title: DSP-1001660008975-G-B03

tag: tissue

value: Colorectal cancer

tag: disease state

value: Colon cancer

value: No Neoadjuvant chemotherapy

value: CK

value: Bordered

tag: slide

tag: roi number

tag: roi x_coordinate


title: C938 [miRNA-seq]

status: Public on Dec 31 2022

type: SRA

city: Atlanta

first: Michael

last: Davis

state: GA

address: 2015 Uppergate Dr

country: USA

institute: Emory University

description: small RNA

library_source: transcriptomic

data_processing:
Base calling was conducted with RTA v3.4.4 and demultiplexing was performed with bcl2fastq v2.20.0.422.
Fastq files were aligned to the human genome using the Qiagen GeneGlobe primary analysis tool.
Supplementary files format and content: *-sRNA.txt: Tab-delimited text files include raw counts.
Supplementary files format and content: sRNA_processed.csv: Comma-separated text files includes raw counts.

molecule: total RNA

organism: Homo sapiens

source_name: c-kit+ progenitor cell isolated from atrial appendage

growth_protocol: CPCs were isolated by c-kit magnetic bead sorting from cardiac biopsies of congenital heart disease patients . CPCs were cultured using Hams F-12 medium with 10% fetal bovine serum, 1% Penicillin-Streptonmycin, 1% L-glutamine, and 0.04% fibroblast growth factor 2.

extract_protocol:
Qiagen miRNeasy kit was used to extract RNA from both CPCs and CPC sEVs.
1 ng of RNA was used as input for library preparation with the Qiagen QIAseq miRNA Library Prep Kit

treatment_protocol: CPCs were serum-depleted 24 h prior to isolate small extracellular vesicles (sEVs). 24 h after serum-depletion, conditioned media were collected and sEVs were isolated by serial ultracentrifugation (7,000 rpm for 30 mins, 32,000 rpm for 210 mins for twice).

tag: patient id

tag: sequence facility

value: Novogene

tag: heart chamber

value: Atrium

tag: age

value: 5 years

tag: Sex

value: Male

tag: diagnosis

value: Subaortic membrane resection, mitral valve ring

tag: cell type


title: F2_D2 individual, grown at 16C [T16_P4.D11_F2_D2]

city: Vienna

first: Rahul

last: Pisupati

address: Dr. Bohrgasse 3

country: Austria

institute: Gregor Mendel Institute

library_source: genomic

data_processing:
Raw sequencing reads were trimmed using cutadapt
Trimmed reads were mapped to reference TAIR10 genome using Bismark
Assembly: TAIR10
Supplementary files format and content: Files are in bedgraph format with "chromosome position strand context mc_score total_reads methylated"

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: leaf

extract_protocol:
DNA was extracted from leaf tissue and performed bisulfite treatment
Libraries were constructed and sequenced through Illumina HiSeq

value: leaf

tag: developmental stage

value: 7-10 leave rosette

tag: genotype

tag: treatment


title: F2_D1 individual, grown at 16C [T16_P4.D10_F2_D1]


title: C894 [miRNA-seq]

description: small RNA

source_name: c-kit+ progenitor cell isolated from appendage

value: Ventricle

value: 6 months

value: Not determined

value: Not known


title: F2_D1 individual, grown at 16C [T16_P4.C6_F2_D1]


title: E2016 [RNA-Seq]

data_processing:
Sequencing from Novogene: Illumina NovaSeq 6000 with PE150 platform); Yerkes: Illumina HiSeq 30000.
Total RNA was aligned and gene counts were determined with STAR aligner in the Illumina BaseSpace app, RNA-Seq Alignment.
Base calling was conducted with RTA v3.4.4 and demultiplexing was performed with bcl2fastq v2.20.0.422
Assembly: Reads aligned with hg19 reference genome.
Supplementary files format and content: raw counts

source_name: c-kit+ progenitor cell-derived small extracellular vesicles

extract_protocol:
Qiagen miRNeasy kit was used to extract RNA from both CPCs and CPC sEVs.
1 ng of RNA was used as input for library preparation with the Takaro Bio SMARTer Stranded Total RNA-Seq Kit v2 Pico Input Mammalian

value: Yerkes Nonhuman Primate Genomics Core

value: 1-2 week

value: Female

value: Coarctation, atrial septal defe ct, ventricular septal defect


title: BMDM Wt1

city: Shanghai

first: Zhiqiang

last: Li

state: Shanghai

address: 301 Middle Yanchang Road

department: Department of Cardiology

country: China

institute: Shanghai Tenth People's Hospital

data_processing:
OE biotech Co., Ltd.  (Shanghai, China).
Raw data (raw reads) were processed using Trimmomatic.
The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat2.
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include counts for each Sample

organism: Mus musculus

source_name: BMDM

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol.
RNA libraries were constructed using TruSeq Stranded  mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s  instructions

tag: cell line

value: BMDM

value: mouse bone marrow-derived macrophages

value: WT

value: LPS treatment


title: C903 [miRNA-seq]

description:
small RNA
sRNA_processed.csv

value: Atrium

value: < 1 week

value: Hypoplastic left heart syndrome

value: c-kit+ progenitor cell isolated from atrial appendage


title: F2_D1 individual, grown at 16C [T16_P4.C5_F2_D1]

value: leaf

value: 7-10 leave rosette


title: DSP-1001660008975-G-B01

city: Tomsk

first: Irina

last: Larionova

state: Tomsk oblast

address: Lenin Ave, 36, Tomsk, Tomsk Oblast, Russia

country: Russia

institute: Tomsk State University

library_source: other

data_processing:
The raw counts were processed in the NanoString’s GeoMx NGS pipeline v.2.1 where they were converted to the digital count conversion (DCC) files
The GeomxTools was used for quality control (QC) and downstream analysis of the DCC files in R
Assembly: hg38
Supplementary files format and content: GeoMx pipeline readable digital counts (DCC)
Library strategy: GeoMx NGS readout

molecule: other

source_name: Colorectal cancer

extract_protocol:
Briefly, once the slides were deparaffinised and subjected to antigen retrieval procedures, samples were co-incubated with fluorescent-labeled visualization antibodies to detect tumor cells (pan-cytokeratin [CK]), all immune cells (CD45), together with DAPI for nuclei detection. Customizable fluorescent morphology markers, conjugated to unique oligonucleotide tags with an ultraviolet (UV) photocleavable linker, helped visualizing the tissue architecture. The samples were imaged and regions of interest (ROIs) were exposed to UV light that cleaved the linker and released the barcoded oligos for capture by microfluidics and GeoMx DSP then were coupled to next generation sequencing (NGS) readout to profile RNA expression for identifying over 1,800 genes in colon and rectal cancers. The 97 areas of illumination (AOIs) across all slides in mixed stroma/tumor regions was selected
After UV illumination, the barcodes were collected in 96-well plates and were used in the NGS readout library preparation procedure protocol. The resulted libraries were sequenced by the Illumina NextSeq 500 platform using 2 x 27 base paired reads

value: Colorectal cancer

value: Colon cancer

tag: patient

value: No Neoadjuvant chemotherapy

tag: segment

value: CK

tag: tissue site

value: Internal

tag: roi y_coordinate


title: E2013 [RNA-Seq]

value: Yerkes Nonhuman Primate Genomics Core

value: 3 months

value: Male

value: Ventricular septal defect


title: F2_D1 individual, grown at 16C [T16_P4.C3_F2_D1]

tag: tissue


title: DSP-1001660008972-H-B01

tag: disease state

value: Rectal cancer

value: Neoadjuvant chemotherapy

tag: slide

tag: roi number

tag: roi x_coordinate


title: F2_D1 individual, grown at 16C [T16_P4.C4_F2_D1]


title: DSP-1001660008972-H-B02

value: Bordered


title: DSP-1001660008972-H-A12

value: External


title: F2_D1 individual, grown at 16C [T16_P4.C1_F2_D1]


title: DSP-1001660008972-H-A11


title: Liver Mier1 KO 0h

first: Yanhao

last: Chen

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

data_processing:
Basecalls were performed using bcl2fastq v2.17
ATAC-seq reads were trimmed by using Trim Galore (v0.6.7), discarding reads left with < 20 bp
ATAC-seq reads were aligned to the reference mouse genome UCSC mm10 by Bowtie 2 (v2.2.5). Only uniquely mapping reads without mismatches were retained. Duplicate reads and reads mapping to the mitochondrial genome were discarded.
ATAC-seq peaks were called and annotated by using HOMER (v4.11) findPeaks function with following parameters “-style dnase -minDist 200 -size 100”. Peak regions overlapping with mm10 ENCODE exclusion list regions were discarded.
To create ATAC-seq coverage plots, regions of interest was extracted from bam files and renormalized to counts per million by ngs.plot (v2.6.1) with following parameters "-L 3000 -FL 100 -MW 4 -SE 0".
bigWig files were generated using the deeptools bamCoverage function. Score represents the normalized coverage of DNA fragments at a given genomic coordinate.
Assembly: mm10
Supplementary files format and content: big wig files

source_name: Liver

extract_protocol:
Nuclei were purified by gradient density centrifugation frome 30mg homogenized frozen liver tissue.
50,000 purified nuclei were used to generated ATAC-seq libraries by TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501). Final libraries were purified and size selected using VAHTS DNA Clean Beads (Vazyme, N411). Library quality was assessed on the Agilent Bioanalyzer 2100 system and qPCR

value: Liver

tag: aav treatment

value: AAV-Mier1 sgRNA

value: PHx 0 h


title: Liver Control 0h

value: AAV-Cre


title: E1097 [RNA-Seq]

tag: patient id

tag: sequence facility

tag: heart chamber

value: Atrium

tag: age

tag: Sex

value: Tetralogy of Fallot


title: E1100 [RNA-Seq]

value: < 1 week

value: Female

tag: diagnosis

value: Hypoplastic left heart syndrome


title: E1099 [RNA-Seq]

value: Yerkes Nonhuman Primate Genomics Core

value: 5 months

value: Complete atrioventricular canal defect, Downs syndrome


title: E1095 [RNA-Seq]

value: 3 months

value: Male

value: Double outlet right ventricle


title: C57BL/6 mice, Fibrinigen, miRNA-Seq, rep3

city: Beijing

first: Huiqing

last: Hou

state: Beijing

address: No.119, South 4th Ring West Road, Fengtai District

department: Neurology

institute: Beijing Tiantan Hospital

data_processing:
Raw sequencing data was firstly filtered by fastx_toolkit (version: 0.0.13.2) fordiscarding the low-quality reads and adaptor sequences were trimmed by cutadapt(version: 1.15)
UMI analysis was conducted with KC-UID (https://github.com/KC-UID/KC-UID)
Reads were mapped to the genome  using bowtie (version: 1.1.2) with default parameters
The package of mirdeep2 (version:2.0.0.8) was used for mapping the reads to the known primary-miRNA in the database of miRBase and predicting the novel miRNA
The TPM of miRNA was count with edgeR package (version: 3.12.1)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: brain

extract_protocol:
RNA was harvested using TRIzol reagent (Invitrogen). Total RNA was used for the construction of sequencing libraries.
miRNA libraries for miRNA-seq were prepared using small RNA Library Prep Kit  for Illumina following manufacturer's protocols.

value: brain

tag: strain

tag: cell type

value: oligodendrocyte progenitor cells

tag: genotype

value: WT

tag: treatment

value: fibrinogen


title: Liver Control 24h

value: Liver

value: PHx 24 h


title: DSP-1001660008972-H-A10

value: Colorectal cancer

value: Colon cancer

tag: patient

value: No Neoadjuvant chemotherapy

tag: segment

tag: tissue site

value: External

tag: roi y_coordinate


title: Liver Mier1 KO 24h

tag: tissue

value: AAV-Mier1 sgRNA


title: DSP-1001660008975-G-B02

tag: disease state

value: Internal

tag: slide

tag: roi number

tag: roi x_coordinate


title: C57BL/6 mice, Fibrinigen, miRNA-Seq, rep2


title: F2_D1 individual, grown at 16C [T16_P4.C11_F2_D1]

value: leaf

tag: developmental stage

value: 7-10 leave rosette


title: C57BL/6 mice, Fibrinigen, miRNA-Seq, rep1


title: F2_D2 individual, grown at 16C [T16_P4.C10_F2_D2]


title: E1083 [RNA-Seq]

tag: patient id

tag: sequence facility

value: Yerkes Nonhuman Primate Genomics Core

tag: heart chamber

value: Atrium

tag: age

value: < 1 week

value: Female

value: Interrupted aortic arch, ventricular septal defect


title: DSP-1001660008972-H-A09

value: Bordered


title: E1066 [RNA-Seq]

value: 6 months

tag: Sex

tag: diagnosis

value: Tricuspid atresia, ventricular septal defect, atrial septal defect


title: DSP-1001660008972-H-A08

tag: treatment

value: CK


title: C57BL/6 mice, Control, miRNA-Seq, rep3

value: brain

tag: strain

tag: cell type

value: oligodendrocyte progenitor cells

tag: genotype

value: WT

value: control


title: F2_D1 individual, grown at 16C [T16_P4.C2_F2_D1]


title: F2_D2 individual, grown at 16C [T16_P4.B9_F2_D2]


title: C57BL/6 mice, Control, miRNA-Seq, rep2


title: DSP-1001660008972-H-A07

value: Colorectal cancer

value: Colon cancer

tag: patient

value: No Neoadjuvant chemotherapy

tag: segment

tag: tissue site

tag: roi y_coordinate


title: F2_D1 individual, grown at 16C [T16_P4.C12_F2_D1]

tag: tissue

value: leaf

value: 7-10 leave rosette


title: E1050 [RNA-Seq]

value: Yerkes Nonhuman Primate Genomics Core

value: Atrium

value: 1 week

value: Hypoplastic left heart syndrome


title: C57BL/6 mice, Control, miRNA-Seq, rep1


title: DSP-1001660008972-H-A06

tag: disease state

value: Bordered

tag: slide

tag: roi number

tag: roi x_coordinate


title: E1045 [RNA-Seq]

tag: patient id

tag: sequence facility

tag: heart chamber

value: < 1 week

value: Female

value: Coarctation of the aorta, ventricular septal defect


title: DSP-1001660008972-H-A04

value: CK

value: Internal


title: F2_D1 individual, grown at 16C [T16_P4.B7_F2_D1]

tag: developmental stage


title: C57BL/6 mice, Fibrinigen, rep2

data_processing:
STRA software (version 2.5.3a)
Sequence reads were trimmed for adaptor sequence/low-quality sequence using  trimmomatic (version 0.39, parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 HEADCROP:0 MINLEN:36)
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR (version 2.7.6a, default parameters)
Read count extraction and normalization were performed using featureCounts (version 1.5.1, parameters: -d 30 -D 1000 -C -s 0 -t exon -g GENE --primary)
RPKM was calculated with edgeR (version 3.12.1)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was harvested using TRIzol reagent (Invitrogen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KCTM Stranded mRNA Library Prep Kit  following manufacturer's protocols.

