title: WD, replicate 3, scRNAseq

value: liver

value: patient with Wilson's disease

value: hepatic mesenchymal cells


title: BaselineCART_ATAC-seq Biorep1

status: Public on Aug 01 2024

type: SRA

city: Rochester

first: Saad

last: Kenderian

state: MN

address: 200 First Street SW

department: Hematology Research

country: USA

institute: Mayo Clinic

library_source: genomic

data_processing:
Quality check was performed first with FASTQC. Then, the Nextera adapter sequences were trimmed and a minimum length of 45 base-pairs was employed per ENCODE recommendations using Cutadapt. FASTQC was then re-run to ensure quality. Next, paired-end reads for each sample were aligned to the UCSC reference genome for human genome 38 (hg38), patch release 13 with Bowtie2. The resulting bam file was sorted with samtools and mitochondrial reads were removed with the BAMQC program. BigWig files were created from sorted BAM files using the bamCoverage function.
Assembly: UCSC reference genome for human genome 38 (hg38), patch release 13
Supplementary files format and content: BigWig files

molecule: genomic DNA

organism: Homo sapiens

source_name: T-cell

extract_protocol:
For all samples, 1x105 cells were washed in PBS and pelleted. The cell pellet was resuspended in 100μL freezing medium, composed of 10% dimethyl sulfoxide (Sigma, St. Louis, MO, USA) and 90% FBS (Sigma, St. Louis, MO, USA). Then, it was stored at -80°C prior to shipment to CD Genomics.
Nextera kit

treatment_protocol: CART19-28ζ cells from three biological replicates were collected before (baseline) or after chronic stimulation (exhausted) in our in vitro model for CART cell exhaustion. In this model, CART cells were chronically stimulated with JeKo-1 cells.

tag: tissue

value: T-cell

tag: treatment

value: Baseline


title: cardiomyocyte,sham, replicate2-53, scRNAseq

city: Bunkyo-ku

first: Manami

last: Katoh

state: Tokyo

address: 7-3-1 Hongo

department: Department of Cardiovascular Medicine

country: Japan

institute: The University of Tokyo

description:
smartseq2
sham_2.xlsx

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Mus musculus

source_name: heart

extract_protocol:
Cardiomyocytes and noncardiomyocyte were isolated using Langendorff perfusion from the left ventricular free wall. Enzymatic dissociation using Langendorff perfusion was performed with 37 °C pre-warmed 35 mL enzyme solution (collagenase Type II 1 mg/mL (Worthington), protease type XIV 0.05 mg/mL (Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, pH 7.4) at a rate of 3 mL/min. Enzymes were neutralized with fetal bovine serum (FBS) at a final concentration of 0.2%. Cell suspensions were filtered through a 100 μm nylon mesh cell strainer and centrifuged at 20 g for 3 min. The supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%, pH 7.4) containing a low concentration of calcium (0.5 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥70%) were collected immediately after isolation from two mice at each condition with a 0.2–2 μL pipette (sample volume, 0.5 μL) and incubated in lysis buffer.The supernatant was collected as non-cardiomyocytes and the cells were continued to lysis process according to the 10X protocol.
Sample 731-736,library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.  Other samples, single-cell cDNA libraries were generated using the Smart-seq2 protocol.  And the efficiency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad) and by examining the dis- tribution of the lengths of cDNA fragments using a LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward, TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse, TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold.

tag: cell type

value: cardiomyocyte

value: heart

tag: strain

tag: age

value: 6-8 weeks old

value: sham


title: T24si-SM-1

city: Guangzhou

first: Liang

last: Cheng

state: Guangdong

address: 107th Yanjiangxi Road

department: Department of Urology

country: China

institute: Sun Yat-sen Memorial Hospital

library_source: transcriptomic

data_processing:
Base-calling using bcl2fastq2 v2.19.1 with -r 4 -p 16 -w 4  --barcode-mismatches 0
Adaptor contamination was remove from reads (the number of bases contaminated by the adaptor in reads is greater than 5bp. For pair-end sequencing, if one end is contaminated by the adaptor, the Reads at both ends are removed)；Remove low-quality reads (Reads with more than 50% of the total bases are bases with a mass value of Q ≤ 19 . For pair-end sequencing, if one pair is low-quality reads, the both reads will be removed)；Remove the reads with N rate greater than 5%  (For pair-end sequencing, if one pair contains more than 5% N, the both reads will be removed)
Fastq reads were mapped to genome using hisat2 v2.1.0 with default parameters
Reads count of echo gene was calculated using htseq-count v0.6.1 with -t exon -f bam -s no -a 10
Assembly: hg19(ftp://ftp.ensembl.org/pub/grch37/current/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna.toplevel.fa.gz)
Supplementary files format and content: excel files include normalize values for each Sample

source_name: bladder

growth_protocol: T24 was cultured in RPMI-1640 (Gibco) and UM-UC-3 was cultured in DMEM (Gibco) supplemented with 10% FBS (Biological Industries) and 1% penicillin/streptomycin (Gibco). Cells were grown in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using Trizol reagent and was further purified using Qiagen RNeasy Mini Kit according to the manufactures’ instructions. The RNA quality was assessed by formaldehyde agarose gel electrophoresis and was quantitated spectrophotometrically.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 1 OD SiRNA was  diluted at a stocking solution of 125 μL in sterile DEPC-treated water, and cells were treated for 48h with 5 μL of SiRNA.

value: bladder

tag: cell line

value: bladder cancer cell

tag: genotype

value: SLC2A11-MIF knockdown


title: MoAM WT D2 rep2

city: Chicago

first: kishore

last: Anekalla

state: IL

address: 303 E. Superior

department: Pulmonary and Critical Care

institute: Northwestern University

data_processing:
Fpkm
Genome_build: mm10
Supplementary_files_format_and_content: Fpkm_counts_MoAMs_013019.xlsx

source_name: Lung

extract_protocol: Total RNA was isolated using RNeasy Plus Mini kits (Qiagen). Using poly(A) mRNA magnetic enrichment  kits from NEBNext (New England Biolabs), mRNA was isolated. cDNA libraries were prepared  using NEBNext Ultra DNA library kits (New England BioLabs) for Illumina. Libraries were  sequenced using high-output 75-cycle single-end kits on an Illumina NextSeq 500 sequencer

treatment_protocol: Mice were anesthetized using isoflurane and intratracheally (i.t.) infected with 200 pfu WSN

value: Monocyte derived alveolar macrophages

tag: agent

value: Influenza A virus

tag: time point

value: MoAM WT


title: cardiomyocyte,sham, replicate2-52, scRNAseq

description:
smartseq2
sham_2.xlsx


title: MoAM WT D3 rep3


title: Adipocytes, Day14, Rep3

city: Boston

first: Claire

last: Moore

state: MA

address: 150 Harrison Ave

institute: Tufts University

description:
normalized_abundance_DESeq2.csv
UTR_APA.xlsx
intronic_APA.xlsx

data_processing:
For differential gene expression and generation of normalized_abundance_DESeq2.csv file, raw R1 reads were trimmed using Cutadapt (v2.8) and aligned using STAR (2.6.1d) to Human hg38 genome. Aligned reads were then quantified using featurecounts (v1.6.3) and log2-fold changes were calculated using DESeq2 (1.40.2) using default parameters.
For alternative polyadenylation analysis and generation of UTR-APA and intronic_APA files, raw R2 reads were trimmed using Trim Galore (v0.6.10) and mapped to the human hg38 genome using bowtie2. The last aligned position (LAP) of each read was matched to annotated PASs in the polyA_DB database and these matched reads were used for further analysis. For UTR-APA analysis, two pA sites with the highest usage in the 3'-UTR were compared, and for intronic APA analysis, the intronic isoform with the highest expression was compared to isoform using pA sites in the terminal exon. A RED value (Relative Expression Difference) was calculated as difference in log2-ratio of isoform abundance (isoforms from use of distal pA sites vs those from proximal pA site) between preadipocytes and adipocytes.
Assembly: hg38
Supplementary files format and content: comma-separated values file includes normalized abundance measurements comparing gene expression for biological replicates at Day 0 versus at Day 14
Supplementary files format and content: Excel worksheet includes RED values representing polyA site usage in 3'-UTR of genes for biological replicates at Day 0 versus at Day 14
Supplementary files format and content: Excel worksheet includes RED values representing intronic polyA site usage in genes for biological replicates at Day 0 versus at Day 14
Supplementary files format and content: FASTQ files show quality of forward (R1) and reverse (R2) reads for each sample.

source_name: Human subcutaneous adipose tissue

growth_protocol: Undifferentiated preadipocytes were cultured using ZenBio’s Preadipocyte Medium (catalog number PM-1) and differentiated adipocytes were maintained in Adipocyte Maintenance medium  (catalog number AM-1) using Zen-Bio's protocol.

extract_protocol:
RNA was isolated by Zen-Bio using modified guanidine thiocyanate techniques
RNA libraries for RNA-seq were prepared using Quant-Seq FWD library kit following manufacturer's protocols

treatment_protocol: Preadipocytes were induced to differentiate using Adipocyte Differentiation medium (catalog number DM-2)

value: Human subcutaneous adipose tissue

value: Adipocytes

tag: time


title: MoAM WT D2 rep4


title: T24si-Ctrl

value: Negative control


title: Preadipocytes, Day0, Rep3

value: Pre-adipocytes


title: MUT, replicate1, scRNA

city: Bad Nauheim

first: Mario

last: Looso

address: Ludwigstrasse 43

country: Germany

institute: Max Planck Institute for Heart and Lung Research

description: 10x genomics

data_processing:
demultiplexing
star solo mapping: '--soloType CB_UMI_Simple --soloBarcodeReadLength 0 --soloCellFilter EmptyDrops_CR 5000 0.99 10 45000 90000 500 0.01 20000 0.01 10000'
Assembly: danio_rerio/101
Supplementary files format and content: 10x based mtx raw count matrix, barcodes and genes

organism: Danio rerio

source_name: whole embryo

value: whole embryo

value: hand2 reporter-expressing single cells

value: hand2 mutants


title: cardiomyocyte,sham, replicate2-51, scRNAseq

description:
smartseq2
sham_2.xlsx

value: cardiomyocyte


title: cardiomyocyte,sham, replicate2-50, scRNAseq

description:
smartseq2
sham_2.xlsx

value: heart


title: Adipocytes, Day14, Rep2


title: Preadipocytes, Day0, Rep2


title: D1-C16

city: Westmead

first: Nader

last: Aryamanesh

state: NSW

address: 214 Hawkesbury Rd

department: Bioinformatics

country: Australia

institute: CMRI

description: 10x Genomics

data_processing:
see Aryamanesh 2022, DOI: 10.1007/978-1-0716-2281-0_10
Assembly: hg38
Supplementary files format and content: cellranger output files

extract_protocol:
hiPSCs were dissociated using Accutase and counted to load 10,000 cells into on channel of a 10X Chromium chip. One channel per sample was used. After emulsion cell lysis and RNA was extracted followed by library preparation. Libraries were sent to Novogene for sequencing. Single cell suspensions were passed through 40μm cell strainer (Corning) and concentration was adjusted to 1000 cells/μL. Suspensions were loaded in single-cell-G Chip (10X Genomics) for target output of 10,000 cells per sample. Single-cell droplet capture was performed on the Chromium Controller (10X Genomics).
cDNA library preparation was performed in accordance with the Single-Cell 3’ v 3.0 or v3.1 protocol. Libraries were evaluated for fragment size and concentration using Agilent HSD5000 ScreenTape System (Agilent).

value: human induced pluripotent stem cells

value: WT

value: DE differentiation (STEMCELL Tech)


title: D4-C16

description: 10x Genomics


title: Mo17-SCMV-3

city: shenyang

first: jun

last: zhang

address: liaoning

institute: Shenyang 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 mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads 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.
Assembly:  ftp://ftp.ensemblgenomes.org/pub/release-45/plants/fasta/zea_mays/dna/
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Zea mays

source_name: leaves

growth_protocol: The maize (Zea mays L.) inbred lines Chang7-2 and Mo17 were grown in growth chambers (28 oC, 16 h day and 22 oC, 8 h night cycles).

extract_protocol:
Total RNA was isolated from mock and SCMV-infected 1SL of Chang7-2 and Mo17 using reagent.
For mRNA, lncRNA and circRNA, the Ribo-Zero™ rRNA Removal Kit (Illumina, San Diego, USA) was used to remove ribosomal RNA and construct the chain-specific library.For miRNA, the six small RNA library was prepared by TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, USA).

