title: PF3, scRNAseq

city: suzhou

first: zhang

middle: shu

last: yu

address: No. 199, Ren'ai Road

department: soochow university

institute: Soochow University

data_processing:
Quality control
scRNA-seq reads were aligned to the GRCh38 genome assembly using STAR version 2.7.5a
Assembly: aligned bam files were dealing with Featurecounts Version 1.6.2 to get UMI counts of each cell
Supplementary files format and content: expression matrix file using RNA raw count

source_name: SKIN

growth_protocol: In this study, HaCaT cells were maintained in DMEM. All culture media were supplemented with 10% fetal bovine serum (FBS; Biological Industries, Kibbutz Beit-Haemek, Israel). Cells were grown at 37 °C in 5% CO2 incubators.

extract_protocol:
The concentration of single-cell suspension was adjusted to 1×105 cells/mL in PBS.
Single cell suspension was then loaded onto a microfluidic chip (part of Singleron GEXSCOPETM Single Cell RNAseq Kit, Singleron Biotechnologies) and single cell RNA-seq libraries were constructed according to the manufacturer’s instructions (Singleron Biotechnologies).

treatment_protocol: The skin cells were subjected to a conventional radiotherapy schedule of daily 2 Gy irradiation for 5 days per week in one and two weeks respectively. Meanwhile at the end of last time fractionated irradiation, a single 20 Gy irradiation was given for cells in another cultrue dish using X-ray linear accelerator (Rad Source, Suwanee, GA) at a fixed dose rate of 1.15 Gy/min

value: SKIN

value: HaCaT

value: 2 Gyx10


title: PF4, scRNAseq

status: Public on Dec 31 2022

type: SRA

country: China

library_source: transcriptomic single cell

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: cell line

tag: treatment

value: 20 Gy


title: F2_D1 individual, grown at 16C [T16_P5.H11_F2_D1]

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: cell type

tag: genotype


title: EtOH_Control_72h_RNASeq_Rep2

city: London

first: Vlad

middle: Cezar

last: Seitan

address: Guy's Hospital

department: Medical & Molecular Genetics

country: United Kingdom

institute: King's College London

description: total RNA (rRNA-depleted)

library_source: transcriptomic

data_processing:
ChIP-seq: Reads were trimmed and filtered using Cutadapt applying a Phred quality threshold of 25 and a minimal read length of 25 bases. Filtered reads were aligned to the mouse genome (NCBI37/mm9 assembly) with Bowtie 1.1.2 keeping only uniquely aligned reads while allowing a maximum of 2 mismatches (-v 2 -m 1). MACS2 was set to discard PCR/optical duplicates and was used as peak caller within the Irreproducibility Discovery Rate (IDR) pipeline implemented by the ENCODE consortium. The final set of peaks was considered the conservative set for IDR <0.02. From this set we removed blacklisted sites. Peak overlap analysis was carried out in R and normalised read coverage values were obtained using the DiffBind Bioconductor package.
RNA-seq: Bases with a Phred quality score lower than 25 were trimmed from read ends with Cutadapt, and polyA tails were removed using PRINSEQ. Filtered reads were aligned to the mouse transcriptome with STAR using 2-pass mapping, and gene-level counts were generated with HTSeq. Differential gene expression analysis was carried out using the Bioconductor package EdgeR.
Genome_build: mm9

organism: Mus musculus

source_name: Embryonic Stem Cells

growth_protocol: Mouse embryonic stem cells were maintained in feeder-free conditions, on gelatin-coated plates, in KO DMEM supplemented with 10% foetal bovine serum, LIF, L-Glutamine, 2-mercaptoethanol, non-essential amino acids, penicillin and streptomycin

extract_protocol:
1μg total RNA was used as starting material for each library. rRNA was depleted using the NEBNext rRNA Depletion Kit (E6310, New England Biolabs)
Directional RNA-seq libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420, New England Biolabs).

treatment_protocol: To induce Zbtb11 KO, growth media was supplemented with 4-hydroxytamoxifen (4OHT) pre-slubilised in ethanol. 4OHT was added to a final concentration of 250nM from a 1000x stock solution. As control, Zbtb11lox/lox Rosa26ERt2-Cre were treated with the carrier ethanol, or Zbtb11WT/WT Rosa26WT were treated with 4OHT.

tag: parental esc line

tag: zbtb11 locus genotype

tag: rosa26 locus genotype

value: ethanol


title: EtOH_Control_72h_RNASeq_Rep1

description: total RNA (rRNA-depleted)


title: G25S NDM-1

city: Baltimore

first: Marc

last: Ostermeier

state: MD

address: 3400 N. Charles St.

