraries were purified one more time with SPRISelect reagent (Beckman Coulter, 1.5x). Libraries were quantified using a Qubit fluorimeter (Life technologies) and a nucleosomal pattern of fragment size distribution was verified using a Tapestation (High Sensitivity D1000, Agilent). Libraries were sequenced on a NextSeq500 or HiSeq4000 sequencer (Illumina) using custom sequencing primers with following read lengths: 50 + 10 + 12 + 50 (Read1 + Index1 + Index2 + Read2).
OTHER: single cell ATAC-seq

tag: sample type

value: normal

tag: biosample

value: flash-frozen tissue

tag: donor age (years)

tag: donor sex

value: male

tag: race

value: white

tag: case of death

value: anoxia


title: MRC5_VA UV_30 min Cytoplasm (re-analysis)

tag: cell line

value: normal lung tissue-derived fibroblast cells


title: Cluster1 Child3 Positive Interval1

value: whole blood

tag: sars-cov-2 infection

tag: age (years)

tag: time point

value: POS interval 1


title: MRC5_VA no UV Chromatin (re-analysis)

value: untreated


title: CTX_Het_Male_11 [RNA-Seq]

value: m


title: Cluster1 Child2 Positive Interval5

value: Positive

value: POS interval 5


title: CTX_Het_Female_10 [RNA-Seq]

value: f


title: MRC5_VA no UV Cytoplasm (re-analysis)


title: PVC_WT

city: Suwon

first: Jae-Il

last: Choi

address: 164, World cup-ro, Yeongtong-gu

department: Pathology

country: South Korea

institute: Ajou University School of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to mm9 whole genome using Tophat-2.0.9 with parameters --bowtie1 --segment-length 21
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated by Cufflinks with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: Perivascular cell

growth_protocol: WT or Kai1 KO PVCs were grown in DMEM containing 10% FBS.

extract_protocol:
RNA was extracted from TRIZOL (Invitrogen) or RNeasy RNA isolation kit (Qiagen).
Sequencing libraries were manually generated for high-throughput sequencing. Either end of DNA strands was filled using the Epicentre DNA END-Repair kit (Epicentre Biotechnologies, Madison, WI). Adenine was added at 3’ ends by Taq DNA polymerase (New England Biolabs, Beverly, MA) under dATP conditions. Illumina’s adaptor oligomers was ligated at both ends using Quick Ligation kit (Qiagen). After purified twice, DNA libraries are amplified using Solexa primers (Illumina, San Diego, CA) and Pusion PCR master mix (Thermo Scientific, Hudson, NH).

tag: strain background

tag: genotype/variation

value: wild type

value: Aorta

value: Perivascular cell (PVC)


title: Vso

city: Tomsk

first: Sofia

middle: Yuryevna

last: Zolotaryova

address: pereulok Kooperativny, 5

country: Russia

institute: Cancer Research Institute Tomsk NRMS

data_processing:
Raw reads were aligned using STAR v. 2.7.3a
The number of mapped reads was counted by the featureCounts tool
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Breast

extract_protocol:
7 µm sections of fresh frozen tumor tissue were stained according to the protocol preserving RNA, the microenvironment of morphological structures was isolated using laser caption microdissection. RNA was extracted from the microdissected samples using Single Cell RNA Purification Kit (Norgen, Thorold, ON, Canada). RNA samples were immediately used to generate cDNA libraries using SMARTer Stranded Total RNA-Seq Kit v2 — Pico Input Mammalian (Takara, Mountain View, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: breast

tag: patient code

value: V

tag: morphological structure

value: solid


title: Vtr

value: trabecular


title: NCI-H660_YAP1_OE_3

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

data_processing:
Sequencing reads were mapped to the hg38 human genome using STAR.v2.7.3a.
Gene level abundance was quantitated from the filtered human alignments in R using the Genomic Alignments Bioconductor package using the summarizeOverlaps function with mode=IntersectionStrict, counting reads mapping to the exonic regions of genes.
Genome_build: hg38
Supplementary_files_format_and_content: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

source_name: NCI-H660 with YAP1 overexpression human prostate tumor cell line

extract_protocol:
Total RNA from cell lines/cell pellets in triplicate replicates was extracted using RNeasy kit (Qiagen), following the manufacturer instructions.
RNA sequencing of triplicate cell line replicates was performed at Novogene. In brief, messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by second strand cDNA synthesis using dUTP.