treatment_protocol: The crude extracts of maize leaves tissue infected with SCMV were prepared by mixing 0.01M phosphate buffer solution (0.01 M KH2PO4: 0.01 M Na2HPO4 = 49: 51 (V/V), pH 7.0) at a ratio of 1:10 (W/V).The crude extracts were inoculated on the second leaves of six-day-old Chang7-2 and Mo17 maize seedlings, and buffer-inoculated plants were used as control.

value: leaves

value: inbred line

value: No


title: Vector-SB-2

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

data_processing:
Paired-end 75 bp reads of bulk RNA-seq data were aligned to hg19 reference genome (ENSEMBL, version 67) using STAR alignment tool (version 2.7.3a) with default parameters.
Uniquely mapped reads were employed to quantify gene expression using RSEM software (version 1.3.1).2 Transcripts per million mapped reads (TPM) were calculated to estimate the gene expression levels, normalized for sequencing depth.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes TPM counts for each Sample

extract_protocol:
total RNA was purified from the HEK293 cell line using RNeasy RNA isolation Kit (Qiagen) coupled with an on-column DNase I digestion to eliminate residual DNA. The mRNA was purified from 2 μg of total RNA.
libraries for massive parallel sequencing were constructed with NEBNext® UltraTM RNA Library Prep Kit for Illumina (NEB). Library quality was assessed with Agilent Bioanalyzer 2100 system. Next-generation sequencing was performed on an Illumina HiSeq 4000 platform.

value: Vector-SB


title: T24si-SM-2

value: bladder

value: bladder cancer cell

value: SLC2A11-MIF knockdown


title: cardiomyocyte,sham, replicate2-49, scRNAseq

description:
smartseq2
sham_2.xlsx

value: 6-8 weeks old

value: sham


title: Adipocytes, Day14, Rep1

value: Human subcutaneous adipose tissue

value: Adipocytes


title: D0-C16

description: 10x Genomics


title: Mo17-SCMV-2


title: Mo17-SCMV-1


title: cardiomyocyte,sham, replicate2-48, scRNAseq

description:
smartseq2
sham_2.xlsx


title: Preadipocytes, Day0, Rep1

value: Pre-adipocytes


title: D4-C11

description: 10x Genomics


title: cardiomyocyte,sham, replicate2-47, scRNAseq

description:
smartseq2
sham_2.xlsx

value: cardiomyocyte


title: D1-C11

description: 10x Genomics


title: Chang7-2-SCMV-3


title: MCF7_WT_med

city: Leiden

first: Tom

last: van Wezel

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: Leiden University Medical Center

data_processing:
Quality control of the RNA-sequencing reads as well as adapter clipping, read alignment and gene expression quantification was done using the BIOWDL RNAseq pipeline v4.0.0 (https://doi.org/10.5281/zenodo.3975552).
Reads were aligned to the human reference genome (hg38 build) using STAR v2.7.5a, followed by gene expression quantification by htseq-count v0.12.4.
For expression quantification gencode v35 (corresponding to Ensembl 101) was used for gene annotation.
Assembly: human reference genome (hg38 build)
Supplementary files format and content: Tab-delimited text file containing the raw counts per sample

growth_protocol: Cells were cultured in DMEM (Gibco) or RPMI-1640 medium (Gibco), supplemented with 10% heat-inactivated fetal bovine serum (Sigma) and 50 units/ml penicillin-streptomycin (Gibco).

extract_protocol:
RNA was isolated with the Nucleospin RNA kit (Macherey-Nagel). cDNA conversion of mRNA was performed with AMV Reverse Transcriptase (Roche) and OdT primers.
RNA-sequencing library preparation was performed with TruSeq Stranded Total RNA with Ribo-Zero Gold

value: breast cancer cell line

value: medium


title: MCF7_BSL_med

value: BSL


title: cardiomyocyte,sham, replicate2-46, scRNAseq

description:
smartseq2
sham_2.xlsx

value: heart


title: D0-C11

description: 10x Genomics

value: human induced pluripotent stem cells

value: WT

value: DE differentiation (STEMCELL Tech)


title: Chang7-2-SCMV-2

value: leaves

value: inbred line

value: No


title: cardiomyocyte,sham, replicate2-45, scRNAseq

description:
smartseq2
sham_2.xlsx


title: WT, replicate 1, scRNA

description: 10x genomics

value: whole embryo

value: hand2 reporter-expressing single cells


title: cardiomyocyte,sham, replicate2-44, scRNAseq

description:
smartseq2
sham_2.xlsx

value: 6-8 weeks old

value: sham


title: HCT116_BSL_med

value: colorectal cancer cell line


title: Chang7-2-SCMV-1


title: C32_replicate C

data_processing:
see Aryamanesh 2022, DOI: 10.1007/978-1-0716-2281-0_10
Assembly: hg38
Supplementary files format and content: counts

extract_protocol:
hiPSC were collected at Day1 of the DE diff protocol (STEMDiff)
Library prep was performed by GENEWIZ (https://www.genewiz.com/Public/Services/Next-Generation-Sequencing)


title: C32_replicate B


title: HCT116_WT_med


title: C32_replicate A


title: Mo17-mock-2


title: Mo17-mock-3


title: C7_replicate C


title: cardiomyocyte,sham, replicate2-43, scRNAseq

description:
smartseq2
sham_2.xlsx


title: OCI-LY1 cells, Bendamustine+Rituximab2

first: Xiao

last: Ruipei

address: Guangzhou North Stress

institute: Southern Medical University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Hisat2 tools soft were used to map with reference genome.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Differential expression analysis of two conditions/groups was performed using the DESeq2.
Assembly: hg38
Supplementary files format and content: TXT files include FPKM values for each Sample

growth_protocol: RPMI medium supplemented with 10% FBS, 1% penicillin G/streptomycin, cells were cultured at 37°C at 5%CO2.

extract_protocol:
Total RNA of OCI-LY1 cells was prepared using RNAex Pro RNA Reagent(AG,AG21102) after treatment.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: OCI-LY1 cells were planted in 48-well culture plates at a concentration of 2x105 per well. B (Bendamustine) group was treated the same as control group for 1 day before exposed to 200uM Bendamustine for 1.5 days. R (Rituximab) group exposed to 10uM Rituximab for 2.5 days. BR (Bendamustine+Rituximab) group exposed to 10uM Rituximab for 1 days before exposed to 200uM Bendamustine and 10uM Rituximab for 1.5 days. The control group was grown in the same culture conditions for 2.5 days without the addition of any drugs.

value: Diffuse Large B-cell lymphoma cell

value: Bendamustine+Rituximab


title: cardiomyocyte,sham, replicate2-42, scRNAseq

description:
smartseq2
sham_2.xlsx

value: cardiomyocyte


title: Mo17-mock-1


title: C7_replicate B


title: OCI-LY1 cells, Bendamustine+Rituximab1


title: Chang7-2-mock-3


title: cardiomyocyte,sham, replicate2-41, scRNAseq

description:
smartseq2
sham_2.xlsx


title: cardiomyocyte,sham, replicate2-40, scRNAseq

description:
smartseq2
sham_2.xlsx


title: Chang7-2-mock-1


title: C9_replicate C


title: Chang7-2-mock-2


title: OCI-LY1 cells, Bendamustine2

value: Bendamustine


title: OCI-LY1 cells, Bendamustine3


title: cardiomyocyte,sham, replicate2-39, scRNAseq

description:
smartseq2
sham_2.xlsx


title: C7_replicate A


title: C9_replicate B


title: cardiomyocyte,sham, replicate2-38, scRNAseq

description:
smartseq2
sham_2.xlsx


title: Tradition replicate 3

city: Saskatoon

first: Peng

last: Gao

state: Saskatchewan

address: 107 Science Place

country: Canada

institute: Agriculture and Agri-Food Canada

data_processing:
Illumina Casava software used for basecalling.
Trimming the adaptor sequences, filtering low-quality reads  and eliminating short reads using Trimmomatic.
Filtered reads were mapped to IWGSC RefSeq v2.1 complete reference genome.
Reads quantification was performed by Salmon.
Normalized counts were obtained from R tximport and DESeq2 package.
Assembly: IWGSC RefSeq v2.1 complete wheat reference genome
Supplementary files format and content: Matrix table file includes normalized counts for each sample

organism: Triticum aestivum

source_name: flag leaf

growth_protocol: Four wheat varieties were grown in the field at the Llewellyn Farm, Agriculture and Agri-Food Canada (AAFC), Saskatoon, Saskatchewan from May to August 2021. The plots were seeded on May 21st, 2021 at 263 seeds/m2, with 5 rows spaced 0.18 m and 4.26 m long for a seeded area of 3.79 m2.

extract_protocol:
RNA was extracted from 0.1 g of each sample using a Qiagen RNeasy Mini Kit, and checked for quality using a Thermo Scientific NanoDrop™ One/OneC Microvolume UV-Vis Spectrophotometer.
Libraries were generated with the TruSeq UD V1.5 Kit following the instruction manual. Samples were loaded on the Illumina NovaSeq 6000 platform for pair-end sequencing with 150 cycles at the Omics and Precision Agriculture Laboratory.

treatment_protocol: On July 8th 2021, two fully expanded flag leaves were collected from the middle of each plot in 15 mL falcon tubes and placed in a dry ice container.

value: flag leaf

value: AAC Tradition

value: Control


title: C9_replicate A

value: human induced pluripotent stem cells

value: WT


title: OCI-LY1 cells, Rituximab3

value: Rituximab


title: cardiomyocyte,sham, replicate2-37, scRNAseq

description:
smartseq2
sham_2.xlsx

value: heart


title: OCI-LY1 cells, Bendamustine+Rituximab3


title: OCI-LY1 cells, Bendamustine1


title: Tradition replicate 2


title: cardiomyocyte,sham, replicate2-36, scRNAseq

description:
smartseq2
sham_2.xlsx


title: Tradition replicate 1


title: C11_replicate C

value: DE differentiation (STEMCELL Tech)


title: OCI-LY1 cells, Rituximab2


title: C11_replicate B


title: OCI-LY1 cells, Rituximab1


title: Starbuck replicate 3

value: AAC Starbuck


title: cardiomyocyte,sham, replicate2-33, scRNAseq

description:
smartseq2
sham_2.xlsx


title: OCI-LY1 cells, control3


title: cardiomyocyte,sham, replicate2-34, scRNAseq

description:
smartseq2
sham_2.xlsx


title: Starbuck replicate 2


title: C16_replicate C


title: OCI-LY1 cells, control1


title: C16_replicate B


title: cardiomyocyte,sham, replicate2-31, scRNAseq

description:
smartseq2
sham_2.xlsx


title: C16_replicate A


title: Magnet replicate 3

value: AAC Magnet


title: cardiomyocyte,sham, replicate2-32, scRNAseq

description:
smartseq2
sham_2.xlsx

value: 6-8 weeks old


title: OCI-LY1 cells, control2


title: Starbuck replicate 1


title: cardiomyocyte,sham, replicate2-29, scRNAseq

description:
smartseq2
sham_2.xlsx

value: sham


title: Magnet replicate 2


title: WNK2 deleted T/C-28a2 cells, Sorbitol, 04

city: Saltlake city

first: Michael

last: Jurynec

state: UT

institute: University of Utah

data_processing:
Raw data were analyzed for per base sequence quality (>30), per sequence GC content, adapter (universal Illumina adapter) removal using FASTQC v0.11.9.
The sequencing reads were mapped to the human reference genome (GRCh38 release 108 ) using HISAT2 v2.2.1 .
Aligned reads were counted using HTSeq v2.0.2, and the counts were then analyzed for differential gene expression using median-ratio-normalization with Deseq2 v1.38.3.
Assembly: hs39
Supplementary files format and content: tab-deliminated text file_including raw counts for each samples

growth_protocol: The human chondrocyte cell line, T/C-28A2 (MilliporeSigma, Burlington, MA), were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum , 4.5 g/L glucose, 1 mM sodium pyruvate, sodium pyruvate, and 100 U/mL penicillin/streptomycin in a 5% CO2 humidified atmosphere incubator at 37 °C.

extract_protocol:
After cell lysis, impurities removal, and inhibition of RNAse activity, total RNA was extracted by using the phase separation method from cell debris. Then Agilent bioanalyzer 2100 was used to check RNA integrity and concentration.
Sequencing libraries were generated using NEBNext® UltraTM RNALibrary Prep Kit for Illumina® (NEB, USA) following the manufacturer’s recommendations. mRNA is captured with the PolyA enrichment method.

treatment_protocol: We transfected T/C-28a2 cells with WNK2 and used sorbitol to alter the osmolarity of the media.