value: brain

tag: cell line

value: oligodendrocyte progenitor cells

value: WT

tag: treatment

value: fibrinogen


title: F2_D1 individual, grown at 16C [T16_P4.B8_F2_D1]

tag: cell type


title: E1010 [RNA-Seq]

tag: age

value: 9 weeks

tag: Sex

value: Male

tag: diagnosis

value: Tetralogy of Fallot


title: C57BL/6 mice, Fibrinigen, rep3

tag: genotype


title: DSP-1001660008972-H-A05

value: Colorectal cancer

value: Colon cancer

tag: patient

value: No Neoadjuvant chemotherapy

tag: segment

tag: tissue site

tag: roi y_coordinate


title: F2_D1 individual, grown at 16C [T16_P4.B5_F2_D1]

tag: tissue

value: leaf

value: 7-10 leave rosette


title: C57BL/6 mice, Fibrinigen, rep1


title: F2_D2 individual, grown at 16C [T16_P4.B4_F2_D2]


title: DSP-1001660008972-H-A03

tag: disease state

tag: slide

tag: roi number

tag: roi x_coordinate


title: E1007 [RNA-Seq]

tag: patient id

tag: sequence facility

value: Yerkes Nonhuman Primate Genomics Core

tag: heart chamber

value: Atrium

value: 6 months

value: Ventricular septal defect, congenial/subaortic stenosis repair defect


title: DSP-1001660008972-H-A02

tag: treatment

value: CK

value: Internal


title: E1006 [RNA-Seq]

tag: age

value: Female

value: Complete atrioventricular canal defect


title: C57BL/6 mice, Control, rep3

value: brain

tag: cell line

tag: cell type

value: oligodendrocyte progenitor cells

value: WT

value: control


title: E1063 [RNA-Seq]

value: 3 years

tag: Sex

value: Male

tag: diagnosis

value: Ventricular septal defect


title: F2_D2 individual, grown at 16C [T16_P4.B3_F2_D2]

value: leaf

tag: developmental stage

tag: genotype


title: E1004 [RNA-Seq]

value: 12 months

value: Anomalous right superior vena cava to left atrium, no left superior vena cava


title: C57BL/6 mice, Control, rep2


title: F2_D1 individual, grown at 16C [T16_P4.B2_F2_D1]

value: 7-10 leave rosette


title: E985 [RNA-Seq]

value: Yerkes Nonhuman Primate Genomics Core

value: Atrium

value: 2 weeks

value: Interrupted aortic arch


title: C57BL/6 mice, Control, rep1


title: F2_D2 individual, grown at 16C [T16_P4.B6_F2_D2]


title: F2_D2 individual, grown at 16C [T16_P4.B12_F2_D2]


title: E957 [RNA-Seq]

value: 7 months

value: Partial anomalous pulmonary venous return


title: TNBC-L, replicate 1, scRNAseq

city: Wuhan

first: Li

last: Su

state: Hubei

address: Luoyu Road 1037

institute: Huazhong university of science and technology

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Breast cancer in situ from patient

extract_protocol:
Freshly collected Breast cancer in situ from patient were flushed with ice-cold HBSSwo (Mg2+/Ca2+ free supplemented with 10mM HEPES, pH 7.2) to remove luminal content. The tissue was inverted and inflated by injection of HBSSwo. Epithelial isolation was performed by incubation of tissue with pre-digestion buffer (HBSSwo, 5 mM EDTA, 5% v/v FCS, 1 mM DTT) in a shaking incubator. The isolated epithelial cells were resuspended in digestion buffer (HBSS with Mg2+/Ca2+ supplemented with 2 mg/ml collagenase type I and 40 U/ml DNase I) and incubated at 37 °C for 30 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (HBSSwo, 2% v/v FCS, 5mM EDTA).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 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.

value: stage III triple-negative breast cancer

value: epithelial cells

value: subcutaneous metastatic sample


title: F2_D2 individual, grown at 16C [T16_P4.B10_F2_D2]


title: Day 14 post-CTX MmSCs

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: scRNA-seq of MmSCs 14 days post CTX injury

data_processing:
Sequenced reads were demultiplexed (only for MDX-DBA dataset), aligned, assigned to cells, and output as count matrices using Cell Ranger (10x Genomics).
Hash-by-cell matrices (only for MDX-DBA dataset) were computed using CITE-seq-count.
Cells with no or multiple hashes (only for MDX-DBA dataset), high mitochondrial content, low gene number, low UMI number, or lineage markers of contaminants were filtered out in Seurat (v4.1.2)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Skeletal muscle

extract_protocol:
Cells were isolated by first enzymatically digesting the hindlimb muscles and then purified by fluorescence-activated cell sorting. Single cells were then sent to the Broad Institute Genomics Platform, which performed encapsulation following 10x Genomics protocols.
10x Genomics library prep, 3' v2 chemistry (CTX), 3' v3 chemistry (MDX-DBA)

treatment_protocol: For CTX time-course dataset, mice were injected with 0.03 mL of Naja mossambica CTX (0.03 mg/mL) intramuscularly (i.m.) in their hindlimb muscles (tibialis anterior, gastrocnemius, quadriceps)

value: Skeletal muscle

value: MmSCs

tag: strain

value: 14 day after cardiotoxin-induced hindlimb skeletal muscle injury


title: E956 [RNA-Seq]

value: 5 months

value: Female

value: Complete atrioventricular canal defect


title: F2_D1 individual, grown at 16C [T16_P4.A9_F2_D1]

tag: tissue

value: leaf


title: Day 7 post-CTX MmSCs

description: scRNA-seq of MmSCs 7 days post CTX injury

value: Male

value: 7 day after cardiotoxin-induced hindlimb skeletal muscle injury


title: JDM.RN.9.1063.MR,  Juvenile Dermatomyositis, during treatment, CD14

city: London

first: Meredyth

middle: G Ll

last: Wilkinson

state: London

address: 30 Guilford Street

country: United Kingdom

institute: UCL GOS Institute of Child Health

data_processing:
Run data were demultiplexed and converted to fastq files using Illuminas bcl2fastq Conversion Software v2.16. Sequencing reads (in fastq format) were aligned to the GRCh38 reference sequence using TopHat v2.1.0.
Assembly: GRCh38
Supplementary files format and content: 221215_HIGH5_expression_matrix_rpkm_JDM
Supplementary files format and content: 221215_HIGH5_expression_matrix_raw_counts_JDM

source_name: Blood

extract_protocol:
Sorted B cell RNA was extracted using the Arcturus PicoPure RNA Isolation Kit.
Samples were processed using Illuminas TruSeq Stranded mRNA LT sample preparation kit (p/n RS-122-2101) according to manufacturers instructions.
Samples were sequenced on the NextSeq 500 instrument (Illumina, San Diego, US) using a 43 bp paired end run resulting in >15million reads per sample.

treatment_protocol: Sample processing: CD19+ B cells, CD14+ monocytes, CD4+ T cells, CD8+ T cells were sorted from freeze-thawed peripheral blood mononuclear cells (PBMC) by flow cytometry (FACS Aria III). DAPI was used to exclude dead cells.

tag: disease

value: Juvenile Dermatomyositis

value: Blood

value: F


title: E930 [RNA-Seq]

value: Yerkes Nonhuman Primate Genomics Core

value: Atrium

value: < 1 week

value: Total anomalous pulmonary venous return, unbalanced atriovantricular canal defect


title: JDM.RN.9.1064.MR, Juvenile Dermatomyositis, during treatment, CD19


title: JDM.RN.9.1062.MR, Juvenile Dermatomyositis, during treatment, CD8


title: E975 [RNA-Seq]

value: 6 months

value: Tetralogy of Fallot


title: Day 3 post-CTX MmSCs

description: scRNA-seq of MmSCs 3 days post CTX injury

value: Skeletal muscle

value: MmSCs

value: 3 day after cardiotoxin-induced hindlimb skeletal muscle injury


title: JDM.RN.9.1059.MR, Juvenile Dermatomyositis, pre treatment, CD14


title: E926 [RNA-Seq]

value: 14 months

value: Ventricular septal defect


title: MmSCs from 2.5-, 5- , 12.5-wk-old Dmdmdx; 2.5- , 12.5-wk-old DBA/2J mice

description: scRNA-seq of MmSCs from hindlimb muscle

value: Dmdmdx, DBA/2J

value: No treatment

tag: hashid

value: 2.5-wk-old MDX:Hash5-TACAGTCGCTTGGCA

value: 5-wk-old MDX:Hash7-GGGCTTATCATTAAG

value: 12.5-wk-old MDX:Hash9-TGGAGTATCACCAAT

value: 2.5-wk-old DBA:Hash6-CTCTCCCTTTGTAGT

value: 12.5-wk-old DBA:Hash4-AAAGCATGACCAGTA


title: F2_D1 individual, grown at 16C [T16_P4.A8_F2_D1]

value: leaf

value: 7-10 leave rosette


title: Day 1 post-CTX MmSCs

description: scRNA-seq of MmSCs 1 day post CTX injury

value: Male

value: 1 day after cardiotoxin-induced hindlimb skeletal muscle injury


title: E925 [RNA-Seq]

value: Yerkes Nonhuman Primate Genomics Core

value: Atrium

value: < 1 week

value: Female

value: Total anomalous pulmonary venous return


title: F2_D2 individual, grown at 16C [T16_P4.A7_F2_D2]


title: JDM.RN.9.1058.MR, Juvenile Dermatomyositis, pre treatment, CD8

value: Juvenile Dermatomyositis

value: Blood

value: F


title: Day half post-CTX MmSCs

description: scRNA-seq of MmSCs 0.5 days post CTX injury

value: Skeletal muscle

value: MmSCs

value: 0.5 days after cardiotoxin-induced hindlimb skeletal muscle injury


title: F2_D2 individual, grown at 16C [T16_P4.A6_F2_D2]


title: E924 [RNA-Seq]

value: 2 months


title: F2_D1 individual, grown at 16C [T16_P4.A5_F2_D1]


title: Uninjured MmSCs

description: scRNA-seq of MmSCs from uninjured hindlimb muscle

value: No treatment


title: RNAseq_GE_2483-9_KO

first: Yan

last: Jiang

address: 131 Dongan rd

department: Institutes of Brain Science

institute: Fudan University

data_processing:
ATACseq:
Sequenced reads were trimmed for adapter sequence, and masked for low-complexity or low-quality sequence (--quality 20 --phred33 --stringency 1 --length 20 --paired), then mapped to mm10 whole genome using Bowtie2 v2.3.4.3 with --phred33, --sensitive, look for multiple alignments and report best with MAPQ, --maxins 1000.
MACS2 was used for peak calling with --keep-dup 1 --shift -100 --extsize 200 –nomodel
RNA-seq:
Sequenced reads were trimmed for adapter sequence, and masked for low-complexity or low-quality sequence (--quality 20 --phred33 --stringency 1 --length 20 --paired), then mapped to mm10 whole genome using Tophat2 v2.1.1 with parameters --max-multihits 20 --transcriptome-max-hits 60.
The number of reads falling in the exons were counted by FeatureCounts v1.6.3 with GTF file (gencode.vM20.annotation.gtf).
Supplementary_files_format_and_content: Peak text files
Supplementary_files_format_and_content: Raw counts text files

source_name: Ganglionic eminence

extract_protocol:
ATAC-Seq: 50,000 to 100,000 nuclei from GE_NPC were used for ATAC-seq library preparation.
ATAC-seq library preparation using reagents from TruePrep DNA Library Preparation Kit V2 (Vazyme, TD501-02, China) following the manufactory's protocol with modifications.
RNA-seq: Total RNA was extracted from fresh frozen GE_NPCs and GE tissue at E15.5 by Direct-zolTM RNA MicroPrep kit (ZYMO RESEARCH, catalog #R2060) and RNeasy Lipid Tissue Mini Kit (Qiagen, catalog #74804), respectively.
mRNA-seq libraries from GE_NPCs were prepared by BGI Genomics, China. Total RNA-seq libraries from GE tissue were prepared using QIAseq™ Stranded Total RNA Lib Kit (Qiagen, Cat#180745) following the manufacturer’s instructions.