department: Chemical & Department of Chemical & Biomolecular Engineering

country: USA

institute: Johns Hopkins University

data_processing:
Reads were analyzed for per base sequence quality using FastQC v0.11.9.
We indexed the genome of NEB 5-alpha F'Iq cells (NCBI Reference Sequence: NZ_CP053607.1) and mapped our paired end reads to the transcriptome using STAR version 2.7.0c
Mapped reads were quantified and tabulated using featureCounts from the Subread package v1.6.4.
Normalized counts per million for the two biological replicates of RNA-Seq were tabulated with edgeR version 3.8.
Calculations for the fold-difference in gene expression and statistical analysis were performed in Microsoft Excel 2016
Assembly: Escherichia coli strain K-12 NEB 5-alpha F'Iq
Supplementary files format and content: The processed data file consists of tabs for raw counts of mapped reads, fold-difference in gene expression, variance in fold-difference, and p-values. Each tab is organized with the sample name listed in columns and genes listed in rows.

organism: Escherichia coli

source_name: NEB 5-alpha F'Iq Competent E. coli

growth_protocol: Frozen stocks of NEB 5-alpha LacIq cells containing single-codon substitutions of either the NDM-1, CAT-I, or aadB antibiotic resistance genes were diluted into 10 ml media containing 50 μg/ml spectinomycin and 2% w/v glucose and incubated overnight at 37 °C. The overnight cultures were diluted to an OD of 0.020 in 100 ml media containing 50 μg/ml spectinomycin and 2% w/v glucose, and incubated at 37 °C with shaking until the OD was about 0.5. The culture was diluted back to an OD of 0.020 in 100 ml of media in a shake flask. At time zero, IPTG was added to a concentration of 1 mM and the flasks were incubated at 37°C with shaking until the OD of the controls was approximately 0.640 (5 generations of growth). The culture was then diluted back to an OD of 0.020 in 100 ml of prewarmed media in a separate shake flask and incubated at 37°C with shaking until 330 minutes had passed since first inducing the cultures.

extract_protocol:
Microcentrifuge tubes that had been chilled on ice were filled with 1.5 ml of bacteria culture and centrifuged at 6000 x g and 4°C for 5 minutes. Supernatant was decanted and the cell pellet resuspended in 200 μl of Max Bacterial Enhancement Reagent (Invitrogen) that had been preheated to 95°C. The tubes were incubated at 95°C for 4 minutes before 1 ml of TRIzol Reagent (Invitrogen) was added. Sample lysis, separation of the RNA aqueous phase, and subsequent precipitation and wash steps were performed according to the TRIzol user manual. The resulting RNA pellet was resuspended in 50 μl of nuclease-free water. A second RNA precipitation was performed to remove residual salt as recommended by the MICROBExpress Bacterial mRNA Enrichment Kit (Invitrogen). RNA was resuspended in 0.1X TE buffer (NEB). Concentration of RNA was measured by NanoDrop spectrophotometer. RNA integrity was examined by native agarose gel electrophoresis with 300 ng of total RNA loaded in each lane of a 1.0% TAE gel containing ethidium bromide. mRNA enrichment was completed using the MICROBExpress Bacterial mRNA Enrichment Kit. The enriched mRNA was treated with DNase using the TURBO DNA-free Kit (Invitrogen).
Double-stranded cDNA was synthesized, purified, and end prepped with the NEBNext Ultra II Directional RNA Library Prep Kit with Sample Purification Beads (NEB). NEBNext Adaptor for Illumina (NEB) was ligated to the cDNA. The ligation reactions were purified using NEBNext Sample Purification Beads and PCR enriched using a unique index primer from the NEBNext Multiplex Oligos for Illumina Kit (NEB) for each sample. PCR products were cleaned with NEBNext Sample Purification Beads and pooled for Illumina Tru-Seq (2 x 75 bp reads) at the Transcriptomics and Deep Sequencing core at Johns Hopkins University.

treatment_protocol: Monoculture growth at 37°C for 330 minutes.

tag: strain

value: NEB 5-alpha LacIq

value: G25S NDM-1


title: C26S NDM-1

value: C26S NDM-1


title: G25T NDM-1

value: G25T NDM-1


title: G25C NDM-1

value: G25C NDM-1


title: PF2, scRNAseq

value: 2 Gyx5


title: F2_D1 individual, grown at 16C [T16_P5.H10_F2_D1]


title: Induced WT NDM-1

value: Induced WT NDM-1


title: Uninduced WT NDM-1

value: Uninduced WT NDM-1


title: F2_D1 individual, grown at 16C [T16_P5.G9_F2_D1]


title: PF1, scRNAseq

value: 0 Gy


title: F2_D2 individual, grown at 16C [T16_P5.G8_F2_D2]


title: high lipid Huh-7 cells, Experimental03

city: Nanchang

first: Songhua

last: Wang

address: 605 Fenglin Road, Jingkai District

institute: Jiangxi Science and Technology Normal University

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Assembly: GRCh38.104
Supplementary files format and content: tab-delimited text files include count and FPKM values for each Sample.