value: human chondrocyte cells

value: WNK2 knockout

value: Sorbitol


title: WNK2 deleted T/C-28a2 cells, Sorbitol, 03


title: WNK2 deleted T/C-28a2 cells, Sorbitol, 02


title: C16-MKO_repC

data_processing:
ATAC-seq reads were processed using the alignment and filtering functions of the PreNet pipeline53. Paired-end reads were mapped to the hg38 genome using bowtie2, allowing for local mapping, a maximum insert size of 2000 bp and a maximum of 4 multimapping hits (–local -X 2000 -k 4).
Multimapping reads were allocated using ’assignmultimappers.py’ from the ENCODE ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline/tree/master/src). Reads with MAPQ < 30 were excluded and only unique, paired reads that aligned outside blacklisted regions were used for subsequent analyses. Filtering steps were performed using samtools and sambamba.
Qualifying reads were then converted to pseudo-single end reads and peaks were detected using MACS2, with BED input files and reads shifted by -100 bp and extended to 200bp to capture Tn5 transposase events: -f BED –shift -100 –extend 200 -q 0.05. Biological replicates were analyzed individually and then consensus peak list was created to include only peaks appearing in at least two of the three replicates. Accessibility within a pooled consensus peak list was estimated by quantifying Tn5 events in each of the biological replicates using featureCounts.
The DESeq2 package within R was used to identify differentially accessible regions. The regions were filtered for adjusted P¬-value < 0.05 and an absolute Log2(Fold change) > 1. Coverage tracks were created using the bamCoverage function of deepTools (–normalization RPKM -bs 10) and visualized within Integrative Genomics Viewer.
62 findMotifsGenome.pl from HOMER was used to identify over enriched motifs, between 6 bp and 12 bp in size, within regions of differential accessibility using a repeat masked version of the hg38 sequence (-mask -len 6,7,8,9,10,11,12). Coverage tracks summarizing and combining biological replicates were created using WiggleTools to quantify the mean coverage per 10 bp bin. These tracks were used for heatmap visualizations created using plotHeatmap from deeptools.
Assembly: hg38
Supplementary files format and content: narrowPeak

extract_protocol:
hiPSC were collected at Day1 of the DE diff protocol (STEMDiff) and were processed following Salehin et al. 2020. Briefly, 5 x 104 cells were collected at Day 1 of DE differentiation and lysed in cold lysis buffer (10 mM Tris·Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) Igepal CA-630). Intact nuclei were separated by centrifugation at 500xg and immediately digested in transposase mix containing 25μl 2x Tagment DNA buffer, 2.5μl Tagment DNA enzyme I (Illumina) and 22.5μl nuclease-free water for 30min at 37°C. Digested chromatin fragments were then purified using the MinElute PCR Purification Kit (Qiagen), according to manufacturer’s instructions.
The fragments of DNA were then pre-amplified by adding 10μL purified DNA sample, 10μL RNase-free water, 2.5μL of each primer (Supplementary Table 3, where each reaction had non-barcoded primer "Ad1_noMix" and one barcoded primer ’Ad2.1’ - ’Ad2.9’ added) and 25μL NEBNext High-Fidelity 2x PCR Master Mix (NEB) and was run under the following conditions: 72°C for 5min, 98°C for 30secand then 5 cycles of 98°C for 10sec, 63°C for 30sec and 72°C for 1min. The number of additional cycles to run was calculated by running a RT-qPCR side reaction - a reaction mixture containing 5μL of the pre-amplified PCR product, 3.9μL nuclease-free water, 0.25μL of each primer, 0.6μl 25x SYBR Green and 5μL NEBNext High-Fidelity 2x PCR Master Mix was run under the following conditions: 98°C for 30secand then 20 cycles of 98°C for 10sec, 63°C for 30sec and 72°C for 1min. The linear fluorescence versus cycle number was plotted and the cycle number (N) required to reach one-third of the maximum relative fluorescence was determined. The final amplification reaction (the remaining 45μl pre-amplified PCR product) was run under the following conditions: 98°C for 30sec and then N cycles of 98°C for 10sec, 63°C for 30sec and 72°C for 1min. Amplified samples were then purified using AMPure XP magnetic beads (Beckman Coulter) to remove small fragments and primer-dimers less than 100 bp long (1.3x beads) and large fragments (0.5x beads) using a Dynamag-2 magnet (Thermo Fisher Scientific). To determine the integrity, fragment size and concentration, the DNA library was analyzed using the Agilent HSD5000 ScreenTape System (Agilent). Libraries were then 101 bp paired-end sequenced on an Illumina HiSeq 4000 (Illumina)


title: cardiomyocyte,sham, replicate2-35, scRNAseq

description:
smartseq2
sham_2.xlsx

value: cardiomyocyte


title: C16-MKO_repB


title: cardiomyocyte,sham, replicate2-30, scRNAseq

description:
smartseq2
sham_2.xlsx


title: Magnet replicate 1


title: Concord replicate 3

value: AAC Concord


title: cardiomyocyte,sham, replicate2-28, scRNAseq

description:
smartseq2
sham_2.xlsx


title: C11_replicate A


title: WNK2 deleted T/C-28a2 cells, Sorbitol, 01


title: C16-MKO_repA


title: WNK2 deleted T/C-28a2 cells, 04


title: Concord replicate 2

value: flag leaf


title: cardiomyocyte,sham, replicate2-26, scRNAseq

description:
smartseq2
sham_2.xlsx


title: C16_repC


title: WNK2 deleted T/C-28a2 cells, 03


title: cardiomyocyte,sham, replicate2-25, scRNAseq

description:
smartseq2
sham_2.xlsx


title: C16_repA


title: WNK2 deleted T/C-28a2 cells, 02


title: t9_mock_rep3

city: Haifa

first: Tamar

last: Lahav

address: Zor

department: Biology

country: Israel

institute: Technion

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using catadapt
Trimmed sequence reads were mapped to GRCh38 using STAR
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: First-trimester decidua

extract_protocol:
RNA was harvested using NucleoSpin RNA isolation kit (Macherey-Nagel).
RNA libraries for 3' RNA sequencing were prepared using the CEL-seq2 protocol

value: First-trimester decidua

value: Mock infected

tag: time post_infection

value: 24 hours

tag: donor #

tag: donor hcmv-serostatus

value: ask tamar hashimshony


title: cardiomyocyte,sham, replicate2-23, scRNAseq

description:
smartseq2
sham_2.xlsx


title: T/C-28a2 cells, WNK2 transfection +Sorbitol, 04

value: WT

value: WNK2 transfection +Sorbitol


title: cardiomyocyte,sham, replicate2-27, scRNAseq

description:
smartseq2
sham_2.xlsx

value: heart


title: cardiomyocyte,sham, replicate2-22, scRNAseq

description:
smartseq2
sham_2.xlsx


title: Test StwlEY_Replicate 2

city: Zurich

first: Madhav

last: Jagannathan

address: Otto Stern-Weg 3

country: Switzerland

institute: ETH Zurich

data_processing:
Raw reads (28.3 million reads per sample) were cleaned by adaptor sequence removal, low -quality end trimming and removal of low-quality reads using BBTools v38.18
More information on exact commands
Transcript abundances were quantified using Salmon v1.10.1 and BDGP6.32.
Differential geen expression analysis was done usin Bioconductor R package DESeq2 v1.37.4
Assembly: Dm6
Supplementary files format and content: tab-delimited file containing raw counts of TPM for control (Stwl) and Test_StwlEY (Stwl overexpression)

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: ovaries enriched for GSCs

growth_protocol: Drosophila melanogatser females (4-5 day old) of the correct genotypes, with and without Stwl overexpression were selected for RNA extraction.

extract_protocol:
RNA extraction was performed using the RNA-easy kit (Qiagen). Samples were additionally treated with DNAse after extraction and RNA purification step was performed.
RNA libraries were prepared by the Functional Genomic Center Zurich (FCGZ) using Tru-Seq mRNA library kit )as per manufacturer's protocol

treatment_protocol: ~ 35 ovaries were dissected  per sample in 1XPBS and were frozen at -80C until RNA extraction

value: ovaries enriched for GSCs

value: GSC-like cells

value: Stwl overexpression

value: with Stwl overexpression


title: WNK2 deleted T/C-28a2 cells, 01

value: human chondrocyte cells

value: Control


title: cardiomyocyte,sham, replicate2-21, scRNAseq

description:
smartseq2
sham_2.xlsx

value: 6-8 weeks old

value: sham


title: T/C-28a2 cells, WNK2 transfection +Sorbitol, 03


title: Test StwlEY_Replicate 4


title: Control Stwl_Replicate 4

value: without Stwl overexpression


title: Test StwlEY_Replicate 1


title: T/C-28a2 cells, WNK2 transfection +Sorbitol, 02


title: Control Stwl_Replicate 3


title: t9_cmv_rep2

value: HCMV infected


title: C16_repB

value: human induced pluripotent stem cells

value: DE differentiation (STEMCELL Tech)


title: Concord replicate 1

value: flag leaf

value: AAC Concord


title: cardiomyocyte,sham, replicate2-20, scRNAseq

description:
smartseq2
sham_2.xlsx

value: cardiomyocyte


title: t8_mock_rep3

value: First-trimester decidua

value: Mock infected

value: 24 hours

value: ask tamar hashimshony


title: Control Stwl_Replicate 2

value: ovaries enriched for GSCs

value: GSC-like cells


title: Test StwlEY_Replicate 3

value: Stwl overexpression

value: with Stwl overexpression


title: cardiomyocyte,sham, replicate2-24, scRNAseq

description:
smartseq2
sham_2.xlsx

value: heart

value: 6-8 weeks old


title: t9_mock_rep2


title: t8_mock_rep2


title: t9_cmv_rep3


title: T/C-28a2 cells, WNK2 transfection, 04

value: human chondrocyte cells

value: WT

value: WNK2 transfection


title: cardiomyocyte,sham, replicate2-18, scRNAseq

description:
smartseq2
sham_2.xlsx

value: sham


title: t8_cmv_rep2

value: HCMV infected


title: cardiomyocyte,sham, replicate2-17, scRNAseq

description:
smartseq2
sham_2.xlsx


title: 220118_13_NA_CUTTAG_T180_H3K9me2_WT_PFA_st17_rep1

city: Milano

first: Yinxiu

last: Zhan

address: Via Adamello 16

country: Italy

institute: European Institute for Oncology

description:
220118_H3K9me2_T180_st17.pooled.broad_peaks.broadPeak
220118_H3K9me2_T180_st17.pooled.bw

data_processing:
The Cut&Tag data was processed using snakePipes version 2.4.0 (parameters: --trim --fastqc --properPairs –dedup --mapq 1) with specific Cut&Tag Bowtie2 alignment option (--alignerOpts="--local --very-sensitive-local --no-discordant --no-mixed -I 10 -X 700"), as reported in Kaya-Okur et al., 2019. Since the Cut&Tag contains lambda phage spike-ins for reliable quantification of global effects, the libraries were mapped to a constructed hybrid genome of dm6 and lambda phage (NCBI GenBank ID: J02459.1).
Assembly: dm6.22; ensembl96
Supplementary files format and content: Bigwig files were generated by bamCoverage using --scaleFactor to normalise for lambda dna and H3. peak files were generated using macs2 with -q 0.05 --broad options
Library strategy: Cut&Tag

source_name: stage 17 embryo

growth_protocol: Embryos were aged at 25C

extract_protocol:
The snap-frozen embryos were defrosted and resuspended in ice-cold digitonin wash buffer (20mM HEPES (pH7.5),150mM NaCl, 0.5mM Spermidine, 5mM Sodium butyrate, 0.01% Digitonin, 2mM EDTA and 1x Protease inhibitor cocktail). The nuclei were extracted by breaking the embryo using a pestle for 30s. H3 was used as a loading control and for that, after extracting nuclei, the suspension was equally divided into Eppendorf tubes. The rest of the protocol was performed according to Kaya-Okur et al. 2019,  Nat Comm
The library was constructed according to Kaya-Okur et al. 2019,  Nat Comm

treatment_protocol: PFA fixed and snap frozen until the experiment

value: stage 17 embryo

tag: antibody

value: control

tag: spike in

value: 1pg lambdaphage DNA


title: T/C-28a2 cells, WNK2 transfection, 02


title: cardiomyocyte,sham, replicate2-15, scRNAseq

description:
smartseq2
sham_2.xlsx

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

value: cardiomyocyte


title: 220118_12_NA_CUTTAG_T180_H3K9me3_WT_PFA_st17_rep2

description:
220118_H3K9me3_T180_st17.pooled.broad_peaks.broadPeak
220118_H3K9me3_T180_st17.pooled.bw