value: Brain homogenate

value: Nestin-KO

tag: gender

value: male


title: F2_D1 individual, grown at 16C [T16_P4.A4_F2_D1]

value: leaf

value: 7-10 leave rosette


title: E902 [RNA-Seq]

value: Yerkes Nonhuman Primate Genomics Core

value: Atrium

value: 4 years

value: Male

value: Atrial septal defect


title: RNAseq_GE_2483-7_KO


title: E896 [RNA-Seq]

value: 12 months

value: Female

value: Ventricular septal defect


title: JDM.RN.7.1048.MR, Juvenile Dermatomyositis, pre treatment, CD19

value: Juvenile Dermatomyositis

value: Blood

value: F


title: F2_D2 individual, grown at 16C [T16_P4.A3_F2_D2]


title: F2_D1 individual, grown at 16C [T16_P4.A2_F2_D1]


title: E894 [RNA-Seq]

value: Ventricle

value: 6 months

value: missing

value: Not known


title: JDM.RN.7.1047.MR, Juvenile Dermatomyositis, pre treatment, CD14


title: F2_D2 individual, grown at 16C [T16_P4.A1_F2_D2]

value: leaf


title: JDM.RN.7.1046.MR, Juvenile Dermatomyositis, pre treatment, CD8


title: JDM.RN.9.1057.MR, Juvenile Dermatomyositis, pre treatment, CD4


title: RNAseq_GE_2483-2_WT

value: Brain homogenate

value: WT

value: male


title: C2013 [RNA-Seq]

source_name: c-kit+ progenitor cell isolated from artial appendage

value: Novogene

value: Atrium

value: 3 months


title: E903 [RNA-Seq]

value: Yerkes Nonhuman Primate Genomics Core

value: < 1 week

value: Hypoplastic left heart syndrome


title: JDM.RN.7.1052.MR,  Juvenile Dermatomyositis, during treatment, CD19

value: Juvenile Dermatomyositis


title: C1100 [RNA-Seq]

value: Female


title: ATACseq_NPC_4643_KO

source_name: Neurosphere culture from Ganglionic eminence

value: Neural progenitor cells

value: Nestin-KO


title: JDM.RN.6.1044.MR, Juvenile Dermatomyositis, during treatment, CD19

value: Blood

value: F


title: F2_D1 individual, grown at 16C [T16_P4.A10_F2_D1]

value: 7-10 leave rosette


title: C1099 [RNA-Seq]

value: 5 months

value: Complete atrioventricular canal defect, Downs syndrome


title: JDM.RN.6.1043.MR, Juvenile Dermatomyositis, during treatment, CD14


title: ATACseq_NPC_3043_KO


title: RNAseq_GE_2483-4_WT

value: Brain homogenate

value: WT


title: C2016 [RNA-Seq]

value: Novogene

value: 1-2 week

value: Coarctation, atrial septal defe ct, ventricular septal defect


title: F2_D2 individual, grown at 16C [T16_P3.H9_F2_D2]

value: leaf


title: JDM.RN.6.1042.MR, Juvenile Dermatomyositis, during treatment, CD8


title: JDM.RN.7.1045.MR, Juvenile Dermatomyositis, pre treatment, CD4


title: C1097 [RNA-Seq]

value: Atrium

value: 3 months

value: Male

value: Tetralogy of Fallot


title: ATACseq_NPC_5088_WT

value: Neural progenitor cells

value: female


title: F2_D2 individual, grown at 16C [T16_P3.H8_F2_D2]


title: F2_D2 individual, grown at 16C [T16_P3.H7_F2_D2]


title: ATACseq_NPC_5084_KO

value: Nestin-KO


title: C1095 [RNA-Seq]

value: Yerkes Nonhuman Primate Genomics Core

value: Double outlet right ventricle


title: C1092 [RNA-Seq]

value: 4 years

value: Female

value: Atrial septal defect


title: JDM.RN.6.1041.MR, Juvenile Dermatomyositis, during treatment, CD4

value: Juvenile Dermatomyositis

value: Blood

value: F


title: JDM.RN.6.1039.MR, Juvenile Dermatomyositis, pre treatment, CD14


title: ATACseq_NPC_3046_WT

value: WT


title: F2_D1 individual, grown at 16C [T16_P3.H6_F2_D1]

value: leaf

value: 7-10 leave rosette


title: C1083 [RNA-Seq]

value: Novogene

value: Atrium

value: < 1 week

value: Interrupted aortic arch, ventricular septal defect


title: JDM.RN.6.1037.MR,  Juvenile Dermatomyositis, pre treatment, CD4


title: C1066 [RNA-Seq]

value: 6 months

value: Tricuspid atresia, ventricular septal defect, atrial septal defect


title: JDM.RN.5.1036.MR, Juvenile Dermatomyositis, during treatment, CD19

value: M


title: C1063 [RNA-Seq]

value: Yerkes Nonhuman Primate Genomics Core

value: 3 years

value: Male

value: Ventricular septal defect


title: F2_D2 individual, grown at 16C [T16_P3.H4_F2_D2]


title: F2_D2 individual, grown at 16C [T16_P3.H3_F2_D2]


title: C1050 [RNA-Seq]

value: 1 week

value: Female

value: Hypoplastic left heart syndrome


title: RNA-seq AB1 Ts15 rep2

first: Mengfan

address: No.5 Yiheyuan Road

institute: Peking University

description:
processed data file:
raw_counts.txt
Ts15_fpkm_DESeq2_output.txt
Ts-15-2_HVNNMCCXX_L7

data_processing:
All RNA-seq reads were aligned to mouse mm10 reference genome using Hisat2 (Kim et al., 2015) with default parameters and assigned to each gene using the summarizeOverlaps function in Bioconductor (Lawrence et al., 2013). Low FPKM values were usually experimental or sequencing noise rather than truly expressed genes, so genes whose FPKM values less than 1 in both comparing samples were removed and not included in the downstream analysis (Mortazavi et al., 2008). DESeq2 (Love et al., 2014) was used to identify differentially expressed genes (FDR < 0.05, fold change > 1.2). Differentially expressed genes in at least two trisomic mESCs compared with the WT mESC were regarded as shared differentially expressed genes. Enrichr was used to perform GO and KEGG pathway enrichment analysis (Kuleshov et al., 2016).
Genome_build: mm10

molecule: polyA RNA

source_name: RNA-seq Ts15_mESCs

growth_protocol: WT and trisomic mESCs were cultured on a layer of γ-irradiated mouse embryonic fibroblasts (i-MEFs) in KnockOut DMEM (Gibco, 10829018) supplemented with 15% fetal bovine serum (FBS, Sigma, F4135), 1000 U/ml leukemia inhibitory factor (LIF, ESG1107), 2 mM GlutaMAX-1 (Gibco, 35050061), 1% non-essential amino acids (NEAA) (Gibco, 1140050), and 100 μM β-mercaptoethanol (Gibco, 21985023). Cells were cultured at 37°C in a 5% CO2 incubator, and were dissociated into single cell suspension with 0.05% Trypsin-EDTA (Gibco, 25300062) at 37°C for 10 min. For the following RNA-seq and Hi-C experiments, cells were then sedimented in the cell culture dishes for 30 min to remove the feeder cells.

extract_protocol:
Total RNA of WT and trisomic mESCs was isolated following TRIZOL RNA extraction method, and poly(A) based mRNA enrichment was performed. Then mRNA was fragmented and cDNA was synthesized from mRNA library.
RNA-seq library was prepared following DNA end repair, dATP tailing, adapter ligation and PCR.

value: mouse embryonic stem cells (mESCs)

tag: karyotype

value: trisomy 15


title: RNA-seq AB1 Ts15 rep1

description:
processed data file:
raw_counts.txt
Ts15_fpkm_DESeq2_output.txt
Ts-15-1_HVNNMCCXX_L7


title: JDM.RN.5.1034.MR, Juvenile Dermatomyositis, during treatment, CD8

value: Juvenile Dermatomyositis

value: Blood


title: JDM.RN.5.1035.MR, Juvenile Dermatomyositis, during treatment, CD14


title: RNA-seq AB1 Ts11 rep3

description:
processed data file:
raw_counts.txt
Ts11_fpkm_DESeq2_output.txt
Ts-11-3_HVNNMCCXX_L7

source_name: RNA-seq Ts11_mESCs

value: trisomy 11


title: F2_D2 individual, grown at 16C [T16_P3.H2_F2_D2]

value: leaf

value: 7-10 leave rosette


title: JDM.RN.5.1033.MR, Juvenile Dermatomyositis, during treatment, CD4


title: C1048 [RNA-Seq]

tag: patient id

value: Novogene

value: Atrium

value: 6 years

value: Atrial septal defect


title: F2_D2 individual, grown at 16C [T16_P3.H1_F2_D2]


title: RNA-seq AB1 Ts11 rep2

description:
processed data file:
raw_counts.txt
Ts11_fpkm_DESeq2_output.txt
Ts-11-2_HVNNKCCXX_L3


title: RNA-seq AB1 Ts15 rep3

description:
processed data file:
raw_counts.txt
Ts15_fpkm_DESeq2_output.txt
Ts-15-3_HVNNMCCXX_L7


title: C1045 [RNA-Seq]

tag: sequence facility

value: Yerkes Nonhuman Primate Genomics Core

value: < 1 week

value: Coarctation of the aorta, ventricular septal defect


title: JDM.RN.4.1079.MR, Juvenile Dermatomyositis, during treatment, PBMC

value: PBMC

value: M


title: F2_D2 individual, grown at 16C [T16_P3.H5_F2_D2]


title: RNA-seq AB1 Ts11 rep1

description:
processed data file:
raw_counts.txt
Ts11_fpkm_DESeq2_output.txt
Ts-11-1_HVNNMCCXX_L7


title: F2_D1 individual, grown at 16C [T16_P3.H12_F2_D1]


title: C1010 [RNA-Seq]

tag: heart chamber

value: 9 weeks

value: Male

value: Tetralogy of Fallot


title: F2_D2 individual, grown at 16C [T16_P3.H11_F2_D2]

tag: treatment


title: JDM.RN.4.1032.MR, Juvenile Dermatomyositis, during treatment, CD19

value: Juvenile Dermatomyositis

tag: age


title: RNA-seq AB1 Ts8 rep2

description:
processed data file:
raw_counts.txt
Ts8_fpkm_DESeq2_output.txt
Ts-8-2_HVNNMCCXX_L7

source_name: RNA-seq Ts8_mESCs

value: mouse embryonic stem cells (mESCs)

tag: cell line

value: trisomy 8


title: F2_D1 individual, grown at 16C [T16_P3.H10_F2_D1]

value: leaf

tag: cell type


title: JDM.RN.9.1060.MR, Juvenile Dermatomyositis, pre treatment, CD19

value: Blood

tag: Sex

value: F


title: C1007 [RNA-Seq]

value: Novogene

value: Atrium

value: 6 months

tag: diagnosis

value: Ventricular septal defect, congenial/subaortic stenosis repair defect


title: RNA-seq AB1 Ts8 rep3

description:
processed data file:
raw_counts.txt
Ts8_fpkm_DESeq2_output.txt
Ts-8-3_HVNNMCCXX_L7


title: JDM.RN.4.1078.MR, Juvenile Dermatomyositis, pre treatment, PBMC


title: C1004 [RNA-Seq]

value: 12 months

value: Anomalous right superior vena cava to left atrium, no left superior vena cava


title: RNAseq_GE_2483-6_KO

value: Brain homogenate

value: Nestin-KO

value: male


title: F2_D2 individual, grown at 16C [T16_P4.A12_F2_D2]

tag: developmental stage

value: 7-10 leave rosette


title: F2_D1 individual, grown at 16C [T16_P4.A11_F2_D1]

tag: genotype


title: C1006 [RNA-Seq]

value: Female

value: Complete atrioventricular canal defect


title: JDM.RN.4.1030.MR, Juvenile Dermatomyositis, during treatment, CD8

value: Juvenile Dermatomyositis

value: M


title: JDM.RN.7.1049.MR, Juvenile Dermatomyositis, during treatment, CD4


title: F2_D2 individual, grown at 16C [T16_P3.G9_F2_D2]

value: leaf


title: JDM.RN.4.1031.MR,  Juvenile Dermatomyositis, during treatment, CD14

value: Blood


title: RNA-seq AB1 Ts6 rep3

description:
processed data file:
raw_counts.txt
Ts6_fpkm_DESeq2_output.txt
Ts-6-3_HVNNMCCXX_L7

source_name: RNA-seq Ts6_mESCs

value: mouse embryonic stem cells (mESCs)

tag: strain

value: trisomy 6


title: C985 [RNA-Seq]

value: Yerkes Nonhuman Primate Genomics Core

value: Atrium

value: 2 weeks

value: Male

value: Interrupted aortic arch


title: JDM.RN.4.1029.MR, Juvenile Dermatomyositis, during treatment, CD4

tag: tissue


title: F2_D1 individual, grown at 16C [T16_P3.G7_F2_D1]

source_name: leaf


title: RNA-seq AB1 Ts6 rep2

description:
processed data file:
raw_counts.txt
Ts6_fpkm_DESeq2_output.txt
Ts-6-2_HVNNMCCXX_L6


title: JDM.RN.4.1028.MR,  Juvenile Dermatomyositis, pre treatment, CD19

tag: disease


title: ATACseq_NPC_4647_WT

value: Neural progenitor cells

value: WT


title: RNA-seq AB1 Ts6 rep1

description:
processed data file:
raw_counts.txt
Ts6_fpkm_DESeq2_output.txt
Ts-6-1_HVNNMCCXX_L6


title: P_6046 individual, grown at 16C [T16_P3.G6_P_6046]


title: RNA-seq AB1 Ts8 rep1

description:
processed data file:
raw_counts.txt
Ts8_fpkm_DESeq2_output.txt
Ts-8-1_HVNNMCCXX_L8

value: trisomy 8


title: JDM.RN.4.1027.MR, Juvenile Dermatomyositis, pre treatment, CD14


title: C957 [RNA-Seq]

value: 7 months

value: Partial anomalous pulmonary venous return


title: RNA-seq AB1 WT rep3

description:
processed data file:
raw_counts.txt
WT-3_HVNNMCCXX_L6

source_name: RNA-seq WT_mESCs

value: diploid


title: F2_D1 individual, grown at 16C [T16_P3.G5_F2_D1]

value: 7-10 leave rosette


title: RNA-seq AB1 WT rep2

description:
processed data file:
raw_counts.txt
WT-2_HVNNMCCXX_L6


title: F2_D1 individual, grown at 16C [T16_P3.G4_F2_D1]


title: JDM.RN.4.1025.MR, Juvenile Dermatomyositis, pre treatment, CD4

value: Juvenile Dermatomyositis

value: M


title: RNA-seq AB1 WT rep1

description:
processed data file:
raw_counts.txt
WT-1_HVNNMCCXX_L6


title: F2_D1 individual, grown at 16C [T16_P3.G3_F2_D1]

value: leaf


title: Hi-C AB1 Ts15 rep2

description:
processed data file:
Ts15_1000000_raw_wholeGenome_adjLibSize.matrix.gz
Ts15_100000_iced_chr_matrix.tar.gz
Ts15_40000_iced_chr_matrix.tar.gz
Ts15_r2

data_processing:
Hi-C pre-processing was performed using the HiC-Pro pipeline (Servant et al., 2015). Briefly, sequencing reads were aligned to the mouse mm10 reference genome using the two-step mode. Unaligned read pairs, singletons, multiple aligned read pairs were discarded. Uniquely mapped read pairs were mapped to MboI restriction fragments. Then the invalid read pairs and PCR duplicates were removed. Valid read pairs were used to build Hi-C contact maps. For the following steps, Hi-C raw matrices were used for inter-chromosomal interaction analysis, and ICE (Imakaev et al., 2012) normalized matrices were used for intra-chromosomal interaction analysis, such as A/B compartment and TAD calling.
Genome_build: mm10

source_name: Hi-C Ts15_mESCs

extract_protocol:
Crosslinked cells were lysed in ice-cold Hi-C lysis buffer and treated with SDS. SDS was then quenched with Triton X-100. Chromatin was digested with MboI restriction enzyme and digested overhang was labeled with biotin-14-dATP. DNA fragments were ligated. After that, crosslinking was reversed and DNA was purified. DNA was sheared to 300-500 bp and biotin-labeled DNA was enriched using Dynabeads MyOne Streptavidin T1 beads.
The following library construction steps were performed on beads. Briefly, sheared DNA ends were repaired and ligated with dATP tailing. Then Illumina adapters were ligated to DNA fragments and 8-10 cycles of PCR was performed. Finally, PCR products were purified and size-selected using AMPure beads for Illumina sequencing.