tag: gender

value: male

value: prostate cancer

value: LNCaP (ATCC CRL-5813)

value: YAP1 overexpression

tag: cell culture media

value: cells were maintained in HITES medium (RPMI 1640, supplemented with insulin, transferrin, beta-estradiol, hydrocortisone and sodium selenite).


title: Cluster1 Child2 Positive Interval4

source_name: whole blood

tag: tissue

value: whole blood

value: POS interval 4


title: Vdc

value: single tumor cells


title: Cluster1 Child2 Positive Interval3

value: Positive

value: POS interval 3


title: Adult_PFC_Het_Male_09 [RNA-Seq]

source_name: Prefrontal Cortex

tag: genotype

value: Het

tag: Sex

value: m


title: CTX_Hom_Female_01 [RNA-Seq]

value: Hom

value: f


title: Val

value: breast

value: V

value: alveolar


title: NCI-H660_YAP1_OE_1

value: male

tag: cell type


title: Adult_PFC_Het_Female_07 [RNA-Seq]


title: Cluster1 Child2 Positive Interval2

value: POS interval 2


title: ATAC-Seq colon_transverse_SM-CSSDA

source_name: transverse colon

tag: sample type

value: normal

tag: biosample

value: flash-frozen tissue

tag: donor age (years)

tag: donor sex

value: white

value: anoxia


title: NCI-H660_Control_3

source_name: NCI-H660 human prostate tumor cell line

value: prostate cancer

tag: cell line

value: LNCaP (ATCC CRL-5813)

value: cells were maintained in HITES medium (RPMI 1640, supplemented with insulin, transferrin, beta-estradiol, hydrocortisone and sodium selenite).


title: Trtr

value: Tr

value: trabecular


title: Cluster1 Child2 Positive Interval1

value: whole blood

tag: sars-cov-2 infection

value: Positive

tag: age (years)

value: POS interval 1


title: Trsol

value: breast

value: solid


title: NCI-H660_Control_2


title: Adult_PFC_WT_Female_06 [RNA-Seq]

value: WT

value: f


title: Trdc

value: single tumor cells


title: Adult_PFC_Het_Female_04 [RNA-Seq]

value: Het


title: Cluster1 Child1 Positive Interval4

tag: time point

value: POS interval 4


title: Cluster1 Child1 Positive Interval5

value: POS interval 5


title: NCI-H660_Control_1

value: male


title: Cluster1 Child1 Positive Interval3

value: POS interval 3


title: Adult_PFC_WT_Male_11 [RNA-Seq]

value: m


title: Str

value: S


title: Tral

value: Tr

value: alveolar


title: Adult_PFC_Het_Female_02 [RNA-Seq]


title: Cluster1 Child1 Positive Interval1

value: whole blood


title: DU145_YAP1_KD_clone2_3

source_name: DU145 with YAP1 knockdown clone 2 human prostate tumor cell line

value: prostate cancer

value: LNCaP (ATCC HTB-81)

tag: genotype/variation

value: YAP1 knockdown clone 2

value: cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin.


title: DU145_YAP1_KD_clone2_1


title: NCI-H660_YAP1_OE_2

value: LNCaP (ATCC CRL-5813)

value: YAP1 overexpression

value: cells were maintained in HITES medium (RPMI 1640, supplemented with insulin, transferrin, beta-estradiol, hydrocortisone and sodium selenite).


title: Adult_PFC_WT_Female_10 [RNA-Seq]

value: WT

value: f


title: Adult_PFC_Het_Male_08 [RNA-Seq]

value: Het


title: Cluster1 Child1 Positive Interval2

value: Positive

value: POS interval 2


title: Smtr

value: breast

tag: patient code

value: Sm

value: trabecular


title: DU145_YAP1_KD_clone1_3

source_name: DU145 with YAP1 knockdown clone 1 human prostate tumor cell line

value: male

value: YAP1 knockdown clone 1


title: Smdc

tag: morphological structure

value: single tumor cells


title: Sso

value: S

value: solid


title: DU145_YAP1_KD_clone1_1

tag: gender

value: prostate cancer

value: LNCaP (ATCC HTB-81)

value: cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin.