title: t6_mock_rep3

value: First-trimester decidua

value: Mock infected

value: 24 hours


title: T/C-28a2 cells, WNK2 transfection, 01


title: 220118_11_NA_CUTTAG_T180_H3K9me3_WT_PFA_st17_rep1


title: t6_mock_rep2

value: ask tamar hashimshony


title: cardiomyocyte,sham, replicate2-19, scRNAseq

description:
smartseq2
sham_2.xlsx


title: t6_cmv_rep3


title: cardiomyocyte,sham, replicate2-14, scRNAseq

description:
smartseq2
sham_2.xlsx


title: T/C-28a2 cells, Sorbitol, 04

value: Sorbitol


title: T/C-28a2 cells, Sorbitol, 03


title: T/C-28a2 cells, WNK2 transfection +Sorbitol, 01

value: WNK2 transfection +Sorbitol


title: cardiomyocyte,sham, replicate2-13, scRNAseq

description:
smartseq2
sham_2.xlsx

value: heart


title: Control Stwl_Replicate 1

value: ovaries enriched for GSCs

value: GSC-like cells

value: Control

value: without Stwl overexpression


title: t8_cmv_rep3


title: T/C-28a2 cells, Sorbitol, 02

value: human chondrocyte cells

value: WT


title: t6_cmv_rep2

value: HCMV infected


title: 220118_14_NA_CUTTAG_T180_H3K9me2_WT_PFA_st17_rep2

value: stage 17 embryo

value: control


title: T/C-28a2 cells, WNK2 transfection, 03

value: WNK2 transfection


title: 220118_09_NA_CUTTAG_T180_H3_WT_PFA_st17_rep1

description: 220118_H3_T180_st17.pooled_peaks.narrowPeak

value: 1pg lambdaphage DNA


title: cardiomyocyte,sham, replicate2-12, scRNAseq

description:
smartseq2
sham_2.xlsx

value: cardiomyocyte

value: 6-8 weeks old

value: sham


title: cardiomyocyte,sham, replicate2-16, scRNAseq

description:
smartseq2
sham_2.xlsx


title: T/C-28a2 cells, Sorbitol, 01

value: Sorbitol


title: t5_mock_rep3

value: First-trimester decidua

value: Mock infected

value: 24 hours

value: ask tamar hashimshony


title: 220118_06_NA_CUTTAG_T180_H3K9me2_WT_PFA_st5_rep2

source_name: cycle 14  embryo

value: cycle 14  embryo


title: t5_mock_rep2


title: t5_cmv_rep3


title: cardiomyocyte,sham, replicate2-11, scRNAseq

description:
smartseq2
sham_2.xlsx

value: heart


title: cardiomyocyte,sham, replicate2-10, scRNAseq

description:
smartseq2
sham_2.xlsx


title: 220118_05_NA_CUTTAG_T180_H3K9me2_WT_PFA_st5_rep1


title: T/C-28a2 cells, Control, 04

value: human chondrocyte cells

value: Control


title: 220118_10_NA_CUTTAG_T180_H3_WT_PFA_st17_rep1


title: T/C-28a2 cells, Control, 02

value: WT


title: t4_mock_rep3


title: 220118_04_NA_CUTTAG_T180_H3K9me3_WT_PFA_st5_rep2


title: t5_cmv_rep2

value: HCMV infected


title: cardiomyocyte,sham, replicate2-8, scRNAseq

description:
smartseq2
sham_2.xlsx


title: cardiomyocyte,sham, replicate2-9, scRNAseq

description:
smartseq2
sham_2.xlsx


title: 220118_02_NA_CUTTAG_T180_H3_WT_PFA_st5_rep2

description: 220118_H3_T180_st5.pooled_peaks.narrowPeak

value: control


title: T/C-28a2 cells, Control, 01


title: cardiomyocyte,sham, replicate2-7, scRNAseq

description:
smartseq2
sham_2.xlsx


title: t4_mock_rep2


title: 220118_03_NA_CUTTAG_T180_H3K9me3_WT_PFA_st5_rep1


title: cell clusters within microspheres, 6 days after bioprinting 2

city: 北京

first: yixue

last: Luo

state: 北京市

address: Biomanufacturing and Rapid Forming Technology Key Laboratory of Beijing, Department of Mechanical Engineering, Tsinghua University, Beijing 100084, China

institute: 清华大学

data_processing:
The basic principle of sequencing is to synthesize and sequence at the sametime (Sequencing by Synthesis).
Four fluorescent labeled dNTP, DNApolymeraseand splice primers were added to the sequenced flowcell and amplified.
The sequencer captures thefluorescence signal and converts the optical signal into the sequencing peakbycomputer software, so as to obtain the sequence information of the fragment tobetested.
The image data measured by the high-throughput sequencer are convertedintosequence data (reads) by CASAVA base recognition.
Raw data (rawreads) of fastqformat were firstly processed through in-house perl scripts. I
Assembly: Hisat2(v2.0.5)
Supplementary files format and content: table-delimited text file induces raw counts for each sample
Supplementary files format and content: table-delimited text files induce FPKM values for each sample

source_name: Nuwacell hiPSC

growth_protocol: Human iPSCs (hiPSCs) were grown on matrigel-coated 6-well plates using the commercial serum-free medium at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
RNA was harvest using the HiPure Total RNA Mini Kit.
It was completed by Novogene.Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature inFirst Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseHtodegrade the RNA. Second strand cDNA synthesis was subsequently performed usingDNA Polymerase I and dNTP. Remaining overhangs were converted into blunt endsvia exonuclease/polymerase activities. After adenylation of 3’ ends of DNAfragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bpinlength, the library fragments were purified with AMPure XP system(BeckmanCoulter, Beverly, USA). Then PCR amplification, the PCR product was purifiedbyAMPure XP beads, and the library was finally obtained.

treatment_protocol: Single hiPSCs wrapped in hydrogel were bioprinted and cultured in commercial serum-free medium with 2.5 μM blebbistatin being added for 3 days.

value: Nuwacell hiPSC

value: induced pluripotent stem cell

value: bioprinting


title: cardiomyocyte,sham, replicate2-6, scRNAseq

description:
smartseq2
sham_2.xlsx

extract_protocol:
Cardiomyocytes and noncardiomyocyte were isolated using Langendorff perfusion from the left ventricular free wall. Enzymatic dissociation using Langendorff perfusion was performed with 37 °C pre-warmed 35 mL enzyme solution (collagenase Type II 1 mg/mL (Worthington), protease type XIV 0.05 mg/mL (Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, pH 7.4) at a rate of 3 mL/min. Enzymes were neutralized with fetal bovine serum (FBS) at a final concentration of 0.2%. Cell suspensions were filtered through a 100 μm nylon mesh cell strainer and centrifuged at 20 g for 3 min. The supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%, pH 7.4) containing a low concentration of calcium (0.5 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥70%) were collected immediately after isolation from two mice at each condition with a 0.2–2 μL pipette (sample volume, 0.5 μL) and incubated in lysis buffer.The supernatant was collected as non-cardiomyocytes and the cells were continued to lysis process according to the 10X protocol.
Sample 731-736,library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.  Other samples, single-cell cDNA libraries were generated using the Smart-seq2 protocol.  And the efficiency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad) and by examining the dis- tribution of the lengths of cDNA fragments using a LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward, TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse, TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold.

value: cardiomyocyte

value: 6-8 weeks old


title: 220118_01_NA_CUTTAG_T180_H3_WT_PFA_st5_rep1

value: 1pg lambdaphage DNA


title: t4_cmv_rep3

value: First-trimester decidua


title: cardiomyocyte,sham, replicate2-5, scRNAseq

description:
smartseq2
sham_2.xlsx

value: sham


title: t4_cmv_rep2

value: 24 hours


title: cell clusters within microspheres, 6 days after bioprinting 1


title: 211125_13_NA_CUTTAG_NI842xNI746_H3K9me3_MR_PFA_st17_rep1_2

description:
211125_H3K9me3_NI842xNI746_st17.pooled.broad_peaks.broadPeak
211125_H3K9me3_NI842xNI746_st17.pooled.bw

value: stage 17 embryo

value: dSetDB1 maternal rescue


title: cell clusters within microspheres, 4 days after bioprinting 2


title: 211125_14_NA_CUTTAG_NI842xNI746_H3K9me3_MT_PFA_st17_rep2_2


title: cardiomyocyte,sham, replicate2-4, scRNAseq

description:
smartseq2
sham_2.xlsx

value: heart


title: T/C-28a2 cells, Control, 03

value: human chondrocyte cells


title: t3_mock_rep3

value: Mock infected

value: ask tamar hashimshony


title: cell clusters within microspheres, 3 days after bioprinting 2


title: t3_mock_rep2


title: cell clusters within microspheres, 4 days after bioprinting 1


title: 210908_06_NA_CUTTAG_NI762xNI746xNI677_H3K9me3_WT_PFA_st17_rep2

description:
210908_H3K9me3_NI762xNI746xNI677_st17.pooled.broad_peaks.broadPeak
210908_H3K9me3_NI762xNI746xNI677_st17.pooled.bw

value: zygotic rescue


title: cardiomyocyte,sham, replicate2-2, scRNAseq

description:
smartseq2
sham_2.xlsx


title: 210908_05_NA_CUTTAG_NI762xNI746xNI677_H3K9me3_WT_PFA_st17_rep1


title: t3_cmv_rep3

value: HCMV infected


title: cardiomyocyte,sham, replicate2-1, scRNAseq

description:
smartseq2
sham_2.xlsx


title: 210908_04_NA_CUTTAG_NI762xNI746_H3K9me3_TM_PFA_st17_rep2

description:
210908_H3K9me3_NI762xNI746_st17.pooled.broad_peaks.broadPeak
210908_H3K9me3_NI762xNI746_st17.pooled.bw

value: triple mutant


title: hiPSCs, cultured in 2D substrate 2

value: Nuwacell hiPSC

value: induced pluripotent stem cell

value: no bioprinting


title: cell clusters within microspheres, 3 days after bioprinting 1

value: bioprinting


title: cardiomyocyte,sham, replicate1-86, scRNAseq

description:
smartseq2
sham_1.xlsx

value: cardiomyocyte

value: 6-8 weeks old


title: t2_mock_rep3

value: First-trimester decidua


title: t3_cmv_rep2

value: 24 hours


title: 210908_02_NA_CUTTAG_T180_H3K9me3_WT_PFA_st17_rep2

description:
210908_H3K9me3_T180_st17.pooled.broad_peaks.broadPeak
210908_H3K9me3_T180_st17.pooled.bw

value: stage 17 embryo

value: control

value: 1pg lambdaphage DNA


title: t2_mock_rep2


title: hiPSCs, cultured in 2D substrate 1


title: MGG8 treated with Belinostat & Dasatinib 3

city: Okayama-shi

first: Shuichiro

last: Hirano

address: kita-ku, shikata-cho, 2-5-1

institute: Okayama University

data_processing:
Sequencing was conducted using NovaSeq 6000
Fastq files were quality checked using FastQC
Adapter sequences were removed using Trimmomatic
Quantification of transcript abundance was performed using Kallisto
Assembly: Hallmark
Supplementary files format and content: Csv excel files include TPM values for each Sample

source_name: Glioblastoma

growth_protocol: GSC was cultured in neurobasal medium supplemented with 3 mmol/L l-Glutamine, 1× B27 supplement without vitamin A, 0.5× N2 supplement (Life Technologies), 20 ng/mL recombinant human EGF, 20 ng/mL recombinant human FGF2, and 0.5× penicillin G/streptomycin sulfate/amphotericin B complex.

extract_protocol:
RNA was extracted using All prep RNA/DNA mini kit (QIAGEN) and on-column DNase (Invitrogen).
Library preparation was performed with NEBNext® Ultra™II Directional RNA Library Prep Kit for Illumina® (New England Biolabs).