treatment_protocol: mESCs were digested and crosslinked in 1% formaldehyde solution for 10 min at room temperature, and the reaction was quenched in 0.2 M glycine solution for 5 min. Cell pellet was washed with PBS.

value: mouse embryonic stem cells (mESCs)

value: trisomy 15


title: F2_D2 individual, grown at 16C [T16_P3.G8_F2_D2]


title: C938 [RNA-Seq]

value: Yerkes Nonhuman Primate Genomics Core

value: 5 years

value: Subaortic membrane resection, mitral valve ring


title: C930 [RNA-Seq]

value: Atrium

value: < 1 week

value: Male

value: Total anomalous pulmonary venous return, unbalanced atriovantricular canal defect


title: C975 [RNA-Seq]

value: 6 months

value: Tetralogy of Fallot


title: JDM.RN.34.1266.MR, control, CD19

value: Control

value: Blood

value: F


title: C926 [RNA-Seq]

value: 14 months

value: Ventricular septal defect


title: F2_D2 individual, grown at 16C [T16_P3.G1_F2_D2]

value: leaf

value: 7-10 leave rosette


title: Hi-C AB1 Ts15 rep1

description:
processed data file:
Ts15_1000000_raw_wholeGenome_adjLibSize.matrix.gz
Ts15_100000_iced_chr_matrix.tar.gz
Ts15_40000_iced_chr_matrix.tar.gz
Ts15_r1

value: mouse embryonic stem cells (mESCs)

value: trisomy 15


title: C925 [RNA-Seq]

value: Novogene

value: Female

value: Total anomalous pulmonary venous return


title: JDM.RN.34.1264.MR, control, CD8


title: Hi-C AB1 Ts11 rep3

description:
processed data file:
Ts11_1000000_raw_wholeGenome_adjLibSize.matrix.gz
Ts11_100000_iced_chr_matrix.tar.gz
Ts11_40000_iced_chr_matrix.tar.gz
Ts11_r3

source_name: Hi-C Ts11_mESCs

value: trisomy 11


title: F2_D1 individual, grown at 16C [T16_P3.G12_F2_D1]


title: C956 [RNA-Seq]

value: Yerkes Nonhuman Primate Genomics Core

value: Atrium

value: 5 months

value: Complete atrioventricular canal defect


title: JDM.RN.4.1026.MR, Juvenile Dermatomyositis, pre treatment, CD8

value: Juvenile Dermatomyositis

value: M


title: Hi-C AB1 Ts11 rep2

description:
processed data file:
Ts11_1000000_raw_wholeGenome_adjLibSize.matrix.gz
Ts11_100000_iced_chr_matrix.tar.gz
Ts11_40000_iced_chr_matrix.tar.gz
Ts11_r2


title: JDM.RN.9.1061.MR,  Juvenile Dermatomyositis, during treatment, CD4

value: Blood

value: F


title: JDM.RN.35.1269.MR, control, CD14

value: Control


title: JDM.RN.33.1272.MR, control, PBMC

value: PBMC


title: P_6046 individual, grown at 16C [T16_P3.G11_P_6046]

value: leaf

value: 7-10 leave rosette


title: F2_D2 individual, grown at 16C [T16_P3.G2_F2_D2]


title: JDM.RN.34.1263.MR, control, CD4


title: Hi-C AB1 Ts11 rep1

description:
processed data file:
Ts11_1000000_raw_wholeGenome_adjLibSize.matrix.gz
Ts11_100000_iced_chr_matrix.tar.gz
Ts11_40000_iced_chr_matrix.tar.gz
Ts11_r1

value: mouse embryonic stem cells (mESCs)


title: P_6191 individual, grown at 16C [T16_P3.G10_P_6191]


title: C924 [RNA-Seq]

value: 2 months

value: Male


title: F2_D1 individual, grown at 16C [T16_P3.F9_F2_D1]


title: C896 [RNA-Seq]

value: 12 months

value: Female

value: Ventricular septal defect


title: C903 [RNA-Seq]

value: Yerkes Nonhuman Primate Genomics Core

value: Atrium

value: < 1 week

value: Hypoplastic left heart syndrome


title: C902 [RNA-Seq]

value: 4 years

value: Atrial septal defect


title: F2_D1 individual, grown at 16C [T16_P3.F8_F2_D1]


title: JDM.RN.33.1260.MR, control, CD8

value: Blood

value: F


title: JDM.RN.33.1261.MR, control, CD14

value: Control


title: Hi-C AB1 Ts8 rep2

description:
processed data file:
Ts8_1000000_raw_wholeGenome_adjLibSize.matrix.gz
Ts8_100000_iced_chr_matrix.tar.gz
Ts8_40000_iced_chr_matrix.tar.gz
Ts8_r2

source_name: Hi-C Ts8_mESCs

value: trisomy 8


title: JDM.RN.33.1262.MR, control, CD19


title: F2_D1 individual, grown at 16C [T16_P3.F7_F2_D1]

value: leaf

value: 7-10 leave rosette


title: YAP-KO3

city: xinxiang

first: xiaofeng

last: zhou

address: No. 601 Jinsui Avenue

institute: xinxiang medical university

data_processing:
Using the Illumina paired-end RNA-seq approach
we aligned reads of  all samples to the (http://mascotton.njau.edu.cn/info/1054/1118.htm) TM-1 reference genome using HISAT package
StringTie and Ballgown was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM
The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package – Ballgown.
Assembly: TM-1
Supplementary files format and content: xls include FPKM values for each Sample

source_name: esophagus

growth_protocol: EC9706 cells were cultured in RPMI 1640 Medium containing 10% fetal bovine serum 1%penicillin/streptomycin.

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit .  RNA was quantified using a NanoDrop-1000 spectrophotometer.
Approximately 10 μ g of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligo attached magnetic beads (Invitrogen). Following purification, using divalent cations, the poly (A) - or poly (A) + RNA fractions were fragmented into small pieces under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to the final cDNA library according to the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp ( ± 50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 4000 at the (lc-bio, China) following of the merchant's recommended protocol.

treatment_protocol: Using CRISPR to generate YAP knock-out EC9706 cell lines

value: YAP-/-


title: JDM.RN.33.1259.MR, control, CD4


title: C894 [RNA-Seq]

source_name: c-kit+ progenitor cell isolated from appendage

value: Ventricle

value: 6 months

value: missing

value: Not known


title: Hi-C AB1 Ts8 rep1

description:
processed data file:
Ts8_1000000_raw_wholeGenome_adjLibSize.matrix.gz
Ts8_100000_iced_chr_matrix.tar.gz
Ts8_40000_iced_chr_matrix.tar.gz
Ts8_r1

value: mouse embryonic stem cells (mESCs)


title: Hi-C AB1 Ts6 rep3

description:
processed data file:
Ts6_1000000_raw_wholeGenome_adjLibSize.matrix.gz
Ts6_100000_iced_chr_matrix.tar.gz
Ts6_40000_iced_chr_matrix.tar.gz
Ts6_r3

source_name: Hi-C Ts6_mESCs

value: trisomy 6


title: F2_D2 individual, grown at 16C [T16_P4.B11_F2_D2]


title: YAP-KO2


title: JDM.RN.32.1255.MR, control, CD4


title: Hi-C AB1 Ts6 rep2

description:
processed data file:
Ts6_1000000_raw_wholeGenome_adjLibSize.matrix.gz
Ts6_100000_iced_chr_matrix.tar.gz
Ts6_40000_iced_chr_matrix.tar.gz
Ts6_r2


title: YAP-KO1


title: JDM.RN.3.1024.MR, Juvenile Dermatomyositis, during treatment, CD19

value: Juvenile Dermatomyositis

value: M


title: Hi-C AB1 Ts8 rep3

description:
processed data file:
Ts8_1000000_raw_wholeGenome_adjLibSize.matrix.gz
Ts8_100000_iced_chr_matrix.tar.gz
Ts8_40000_iced_chr_matrix.tar.gz
Ts8_r3


title: Hi-C AB1 Ts6 rep1

description:
processed data file:
Ts6_1000000_raw_wholeGenome_adjLibSize.matrix.gz
Ts6_100000_iced_chr_matrix.tar.gz
Ts6_40000_iced_chr_matrix.tar.gz
Ts6_r1


title: F2_D1 individual, grown at 16C [T16_P3.F4_F2_D1]


title: F2_D2 individual, grown at 16C [T16_P3.F5_F2_D2]


title: Hi-C AB1 WT rep3

description:
processed data file:
WT_1000000_raw_wholeGenome_adjLibSize.matrix.gz
WT_100000_iced_chr_matrix.tar.gz
WT_40000_iced_chr_matrix.tar.gz
wt_r3

source_name: Hi-C WT_mESCs

value: diploid


title: YAP-WT2

value: wild type


title: Hi-C AB1 WT rep2

description:
processed data file:
WT_1000000_raw_wholeGenome_adjLibSize.matrix.gz
WT_100000_iced_chr_matrix.tar.gz
WT_40000_iced_chr_matrix.tar.gz
wt_r2


title: F2_D2 individual, grown at 16C [T16_P3.F3_F2_D2]


title: YAP-WT3


title: JDM.RN.3.1021.MR,  Juvenile Dermatomyositis, during treatment, CD4

source_name: Blood

value: Blood


title: YAP-WT1


title: JDM.RN.3.1022.MR, Juvenile Dermatomyositis, during treatment, CD8


title: JDM.RN.3.1020.MR,  Juvenile Dermatomyositis, pre treatment, CD19


title: F2_D2 individual, grown at 16C [T16_P3.F2_F2_D2]


title: JDM.RN.3.1023.MR, Juvenile Dermatomyositis, during treatment, CD14


title: Hi-C AB1 WT rep1

description:
processed data file:
WT_1000000_raw_wholeGenome_adjLibSize.matrix.gz
WT_100000_iced_chr_matrix.tar.gz
WT_40000_iced_chr_matrix.tar.gz
wt_r1


title: F2_D1 individual, grown at 16C [T16_P3.F1_F2_D1]


title: JDM.RN.3.1017.MR,  Juvenile Dermatomyositis, pre treatment, CD4


title: hippocampus from rapa-treated mother rep3

first: Wenjie

last: Shu

address: Taiping Road 27

institute: Beijing Institute of Radiation Medicine

description: F1_ORa3_ hippocampus

data_processing:
Raw reads were processed with trim galore to obtain clean data
Clean reads were mapped to mm10 using Bismark
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph, containing the CpG sites and methylated read counts

source_name: hippocampus from rapa-treated mother

growth_protocol: Mice were housed under SPF environmental conditions with free access to water and food, 20–22°C ,50–70% humidity, and a 12/12-hour light and dark cycle in the Animal Core Facility of Nanjing Medical University. Animal care and experimental procedures were conducted according to the guidelines of the Animal Research Committee of Nanjing Medical University.

extract_protocol:
Before scBS seq, 2 × lysis buffer and 0.5 μ lproteinase K were added followed by incubation at 37 C for 1 h. For hippocampus WGBS, 200-300mg tissue were used, genome DNA concentration per sample were all >= 50 ng/μl.The A260/A280 ratio of gDNA was 1.8~2.0 and the electropherogram of gDNA was without RNA protein and degradation.
For WGBS of hippocanpus,a total volume of 80 μl gDNA unmethylated lambda DNA were combined and fragment the DNA to 300bp.Then the next protocol include End repair, dA Tailing, Methylated a dapt o r ligation, and bisulfite conversion. The uracil binding pocket of KAPA HiFi DNA Polymerase has been inactivat was then used in PCR amplification, enabling amplification of uracil containing DNA .
For scBs seq, before incubation at 65 C for 3 min ,50 U of Klenow exo (Sigma) were added and the samples incubated at 4 C for 5 min, 37 C for 30 min. Samples were incubated at 95 C  for 1 min and transferred immediately to ice before addition of fresh oligo 1 (10 pmol), Klenow exo (25 U), and dNTPs (1 nmol) in 2.5 μ l total. The samples were incubated at 4 C for 5 min , 37 C for 30 min. This ran dom priming and extension was repeated a further three times (five rounds in total). Samples were then incubated with 40 U exonuclease I (NEB) for 1 h at 37 C before DNA was purified using 0 .8 × Agencourt Ampure XP beads.Samples were eluted in 10 mM TrisCl (pH 8.5) and incubated with washed M 280 Streptavidin Dynabeads (Life Technologies) for 20 min with rotation at room temperature. Beads were washed twice  and resuspended in dNTPs, 0.4 μ M oligo 2 and 1 × Blue Buffer. Samples were  incubated at 95 C for 45 s and transferred immediately to ice before addi tion of 100 U Klenow  exo (Sigma) and incubation at 4 C for 5 min, +1 C/15 s to 37 C, 37 C for 90 min.Libraries were then amplified by PCR as follows: 95 2 min, 12 13 repeats of (94 C 80 s, 65 C 30 s, 72 C 30 s), 72 C 3 min and 4 C hold.
Whole Genome Bisulfite Sequencing (WGBS)

treatment_protocol: 8-week-old female mice were intraperitoneally injected with rapamycin (2mg/kg) or  vehicle for 40 weeks. At the end of experiment, 4-week-old, 48-week-old and 48-week-old rapa-treated female mice were paired with  young adult (~4 mo old) males to produce F1 offspring. An F2 generation (OF2 and ORaF2) resulted from mating F1 female at 44~48 weeks of age  with  young adult males. Females from F0, F1 and F2 generations were  intraperitoneally injected with pregnant mare serum gonadotropin (PMSG, 5 IU for 4 wks and 10 IU for 48 wks, Ningbo Sansheng Pharmaceutical Corporation, Zhejiang, China) followed by human chorionic gonadotrophin (hCG, 5 IU for 4wk and 10 IU for 48 wks) 46-48 h later to collect M2 matured oocytes.  The cumulus cells were removed by pipetting in M2 medium containing 0.1% hyaluronidase (Sigma-Aldrich).  Males from F1 and F2 generatios were used to collect sperm from  epididymis.  Adult female (about 10 month of age) F1 offspring were used to collect hippocampus, and one of hippocampus was fresh frozen in dry ice.