source_name: Huh-7 cell line

growth_protocol: Huh-7 cell was maintained in DMEM supplemented with 100 IU/ml penicillin-streptomycin containing 10% FBS.

extract_protocol:
RNA was harvested using TRIzol reagent kit (Thermo). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS® Universal V8 RNA-seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Huh-7 was induced to a high lipid model by incubating with oleic acid at 100 µM for 24 h. Then, Huh-7 cells were planted in a six-well plate at a density of 1.5 × 106 cells per well and treated with 0 and 100 μM Pectolinarigenin for 24 h after being starved.

value: Huh-7 cell line

value: high lipid Huh-7 cells

value: Pectolinarigenin(100uM, 24h)


title: Rcb13 [excluded]

city: Tomsk

first: Irina

last: Larionova

state: Tomsk oblast

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

country: Russia

institute: Tomsk State University

data_processing:
Raw data quality control was performed using FastQC (FastQC, RRID:SCR_014583) and visualized by MultiQC (MultiQC, RRID:SCR_014982)
Read alignment was performed using STAR aligner (STAR, RRID:SCR_004463) with GRCh38 genome and Gencode annotations
The numbers of reads assigned to genomic features were calculated using QoRTs software (QoRTs, RRID:SCR_018665)
Subsequent analysis steps were performed using DESeq2 software (DESeq2, RRID:SCR_015687)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: PBMC

extract_protocol:
For RNA sequencing, the peripheral blood mononuclear cells (PBMCs) were separated from whole blood by density gradient centrifugation using Lymphosep, Lymphocyte Separation Media (#L0560-500, Biowest, France), density 1.077 g/ml. After that, CD14+ monocytes from PBMC fraction were obtained by FACS. Cells were resuspended in 150 μl of staining buffer (#2701005, Cell Staining Buffer, Sony, Japan). Monocytes were defined as CD45+CD56-CD14+7-AAD- population. Conjugated monoclonal antibodies to CD45, CD56, CD14, 7-AAD were added to the cell suspension. Samples were analyzed on a MoFlo XDP cell sorter (RRID:SCR_019665, Beckman Coulter, USA). Sorting of monocytes was carried out in the Purify 1-2 mode, the sorting efficiency was 70%, the purity of the target population was 96-99%
RNA libraries were prepared with NEX 160 T flex Rapid Directional qRNA-SeqKit using indexed barcodes NEXTflex-qRNA-8nt-Barcodes (#NOVA-5198-02, Bioo Scientific, PerkinElmer Applied Genomics, USA) according manufacture`s protocols. Ribosomal RNA depletion was performed with NEBNext® rRNA Depletion Kit (Human/Mouse/Rat) (NEB #E7400, New England Biolabs Inc., USA)

value: PBMC

value: CD14+ Monocytes

tag: disease state

value: Rectal cancer

tag: patient

value: XELOX (Capecitabine plus Oxaliplatin) or FOLFOX-4 (oxaliplatin, L-leucovorin and fluorouracil) NAC


title: Rcb12


title: high lipid Huh-7 cells, Experimental02


title: F2_D2 individual, grown at 16C [T16_P5.G7_F2_D2]

value: leaf

value: 7-10 leave rosette


title: F2_D1 individual, grown at 16C [T16_P5.G6_F2_D1]


title: high lipid Huh-7 cells, Experimental01


title: G202K CAT-I

value: NEB 5-alpha LacIq

value: G202K CAT-I


title: high lipid Huh-7 cells, Control03

value: DMSO


title: Rcb11


title: S155R CAT-I

value: S155R CAT-I


title: Q30M CAT-I

value: Q30M CAT-I


title: Rcb15 [excluded]


title: Rcb10


title: F2_D1 individual, grown at 16C [T16_P5.G5_F2_D1]


title: F2_D1 individual, grown at 16C [T16_P5.G4_F2_D1]


title: high lipid Huh-7 cells, Control02


title: Rcb9


title: Rcb14 [excluded]


title: Rcb6


title: Induced WT CAT-I

value: Induced WT CAT-I


title: F2_D1 individual, grown at 16C [T16_P5.G2_F2_D1]


title: Rcb5


title: U937 Control PMA+Z-VAD-fmk+Cyclohexamide+TNF, replicate 2

city: Seoul

first: Yeongun

last: Lee

state: State...