treatment_protocol: MGG8 GSC were treated as follows; 500 nM of Belinostat (Belinostat group), 50 nM of Dasatinib (Dasatinib group), 500 nM of Belinostat and 50 nM of Dasatinib (Combination group), or 0.1% Dimethyl sulfoxide (DMSO, Control group) for 72hours

value: Glioblastoma

value: Glioblastoma stem cell

value: WT

value: Combination of Belinostat & Dasatinib


title: 210908_03_NA_CUTTAG_NI762xNI746_H3K9me3_TM_PFA_st17_rep1


title: 210908_01_NA_CUTTAG_T180_H3K9me3_WT_PFA_st17_rep1


title: cardiomyocyte,sham, replicate1-84, scRNAseq

first: Manami

last: Katoh

institute: The University of Tokyo

description:
smartseq2
sham_1.xlsx

value: heart

value: sham


title: t2_cmv_rep3

value: HCMV infected

value: ask tamar hashimshony


title: MGG8 treated with Belinostat & Dasatinib 2


title: 210802_9_NA_CUTTAG_T180_HP1a_WT_PFA_st5_rep1

value: cycle 14  embryo


title: t2_cmv_rep2


title: cardiomyocyte,sham, replicate2-3, scRNAseq

description:
smartseq2
sham_2.xlsx


title: cardiomyocyte,sham, replicate1-85, scRNAseq

description:
smartseq2
sham_1.xlsx


title: 210802_14_NA_CUTTAG_NI635xNI743_HP1a_dSetDB1KD_PFA_st5_rep2


title: cardiomyocyte,sham, replicate1-83, scRNAseq

description:
smartseq2
sham_1.xlsx


title: MGG8 treated with Belinostat & Dasatinib1


title: t1_mock_rep3

value: Mock infected


title: cardiomyocyte,sham, replicate1-82, scRNAseq

description:
smartseq2
sham_1.xlsx

value: cardiomyocyte


title: MGG8 treated with Dasatinib3

value: 50nM of Dasatinib


title: 210802_13_NA_CUTTAG_NI635xNI743_HP1a_dSetDB1KD_PFA_st5_rep1


title: cardiomyocyte,sham, replicate1-81, scRNAseq

description:
smartseq2
sham_1.xlsx

value: 6-8 weeks old


title: t1_mock_rep2

value: First-trimester decidua

value: 24 hours


title: MGG8 treated with Dasatinib2


title: 210802_12_NA_CUTTAG_NI665_HP1a_Suvar3-9KO_PFA_st5_rep2

description: 210802_HP1a_Suvar3-9KO_PFA_st5.pooled.bw


title: t1_cmv_rep3


title: cardiomyocyte,sham, replicate1-80, scRNAseq

description:
smartseq2
sham_1.xlsx


title: cardiomyocyte,sham, replicate1-79, scRNAseq

description:
smartseq2
sham_1.xlsx


title: 210802_11_NA_CUTTAG_NI665_HP1a_Suvar3-9KO_PFA_st5_rep1


title: 210802_10_NA_CUTTAG_T180_HP1a_WT_PFA_st5_rep2

value: control


title: MGG8 treated with Belinostat3

value: 500nM of Belinostat


title: cardiomyocyte,sham, replicate1-78, scRNAseq

description:
smartseq2
sham_1.xlsx


title: w13_cmv_pos_rep2

value: Seropositive


title: 210728_9_NA_CUTTAG_T180_H3K9me2_WT_PFA_st5_rep1

value: 1pg lambdaphage DNA


title: MGG8 treated with Belinostat2

value: Glioblastoma

value: Glioblastoma stem cell

value: WT


title: cardiomyocyte,sham, replicate1-77, scRNAseq

description:
smartseq2
sham_1.xlsx

value: heart

value: sham


title: MGG8 treated with Belinostat1


title: 210728_6_NA_CUTTAG_NI635xNI743_H3K9me3_dSetDB1KD_PFA_st5_rep2

description: 210728_H3K9me3_dSetDB1KD_PFA_st5.pooled.bw


title: cardiomyocyte,sham, replicate1-76, scRNAseq

description:
smartseq2
sham_1.xlsx


title: w13_cmv_pos_rep1

value: HCMV infected


title: w13_mock_pos_rep2


title: Control of MGG8-3

value: 0.1percent DMSO


title: 210728_5_NA_CUTTAG_NI635xNI743_H3K9me3_dSetDB1KD_PFA_st5_rep1

value: cycle 14  embryo


title: w13_mock_pos_rep1

value: Mock infected


title: Control of MGG8-2


title: cardiomyocyte,sham, replicate1-74, scRNAseq

description:
smartseq2
sham_1.xlsx

value: cardiomyocyte


title: w8_cmv_pos_rep2

value: Seronegative


title: 210728_4_NA_CUTTAG_NI665_H3K9me3_Suvar3-9KO_PFA_st5_rep2

description: 210728_H3K9me3_Suvar3-9KO_PFA_st5.pooled.bw


title: cardiomyocyte,sham, replicate1-75, scRNAseq

description:
smartseq2
sham_1.xlsx

value: 6-8 weeks old


title: Control of MGG8-1


title: t1_cmv_rep2

value: First-trimester decidua

value: 24 hours

value: ask tamar hashimshony


title: w8_cmv_pos_rep1


title: cardiomyocyte,sham, replicate1-73, scRNAseq

description:
smartseq2
sham_1.xlsx


title: 210728_2_NA_CUTTAG_T180_H3K9me3_WT_PFA_st5_rep2

value: control


title: MGG8 treated with Dasatinib1

value: 50nM of Dasatinib


title: 210728_3_NA_CUTTAG_NI665_H3K9me3_Suvar3-9KO_PFA_st5_rep1

value: 1pg lambdaphage DNA


title: HIVHBV_X2_SP

city: London

first: Dimitra

last: Peppa

address: Gower St

country: United Kingdom

institute: University College London

description: 10X Genomics

library_source: other

data_processing:
Library quality assessed. Exclusion of for barcodes with less than 200 transcripts, retaning those with a number of genes less than 3000. Aells with a high proportion (> 10%) of mitochondrial-encoded genes were removed. Genes were considered if they were expressed in at least 5 cells.
Hashtagged samples were demultiplexed using the Scanpy external implementation of Hashsolo with default settings. Once demultiplexed, doublet exclusion was performed within multiplexed pools using Solo.
Dataset integration, dimensionality reduction, embedding and clustering
Autoated and manul cell type annotation
Differential Gene Expression & Functional analysis
Assembly: GRCh38

molecule: protein

source_name: Peripheral blood mononuclear cells

growth_protocol: PBMC isolated from whole blood, no further growth of cells required

extract_protocol:
cDNA libraries were prepared as per 10x Genomics Single Cell 5’ reagent kit user guide with calculations based on the amount of input cDNA.
Library construction was performed using the 10x next GEM Chips Chromium single cell library 5’ construction kit

treatment_protocol: The cells were not treated

value: Peripheral blood mononuclear cells


title: w8_mock_pos_rep2


title: HIVHBV_X2_GEX

description: 10X Genomics


title: 210728_1_NA_CUTTAG_T180_H3K9me3_WT_PFA_st5_rep1


title: cardiomyocyte,sham, replicate1-72, scRNAseq

city: Bunkyo-ku

address: 7-3-1 Hongo

description:
smartseq2
sham_1.xlsx


title: HBV_X2_SP

description: 10X Genomics


title: 210728_14_NA_CUTTAG_NI635xNI743_H3K9me2_dSetDB1KD_PFA_st5_rep2

description: 210728_H3K9me2_dSetDB1KD_PFA_st5.pooled.bw


title: cardiomyocyte,sham, replicate1-70, scRNAseq

description:
smartseq2
sham_1.xlsx


title: w6_cmv_pos_rep2

value: Seropositive


title: HBV_X2_GEX

description: 10X Genomics


title: cardiomyocyte,sham, replicate1-71, scRNAseq

description:
smartseq2
sham_1.xlsx

value: heart


title: w8_mock_pos_rep1


title: 210728_13_NA_CUTTAG_NI635xNI743_H3K9me2_dSetDB1KD_PFA_st5_rep1


title: cardiomyocyte,sham, replicate1-68, scRNAseq

description:
smartseq2
sham_1.xlsx

value: sham


title: cardiomyocyte,sham, replicate1-69, scRNAseq

description:
smartseq2
sham_1.xlsx


title: HIVHBV_Tre_SP_5

description: 10X Genomics


title: w6_cmv_pos_rep1

value: HCMV infected


title: 210728_12_NA_CUTTAG_NI665_H3K9me2_Suvar3-9KO_PFA_st5_rep2

description: 210728_H3K9me2_Suvar3-9KO_PFA_st5.pooled.bw


title: cardiomyocyte,sham, replicate1-67, scRNAseq

description:
smartseq2
sham_1.xlsx


title: HIVHBV_Tre_GEX_5

description: 10X Genomics


title: 210728_11_NA_CUTTAG_NI665_H3K9me2_Suvar3-9KO_PFA_st5_rep1


title: w6_mock_pos_rep1


title: 210728_10_NA_CUTTAG_T180_H3K9me2_WT_PFA_st5_rep2


title: HH_Tre_SP_4

description: 10X Genomics


title: 210530_16_NA_CUTTAG_NI762xNI746_HP1a_TM_PFA_st5_rep3

description:
210301_HP1a_NI762xNI746_st5.pooled.broad_peaks.broadPeak
210301_HP1a_NI762xNI746_st5.pooled.bw

value: triple mutant


title: HH_Tre_GEX_4

description: 10X Genomics


title: cardiomyocyte,sham, replicate1-65, scRNAseq

description:
smartseq2
sham_1.xlsx


title: cardiomyocyte,sham, replicate1-66, scRNAseq

description:
smartseq2
sham_1.xlsx


title: w4_cmv_pos_rep1


title: w4_mock_pos_rep2


title: 210530_14_NA_CUTTAG_T180_HP1a_WT_PFA_st5_rep3

description:
210301_HP1a_T180_st5.pooled.broad_peaks.broadPeak
210301_HP1a_T180_st5.pooled.bw

value: cycle 14  embryo


title: cardiomyocyte,sham, replicate1-64, scRNAseq

description:
smartseq2
sham_1.xlsx


title: 210530_10_NA_CUTTAG_NI762xNI746_H3K9me2_TM_PFA_c9-13_rep3

description:
210530_H3K9me2_NI762xNI746_c9-13.pooled.broad_peaks.broadPeak
210530_H3K9me2_NI762xNI746_c9-13.pooled.bw

source_name: cycle 9-13

value: cycle 9-13


title: cardiomyocyte,sham, replicate1-63, scRNAseq

description:
smartseq2
sham_1.xlsx

value: cardiomyocyte


title: 210530_09_NA_CUTTAG_NI762xNI746_H3K9me3_TM_PFA_c9-13_rep3

description:
210303_H3K9me3_NI762xNI746_c9-13.pooled.broad_peaks.broadPeak
210303_H3K9me3_NI762xNI746_c9-13.pooled.bw


title: w4_mock_pos_rep1

value: Mock infected


title: cardiomyocyte,sham, replicate1-62, scRNAseq

description:
smartseq2
sham_1.xlsx

value: 6-8 weeks old


title: w6_mock_pos_rep2

value: First-trimester decidua


title: 210530_08_NA_CUTTAG_NI762xNI746_H3K9me2_TM_PFA_bc9_rep3

description:
210303_H3K9me2_T180_bc9.pooled.broad_peaks.broadPeak
210303_H3K9me2_T180_bc9.pooled.bw

source_name: before cycle 9

value: before cycle 9


title: HBV_Tre_GEX_2

description: 10X Genomics


title: w12_cmv_neg_rep1

value: 24 hours

value: Seronegative


title: cardiomyocyte,sham, replicate1-61, scRNAseq

description:
smartseq2
sham_1.xlsx


title: 210530_07_NA_CUTTAG_NI762xNI746_H3K9me3_TM_PFA_bc9_rep3

description:
210303_H3K9me3_T180_bc9.pooled.broad_peaks.broadPeak
210303_H3K9me3_T180_bc9.pooled.bw


title: cardiomyocyte,sham, replicate1-60, scRNAseq

description:
smartseq2
sham_1.xlsx


title: w12_mock_neg_rep2


title: HBV_Tre_GEX_1

description: 10X Genomics


title: cardiomyocyte,sham, replicate1-59, scRNAseq

description:
smartseq2
sham_1.xlsx


title: 210530_04_NA_CUTTAG_T180_H3K9me2_WT_PFA_c9-13_rep3

description:
210301_H3K9me2_NI762xNI746_st5.pooled.broad_peaks.broadPeak
210301_H3K9me2_NI762xNI746_st5.pooled.bw

value: control


title: w12_mock_neg_rep1


title: cardiomyocyte,sham, replicate1-58, scRNAseq

description:
smartseq2
sham_1.xlsx


title: Healthy_SP

description: 10X Genomics


title: HBV_Tre_SP_3

description: 10X Genomics


title: HBV_Tre_GEX_3

description: 10X Genomics


title: w9_cmv_neg_rep2


title: 210530_03_NA_CUTTAG_T180_H3K9me3_WT_PFA_c9-13_rep3

description:
210301_H3K9me3_NI762xNI746_st5.pooled.broad_peaks.broadPeak
210301_H3K9me3_NI762xNI746_st5.pooled.bw