value: hippocampus

tag: generation

value: Rapa-treated


title: hippocampus from rapa-treated mother rep2

description: F1_ORa2_ hippocampus


title: F2_D1 individual, grown at 16C [T16_P3.F11_F2_D1]


title: F2_D1 individual, grown at 16C [T16_P3.F12_F2_D1]


title: 8808R2_278_IndexUDI0028_TCCAACGC+TTGGACTT_L002_001

city: Frankfurt am Main

first: Daniel

last: Margerie

address: Industrial Park Hoechst, Building H831

department: R&D, Digital Data Sciences

country: Germany

institute: Sanofi-Aventis Deutschland GmbH

data_processing:
Bioinformatics analyses of RNA-seq raw data were performed using the OmicSoft studio software package version 10.1.2.9 (Qiagen)
Mapping of RNA-seq reads (fastq files) to the human genome was done using OmicSoftGenCode V19 as gene model with B.38 as reference genome and OSA4 as aligner
Genes with FPKM <1 were filtered out according to a 50% fraction rule for each sample group to exclude minimally expressed genes. Differentially expressed genes were detected by applying the DESeq2 statistical test and P-values were adjusted by the Benjamini-Hochberg procedure to control FDR
Supplementary files format and content: Tab-delimited text file include FPKM values for each sample

source_name: RA-FLS and T-cells

extract_protocol:
RNA was isolated with the Qiagen RNeasy Micro Kit for cell cultures according to the manufacturer´s instructions.
For RNA-seq library preparation the Ovation RNA-Seq System V2 combined with Illumina Nextera XT Library Preparation Kit was used for cell cultures. RNA libraries were subjected to paired-end sequencing on a Novaseq 6000 system with a reading depth of 80 million raw reads per sample.

treatment_protocol: Firstly, a coculture of fibroblast-like synoviocytes from RA donors with CD4 T cells from healthy donors was stimulated with 1ng/ml recombinant human TNF, 10ng/ml IL-6 with 100ng/ml sIL-6R or a combination of TNF and IL-6/sIL-6R for 24h. Secondly, a coculture of fibroblast-like synoviocytes from RA donors with CD4 T cells from healthy donors was stimulated with IL-17, sIL-6R and anti-CD3 (100ng/ml each) for 24h. Monospecific antibodies against TNF, IL-6 or a combination of them as well as anti-TNF/IL-6 NANOBODY® VHH  and corresponding isotype controls were added to the coculture in 200nM concentration (combination 200nM each; n=9, 3 RA-FLS donors combined with 3 different CD4 donors).

tag: fls donor

tag: blood t-cell donor

value: Fibroblast-like synoviocytes from rheumatoid arthritis (RA) donors cocultured with CD4 T cells from healthy donors

value: recombinant hTNFa


title: 8808R2_280_IndexUDI0030_TTACAGGA+TGACAAGC_L002_001

value: recombinant hTNFa  + hIL-6


title: 8808R2_279_IndexUDI0029_CCGTGAAG+CAGTGGAT_L002_001

value: recombinant hIL-6


title: F2_D1 individual, grown at 16C [T16_P3.F6_F2_D1]

value: leaf

value: 7-10 leave rosette


title: JDM.RN.21.1152.MR, control, CD19

value: Control


title: hippocampus from rapa-treated mother rep1

description: F1_ORa1_ hippocampus


title: F2_D2 individual, grown at 16C [T16_P3.F10_F2_D2]


title: 8808R2_276_IndexUDI0026_GTCGGAGC+GGTTATAA_L002_001

value: anti-TNF/IL-6 NANOBODY® VHH


title: JDM.RN.21.1151.MR, control, CD14


title: hippocampus from aged mother rep3

description: F1_Old3_ hippocampus

source_name: hippocampus from aged mother


title: 8808R2_273_IndexUDI0023_GCAGAATT+ACCGGCCA_L002_001

value: anti-TNF +anti-IL-6 mAb


title: hippocampus from aged mother rep2

description: F1_Old2_ hippocampus


title: F2_D2 individual, grown at 16C [T16_P3.E9_F2_D2]


title: 8808R2_271_IndexUDI0021_GGTACCTT+AAGACGTC_L002_001

value: anti-TNF mAb


title: hippocampus from aged mother rep1

description: F1_Old1_ hippocampus


title: JDM.RN.20.1137.MR, control, CD4


title: 8808R2_272_IndexUDI0022_AACGTTCC+GGAGTACT_L002_001

value: anti-IL-6 mAb


title: hippocampus from young mother rep3

description: F1_Y3_ hippocampus

source_name: hippocampus from young mother


title: JDM.RN.2.1077.MR, Juvenile Dermatomyositis, during treatment, PBMC

value: Juvenile Dermatomyositis

value: PBMC

value: F


title: F2_D1 individual, grown at 16C [T16_P3.E8_F2_D1]


title: F2_D1 individual, grown at 16C [T16_P3.E5_F2_D1]


title: F2_D1 individual, grown at 16C [T16_P3.E7_F2_D1]


title: 8808R2_269_IndexUDI0019_ATGTAAGT+ACTCTATG_L004_001

value: IgG1 isotype control


title: JDM.RN.2.1015.MR,  Juvenile Dermatomyositis, during treatment, CD14

value: Blood


title: hippocampus from young mother rep2

description: F1_Y2_ hippocampus

value: hippocampus

value: wild type


title: 8808R2_268_IndexUDI0018_CGGCGTGA+GCGCCTGT_L004_001

value: Fibroblast-like synoviocytes from rheumatoid arthritis (RA) donors cocultured with CD4 T cells from healthy donors

value: stimulated


title: F2_D1 individual, grown at 16C [T16_P3.E4_F2_D1]


title: P_6191 individual, grown at 16C [T16_P3.E3_P_6191]


title: sperm from ORaF1 rep3

source_name: sperm from ORaF1

value: sperm

value: Rapa-treated


title: hippocampus from young mother rep1

description: F1_Y1_ hippocampus


title: JDM.RN.2.1014.MR, Juvenile Dermatomyositis, during treatment, CD8


title: 8808R2_267_IndexUDI0017_TAATACAG+ATATTCAC_L004_001

value: unstimulated


title: sperm from ORaF1 rep2


title: JDM.RN.2.1013.MR, Juvenile Dermatomyositis, during treatment, CD4


title: F1_D2 individual, grown at 16C [T16_P3.E2_F1_D2]

value: leaf

value: 7-10 leave rosette


title: JDM.RN.21.1148.MR, control, CD4

value: Control

value: M


title: F2_D1 individual, grown at 16C [T16_P3.E6_F2_D1]


title: 8808R2_270_IndexUDI0020_GCACGGAC+GTCTCGCA_L002_001

value: NANOBODY® isotype control


title: JDM.RN.2.1011.MR, Juvenile Dermatomyositis, pre treatment, CD14

value: Juvenile Dermatomyositis


title: sperm from ORaF1 rep1


title: sperm from OF1 rep3

source_name: sperm from OF1


title: P_6046 individual, grown at 16C [T16_P3.E12_P_6046]


title: JDM.RN.2.1076.MR, Juvenile Dermatomyositis, pre treatment, PBMC

value: PBMC


title: 8808R2_265_IndexUDI0015_GGCTTAAG+TCGTGACC_L004_001

value: recombinant hIL-6


title: F2_D1 individual, grown at 16C [T16_P3.E1_F2_D1]


title: JDM.RN.2.1010.MR, Juvenile Dermatomyositis, pre treatment, CD8

value: F


title: sperm from OF1 rep2


title: 8808R2_264_IndexUDI0014_TTGGACTC+GGAAGCAG_L004_001

value: recombinant hTNFa


title: JDM.RN.2.1009.MR,  Juvenile Dermatomyositis, pre treatment, CD4

value: Blood


title: 8808R2_262_IndexUDI0012_CTCTCGTC+TATAACCT_L004_001

value: anti-TNF/IL-6 NANOBODY® VHH


title: JDM.RN.19.1135.MR, control, CD14


title: F2_D2 individual, grown at 16C [T16_P3.E10_F2_D2]


title: 8808R2_258_IndexUDI0008_TGGATCGA+GTGCGATA_L004_001

value: Fibroblast-like synoviocytes from rheumatoid arthritis (RA) donors cocultured with CD4 T cells from healthy donors

value: anti-IL-6 mAb


title: F2_D2 individual, grown at 16C [T16_P3.D9_F2_D2]


title: JDM.RN.19.1134.MR, control, CD8


title: JDM.RN.19.1133.MR, control,CD4


title: 8808R2_266_IndexUDI0016_AATCCGGA+CTACAGTT_L004_001

value: recombinant hTNFa  + hIL-6


title: sperm from young mother rep2

source_name: sperm from young mother

value: sperm

value: wild type


title: F2_D2 individual, grown at 16C [T16_P3.D8_F2_D2]

source_name: leaf

value: leaf


title: sperm from young mother rep1


title: sperm from young mother rep3


title: JDM.RN.2.1012.MR, Juvenile Dermatomyositis, pre treatment, CD19


title: 8808R2_257_IndexUDI0007_CAAGCTAG+ACATAGCG_L004_001

value: anti-TNF mAb


title: JDM.RN.18.1132.MR, control, CD19

value: Control


title: JDM.RN.17.1167.MR, Juvenile Dermatomyositis, during treatment, CD14


title: F2_D2 individual, grown at 16C [T16_P3.D7_F2_D2]

value: 7-10 leave rosette


title: 8808R2_255_IndexUDI0005_ATCCACTG+AGGTGCGT_L004_001

value: IgG1 isotype control


title: F2_D2 individual, grown at 16C [T16_P3.D6_F2_D2]


title: 8808R2_256_IndexUDI0006_GCTTGTCA+GAACATAC_L004_001

value: NANOBODY® isotype control


title: sperm from rapa-treated mother rep3

source_name: sperm from rapa-treated mother

value: Rapa-treated


title: F2_D1 individual, grown at 16C [T16_P3.E11_F2_D1]


title: sperm from rapa-treated mother rep2


title: sperm from OF1 rep1


title: JDM.RN.17.1166.MR, Juvenile Dermatomyositis, during treatment, CD14

value: Juvenile Dermatomyositis


title: 8808R2_254_IndexUDI0004_AAGTCCAA+TATGAGTA_L004_001

value: stimulated


title: sperm from rapa-treated mother rep1


title: JDM.RN.17.1165.MR, Juvenile Dermatomyositis, during treatment, CD8

value: F


title: 8808R2_259_IndexUDI0009_AGTTCAGG+CCAACAGA_L004_001

value: anti-TNF +anti-IL-6 mAb


title: sperm from aged mother rep3

source_name: sperm from aged mother


title: 8808R2_253_IndexUDI0003_GGACTTGG+CGCAGACG_L004_001

value: unstimulated


title: F2_D1 individual, grown at 16C [T16_P3.D4_F2_D1]


title: F2_D1 individual, grown at 16C [T16_P3.D5_F2_D1]


title: 8808R2_224_IndexUDI0002_TTATAACC+GATATCGA_L004_001

value: Fibroblast-like synoviocytes from rheumatoid arthritis (RA) donors cocultured with CD4 T cells from healthy donors


title: sperm from aged mother rep2


title: JDM.RN.17.1164.MR, Juvenile Dermatomyositis, during treatment, CD8

value: Blood


title: F2_D2 individual, grown at 16C [T16_P3.D1_F2_D2]


title: JDM.RN.17.1157.MR, Juvenile Dermatomyositis, pre treatment, CD14


title: sperm from aged mother rep1


title: 8808R2_223_IndexUDI0001_CCGCGGTT+AGCGCTAG_L004_001

value: recombinant hIL-6


title: JDM.RN.17.1154.MR, Juvenile Dermatomyositis, pre treatment,  CD4


title: 8808R2_222_IndexUDI0096_CTAGCGCT+GTGTAGAC_L004_001

value: recombinant hTNFa


title: 8808R2_220_IndexUDI0094_CGTCTGCG+TTCACAAT_L004_001

value: anti-TNF/IL-6 NANOBODY® VHH


title: JDM.RN.16.1145.MR, Juvenile Dermatomyositis, pre treatment, CD19


title: oocyte from ORaF1 rep2

source_name: oocyte from ORaF1

value: M2 oocyte

value: wild type


title: oocyte from ORaF1 rep1


title: F2_D2 individual, grown at 16C [T16_P3.D2_F2_D2]

value: leaf


title: 8808R2_217_IndexUDI0091_GTATGTTC+AACAGGAA_L004_001


title: F2_D1 individual, grown at 16C [T16_P3.D11_F2_D1]