title: DU145_YAP1_KD_clone1_2

tag: cell culture media


title: DU145_Control_3

source_name: DU145 human prostate tumor cell line


title: Smsol

tag: tissue


title: Adult_PFC_WT_Male_07 [RNA-Seq]

tag: genotype

value: m


title: Adult_PFC_WT_Male_03 [RNA-Seq]

value: WT

tag: Sex


title: PVC_Kai1 KO

tag: strain background

value: Kai1 KO

value: Aorta

tag: cell type

value: Perivascular cell (PVC)


title: Cluster1 Adult2 Negative Visit3

value: whole blood

value: Negative

value: Negative visit 3


title: CTX_HOM_Litter2_65 [ATAC-Seq]

source_name: Cortex

value: Hom

tag: litter


title: DU145_YAP1_KD_clone2_2

value: male

value: YAP1 knockdown clone 2


title: CTX_HET_Litter2_64 [ATAC-Seq]

value: Het


title: Adult_PFC_Het_Male_05 [RNA-Seq]


title: LNCaP_YAP1_KD_clone2_3

source_name: LNCaP with YAP1 knockdown clone 2 human prostate tumor cell line

value: LNCaP (ATCC CRL-1740)


title: Smal

value: breast

value: Sm

value: alveolar


title: Mtr

value: M

value: trabecular


title: Adult_PFC_WT_Female_04 [RNA-Seq]

value: WT

value: f


title: CTX_HOM_Litter1_61 [ATAC-Seq]


title: Cluster1 Adult1 Positive Interval2

value: Positive

value: POS interval 2


title: Cluster1 Adult2 Negative Visit1

value: whole blood

value: Negative visit 1


title: Cluster1 Adult1 Positive Interval5

value: POS interval 5


title: Mdc

value: single tumor cells


title: Cluster1 Adult1 Positive Interval1

value: POS interval 1


title: Cluster1 Adult2 Negative Visit5

value: Negative

value: Negative visit 5


title: Cluster1 Adult2 Negative Visit2

value: Negative visit 2


title: Sal

value: breast

value: S


title: Cluster1 Adult1 Positive Interval4

value: POS interval 4


title: Cluster1 Adult1 Positive Interval3

value: POS interval 3


title: DU145_Control_2

value: male

value: prostate cancer

value: LNCaP (ATCC HTB-81)

value: cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin.


title: Adult9 Positive Interval5

value: Positive


title: LNCaP_YAP1_KD_clone2_2

value: LNCaP (ATCC CRL-1740)

value: YAP1 knockdown clone 2


title: Mso

value: M

value: solid


title: CTX_HOM_Litter1_54 [ATAC-Seq]

value: Hom


title: Sdc

value: single tumor cells


title: DU145_Control_1


title: CTX_WT_Litter1_46 [ATAC-Seq]

value: WT


title: LNCaP_YAP1_KD_clone1_2

source_name: LNCaP with YAP1 knockdown clone 1 human prostate tumor cell line

value: YAP1 knockdown clone 1


title: Dso

value: breast

value: D


title: Adult9 Positive Interval4

value: whole blood

value: POS interval 4


title: CTX_HET_Litter2_49 [ATAC-Seq]

value: Het


title: LNCaP_YAP1_KD_clone1_3

value: male

value: prostate cancer


title: Dtr

value: trabecular


title: Adult9 Positive Interval3

value: Positive

value: POS interval 3


title: CTX_WT_Litter1_57 [ATAC-Seq]


title: LNCaP_YAP1_KD_clone2_1

value: LNCaP (ATCC CRL-1740)

value: YAP1 knockdown clone 2

value: cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin.