value: 1pg lambdaphage DNA


title: w4_cmv_pos_rep2


title: HBV_Tre_SP_1

description: 10X Genomics

value: Peripheral blood mononuclear cells


title: cardiomyocyte,sham, replicate1-57, scRNAseq

description:
smartseq2
sham_1.xlsx


title: 210530_02_NA_CUTTAG_T180_H3K9m2_WT_PFA_bc9_rep3


title: HBV_Tre_SP_2

description: 10X Genomics


title: Healthy_GEX

description: 10X Genomics


title: w12_cmv_neg_rep2


title: cardiomyocyte,sham, replicate1-56, scRNAseq

description:
smartseq2
sham_1.xlsx


title: HBV_C_SP

description: 10X Genomics


title: HBV_C_GEX

description: 10X Genomics


title: w9_mock_neg_rep2

value: Seropositive


title: 210530_01_NA_CUTTAG_T180_H3K9me3_WT_PFA_bc9_rep3


title: cardiomyocyte,sham, replicate1-55, scRNAseq

description:
smartseq2
sham_1.xlsx

value: heart


title: 210413_08_NA_CUTTAG_NI762xNI746_H3K9me2_TM_PFA_st5_rep2


title: HIVHBV_C_SP

description: 10X Genomics


title: cardiomyocyte,sham, replicate1-54, scRNAseq

description:
smartseq2
sham_1.xlsx

value: sham


title: w9_mock_neg_rep1


title: cardiomyocyte,sham, replicate1-51, scRNAseq

description:
smartseq2
sham_1.xlsx


title: 210413_06_NA_CUTTAG_NI762xNI746_H3_mouse_TM_PFA_st5_rep2

description: 220118_H3_T180_st5.pooled_peaks.narrowPeak


title: cardiomyocyte,iPS_plus_Igfbp7_vac_2, bulk RNAseq

data_processing:
none provided
Supplementary files format and content: mm10,GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: iPS

extract_protocol:
Cardiomyocytes and noncardiomyocyte were isolated using Langendorff perfusion from the left ventricular free wall. Enzymatic dissociation using Langendorff perfusion was performed with 37 °C pre-warmed 35 mL enzyme solution (collagenase Type II 1 mg/mL (Worthington), protease type XIV 0.05 mg/mL (Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, pH 7.4) at a rate of 3 mL/min. Enzymes were neutralized with fetal bovine serum (FBS) at a final concentration of 0.2%. Cell suspensions were filtered through a 100 μm nylon mesh cell strainer and centrifuged at 20 g for 3 min. The supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%, pH 7.4) containing a low concentration of calcium (0.5 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥70%) were collected immediately after isolation from two mice at each condition with a 0.2–2 μL pipette (sample volume, 0.5 μL) and incubated in lysis buffer.The supernatant was collected as non-cardiomyocytes and the cells were continued to lysis process according to the 10X protocol. iPS cells were differentiated into CMs as described below. On day 0, the medium was replaced with the AscleStem cardiomyocyte differentiation medium kit (CDM; Nacalai Tesque) containing 6 μM CHIR99021 (Tocris, Bristol, UK). On day 2, the medium was replaced with CDM supplemented with 5 μM IWP-2 (Tocris) and 5 μM SB431542 (Wako, Osaka, Japan). From day 4 onward, the medium was replaced with fresh CDM every other day. On day 10, the cells were dissociated into single cells using Liberase solution (Roche) supplemented with DNase I (Roche). On day 11, cells were purified using glucose- and glutamine-free Dulbecco’s modified Eagle’s medium (DMEM) (Life Technologies, Carlsbad, CA) and 4 mM lactic acid (Wako). The glucose-free lactic acid medium was changed every 2 days for 6 to 8 days. After purification, the cells were maintained in DMEM containing 10% FBS (Thermo Fisher Scientific) and then subjected to analysis around day 35. Prepared hiPSCMs were treated with DMEM containing 200 ng/mL human recombinant IGFBP7 (#350-09, Pepro Tech) and 9% mouse serum (vaccinated and unvaccinated), and RNA samples were collected for bulk RNA-seq 24 hours later. "
single-cell cDNA libraries were generated using the Smart-seq2 protocol.  And the efficiency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad) and by examining the dis- tribution of the lengths of cDNA fragments using a LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward, TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse, TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold.
scRNA-seq, Bulk RNA-seq

value: iPS


title: 210413_01_NA_CUTTAG_T180_H3_mouse_WT_PFA_st5_rep2


title: 210413_03_NA_CUTTAG_T180_H3K9m2_WT_PFA_st5_rep2

description:
210301_H3K9me2_T180_st5.pooled.broad_peaks.broadPeak
210301_H3K9me2_T180_st5.pooled.bw


title: w5_cmv_neg_rep1

value: HCMV infected


title: cardiomyocyte,sham, replicate1-52, scRNAseq

description:
smartseq2
sham_1.xlsx

source_name: heart


title: w2_cmv_neg_rep2


title: cardiomyocyte,iPS_plus_Igfbp7_vac_1, bulk RNAseq


title: cardiomyocyte,iPS_plus_Igfbp7_vac_4, bulk RNAseq


title: cardiomyocyte,sham, replicate1-50, scRNAseq

description:
smartseq2
sham_1.xlsx


title: cardiomyocyte,iPS_plus_Igfbp7_vac_3, bulk RNAseq


title: w5_cmv_neg_rep2


title: cardiomyocyte,sham, replicate1-49, scRNAseq

description:
smartseq2
sham_1.xlsx


title: 210303_11_NA_CUTTAG_NI762xNI746_H3K9me3_TM_PFA_c9-13_rep1

value: triple mutant


title: HIVHBV_C_GEX

description: 10X Genomics


title: w2_cmv_neg_rep1


title: w9_cmv_neg_rep1


title: 210413_02_NA_CUTTAG_T180_H3K9me3_WT_PFA_st5_rep2

description:
210301_H3K9me3_T180_st5.pooled.broad_peaks.broadPeak
210301_H3K9me3_T180_st5.pooled.bw

value: cycle 14  embryo


title: 210303_09_NA_CUTTAG_NI762xNI746_H3K9me2_TM_PFA_bc9_rep1

description:
210303_H3K9me2_NI762xNI746_bc9.pooled.broad_peaks.broadPeak
210303_H3K9me2_NI762xNI746_bc9.pooled.bw


title: w5_mock_neg_rep2


title: cardiomyocyte,sham, replicate1-53, scRNAseq

description:
smartseq2
sham_1.xlsx

value: cardiomyocyte


title: cardiomyocyte,sham, replicate1-48, scRNAseq

description:
smartseq2
sham_1.xlsx


title: cardiomyocyte,iPS_plus_Igfbp7_3, bulk RNAseq


title: cardiomyocyte,sham, replicate1-47, scRNAseq

description:
smartseq2
sham_1.xlsx


title: cardiomyocyte,iPS_plus_Igfbp7_4, bulk RNAseq


title: w2_mock_neg_rep2

value: Mock infected


title: 210413_07_NA_CUTTAG_NI762xNI746_H3K9me3_TM_PFA_st5_rep2


title: w5_mock_neg_rep1


title: w2_mock_neg_rep1


title: 210303_05_NA_CUTTAG_T180_H3K9me3_WT_PFA_c9-13_rep1

description:
210303_H3K9me3_T180_c9-13.pooled.broad_peaks.broadPeak
210303_H3K9me3_T180_c9-13.pooled.bw

value: cycle 9-13


title: cardiomyocyte,sham, replicate1-45, scRNAseq

description:
smartseq2
sham_1.xlsx

value: 6-8 weeks old


title: TS_7d_32_tech2

city: Shanghai

first: Huaxin

last: Song

address: Shanghai Jiao Tong University School of Medicine

description: Temperature-sensitive mutation screening.xlsx

data_processing:
Library strategy: DNA-seq
NGS data were processed with the ORFCall software developed by the Broad Institute and aligned to the TP53 reference sequence. The raw read counts were standardized to the fraction of counts at each codon position. Then, the reads of each p53 variant were normalized so that the average reads of 5 nonsense variants in different libraries will be equal.
Genome_build: TP53 CDS
Supplementary_files_format_and_content: Excel table includes normalized reads of each sample

source_name: Myeloid malignant cell line

growth_protocol: U937 cells were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum (Moregate) and cultured in a humidified incubator at 32 or 37℃ under 5% CO2.

extract_protocol:
gDNA was purified from a minimum of 1 × 106 library cells using Blood Genomic DNA Mini Kit (CW2087, Cwbio). Three PCR reactions were performed for each gDNA sample to amplify the p53 region. Each reaction contained a total volume of 50 μL with 1 μg gDNA, 25 μL of VAHTS® HiFi Amplification Mix (N616-02, Vazyme) and 2.5 μL of each (5 μM) library amplification primer. The parameters for PCR were 95 °C for 3 min, 27 cycles of 98 °C for 20 s, 58 °C for 15 s, and 72 °C for 45 s, followed by one cycle of 72 °C for 5 min. Amplicons were separated from nonspecific fragments by electrophoresis on a 1% agarose gel, extracted from the gel and purified using a Wizard® SV Gel and PCR Clean-Up System (A9282, Promega).
Sequencing sample preparations reactions were performed using TruePrep DNA Library Prep Kit V2 for Illumina (TD501, Vazyme), followed by sequenced on an Illumina Novaseq6000 (Illumina) using two reads, each 150 bases in length.

treatment_protocol: no treatment/0.6 μg/ml ATO/intraperitoneal injection with PBS daily/intraperitoneal injection with 5 mg/kg ATO daily/cell culture at 32 degrees Celsius

tag: experiment

value: cell culture at 32 degrees Celsius


title: cardiomyocyte,iPS_plus_Igfbp7_1, bulk RNAseq


title: 210303_06_NA_CUTTAG_T180_H3K9me2_WT_PFA_c9-13_rep2

description:
210303_H3K9me2_T180_c9-13.pooled.broad_peaks.broadPeak
210303_H3K9me2_T180_c9-13.pooled.bw


title: 210303_03_NA_CUTTAG_T180_H3K9m2_WT_PFA_bc9_rep1

value: before cycle 9


title: 210303_02_NA_CUTTAG_T180_H3K9me3_WT_PFA_bc9_rep1


title: cardiomyocyte,iPS_plus_Igfbp7_2, bulk RNAseq


title: 210303_08_NA_CUTTAG_NI762xNI746_H3K9me3_TM_PFA_bc9_rep1

description:
210303_H3K9me3_NI762xNI746_bc9.pooled.broad_peaks.broadPeak
210303_H3K9me3_NI762xNI746_bc9.pooled.bw


title: cardiomyocyte,sham, replicate1-44, scRNAseq

description:
smartseq2
sham_1.xlsx


title: cardiomyocyte,sham, replicate1-46, scRNAseq

description:
smartseq2
sham_1.xlsx


title: TS_7d_32_tech1

institute: Shanghai Jiao Tong University School of Medicine


title: TS_7d_37_tech2

value: no treatment


title: 210301_11_NA_CUTTAG_NI762xNI746_HP1_TM_PFA_st5_rep1


title: cardiomyocyte,iPS_Igfbp7_2, bulk RNAseq


title: cardiomyocyte,iPS_Igfbp7_1, bulk RNAseq


title: cardiomyocyte,sham, replicate1-43, scRNAseq

description:
smartseq2
sham_1.xlsx


title: TS_0d


title: Mice_ATO5

description: Mice tumor growth suppression test.xlsx

value: mice tumor growth suppression test

value: intraperitoneal injection with 5 mg/kg ATO daily


title: cardiomyocyte,iPS_Igfbp7_3, bulk RNAseq


title: cardiomyocyte,iPS_Igfbp7_4, bulk RNAseq


title: TS_7d_37_tech1


title: 210301_08_NA_CUTTAG_NI762xNI746_H3K9me3_TM_PFA_st5_rep1

value: 1pg lambdaphage DNA


title: 210301_09_NA_CUTTAG_NI762xNI746_H3K9me2_TM_PFA_st5_rep1


title: cardiomyocyte,sham, replicate1-42, scRNAseq

description:
smartseq2
sham_1.xlsx


title: Mice_ATO4

description: Mice tumor growth suppression test.xlsx


title: cardiomyocyte,iPS_CTRL_3, bulk RNAseq


title: cardiomyocyte,sham, replicate1-40, scRNAseq

description:
smartseq2
sham_1.xlsx


title: cardiomyocyte,sham, replicate1-41, scRNAseq

description:
smartseq2
sham_1.xlsx


title: cardiomyocyte,iPS_CTRL_2, bulk RNAseq


title: 210301_07_NA_CUTTAG_NI762xNI746_H3_mouse_TM_PFA_st5_rep1


title: cardiomyocyte,iPS_CTRL_1, bulk RNAseq


title: cardiomyocyte,sham, replicate1-38, scRNAseq

description:
smartseq2
sham_1.xlsx


title: 210301_03_NA_CUTTAG_T180_H3K9m2_WT_PFA_st5_rep1

value: control


title: Mice_ATO2

description: Mice tumor growth suppression test.xlsx


title: 210301_05_NA_CUTTAG_T180_HP1a_WT_PFA_st5_rep1


title: cardiomyocyte,sham, replicate1-37, scRNAseq

description:
smartseq2
sham_1.xlsx

value: heart


title: cardiomyocyte,sham, replicate1-39, scRNAseq

description:
smartseq2
sham_1.xlsx

value: sham


title: THP-1_HERV-K_KO_1

city: Busan

first: Eun-Ji

last: Ko

address: 2, Busandaehak-ro

country: South Korea

institute: Pusan National University

description: HERV-K119 env KO cells

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to GRCh38 whole genome using Tophat
FPKM calculation using Cufflink
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