value: 7-10 leave rosette


title: F2_D2 individual, grown at 16C [T16_P3.D12_F2_D2]


title: oocyte from OF1 rep2

source_name: oocyte from OF1


title: JDM.RN.16.1143.MR,  Juvenile Dermatomyositis, pre treatment, CD8


title: JDM.RN.16.1142.MR, Juvenile Dermatomyositis, pre treatment, CD4


title: 8808R2_216_IndexUDI0090_CGCTATGT+TCCGACAC_L004_001

value: anti-IL-6 mAb


title: oocyte from OF1 rep1


title: JDM.RN.16.1141.MR, Juvenile Dermatomyositis, pre treatment, PBMC

value: PBMC


title: F2_D1 individual, grown at 16C [T16_P3.C8_F2_D1]


title: F2_D1 individual, grown at 16C [T16_P3.D3_F2_D1]


title: 8808R2_214_IndexUDI0088_TCTGTTGG+TCGAATGG_L004_001

value: NANOBODY® isotype control


title: JDM.RN.15.1127.MR, Juvenile Dermatomyositis, pre treatment, CD19

value: Juvenile Dermatomyositis


title: F2_D2 individual, grown at 16C [T16_P3.C9_F2_D2]


title: 8808R2_215_IndexUDI0089_TATCGCAC+CTTAGTGT_L004_001

value: anti-TNF mAb


title: F2_D2 individual, grown at 16C [T16_P3.D10_F2_D2]


title: oocyte from YF1 rep3

source_name: oocyte from YF1


title: oocyte from YF1 rep2


title: F2_D1 individual, grown at 16C [T16_P3.C7_F2_D1]


title: oocyte from YF1 rep1


title: JDM.RN.14.1116.MR, Juvenile Dermatomyositis, pre treatment, CD14

value: M


title: 8808R2_213_IndexUDI0087_CTCACCAA+CTAGGCAA_L004_001

value: IgG1 isotype control


title: oocyte from rapa-treated mother rep2

source_name: oocyte from rapa-treated mother

value: Rapa-treated


title: F2_D1 individual, grown at 16C [T16_P3.C5_F2_D1]


title: oocyte from rapa-treated mother rep1


title: JDM.RN.13.1111.MR, Juvenile Dermatomyositis, during treatment, CD8

value: F


title: 8808R2_210_IndexUDI0084_TCATCCTT+AGCGAGCT_L004_001

value: Fibroblast-like synoviocytes from rheumatoid arthritis (RA) donors cocultured with CD4 T cells from healthy donors

value: recombinant hTNFa  + hIL-6


title: oocyte from aged mother rep3

source_name: oocyte from aged mother


title: JDM.RN.13.1108.MR, Juvenile Dermatomyositis, pre treatment, CD14

value: Blood


title: F2_D2 individual, grown at 16C [T16_P3.C3_F2_D2]


title: JDM.RN.13.1112.MR, Juvenile Dermatomyositis, during treatment, CD14


title: oocyte from aged mother rep2


title: F2_D2 individual, grown at 16C [T16_P3.C2_F2_D2]


title: JDM.RN.13.1104.MR, Juvenile Dermatomyositis, pre treatment, PBMC


title: JDM.RN.12.1103.MR, Juvenile Dermatomyositis, during treatment, CD19


title: 8808R2_212_IndexUDI0086_GAACCGCG+TGACCTTA_L004_001

value: stimulated


title: F2_D1 individual, grown at 16C [T16_P3.C1_F2_D1]


title: 8808R2_206_IndexUDI0080_GTGAATAT+TCTCATTC_L004_001

value: anti-TNF/IL-6 NANOBODY® VHH


title: JDM.RN.14.1118.MR, Juvenile Dermatomyositis, during treatment, CD4


title: 8808R2_203_IndexUDI0077_TGCGAGAC+CATTGTTG_L004_001

value: anti-TNF +anti-IL-6 mAb


title: oocyte from aged mother rep1

value: M2 oocyte

value: wild type


title: F2_D2 individual, grown at 16C [T16_P3.C12_F2_D2]

value: leaf

value: 7-10 leave rosette


title: oocyte from young mother rep1

source_name: oocyte from young mother


title: F2_D1 individual, grown at 16C [T16_P3.C11_F2_D1]


title: 8808R2_202_IndexUDI0076_GACGTCTT+GGTTCACC_L004_001

value: anti-IL-6 mAb


title: F2_D2 individual, grown at 16C [T16_P3.C6_F2_D2]


title: 8808R2_211_IndexUDI0085_AGGTTATA+CAGTTCCG_L004_001

value: unstimulated


title: F2_D2 individual, grown at 16C [T16_P3.C4_F2_D2]


title: oocyte from young mother rep2


title: 8808R2_201_IndexUDI0075_AGTACTCC+AACCTGTT_L004_001

value: anti-TNF mAb


title: 8808R2_209_IndexUDI0083_CTGCTTCC+GATAGATC_L004_001

value: recombinant hIL-6


title: F2_D2 individual, grown at 16C [T16_P3.C10_F2_D2]


title: JDM.RN.12.1100.MR, Juvenile Dermatomyositis, during treatment, CD4

source_name: Blood

value: Juvenile Dermatomyositis

value: M


title: rapa-treated aged oocyte rep2

source_name: rapa-treated aged oocyte

value: Rapa-treated


title: 8808R2_208_IndexUDI0082_GGTCACGA+GTATTATG_L004_001

source_name: RA-FLS and T-cells

value: Fibroblast-like synoviocytes from rheumatoid arthritis (RA) donors cocultured with CD4 T cells from healthy donors

value: recombinant hTNFa


title: 8808R2_200_IndexUDI0074_TGGCCGGT+TAGAGCGC_L004_001

value: NANOBODY® isotype control


title: JDM.RN.11.1073.MR, Juvenile Dermatomyositis, during treatment, CD19

value: Blood

value: F


title: 8808R2_199_IndexUDI0073_CAATTAAC+CGAGATAT_L004_001

value: IgG1 isotype control


title: JDM.RN.11.1072.MR, Juvenile Dermatomyositis, during treatment, CD14


title: JDM.RN.12.1101.MR, Juvenile Dermatomyositis, during treatment, CD8


title: 8808R2_198_IndexUDI0072_GTCTACAC+GCCAAGGT_L004_001

value: stimulated


title: JDM.RN.11.1071.MR, Juvenile Dermatomyositis, during treatment, CD8


title: F2_D1 individual, grown at 16C [T16_P3.B7_F2_D1]


title: aged oocyte rep3

source_name: aged oocyte

value: M2 oocyte

value: wild type


title: aged oocyte rep2


title: 8808R2_197_IndexUDI0071_ACTCGTGT+ATTGGAAC_L004_001


title: F1_D1 individual, grown at 16C [T16_P3.B6_F1_D1]

value: leaf

value: 7-10 leave rosette


title: JDM.RN.11.1070.MR, Juvenile Dermatomyositis, during treatment, CD4


title: rapa-treated aged oocyte rep3


title: F2_D2 individual, grown at 16C [T16_P3.B5_F2_D2]


title: aged oocyte rep1


title: JDM.RN.10.1068.MR, Juvenile Dermatomyositis, pre treatment, CD19


title: young oocyte rep3

source_name: young oocyte


title: JDM.RN.10.1067.MR, Juvenile Dermatomyositis, pre treatment, CD14


title: 8808R2_167_IndexUDI0069_GCCACAGG+CATGCCAT_L004_001


title: F2_D1 individual, grown at 16C [T16_P3.B4_F2_D1]


title: young oocyte rep2


title: JDM.RN.10.1066.MR, Juvenile Dermatomyositis, pre treatment, CD8


title: F2_D2 individual, grown at 16C [T16_P3.B9_F2_D2]


title: young oocyte rep1


title: rapa-treated aged oocyte rep1


title: F2_D2 individual, grown at 16C [T16_P3.B2_F2_D2]


title: F2_D1 individual, grown at 16C [T16_P3.B3_F2_D1]


title: 8808R2_166_IndexUDI0068_CCTTCACC+GACGCTCC_L004_001


title: JDM.RN.10.1065.MR, Juvenile Dermatomyositis, pre treatment, CD4


title: 8808R2_161_IndexUDI0063_TTGCCTAG+ACCACTTA_L004_001

value: anti-TNF +anti-IL-6 mAb


title: F2_D1 individual, grown at 16C [T16_P3.B8_F2_D1]


title: JDM.RN.1.1170.MR, Juvenile Dermatomyositis, during treatment, CD4


title: F2_D1 individual, grown at 16C [T16_P3.B1_F2_D1]


title: F2_D2 individual, grown at 16C [T16_P3.B12_F2_D2]


title: 8808R2_159_IndexUDI0061_CGGAACTG+CACTACGA_L004_001

value: anti-TNF mAb


title: 8808R2_168_IndexUDI0070_ATTGTGAA+TGCATTGC_L004_001

value: recombinant hTNFa  + hIL-6


title: 8808R2_164_IndexUDI0066_GTGTCGGA+GCTTGCGC_L004_001

value: anti-TNF/IL-6 NANOBODY® VHH


title: Second biological replicate of the hybrid G x Q

city: Rosario

first: Agustina

middle: Paula

last: Fortuny

address: Ocampo y Esmeralda

country: Argentina

institute: IBR (CONICET-UNR)

description:
FG21
mRNA

data_processing:
The quality of raw reads was evaluated with the software FastQC.
High-quality reads were conserved by filtering adapters, over-represented sequences, low-quality reads (Q < 20), and short reads, using the software fastp v0.21.
The software HISAT2 v 2.1.0 was used to align cleaned reads to the tomato reference genome (ITAG 4.0).
Counting reads was performed with the featureCounts program, belonging to the subread package.
The package edgeR of the free software R v.4.0.3 was employed to filter, normalize, and detect differential expression among samples. Lowly expressed genes (< 5-10 counts) were removed. The normalization of read counts was based on sequencing depth and library size, using a trimmed mean of M-values (TMM) between each pair of samples.
Assembly: Tomato reference genome (ITAG 4.0). Reference genome and annotation files were downloaded from the Sol Genomics Network FTP site (ftp://ftp.solgenomics.net/tomato_genome/annotation/ITAG4.0_release/).
Supplementary files format and content: DGEList_norm.txt: Matrix table with filteres and normalized gene counts for every gene and every sample.

organism: Solanum lycopersicum

source_name: tomato fruit mesocarp

growth_protocol: Eight plants per genotype were transplanted into a greenhouse at the Estación Experimental ‘‘José F. Villarino’’ (33° SL and 61° WL), Argentina in 2015-2016. Plants were pruned to a single stem and tied vertically to a top wire. Plants were drip irrigated and supplemented with nitrogen, phosphorus and potassium + magnesium oxide + magnesium and trace elements fertilizer once a week. The crop was grown according to the standard cultural recommendations for the area.

extract_protocol:
Total RNA was extracted from three red ripe fruits (biological replicates) per genotype with Tripure Isolation Reagent, following the manufacturer’s instructions (Roche, Basel, Switzerland) with some minor modifications. It is worthwhile to mention that the samples used for RNA-seq and 1H-NMR were obtained from the same biological material, an important aspect to consider for omics data integration (Cavill et al., 2016). For each sample, 100 mg of frozen mesocarp powder was weighted in a sterile 1.5 ml polypropylene centrifuge tube. Then, 950 µl of cold Tripure Isolation Reagent was added and the sample was homogenised and centrifuged for 7 min, 4 to 10 °C, 12,000 × g. The supernatant obtained was transferred to a sterile 1.5 ml tube with 200 µl of chloroform at room temperature to phase separation. The sample was shaken vigorously for 15 sec and incubated for 5 to 15 min at room temperature. Tubes were centrifuged for 10 min, 4 to 10 °C, 12,000 × g. The colourless upper aqueous phase was transferred to a new sterile 1.5 ml tube. To precipitate RNA, 500 µl of cold isopropanol was added to each tube and it was inverted several times to mix it thoroughly. Samples were incubated for 20 min on ice. Tubes were centrifuged for 10 min, 4 to 10 °C, 12,000 × g. The supernatant was discarded. To wash the RNA pellet, 200 µl of 80% ethanol was added to each centrifuge tube. The samples were vortexed and centrifuged for 5 min, 4 °C, 7,500 × g. Excess of ethanol was removed from the RNA pellet by air-drying for 5 to 10 min. The RNA pellet was resuspended in 40 µl of diethylpyrocarbonate (DEPC)-treated RNase-free water. Finally, the samples were vortexed and centrifuged for 1 min, 4 °C, 7,500 × g. The quality and concentration of total RNA extracted were quantified using a NanoDrop Lite Spectrophotometer (Thermo ScientificTM, USA). The RNA integrity was checked using 1.5% denaturing formaldehyde agarose gel-electrophoresis with 1X MEN buffer (0.02 M MOPS + 5 mM NaOAc + 1 mM EDTA) stained with ethidium bromide. Each sample consisted of 5 µl RNA solution (2 µg RNA with ultrapure sterile water) with loading buffer (5 µl formamide, 1.25 µl 10 X MEN, and 1.5 µl formaldehyde), and was heated 10 min at 65 °C. After quality and quantity assessment, 3 µg of RNA in each sample was diluted with DEPC-water to reach a final volume of 30 µl. Then, 0.1 volume of 3 M Sodium Acetate (NaOAc) pH 5.5 and 2 volumes of 100% ethanol were added to the 30 µl of RNA solution for precipitation, mixing gently after each step.
The cDNA library construction with fragments of 250-300 bp and the paired-end-sequencing (2 x 150 bp) services were hired from Novogene Corporation, Inc. (Sacramento, CA, USA), using an Illumina Novaseq 6000 platform.