title: Doktr

value: Dok


title: LNCaP_Control_3

source_name: LNCaP human prostate tumor cell line


title: LNCaP_YAP1_KD_clone1_1


title: CTX_WT_Litter1_43 [ATAC-Seq]


title: Mal

value: M

value: alveolar


title: Doksol

value: solid


title: LNCaP_Control_2


title: CTX_HET_Litter1_34 [ATAC-Seq]


title: Adult8 Positive Interval3


title: Adult9 Positive Interval1

value: POS interval 1


title: LNCaP_Control_1


title: CTX_HET_Litter1_27 [ATAC-Seq]


title: Dokal

value: breast


title: Dokdc

value: single tumor cells


title: Ddc

value: D


title: Adult8 Positive Interval1

value: whole blood


title: MV4-11_AC220_rep3

city: Gainesville

first: Petr

last: Starostik

state: Florida

institute: University of Florida

description: MV4-11 cells were treated with AC220 for 24 hours_rep3

data_processing:
Reads were aligned to human genome (UCSC hg19) using RNA-Seq aligner STAR (version 2.4.0) .
DESeq2 (version 1.1.0) was used to identify differentially expressed genes after filtering out genes with low reads, resulting in average 35 M reads per sample. Genes with adjusted P value < 0.05 and |log2 (fold change)|≥ 1 were considered as having a significantly altered expression.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: csv files showing the compared gene expression

source_name: peripheral blood

growth_protocol: All cells were cultured in RPMI media supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin maintained at 5% CO2 and 37°C. Cells were expanded and frozen at low passage number and were passaged <20 times before thawing a fresh vial.

extract_protocol:
RNA was isolated using miRNeasy Mini Kit (Qiagen) with genomic DNA depletion
NEBNext® Poly (A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® were used for library preparation.   RNA-Seq 150bp paired-end libraries were sequenced on NextSeq 500 or NovaSeq6000 (Illumina, San Diego, CA).

treatment_protocol: Both MOLM14 and MV4-11 cells were treated with DMSO, 2 nM gilteritinib, 2 nM crenolanib or 2 nM AC220 for 24 hours. The RNA-seq experiments were performed triplicates.

value: acute myeloid leukemia cell line

value: hemizygous FLT3-ITD mutation

tag: treatment

value: AC220 for 24 hours


title: Adult8 Positive Interval2

value: Positive

value: POS interval 2


title: Dal


title: Adult17 Negative Visit5

value: Negative

value: Negative visit 5


title: CTX_HOM_Litter1_40 [ATAC-Seq]

value: Hom


title: Chtr

value: Ch

value: trabecular


title: Adult17 Negative Visit3

value: Negative visit 3


title: MV4-11_Crenolanib_rep3

description: MV4-11 cells were treated with crenolanib for 24 hours_rep3

value: crenolanib for 24 hours


title: Adult9 Positive Interval2


title: MV4-11_AC220_rep2

description: MV4-11 cells were treated with AC220 for 24 hours_rep2


title: CTX_HOM_Litter1_20 [ATAC-Seq]


title: MV4-11_DMSO_rep3

description: MV4-11 cells were treated with DMSO for 24 hours_rep3

value: DMSO for 24 hours


title: Chdc

value: breast


title: Chsol

value: solid


title: Adult17 Negative Visit2

value: Negative visit 2


title: CTX_WT_Litter1_10 [ATAC-Seq]

value: WT


title: CTX_HET_Litter1_31 [ATAC-Seq]

value: Het


title: MV4-11_Crenolanib_rep2

description: MV4-11 cells were treated with crenolanib for 24 hours_rep2

value: acute myeloid leukemia cell line

value: hemizygous FLT3-ITD mutation


title: CTX_HOM_Litter2_06 [ATAC-Seq]


title: Adult17 Negative Visit1

value: whole blood

value: Negative visit 1


title: Chal

value: alveolar


title: Adult15 Positive Interval5

value: Positive

value: POS interval 5


title: CTX_WT_Litter2_25 [ATAC-Seq]


title: MV4-11_Gilteritinib_rep2

description: MV4-11 cells were treated with gilteritinib for 24 hours_rep2

value: gilteritinib for 24 hours


title: Adult15 Positive Interval4

value: POS interval 4


title: Adult_PFC_WT_Male_62 [ATAC-Seq]

value: m


title: MV4-11_Gilteritinib_rep3

description: MV4-11 cells were treated with gilteritinib for 24 hours_rep3


title: MV4-11_DMSO_rep2

description: MV4-11 cells were treated with DMSO for 24 hours_rep2


title: antimir324_4

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

description: Human adipocytes RNA-seq by Illumina NextSeq500

data_processing:
The gene count table was generated by aligning reads to the human transcriptome (Ensembl version 94) using kallisto and converting transcript counts to gene counts using tximport.
Genome_build: Ensembl version 94
Supplementary_files_format_and_content: count table