source_name: Peripheral blood

growth_protocol: RPMI 1640 (Thermo Fisher Scientific) containing 10% fetal bovine serum (FBS) (Invitrogen), 1% penicillin, and L-glutamine (Thermo Fisher Scientific). All cell lines were maintained at 37 °C in a humidified atmosphere containing 5% CO2 and 90% humidity.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

treatment_protocol: At 18h after transfection, cells were treated with 100 μg/mL hygromycin for two days and PMA(1:1000), LPS(1:2000)

value: Peripheral blood

value: monocyte

value: TATTCCAGTCACACTGTAACTGG

value: Hygromycin


title: THP-1_HERV-K_KO_PMA

description: HERV-K119 env KO cells+PMA

value: Hygromycin, PMA


title: Mice_ATO1

description: Mice tumor growth suppression test.xlsx


title: Mice_PBS5

description: Mice tumor growth suppression test.xlsx

value: intraperitoneal injection with PBS daily


title: THP-1_HERV-K_KO_PMA+LPS

description: HERV-K119 env KO cells+PMA+LPS

value: Hygromycin, PMA, LPS


title: THP-1_MOCK_1

description: Control


title: cardiomyocyte,sham, replicate1-36, scRNAseq

description:
smartseq2
sham_1.xlsx

value: cardiomyocyte

value: 6-8 weeks old


title: Mice_PBS3

description: Mice tumor growth suppression test.xlsx


title: cardiomyocyte,sham, replicate1-34, scRNAseq

description:
smartseq2
sham_1.xlsx


title: cardiomyocyte,sham, replicate1-35, scRNAseq

description:
smartseq2
sham_1.xlsx


title: Mice_PBS4

description: Mice tumor growth suppression test.xlsx


title: DCL_S1_L001

first: Facai

last: Zhang

state: Zhejiang

address: 158 Shangtang Road

institute: Zhejiang Provincial People‘s Hospital

data_processing:
Results from Illumina sequencing offline were converted to FASTQ format using bcl2fastq software (version 5.0.1). The scRNA-seq sequencing data were compared to reference genome using CellRanger software. The output CellRanger expression profile matrix was loaded into Seurat (version 4.1.0) for filtering of low quality cells from scRNA-seq data, and the filtered data was downscaled and clustered, and cells were projected into 2D space using UMAP.
Assembly: hg18
Supplementary files format and content: Tab-seperated values and matrix files

source_name: PBMC

growth_protocol: The purified monocytes were labeled with TLR4-acK and FITC-conjugated secondary antibody, then positively stained cells were enriched through the BD FACSAria™ III Cell Sorter.

extract_protocol:
The single-cell suspension was added to the 10x Chromium chip according to the instructions for the 10X Genomics Chromium Single-Cell 3' kit (V3), cDNA amplification and library construction were performed according to standard protocols. Libraries were sequenced by LC-Bio Technology (Hangzhou, China) on an Illumina NovaSeq 6000 sequencing system at a minimum depth of 20,000 reads per cell.
Results from Illumina sequencing offline were converted to FASTQ format using bcl2fastq software (version 5.0.1). The scRNA-seq sequencing data were compared to reference genome using CellRanger software. The output CellRanger expression profile matrix was loaded into Seurat (version 4.1.0) for filtering of low quality cells from scRNA-seq data, and the filtered data was downscaled and clustered, and cells were projected into 2D space using UMAP.

value: PBMC

value: Monocytes

tag: condition

value: sepsis


title: THP-1_MOCK_PMA

description: Control+PMA

tag: tissue


title: 210301_01_NA_CUTTAG_T180_H3_mouse_WT_PFA_st5_rep1

value: cycle 14  embryo


title: IPF1, Spatial Transcriptomic, Visium, frozen tissue

city: New Haven

first: Naftali

last: Kaminski

state: CT

address: 300 Cedar Street

institute: Yale University

description: 10x Genomics

data_processing:
Base calls were converted to reads with the software SpaceRanger’s implementation mkfastq (SpaceRanger v1-2.2). Multiple fastq files from the same library and strand were catenated to single files. Read2 files were subjected to two passes of contaminant trimming with cutadapt (v1.17): for the template switch oligo sequence (AAGCAGTGGTATCAACGCAGAGTACATGGG) anchored on the 5′ end and for poly(A) sequences on the 3′ end. Following trimming, read pairs were removed if the read2 was trimmed below 30 bp. Visium libraries were mapped on the human genome (10X-provided GRCh38 reference), using StarSolo (StarSolo v2.7.6a).
The data measured expression of 60,651 genes at 4,992 spatial locations. We filtered out the spatial location not covered by tissue and the genes not expressed on all spatial locations. Finally, we performed spatial deconvolution on a set of 32,078 genes and 3,532 spatial spots.
Assembly: Hg19
Supplementary files format and content: Tab-separated matrix of raw expression counts and filtered expression counts with gene name and coordinates; Tab-separated file with coordinates and cell barcodes for raw counts and filtered counts; TIFF image file for spatial data.

source_name: Fibrotic Lung

extract_protocol:
Visium technology (10x Genomics) rely on Visium Spatial Gene Expression slides use. Each slide contains 6.5 × 6.5 mm areas are where tissue sections are placed, Hematoxylin and Eosin stained and finally imaged (20X) using a scanning microscope (EvosM700, ThermoFischer Scientific). Each area contains or 5000 printed regions of barcoded mRNA capture probes with the dimensions of 55 μm in diameter and a center-to-center distance of 100 μm. Tissue is permeabilized and mRNAs are hybridized to the barcoded capture probes directly underneath. cDNA synthesis connects the spatial barcode and the captured mRNA.
Library was performed according to the manufacter’s instructions (Visium, 10x Genomics).
a) Slices (thickness, 10 um) of lung tissues OCT are embedded obtain from control or IPF lung; b) Fixation, staining, and permeabilization; c)RT and amplification cDNA library preparation, and transcriptome sequencing on Illumina HiSeq 6000platform (125 million reads per library);

value: Fibrotic Lung


title: cardiomyocyte,sham, replicate1-33, scRNAseq

description:
smartseq2
sham_1.xlsx

tag: treatment


title: Coneal_epithelium_snRNAseq

city: Cambridge

first: Minkyung

last: Sung

address: 25 Cambridge Science Park Milton Rd, Milton

department: Cell informatics

institute: Mogrify

data_processing:
The raw data were demultiplexed using an in-house script that allows 1 base mismatch between the barcode sequence and the index sequence data. Data were trimmed to 100b using bbduk (https://sourceforge.net/projects/bbmap/)
Approximately 6,300 cells were captured using the 10X chromium single cell 3’ library & gel bead kit from 10 limbus samples. We aligned sequencing reads to the human transcriptome (GRCh38) and generated a UMI count matrix using the 10X Genomics cellranger v. 3.1.0 pipeline.
Scran v.16.0 R package was used to normalize UMI counts and resulting normalized matrix was imported in Seurat v.3.2.1 platform and further analysed (dimensional reduction and clustering etc.).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix file

molecule: nuclear RNA

source_name: Eye limbus epithelium from cataract patients (should not affect the epithelium) - 10 samples pooled

extract_protocol:
Human limbus tissue was extracted during cataract surgery and flash frozen on LN2 for preservation of gene expression profiles of the cell sub-types within the ocular surface epithelium.
Healthy human limbal tissue was collected from consenting cataract patients under the Royal Victorian Eye and Ear Hospital Human Research Ethics Committee approved study (ID:10/954H). Limbus tissue samples were snap frozen within 2 minutes of excision using LN2 were pooled and nuclei isolation was carried out using the Nuclei Isolation Kit: Nuclei EX Prep (Sigma, NUC101) as described previously (PMID 28846088).
All steps were carried out on ice. Briefly, tissue samples were homogenized using a glass Dounce grinder in 2ml of ice-cold Nuclei EZ lysis buffer (Sigma N3408, with RNase inhibitor). Samples were transferred to a separate tube on ice while the glass grinder was rinsed with 2mL of Nuclei EZ lysis buffer. This rinse was pooled into the sample for a total of 4mL and then incubated on ice for 5 min. Nuclei were centrifuged at 500 x g for 5 min at 4oC and washed with ice-cold EZ buffer, followed by a second wash in nuclei suspension buffer (NSB) consisting of PBS (Gibco 14190-144), 1% w/v BSA (Sigma, A9576) and 0.2U/uL RNase inhibitor (Takara, 2313A).
Isolated cell nuclei from cornea limbal samples were resuspended in 200uL NSB containing 5ug/mL DAPI (ThermoFisher Scientific, D1306). Nuclei integrity was visually inspected under an inverted phase microscope. Isolated nuclei were then filtered through a 35um nylon mesh cell strainer for nuclei sorting using a FACSAria Fusion sorter (BD Biosciences, 70um nozzle) at a flow rate between 1-3 to achieve no more than 1000 events per second. Nuclei, defined as DAPI-positive singlets, were sorted into microtubes containing 35uL NSB.
Attempts to count Trypan Blue-positive stained nuclei either prior to soring or immediately after sorting indicated that the number of nuclei was too low to accurately count without sacrificing a large portion of the cornea samples. Therefore, nuclei were resuspended in the minimal volume required for each step in the isolation procedure without counting or dilution. The average percentage recovery from the FACSAria Fusion sorter was determined from other samples to be 70%, so the final nuclei count for sequencing was calculated by multiplying the number of DAPI+ nuclei sorted x 0.7. Sorted nuclei were pelleted by centrifugation (500 x g, 2 min, 4C), then carefully resuspended in either an appropriate volume of NSB to yield 100-200k nuclei per mL or a minimum of 20uL NSB (whichever volume was larger).
Library Construction was performed using the Chromium Next GEM Single Cell 3’ Library & Gel Bead kit v3.1 (10x Genomics (PN-1000121) with 18 complementary DNA pre-amplification cycles and sequencing on one-high output lane of the NextSeq 500 (Illumina). Sequencing was performed with libraries pooled and loaded in a single lane of an MGISEQ2000-RS sequencer (MGI Tech Co Ltd).
snRNA-seq

value: limbal

tag: cell type

value: Corneal epithelial

tag: individual

value: cataract patients


title: THP-1_MOCK_PMA+LPS

description: Control+PMA+LPS

value: Peripheral blood


title: Mice_PBS2

description: Mice tumor growth suppression test.xlsx

value: mice tumor growth suppression test


title: Mice_ATO3

description: Mice tumor growth suppression test.xlsx

value: intraperitoneal injection with 5 mg/kg ATO daily


title: cardiomyocyte,sham, replicate1-32, scRNAseq

description:
smartseq2
sham_1.xlsx

value: heart

tag: strain

tag: age

value: sham


title: Mice_PBS1

description: Mice tumor growth suppression test.xlsx

tag: cell line

value: intraperitoneal injection with PBS daily


title: 210301_02_NA_CUTTAG_T180_H3K9me3_WT_PFA_st5_rep1

tag: genotype

value: control

value: 1pg lambdaphage DNA


title: cardiomyocyte,sham, replicate1-31, scRNAseq

description:
smartseq2
sham_1.xlsx

value: cardiomyocyte

value: 6-8 weeks old


title: cardiomyocyte,sham, replicate1-30, scRNAseq

description:
smartseq2
sham_1.xlsx


title: HUVEC+DPSC+CM+MAC  fibrin tissue day 10 sample3

city: Toronto

first: Shira

last: Landau

state: ON

address: 170 College St.,, MB317

institute: University of Toronto

data_processing:
Fastq files were processed through fastp software for adapter and quality trimming as well as QC analyses.
Trimmed reads were aligned to the reference human genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads mapped to each gene and calculate FPKM.
Differential expression analysis was performed using the DESeq2 R package (1.20.0) with a false discovery rate adjusted p-value <0.05 considered significant.
Assembly: Hisat2 v2.0.5
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file include RPKM counts for each sample

source_name: HUVEC+DPSC+cardiomyocytes+macrophages

extract_protocol:
RNA extraction was done by using the PicoPure™ RNA Isolation Kit (Thermo Fisher Scientific KIT0204).
Quantified libraries were pooled and sequenced on an Illumina NovaSeq S4 with a read length of 2x150 paired-end reads to a depth of 20 million reads in each direction.