value: red ripe

value: fruit mesocarp

value: hybrid 2 (G x Q)


title: JDM.RN.1.1075.MR, Juvenile Dermatomyositis, pre treatment, PBMC

value: Juvenile Dermatomyositis

value: PBMC


title: Third biological replicate of the hybrid G x Q

description:
FG23
mRNA


title: 8808R2_158_IndexUDI0060_AGCTCGCT+GCAGAATC_L004_001

value: Fibroblast-like synoviocytes from rheumatoid arthritis (RA) donors cocultured with CD4 T cells from healthy donors

value: NANOBODY® isotype control


title: F2_D2 individual, grown at 16C [T16_P3.B11_F2_D2]

data_processing:
Raw sequencing reads were trimmed using cutadapt
Trimmed reads were mapped to reference TAIR10 genome using Bismark
Assembly: TAIR10
Supplementary files format and content: Files are in bedgraph format with "chromosome position strand context mc_score total_reads methylated"

extract_protocol:
DNA was extracted from leaf tissue and performed bisulfite treatment
Libraries were constructed and sequenced through Illumina HiSeq


title: JDM.RN.1.1074.MR, Juvenile Dermatomyositis, during treatment, PBMC

value: Blood

value: F


title: First biological replicate of the hybrid G x Q

description:
FG19
mRNA


title: Third biological replicate of the hybrid Q x G

description:
FQ17
mRNA

value: hybrid 1 (Q x G)


title: F2_D1 individual, grown at 16C [T16_P3.B10_F2_D1]


title: 8808R2_157_IndexUDI0059_GATCTATC+ATGAGGCT_L004_001

value: IgG1 isotype control


title: JDM.RN.1.1008.MR,  Juvenile Dermatomyositis, pre treatment, CD19


title: F2_D1 individual, grown at 16C [T16_P3.A9_F2_D1]

value: leaf


title: 8808R2_156_IndexUDI0058_CATAATAC+TTCTAACG_L004_001

value: stimulated


title: JDM.RN.1.1007.MR, Juvenile Dermatomyositis, pre treatment, CD14


title: Second biological replicate of the hybrid Q x G

description:
FQ15
mRNA


title: 8808R2_155_IndexUDI0057_TGCGGCGT+CCTCGGTA_L003_001

value: unstimulated


title: First biological replicate of the hybrid Q x G

description:
FQ13
mRNA


title: JDM.RN.1.1006.MR, Juvenile Dermatomyositis, pre treatment, CD8


title: F2_D2 individual, grown at 16C [T16_P3.A8_F2_D2]

value: 7-10 leave rosette


title: F2_D1 individual, grown at 16C [T16_P3.A7_F2_D1]


title: 8808R2_154_IndexUDI0056_GAATGAGA+GAGGCATT_L003_001

value: recombinant hTNFa  + hIL-6


title: Second biological replicate of the parental line G

description:
G9
mRNA

value: parental line G


title: Third biological replicate of the parental line G

description:
G10
mRNA

value: red ripe


title: 8808R2_153_IndexUDI0055_AGGCAGAG+AGAATGCC_L001_001

value: recombinant hIL-6


title: JDM.RN.1.1004.MR, Juvenile Dermatomyositis, during treatment, CD19


title: F2_D2 individual, grown at 16C [T16_P3.A6_F2_D2]


title: 8808R2_152_IndexUDI0054_TGGTGGCA+TCCTGTAA_L003_001

value: recombinant hTNFa


title: F2_D2 individual, grown at 16C [T16_P3.A5_F2_D2]


title: JDM.RN.1.1003.MR, Juvenile Dermatomyositis, during treatment, CD14

value: Juvenile Dermatomyositis


title: Third biological replicate of the parental line Q

description:
Q5
mRNA

value: fruit mesocarp

value: parental line Q


title: Second biological replicate of the parental line Q

description:
Q3
mRNA


title: 8808R2_150_IndexUDI0052_GGTGAACC+GCGTTGGA_L003_001

value: Fibroblast-like synoviocytes from rheumatoid arthritis (RA) donors cocultured with CD4 T cells from healthy donors

value: anti-TNF/IL-6 NANOBODY® VHH


title: First biological replicate of the parental line G

description:
G7
mRNA


title: JDM.RN.1.1002.MR, Juvenile Dermatomyositis, during treatment, CD8

value: Blood

value: F


title: F2_D1 individual, grown at 16C [T16_P3.A4_F2_D1]


title: F2_D2 individual, grown at 16C [T16_P3.A3_F2_D2]


title: UT-143 3 ATAC 22RV1

city: Memphis

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

institute: UTHSC

data_processing:
QC performed using fastqc. Data trimmed for phred > 30
Alignment performed using STAR 2.7.10a and hg38 reference; Gapped mode for RNASeq; no gap for ATAC
RNASeq normalized count using CPM
Peaking calling using HOMER. BigWig files provided.
Supplementary files format and content: bw and  CPM normalized count table

source_name: 22RV1 ATAC-Seq, prostate cancer

growth_protocol: Cells were grown in RPMI+10%FBS. Cells were treated with vehicle (DMSO) or 10 uM UT-143 for 20-24 hours. ATAC-Seq and RNA-Seq were performed

extract_protocol:
Cells were harvested for ATAC-Seq and RNA-Seq
DNA libraries were prepared using Swift Accel-NGS 2S Plus kit in an automated platform

treatment_protocol: Vehicle (DMSO): UT-143 (10 uM)

tag: agent


title: First biological replicate of the parental line Q

description:
Q1
mRNA


title: F2_D1 individual, grown at 16C [T16_P3.A2_F2_D1]


title: UT-143 2 ATAC 22RV1


title: 8808R2_145_IndexUDI0047_GTTCCAAT+AATTCTGC_L003_001

value: anti-TNF mAb


title: 8808R2_146_IndexUDI0048_ACCTTGGC+GGCCTCAT_L003_001

value: anti-IL-6 mAb


title: JDM.RN.1.1005.MR, Juvenile Dermatomyositis, pre treatment, CD4


title: UT-143 1 ATAC 22RV1


title: F2_D2 individual, grown at 16C [T16_P3.A12_F2_D2]

value: leaf


title: 8808R2_144_IndexUDI0046_GCAATGCA+GGAACGTT_L003_001

value: NANOBODY® isotype control


title: Vehicle 3 ATAC 22RV1

value: Vehicle


title: P_6191 individual, grown at 16C [T16_P3.A11_P_6191]

value: 7-10 leave rosette


title: 8808R2_141_IndexUDI0043_AAGATACT+ACTTACAT_L003_001

value: unstimulated


title: Vehicle 1 ATAC 22RV1


title: 8808R2_142_IndexUDI0044_GGAGCGTC+GTCCGTGC_L003_001

value: stimulated


title: 8808R2_098_IndexUDI0042_GCGCAAGC+TCACGCCG_L003_001

value: recombinant hTNFa  + hIL-6


title: Heart Failure Patients after Acute Myocardial Infarction 21

city: Ningbo

first: Jia

state: China

address: Liuting Street No.59

institute: Ningbo No. 1 Hospital

data_processing:
lncRNA + mRNA and circRNA microarray hybridization was performed, which were consisted of RNA purification, transcribing RNA into fluorescent cRNA, and cDNA hybridization on the Agilent human lncRNA + mRNA Array V4.0 and the Agilent human circRNA Array V2.0. The miRNA profiling was performed by an Affymetrix miRNA array, including RNA labelling and hybridization. Finally, the hybridized slides were washed, dyed, and scanned.
After data summarization[13], the Raw data of gene expression were log2-transformed and normalized by using the percentile and quintile normalization method
Array V4.0
Principal Component Analysis (PCA), Correlation Analysis, Pie plots, Venn plots, Hierarchical clustering, Scatter plots and Volcano plots are performed for the expressed tRF & tiRNA in R or perl environment for statistical computing and graphics
Supplementary files format and content: xlsx
Supplementary files format and content: fpkm, count,cpm

source_name: non sacubitril/valsartan resistance

extract_protocol:
After PBMC isolation, total RNA in samples were obtained by using TRIzol reagent, and the purity and concentration of them were determined with the instrument of NanoDrop ND-1000. If the OD was in the range of 1.8-2.0, the RNA was included in the follow-up experiment. According to rtStar tRF & tiRNA Pretreatment Kit protocols (Arraystar, USA), the total RNA samples were pretreated to remove RNA modifications
Sequencing libraries are size-selected for the RNA biotypes to be sequenced using an automated gel cutter.  The libraries are qualified and absolutely quantified using Agilent BioAnalyzer 2100.

value: non sacubitril/valsartan resistance


title: F2_D1 individual, grown at 16C [T16_P3.A10_F2_D1]

source_name: leaf


title: P_6046 individual, grown at 16C [T16_P2.H9_P_6046]


title: F2_D1 individual, grown at 16C [T16_P2.H8_F2_D1]


title: Heart Failure Patients after Acute Myocardial Infarction 20

source_name: sacubitril/valsartan resistance

value: sacubitril/valsartan resistance


title: ExtracellularVesicles_model4

type: RNA

city: Bunkyo

first: Shintaro

last: Mandai

state: Tokyo

address: 1-5-45 Yushima

country: Japan

institute: Tokyo Medical and Dental University, Graduate School of Medical and Dental Sciences

hyb_protocol: We followed protocol of manual that is Hybridization Control Kit (Thermo Fisher Scientific, Inc., cat.#900454) and Hybridization, Wash, and Stain Kit (Thermo Fisher Scientific, Inc.,cat.# 900720) User Manual.

scan_protocol: We followed manufacturer's protocol, and used GeneChip® Scanner 3000 7G.

data_processing: Data acquisition and normalization (RMA+DABG) were used Affymetrix® Expression Console™ Software.

label: biotin

organism: Rattus norvegicus

source_name: Serum small extracellular vesicles

label_protocol: We followed protocol of manual that is FlashTag(tm) Biotin HSR RNA Labeling Kits (Thermo Fisher Scientific, Inc., cat.# 901911) User Manual.

extract_protocol: Total RNAs in small extracellular vesicles were purified by Total Exosome RNA & Protein Isolation Kit (Cat.4478545, Invitrogen).

value: test

value: Wister

tag: gender

value: male

value: 12 weeks

value: serum small extracellular vesicles


title: ExtracellularVesicles_model3


title: F2_D1 individual, grown at 16C [T16_P3.A1_F2_D1]

address: Dr. Bohrgasse 3

institute: Gregor Mendel Institute


title: F2_D2 individual, grown at 16C [T16_P2.H7_F2_D2]


title: Heart Failure Patients after Acute Myocardial Infarction 19


title: F2_D1 individual, grown at 16C [T16_P2.H6_F2_D1]


title: 8808R2_097_IndexUDI0041_ATATGGAT+CTGTATTA_L003_001

value: Fibroblast-like synoviocytes from rheumatoid arthritis (RA) donors cocultured with CD4 T cells from healthy donors

value: recombinant hIL-6


title: 8808R2_143_IndexUDI0045_ATGGCATG+AAGGTACC_L003_001

value: IgG1 isotype control


title: 8808R2_096_IndexUDI0040_CGGACAAC+TCCGGATT_L003_001

value: recombinant hTNFa


title: Heart Failure Patients after Acute Myocardial Infarction 18


title: ExtracellularVesicles_control4

value: control


title: Vehicle 2 ATAC 22RV1

value: Vehicle


title: 8808R2_147_IndexUDI0049_ATATCTCG+ATCTTAGT_L003_001

value: anti-TNF +anti-IL-6 mAb


title: ExtracellularVesicles_model1


title: 8808R2_094_IndexUDI0038_CTACGACA+GAGTCCAA_L003_001

value: anti-TNF/IL-6 NANOBODY® VHH


title: ExtracellularVesicles_control1


title: ExtracellularVesicles_model2


title: ExtracellularVesicles_control2


title: Heart Failure Patients after Acute Myocardial Infarction 17


title: DF-1-Herts/33

first: Chan

last: Ding

address: No.518 Ziyue Road

institute: Shanghai Veterinary Research Institute,Chinese Academy of Agricultural Sciences

description:
10x Genomics
DF-1-Herts/33

data_processing:
The raw deep sequence data were processed using the 10x Genomics software package CellRanger (v5.0.0). The reads were aligned to a concatenation of the chicken reference genome (GRCg6a) and Newcastle disease virus (NDV) genome. The complete genome sequence of the highly virulent Herts/33 strain was from GenBank AY741404.1, and that of the lentogenic strain LaSota was from GenBank JF950510.1. The chicken transcriptome was generated by filtering genome assembly GRCg6a for protein-coding genes defined in the GTF file.  We processed the unique molecular identifier (UMI) count matrix using the Seurat (v3.1.1) R package(Butler et al., 2018). To remove low-quality cells and likely multiplet captures—a major concern in microdroplet-based experiments, we applied a criterion to filter out cells with UMI/gene number of the limit of mean value +/− two-fold standard deviations with a Gaussian distribution of the UMI/gene numbers in each cell. Following visual inspection of the distribution of cells by the fraction of mitochondrial genes expressed, we further discarded low-quality cells where >30% of the counts belonged to mitochondrial genes. In addition, we used the DoubletFinder package (v2.0.2)(McGinnis et al., 2019) to identify potential doublets. After applying these quality control criteria, 91,447 single cells were included in downstream analyses. Library size normalization was performed with the NormalizeData function in Seurat to obtain the normalized count. Specifically, the global-scaling normalization method “LogNormalize” was used to normalize the gene expression measurements for each cell by the total expression, multiplied by a scaling factor (10,000 by default), and the results were log-transformed.  Top variable genes across single cells were identified using the method described in Macosko et al.(Macosko et al., 2015). The most variable genes were selected using FindVariableGenes function (mean.function = FastExpMean, dispersion.function = FastLogVMR) in Seurat. To remove the batch effects in scRNA-seq data, the mutual nearest neighbors method by Marioni et al. was performed with the batchelor R package(Haghverdi et al., 2018). Graph-based clustering was performed to cluster cells according to their gene expression profile using the FindClusters function in Seurat. Cells were visualized using a two-dimensional t-distributed stochastic neighbor embedding (t-SNE) algorithm with the RunTSNE function in Seurat. We used the FindAllMarkers function (test.use = bimod) in Seurat to identify marker genes of each cluster. For a given cluster, FindAllMarkers identified positive markers compared with all other cells.
Clustering results for individual or grouped samples were visualized using t-SNE. Cell   types were classified based on differential expression analysis, with cluster-specific marker genes identified by the FindMarkers function. GO enrichment analysis of cell type-specific marker genes was performed with ToppGene online tools.