source_name: adipocytes

extract_protocol:
Total RNA was isolated by using TRIzol.
The mRNA was captured using oligo-dT beads as part of the KAPA mRNA HyperPrep workflow. cDNA synthesis, adapter ligation, and amplification were conducted subsequently as part of the same workflow. Following amplification, residual primers were eluted away using KAPA Pure Beads in a 0.63× SPRI-based cleanup.

tag: group

tag: donor

value: adipocytes


title: antimir324_3


title: CTX_WT_Litter2_13 [ATAC-Seq]


title: MOLM14_AC220_rep3

description: MOLM14 cells were treated with AC220 for 24 hours_rep3

tag: cell line

value: heterozygous FLT3-ITD mutation

value: AC220 for 24 hours


title: Adult15 Positive Interval2

tag: sars-cov-2 infection

tag: age (years)

value: POS interval 2


title: Adult_PFC_WT_Female_58 [ATAC-Seq]

value: f


title: Adult_PFC_Het_Female_50 [ATAC-Seq]


title: antimir324_1


title: antimir324_2


title: Adult15 Positive Interval1

tag: time point

value: POS interval 1


title: MOLM14_Crenolanib_rep3

description: MOLM14 cells were treated with crenolanib for 24 hours_rep3

value: crenolanib for 24 hours


title: MOLM14_Gilteritinib_rep3

description: MOLM14 cells were treated with gilteritinib for 24 hours_rep3

value: acute myeloid leukemia cell line


title: Adult_PFC_Het_Male_47 [ATAC-Seq]

value: Het


title: Adult13 Positive Interval4

value: whole blood


title: Adult13 Positive Interval3

value: POS interval 3


title: Adult_PFC_Het_Female_44 [ATAC-Seq]


title: antimir186_4


title: MOLM14_DMSO_rep3

description: MOLM14 cells were treated with DMSO for 24 hours_rep3

value: DMSO for 24 hours


title: Adult_PFC_Het_Male_41 [ATAC-Seq]


title: antimir186_3


title: Adult_PFC_WT_Female_35 [ATAC-Seq]

value: WT


title: antimir186_2


title: HCT116-J3-siCoilin-1-RiboMethSeq

city: New Orleans

first: Tina

last: O'Grady

state: LA

address: 1430 Tulane Ave., SL79

institute: Tulane Health Sciences Center

data_processing:
Adapter sequences were removed using Trimmomatic (0.36; LEADING:30 TRAILING:30 SLIDINGWINDOW:4:15 MINLEN:17 AVGQUAL:30). Only reads shorter than 90 nt were used for the analysis based on the length distribution of reads after adapter trimming.
Reads in the forward direction were mapped to an artificial genome containing ribosomal RNA sequences using bowtie2 (2.3.3.1; sensitive).
Mapped reads were analysed using the ‘R’ package ‘RNAmodR.RiboMethSeq’ and the Score C/RiboMethScore was used as a measurement for 2’-O methylation
Genome_build: hg19
Supplementary_files_format_and_content: .ends.csv: number of protected ends
Supplementary_files_format_and_content: .score.csv: scores per position

growth_protocol: Cell were maintained in DMEM + 10% heat-inactivated FBS, at 37°C with 5% CO2

extract_protocol:
TRIzol
150 ng RNA was used to construct RiboMethSeq libraries using the procedure of Marchand et al. (PMID 27302133)
RiboMethSeq

treatment_protocol: Cells were mock-transfected or transfected with 40 nM of non-targeting siRNA, siCoilin #1 or siCoilin #2 and maintained for 1, 2 or 3 days before RNA extraction.