value: HUVEC+DPSC+cardiomyocytes+macrophages


title: HeLa, Ctr, USF1, IP

first: Diletta

last: Dolfini

state: MI

address: Via Celoria, 26

department: Bioscience

institute: University of Milan

description: Peak calling on HeLa cells samples was performed with MACS2 v.2.1.1.20160309 set with fdr < 0.1

data_processing:
ChIP-seq reads were processed using the ENCODE pipeline 2.1.5, setting default peak caller and bowtie2 aligner.
Homo sapiens ChIP-seq reads were aligned to the hg38 v4 genome provided by ENCODE pipeline.
Mus musculus ChIP-seq reads were aligned to the mm10 v4 genome provided by ENCODE pipeline.
Supplementary files format and content: hg38, mm10
Supplementary files format and content: bigWig, bed narrowPeak (except for Input sample)

source_name: HeLa

extract_protocol:
HeLa: material was processed for ChIP.
DNA libraries were prepared using the NEbNext ChIP-Seq Library kit and TruSeq sample prep (Illumina)

treatment_protocol: HeLa cells at 25-30% confluence were transfected with 50 nM siRNA using Lipofectamine 3000 Reagent (ThermoFisher).

value: HeLa

value: Tumor

value: Non-targeting Control Pool D-001810-10-50

tag: chip antibody

value: USF1, IP


title: HeLa, SiYB, USF1, IP


title: Cell_7d_ATO_bio3_tech2

description: Cell growth inhibition test.xlsx

value: cell growth inhibition test

value: 0.6 ug/ml ATO


title: HUVEC+DPSC+CM+MAC  fibrin tissue day 10 sample4


title: HUVEC+DPSC+CM+MAC  fibrin tissue day 10 sample2


title: Cell_7d_ATO_bio3_tech1

description: Cell growth inhibition test.xlsx


title: Cell_7d_bio3_tech2

description: Cell growth inhibition test.xlsx

value: no treatment


title: cardiomyocyte,sham, replicate1-28, scRNAseq

description:
smartseq2
sham_1.xlsx


title: HeLa, SiYB, input


title: HeLa, Ctr, NFYB, IP

value: NFYB, IP


title: cardiomyocyte,sham, replicate1-29, scRNAseq

description:
smartseq2
sham_1.xlsx


title: cardiomyocyte,sham, replicate1-26, scRNAseq

description:
smartseq2
sham_1.xlsx


title: HUVEC+DPSC+CM  fibrin tissue day 10 sample2

source_name: HUVEC+DPSC+cardiomyocytes

value: HUVEC+DPSC+cardiomyocytes


title: HUVEC+DPSC+CM  fibrin tissue day 10 sample3


title: HUVEC+DPSC+CM+MAC  fibrin tissue day 10 sample1


title: HUVEC+DPSC+CM  fibrin tissue day 10 sample4


title: Cell_7d_bio3_tech1

description: Cell growth inhibition test.xlsx


title: cardiomyocyte,sham, replicate1-25, scRNAseq

description:
smartseq2
sham_1.xlsx

value: heart


title: Cell_7d_ATO_bio2_tech2

description: Cell growth inhibition test.xlsx


title: HUVEC+DPSC+CM  fibrin tissue day 10 sample1


title: Mice_time0

description: Mice tumor growth suppression test.xlsx

value: mice tumor growth suppression test


title: cardiomyocyte,sham, replicate1-24, scRNAseq

description:
smartseq2
sham_1.xlsx

value: sham


title: cardiomyocyte,sham, replicate1-23, scRNAseq

description:
smartseq2
sham_1.xlsx


title: HeLa, SiYB, NFYB, IP


title: HUVEC+DPSC  fibrin tissue day 10 sample3

source_name: HUVEC+DPSC

value: HUVEC+DPSC


title: cardiomyocyte,sham, replicate1-27, scRNAseq

description:
smartseq2
sham_1.xlsx


title: M2_3

type: RNA

first: Shiliang

last: Cai

address: 800 Xiangyin Road

institute: Second Military Medical University

description: Gene expression in Hela cells transfected with  mutation 2 preS

hyb_protocol: Sample hybridization was performed for 16 hours at 45°C according to standard protocol. Washing and staining was performed on Fluidics Station 450.

scan_protocol: GeneChips were scanned using a GeneChip scanner 3000.

data_processing: The data were processed with Expression Console Software. Normalization was performed by the Signal Space Transformation-Robust multi-array average method (sst-RMA).

label: biotin

source_name: M2,replicate 3

label_protocol: Labeling was performed according to manufacturer's standard protocol.

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

treatment_protocol: HeLa cell lines expressing wild-type and mutant preS stably was constructed.


title: HeLa, Ctr, input


title: cardiomyocyte,sham, replicate1-22, scRNAseq

description:
smartseq2
sham_1.xlsx


title: Cell_7d_bio2_tech1

description: Cell growth inhibition test.xlsx


title: Cell_0d_bio3_tech1

description: Cell growth inhibition test.xlsx


title: cardiomyocyte,sham, replicate1-21, scRNAseq

description:
smartseq2
sham_1.xlsx


title: Cell_0d_bio2_tech1

description: Cell growth inhibition test.xlsx


title: M2_2

source_name: M2,replicate 2


title: HUVEC+DPSC  fibrin tissue day 10 sample1


title: HUVEC only fibrin tissue day 10 sample3

source_name: HUVEC

value: HUVEC


title: cardiomyocyte,sham, replicate1-19, scRNAseq

description:
smartseq2
sham_1.xlsx

value: cardiomyocyte


title: Cell_7d_ATO_bio1_tech1

description: Cell growth inhibition test.xlsx


title: HUVEC only fibrin tissue day 10 sample2


title: M1_3

description: Gene expression in Hela cells transfected with  mutation 1 preS

source_name: M1,replicate 3


title: Cell_7d_bio2_tech2

description: Cell growth inhibition test.xlsx


title: Cell_7d_ATO_bio2_tech1

description: Cell growth inhibition test.xlsx


title: HUVEC+DPSC  fibrin tissue day 10 sample4


title: cardiomyocyte,sham, replicate1-18, scRNAseq

description:
smartseq2
sham_1.xlsx

value: 6-8 weeks old


title: Cell_7d_bio1_tech2

description: Cell growth inhibition test.xlsx


title: HUVEC only fibrin tissue day 10 sample1


title: M1_2

source_name: M1,replicate 2


title: HUVEC+DPSC  fibrin tissue day 10 sample2


title: cardiomyocyte,sham, replicate1-17, scRNAseq

description:
smartseq2
sham_1.xlsx


title: M1_1

source_name: M1,replicate 1


title: DL_3

description: Gene expression in Hela cells transfected with  preS2 deletion

source_name: preS2 deletion,replicate 3


title: cardiomyocyte,sham, replicate1-16, scRNAseq

description:
smartseq2
sham_1.xlsx

source_name: heart


title: M2_1

source_name: M2,replicate 1


title: Cell_0d_bio1_tech1

description: Cell growth inhibition test.xlsx

source_name: Myeloid malignant cell line


title: shKLF2_rep3

first: Qian

last: Bian

address: Jinzun Road No.115

department: Shanghai Institute of Precision Medicine, Ninth People’s Hospital

description: shKLF2 RNA-seq replicate3

data_processing:
For analyzing RNA-seq data of shControl and shKLF2 HemSCs, adaptor-trimmed sequencing data were aligned to human reference genome (hg38) with STAR (version 2.7.3a). Mapped reads were then counted with HTSeq (version 0.12.4) to generate counts of RNA-seq libraries, which were further normalized with DESeq2 (version 1.38.1).
Reads matching the forward primer sequence were selected from the total fastq files to ensure an overall high quality of the raw data. The primer sequences were then removed from selected reads, which were then mapped to mm10 reference genome with Bowtie2.
Adaptor sequences in CUT&Tag fastq files were trimmed with trim galore.
Differentially expressed genes (DEGs) were identified with cutoff P value<0.05 and |log2Foldchange|>1.
FPKM values of each sample were counted with rnanorm (https://github.com/genialis/RNAnorm).
Assembly: hg38
Supplementary files format and content: counts (mapped counts)
Supplementary files format and content: csv (FPKM)
Supplementary files format and content: csv (DEGs)

source_name: HemSCs

extract_protocol:
Proliferating regions of IH specimens were minced into pieces and digested with collagenase (Sigma-Aldrich) and Dispase (Gibco). After removal of red blood cells with RBC lysis buffer (Sangon), HemSCs were isolated from cell suspension by anti-CD133 magnetic beads (Miltenyi), and were cultured in vitro on fibronectin-coated (Corning) petri dishes or plates in Endothelial Cell Growth Medium-2 (EGM-2, Lonza, Cat#CC-3162) supplemented with 20% FBS (Gibco). HemSCs between passage 3 to passage 6 were used in this study.
Briefly,mRNA was captured from total RNA with VAHTS mRNA Capture Beads (Vazyme, Cat#N401) for fragmentation into short length nucleotides. First-strand cDNA synthesis was then performed with   1st Strand Enzyme Mix 2, followed by generation of second-strand cDNA with 2nd Strand Enzyme Super Mix. Double-stranded cDNA was then ligated with sequencing adapters, purified and amplified with PCR. After size selection, the RNA-seq libraries were sequenced on Illumina Nova Seq 6000 platform at PE150 mode. Three biological replicates of RNA-seq libraries were prepared for shControl and shKLF2 HemSCs respectively.

value: KLF2 Knockdown

value: HemSCs


title: cardiomyocyte,sham, replicate1-20, scRNAseq

description:
smartseq2
sham_1.xlsx


title: DL_2

source_name: preS2 deletion,replicate 2

value: HeLa


title: Cell_7d_ATO_bio1_tech2

description: Cell growth inhibition test.xlsx


title: cardiomyocyte,sham, replicate1-15, scRNAseq

description:
smartseq2
sham_1.xlsx


title: shKLF2_rep1

description: shKLF2 RNA-seq replicate1


title: Sunitinib-Treated rep2 Ribo-Seq

city: Chicago

first: Soroush

last: Tahmasebi

address: 909 S Wolcott, Chicago, IL 60607

institute: University of Illinois

data_processing:
Library strategy: Ribo-seq
adapter AGATCGGAAGAGCACACGTCTGAA was removed with cutadapt version 1.18
Reads aligning to human rRNA were removed (aligned using bowtie 1.0.1)
Reads were aligned to the human GENCODE transcriptome version 25 (aligned using bowtie version 1.0.1)
Read counts were extracted from the CDS regions of principal transcript isoforms (principal isoforms were taken from the APPRIS database)
hg38
Genome_build: Matrix table with raw gene counts for every gene and every sample

source_name: iPSC-Ecs

extract_protocol:
RNA fragments of expected size were isolated after the ribosomal pellet was resolved by electrophoresis through a denaturing gel.
Gel extract footprints were reverse-transcribed and cloned into a cDNA library for RNA sequencing.Randomly fragmented total mRNA libraries were also prepared in parallel for each sample for RNA sequencing.

value: iPSC-EC

tag: molecule subtype

value: Ribosome Protected Fragments


title: cardiomyocyte,sham, replicate1-14, scRNAseq

description:
smartseq2
sham_1.xlsx


title: shControl_rep3

description: shControl RNA-seq replicate3

value: Control


title: Sunitinib-Treated rep1 Ribo-Seq


title: DL_1

source_name: preS2 deletion,replicate 1


title: WT_2

description: Gene expression in Hela cells transfected with  wild type preS

source_name: WT,replicate 2


title: shControl_rep2

description: shControl RNA-seq replicate2


title: WT_3

source_name: WT,replicate 3


title: Control rep2 Ribo-Seq