organism: Gallus gallus

source_name: cell line

extract_protocol:
Infected or PBS-treated chickens were sacrificed by spinal cord injury. Their lungs were subsequently perfused with PBS through the right ventricle, and were divided into two groups that were subjected to different dissociation techniques. Half of the entire pool of lungs was dissected and dissociated into single-cell suspensions using the Multi Tissue Dissociation Kit 1 (Miltenyi Biotec) in combination with a gentle magnetic activated cell sorting (MACS) dissociator (Miltenyi Biotec) and enzymatic dissociation. The other half of the lung pool was minced on ice to <1-mm cubic pieces, suspended in 5 mL of digestion buffer consisting of elastase (3 U/mL; Worthington Biochemical Corporation) and DNase I (0.33 U/mL; Sigma-Aldrich) in DMEM/F12 medium, incubated with frequent agitation at 37°C for 20 min and briefly triturated(Treutlein et al., 2014). Next, an equal volume mixture of DMEM/F12 supplemented with 10% fetal bovine serum (FBS) and penicillin–streptomycin (1 U/mL, Biological Industries) was added to the single-cell suspensions in both groups. Following enzymatic incubation, cells derived from the same lungs (after the two dissociation techniques) were passed through a 100-μm sieve and then through a 70-μm sieve, pelleted again (300 g, 5 min, 4°C), and resuspended in MACS buffer (0.5% bovine serum albumin, 2 mM EDTA in PBS). Red blood cells were removed by depletion with chicken red blood antibody (Fitzgerald Industries International, Inc.) against fluorescein isothiocyanate conjugated to magnetic beads (Miltenyi Biotec). Cell populations were sorted using chicken CD45 antibody (SouthernBiotech) against biotin conjugated to magnetic beads (Miltenyi Biotec).Chicken embryo fibroblast cell lines DF-1 (ATCC, CRL-12203) were seeded in a 15-cm plate and were cultured overnight. When the cell density reached approximately 80% confluence, cells were infected with the highly virulent Herts/33 strain at a multiplicity of infection (MOI) of 1 and were incubated at 37°C with 5% CO2 for 1 h. The growth medium was replaced with DMEM supplemented with 2% FBS and was incubated for 12 h before harvesting. There was an obvious cytopathic effect on DF-1, which confirmed NDV infection. Uninfected cells were considered negative controls. Single-cell suspensions were prepared based on the 10x Genomics protocols.
Cells isolated from each group were captured in droplet emulsions using the 10x Genomics chromium single-cell instrument, and libraries were prepared using the 10x Genomics 3′ Single Cell v2 protocol for the DF-1 cell line group and the 10x Genomics 3′ Single Cell v3 protocol for the chicken group as previously described. All 10x libraries were pooled and sequenced on the NovaSeq 6000 platform (Illumina).

value: cell line


title: 8808R2_091_IndexUDI0035_AGCCTCAT+AGTAGAGA_L003_001


title: Heart Failure Patients after Acute Myocardial Infarction 13


title: F2_D2 individual, grown at 16C [T16_P2.H3_F2_D2]

first: Rahul

value: leaf

value: 7-10 leave rosette


title: 8808R2_090_IndexUDI0034_CGTTAGAA+TTCAGGTC_L003_001

value: anti-IL-6 mAb


title: F2_D2 individual, grown at 16C [T16_P2.H4_F2_D2]


title: Heart Failure Patients after Acute Myocardial Infarction 9

value: non sacubitril/valsartan resistance


title: ExtracellularVesicles_control3

value: Wister


title: lung-LaSota+

description:
10x Genomics
LaSota-CD45+

source_name: lung

value: lung

value: LaSota


title: F2_D2 individual, grown at 16C [T16_P2.H2_F2_D2]


title: 8808R2_089_IndexUDI0033_TACCGAGG+CCTGAACT_L003_001

value: anti-TNF mAb


title: F2_D2 individual, grown at 16C [T16_P2.H5_F2_D2]


title: Heart Failure Patients after Acute Myocardial Infarction 8

value: sacubitril/valsartan resistance


title: Heart Failure Patients after Acute Myocardial Infarction 7


title: 8808R2_088_IndexUDI0032_AATGCCTC+TCGATCCA_L003_001

value: Fibroblast-like synoviocytes from rheumatoid arthritis (RA) donors cocultured with CD4 T cells from healthy donors

value: NANOBODY® isotype control


title: F2_D1 individual, grown at 16C [T16_P2.H12_F2_D1]


title: F1_D1 individual, grown at 16C [T16_P2.H1_F1_D1]


title: lung-LaSota-

description:
10x Genomics
LaSota-CD45-


title: 8808R2_087_IndexUDI0031_GGCATTCT+CTAGCTTG_L003_001

value: IgG1 isotype control


title: Heart Failure Patients after Acute Myocardial Infarction 5


title: lung-Herts/33-

description:
10x Genomics
Herts/33-CD45-


title: lung-Herts/33+

description:
10x Genomics
Herts/33-CD45+


title: 8808R2_085_IndexUDI0029_CCGTGAAG+CAGTGGAT_L003_001

value: unstimulated


title: DF-1-control

description:
10x Genomics
DF-1-control

value: PBS


title: lung-control+

description:
10x Genomics
control-CD45+


title: 8808R2_086_IndexUDI0030_TTACAGGA+TGACAAGC_L003_001

value: stimulated


title: F2_D2 individual, grown at 16C [T16_P2.H10_F2_D2]


title: F2_D2 individual, grown at 16C [T16_P2.H11_F2_D2]


title: lung-control-

description:
10x Genomics
control-CD45-


title: 8808R2_056_IndexUDI0028_TCCAACGC+TTGGACTT_L003_001

value: recombinant hTNFa  + hIL-6


title: F2_D2 individual, grown at 16C [T16_P2.G9_F2_D2]


title: 8808R2_055_IndexUDI0027_CTTGGTAT+CCAAGTCC_L003_001

value: recombinant hIL-6


title: Kse3

city: Trento

first: Peter

last: De Wulf

state: TN

address: via Sommarive, 9

department: Department of Cellular, Computational and Integrative Biology

country: Italy

institute: University of Trento

data_processing:
Sequence reads were mapped to sacCer3 reference genome using STAR v2.5.3 with parameters --alignIntronMin 4 --alignIntronMax 5000 --quantMode GeneCounts
Per-gene read counts were obtained using STAR GeneCounts mode
Genome_build: sacCer3
Supplementary_files_format_and_content: tab delimited file containing raw count of sequencing reads

organism: Saccharomyces cerevisiae

source_name: wild type

growth_protocol: Cells were grown at 25°C in YPDA medium.

extract_protocol:
Exponentially grown yeast cultures (OD600 = 0,8). were isolated from a 5 ml culture sample (3,000 rpm; 3 min, 4°C), washed with ice-cold AE buffer (50mM sodium acetate pH 5.2, 10mM EDTA pH 8.0), and stored at -80°C. Next, total RNA was extracted using phenol and chloroform. Residual genomic DNA was removed (1h, 37°C) with DNase I (New England Biolabs, Cat # M0303L). Total RNA was further purified with the RNeasy Kit (Qiagen). RNA concentrations were measured with a Qubit Fluorometer (Invitrogen), and RNA quality and integrity examined with a 2100 Bioanalyzer using  RNA 6000 Pico Kit (Agilent Technologies)
CDNA libraries were prepared according to the Illumina Script seq manual. From two μg of purified yeast RNA (see above) all rRNA was removed with the Ribo-Zero Gold rRNA Removal Kit Yeast (Illumina, Cat # MRZY1324). Its depletion was confirmed with a 2100 Bioanalyzer RNA 6000 Pico Chip (Agilent Technologies, Cat # 5067-1513). Next, 10ng of the rRNA-depleted RNA was reverse transcribed into cDNA with the ScriptSeq v2 RNA-Seq Library Preparation Kit (Illumina, Cat # SSV21124). cDNA library concentrations were quantified with a Qubit Fluorometer (Invitrogen), and its quality examined on a 2100 Bioanalyzer using the High Sensitivity DNA assay (Agilent Technologies, Cat # 5067-4626). The cDNA library was then deep sequenced in multiplex fashion (4 samples per run) for 76 bases in the paired-end mode on a HiSeq Sequencing System (Illumina) at CIBIO’s Next Generation Sequencing Core facility.

tag: strain bg

tag: genotype/variation

value: wild type


title: Kse2


title: F2_D1 individual, grown at 16C [T16_P2.G7_F2_D1]

last: Pisupati

value: leaf

value: 7-10 leave rosette

tag: treatment


title: 8808R2_054_IndexUDI0026_GTCGGAGC+GGTTATAA_L003_001

value: recombinant hTNFa


title: Kse1


title: F2_D1 individual, grown at 16C [T16_P2.G8_F2_D1]


title: F2_D1 individual, grown at 16C [T16_P2.G6_F2_D1]


title: F2_D1 individual, grown at 16C [T16_P2.G5_F2_D1]


title: 8808R2_049_IndexUDI0021_GGTACCTT+AAGACGTC_L003_001

value: anti-TNF +anti-IL-6 mAb


title: MY9

first: Hailiang

last: Liu

address: NO 1239, siping road

institute: Tongji university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to mmul_1 whole genome using tophat2
Genes expression level is quantified by cuffquant.
Reads aligned to genes were calculated using cufflinks.
Genome_build: mmul_1
Supplementary_files_format_and_content: Read count and FPKM ( Fragments Per Kilobase Million) for each Sample

organism: Macaca mulatta

source_name: monkey blood-derived peripheral blood mononuclear cell

extract_protocol:
Total RNA was extracted using the TRIZOL following the manufacturer's instructions.
Libraries were prepared according to Nextera® XT DNA Library Prep Kit for Illumina

value: PBMC

tag: age

value: Young


title: 8808R2_052_IndexUDI0024_ATGAGGCC+GTTAATTG_L003_001

tag: cell type

value: anti-TNF/IL-6 NANOBODY® VHH


title: 8808R2_048_IndexUDI0020_GCACGGAC+GTCTCGCA_L003_001

value: anti-IL-6 mAb


title: MY8


title: F2_D1 individual, grown at 16C [T16_P2.G4_F2_D1]


title: F2_D2 individual, grown at 16C [T16_P2.G3_F2_D2]


title: Kse4


title: 8808R2_047_IndexUDI0019_ATGTAAGT+ACTCTATG_L003_001

value: Fibroblast-like synoviocytes from rheumatoid arthritis (RA) donors cocultured with CD4 T cells from healthy donors

value: anti-TNF mAb


title: MY10


title: MY7


title: F2_D2 individual, grown at 16C [T16_P2.G2_F2_D2]


title: JDM.RN.12.1102.MR, Juvenile Dermatomyositis, during treatment, CD14

value: Juvenile Dermatomyositis

value: Blood

tag: Sex

value: M


title: MY6


title: F2_D2 individual, grown at 16C [T16_P2.G1_F2_D2]


title: F2_D1 individual, grown at 16C [T16_P2.G12_F2_D1]


title: MY5


title: 8808R2_046_IndexUDI0018_CGGCGTGA+GCGCCTGT_L003_001

value: NANOBODY® isotype control


title: 8808R2_045_IndexUDI0017_TAATACAG+ATATTCAC_L003_001

value: IgG1 isotype control


title: MY4


title: 8808R2_043_IndexUDI0015_GGCTTAAG+TCGTGACC_L003_001

value: unstimulated


title: F2_D2 individual, grown at 16C [T16_P2.G11_F2_D2]


title: 8808R2_044_IndexUDI0016_AATCCGGA+CTACAGTT_L003_001

value: stimulated


title: MY3


title: 8808R2_014_IndexUDI0014_TTGGACTC+GGAAGCAG_L003_001

value: recombinant hTNFa  + hIL-6


title: F2_D1 individual, grown at 16C [T16_P2.G10_F2_D1]

value: leaf

value: 7-10 leave rosette


title: MY2


title: MY1


title: 8808R2_013_IndexUDI0013_CCAAGTCT+AAGGATGA_L003_001

value: recombinant hIL-6


title: MA10

value: PBMC

value: Aged


title: F2_D1 individual, grown at 16C [T16_P2.F8_F2_D1]


title: 8808R2_010_IndexUDI0010_GACCTGAA+TTGGTGAG_L003_001

value: anti-TNF/IL-6 NANOBODY® VHH


title: MA8


title: 8808R2_007_IndexUDI0007_CAAGCTAG+ACATAGCG_L003_001

value: anti-TNF +anti-IL-6 mAb


title: F2_D2 individual, grown at 16C [T16_P2.F7_F2_D2]


title: F2_D1 individual, grown at 16C [T16_P2.F6_F2_D1]


title: MA9


title: 8808R2_005_IndexUDI0005_ATCCACTG+AGGTGCGT_L003_001

value: Fibroblast-like synoviocytes from rheumatoid arthritis (RA) donors cocultured with CD4 T cells from healthy donors


title: MA6


title: 8808R2_004_IndexUDI0004_AAGTCCAA+TATGAGTA_L003_001


title: F2_D2 individual, grown at 16C [T16_P2.F4_F2_D2]


title: F2_D2 individual, grown at 16C [T16_P2.F3_F2_D2]


title: F2_D1 individual, grown at 16C [T16_P2.F5_F2_D1]


title: F2_D2 individual, grown at 16C [T16_P2.F2_F2_D2]


title: MA5


title: F2_D1 individual, grown at 16C [T16_P2.F1_F2_D1]


title: 8808R2_002_IndexUDI0002_TTATAACC+GATATCGA_L003_001


title: MA3


title: F2_D1 individual, grown at 16C [T16_P2.F9_F2_D1]


title: MA2


title: F2_D1 individual, grown at 16C [T16_P2.F12_F2_D1]


title: MA4


title: 8808R2_012_IndexUDI0012_CTCTCGTC+TATAACCT_L003_001

value: recombinant hTNFa