tag: day


title: HCT116-J3-siCtr-RiboMethSeq


title: Adult12 Positive Interval5

value: Positive

value: POS interval 5


title: Adult_PFC_WT_Male_28 [ATAC-Seq]


title: antimir186_1


title: HCT116-J3-mock-RiboMethSeq


title: Adult_PFC_Het_Female_21 [ATAC-Seq]


title: mir20a_4


title: Adult12 Positive Interval4

value: POS interval 4


title: mir20a_3


title: HCT116-J2-siCoilin-2-RiboMethSeq


title: Adult_PFC_Het_Male_11 [ATAC-Seq]

value: m


title: mir20a_1

value: adipocytes


title: Adult12 Positive Interval3


title: HCT116-J2-siCtr-RiboMethSeq


title: HCT116-J2-siCoilin-1-RiboMethSeq


title: Adult12 Positive Interval1


title: Adult_PFC_WT_Male_01 [ATAC-Seq]


title: Adult12 Positive Interval2


title: Adult13 Positive Interval2


title: HCT116-J2-mock-RiboMethSeq


title: HCT116-J3-SiCoilin-2-RiboMethSeq


title: Adult13 Positive Interval1


title: ctrl_4

value: ctrl


title: 4M K5VP16;Pparg Luminal Tumor rep3

city: New York

first: Cathy

last: Mendelsohn

state: NY

address: 1130 St. Nicholas Ave

department: Urology

institute: Columbia University

description: DESeq2_kallisto_CT111_CT113_CT115_vs_CT126_CT128_CT132_CT140_CT143_counts_table_normalized

data_processing:
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.20) for converting BCL to fastq format, coupled with adaptor trimming. We perform a pseudoalignment to a kallisto index created from transcriptomes (Human: GRCh38; Mouse: GRCm38) using kallisto (0.44.0). We test for differentially expressed genes under various conditions using Sleuth, an R package designed to compute transcript and gene-level differential expression from kallisto abundance files.
Differential expression analysis was performed byreading kallisto counts files into R using the R packages tximport (v.1.10.1) and biomaRt (v.2.34.2),and running DESeq2 (v.1.18) to generate log fold change values and p-values between the twoexperimental groups. The heatmap and PCA plots were visualized after transforming the countsusing VST (variance stabilizing transformation)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-deliminated text files include TPM values for each sample

source_name: Urothelium

extract_protocol:
5 month BBNK5VP16;Pparg and control bladders wereflash frozen sagitally in OCT and stored at-80°C. The specimen blocks were placed in the LeicaCM3050 cryostat chamber for 5-10min to temperature equilibrate. The tissue was sectioned at 5μm on Arcturus PEN Membrane glass slides (Applied Biosystems cat#LCM0522) and the slideswere immediately stored at-80°C. 1 hour prior to LCM, slides were removed from the-80°C andstained with Arcturus HistoGene Staining Solution (ThermoFisher Scientificcat#KIT0415)according to the manufacturer’s protocol. Tissue was then laser captured on a ZeissAxioObserver.Z1 inverted microscope into AdhesiveCap 200 opaque caps (Zeiss cat#000830-19).240μL of RLT Lysis Buffer (Qiagen cat#1015750) was then added to the capturedtissue
Cold active protease (CAP), was prepared and stored on ice (5mMCaCl2, Sigma cat#21115, 10mg/mL Bacillus Licheniformis protease, Sigma cat#P5459, 12.5U/mLDNAse, Sigma cat#4716728001). Mice were perfused with 20 mL of CAP using a small veininfusion set (Kawasumi cat#D3K2-23G) and two 10 mL syringes per mouse. Bladders weredissected and immediately put in a 60mm x 15mm petri dish (Fisherbrand cat#FB0875713A)containing CAP on ice for 10 min. The bladders were then transferred to HBSS media(ThermoFisher cat#14170-112) containing 1% Bovine Serum Albumin (Sigma cat#A2058) and0.1% glucose, where they were inverted and the urothelium was manually separated from thestroma. The cell suspension was then collected into a 1.5mL Eppendorf tube on ice and gentlytriturated until the cells were in a single cell suspension
The libraries were prepared using the SMART-Seq® v4Ultra® Low Input RNA Kit for Sequencing (TaKaRa) followed by Nextera XT (Illumina), bothaccording to manufacturer's instructions

treatment_protocol: N-butyl-N-(4-hydroxybutyl)-nitrosamine(BBN) (0.05%; Sigma cat#B8061  -1G) was administered in the water supply daily  for 3.5–24 weeks to induce bladder cancer. Mice were euthanized at 3.5 or 24 weeks

value: 5M BBN

tag: disease state

value: Cancer


title: Adult11 Positive Interval5


title: Adult11 Positive Interval3


title: ctrl_3


title: 4M K5VP16;Pparg Luminal Tumor rep2


title: HCT166-J1-siCoilin-2-RiboMethSeq


title: Adult11 Positive Interval2

value: POS interval 2


title: Adult_PFC_WT_Female_07 [ATAC-Seq]

value: f


title: ctrl_2


title: HCT116-J1-siCtr-RiboMethSeq


title: 4M K5VP16;Pparg Luminal Tumor Bottom rep2

description: DESeq2_kallisto_CT128_CT143_CT148_vs_CT129_CT144_CT149_counts_table_normalized


title: 4M K5VP16;Pparg Luminal Tumor rep1


title: 4M K5VP16;Pparg Luminal Tumor Bottom rep3


title: ctrl_1


title: Adult10 Positive Interval5


title: mir20a_2


title: 4M K5VP16;Pparg Luminal Tumor Bottom rep1


title: Adult10 Positive Interval4


title: P26_iPSC_ATAC_rep2

city: London

first: Marco

last: Trizzino

state: UK

address: Imperial College Road

department: Life Sciences

institute: Imperial College London

data_processing:
ChIP-seq and ATAC-seq data were aligned to hg19 using BWA-mem
ATAC-seq and CHIP-seq peaks were called with MACS2
For input bigwig was made with Deeptools
Genome_build: Hg19
Supplementary_files_format_and_content: peak text files (ChIP-seq, ATAC-seq), Bigwig for input of Chip-seq

growth_protocol: The iPSC lines were expanded in feeder-free, serum-free mTeSR™1 medium (STEMCELL Technologies). Cells were passaged ~1:10 at 80% confluency using ReLeSR (STEMCELL Technologies) and small cell clusters (50–200 cells) were subsequently plated on tissue culture dishes coated overnight with Geltrex™ LDEV-Free hESC-qualified Reduced Growth Factor Basement Membrane Matrix (Fisher-Scientific).

extract_protocol:
RNA-seq Cells were lysed in Tri-reagent (Zymo research) and total RNA was extracted using Quick-RNA Miniprep kit (Zymo research).
RNA libraries were prepared using NEBNext® Poly(A) mRNA Magnetic Isolation Module, NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina® and NEBNext® UltraTM II DNA Library Prep Kit for Illumina® according to the manufacturer’s instructions (New England Biolabs). 1 μg of total RNA input was used for each library
ATAC-seq: 50000 cells per condition were processed as described in the original ATAC-seq protocol paper (Buenrostro et al 2013)
ChIP-seq: Barcoded libraries were made with NEB ULTRA II DNA Library Prep Kit for Illumina, and sequenced on Illumina NextSeq 500, producing 75bp SE reads.

treatment_protocol: Stem cells were differentiated in CNCC using a previously published protocol (Prescot et al.2015). iPSCs were treated with CNCC Derivation media: 1:1 Neurobasal medium/D-MEM F-12 medium,B-27 supplement, N-2 supplement, 20 ng/ml bFGF, 20 ng/ml EGF, 5 µg/ml bovine insulin and 1× Glutamax-I supplement. Three days after the appearance of the migratory CNCC, cells were detached using accutase and placed into geltrex-coated plates. The early migratory CNCCs were then transitioned to CNCC early maintenance media: 1:1 Neurobasal medium/D-MEM F-12 medium, B-27 supplement, N2 supplement , 20 ng/ml , 20 ng/ml EGF, 1 mg/ml bovine serum albumin and 1× Glutamax-I supplement


title: HCT116-J1-mock-RiboMethSeq


title: P26_iPSC_ATAC_rep1


title: Adult10 Positive Interval3


title: 4M K5VP16;Pparg Luminal Tumor Top rep3

description:
DESeq2_kallisto_CT111_CT113_CT115_vs_CT128_CT143_CT148_counts_table_normalized
DESeq2_kallisto_CT128_CT143_CT148_vs_CT129_CT144_CT149_counts_table_normalized