address: 50-1, Yonsei-ro, Seodaemun-gu

country: South Korea

institute: Yonsei university

description: Human monocyte

data_processing:
The RNA-sequencing data was aligned by HISAT2 (version 2.2.1) according to the provided index file from HISAT2 (https://genome-idx.s3.amazonaws.com/hisat/grch38_tran.tar.gz).
The sam files were processed by Samtools (version 1.10) for read sorting.
Read quantification of bam files were conducted by HTSeq (version 0.11.1) to generate the read count data.
Assembly: GRCh38
Supplementary files format and content: Read count data generated via HTSeq

molecule: polyA RNA

source_name: U937, PMA, Z-VAD-fmk, CHX, TNF, replicate 2

growth_protocol: U937 cells (KCLB 21593.1) were maintained in RPMI 1640 (GIBCO 11875119) supplemented with 10% FBS (GIBCO 10099141), 1% penicillin (GIBCO 15070063), 1X MEM-NEAA (GIBCO 11140050), 1% L-Glutamine (GIBCO 25030081), 1% sodium pyruvate (GIBCO 11360070) and 50 M 2-Mercaptoethanol (Sigma-Aldrich Cat#M3148).

extract_protocol: Total RNA samples were isolated using RNeasy Mini Kit (Qiagen 74104).

treatment_protocol: Ctrl, Casp10 KO, and Casp8 KO U937 cells in media or PMA (10 nM of PMA for overnight)-, or PMA+LPS-treated (PMA followed by 1μg/ml of LPS for 3 hours) conditions.  Ctrl, Casp10 KO, and Casp8 KO U937 cells in media or PMA (10 nM of PMA for overnight)- or PMA+LPS-treated(PMA followed by 20 ng/ml TNF-alpha for 3 hours)-treated conditions.   Ctrl, Casp10 KO, and Casp8 KO U937 cells in Media or 1 PMA (10 nM of PMA for overnight)- or PMA+ZCT-treated(20 μM Z-VAD-fmk for 30 min, followed by 20 ng/mL TNF-α and 20 ng/mL cycloheximide for 3 h)-treated conditions

value: Macrophage

value: WT

value: PMA+Z-VAD+CHX+TNF


title: G202R CAT-I

value: G202R CAT-I


title: S27M CAT-I

value: S27M CAT-I


title: Nip_H2O_48_3

city: Fuzhou

first: Haitao

last: Cui

state: Fujian

address: Shangxiadian road 15

department: Plant Immunity Center

institute: Fujian Agriculture and Forestry University

data_processing:
Clean reads were achieved by filtered out the low quality reads using Trimmomatic software.
All clean reads were maaped to the Oryzae sativa L. cv. Nipponbare reference genome using Hisat2 and transformed into a count per gene library using HTseq.
Genome_build: IRGSP-1.0 by The Rice Annotation Project (RAP), https://rapdb.dna.affrc.go.jp
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each gene in each sample

organism: Oryza sativa

source_name: leaves

growth_protocol: The rice plants were grown in a light incubator for 14 days with 12 h light and 12 h dark conditions.

extract_protocol:
Total RNA quality detection was performed with a Nanodrop for determining the RNA concentration; nondenaturing agarose electrophoresis for determining RNA integrity; and an Agilent 2100 Bioanalyser for determining the total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Spore concentration was adjusted to 5 × 105 spores/mL with 0.02% Tween-20, H2O with 0.02% Tween-20 was used as mock treatment. The fungal-inoculated rice seedlings were kept in a dark chamber at 25 ◦C with 85% humidity for 24 hours, then the plants were maintained in the growth chamber at 26/24 ◦C in a 14 h light/10 h dark cycle with 85% humidity.

value: leaves

tag: age

value: 14 days

value: Nipponbare

value: 48h with H2O


title: Uninduced WT CAT-I

value: Uninduced WT CAT-I


title: Rcb4

value: PBMC

value: CD14+ Monocytes

value: Rectal cancer

value: XELOX (Capecitabine plus Oxaliplatin) or FOLFOX-4 (oxaliplatin, L-leucovorin and fluorouracil) NAC


title: Nip_H2O_48_2


title: Nip_H2O_48_1


title: U937 Control PMA+TNF, replicate 2

description: Human monocyte

source_name: U937, PMA, TNF, replicate 2

value: PMA+TNF


title: Rcb3


title: U937 Control PMA+TNF, replicate 1

description: Human monocyte

source_name: U937, PMA, TNF, replicate 1


title: F2_D2 individual, grown at 16C [T16_P5.G3_F2_D2]

value: leaf

value: 7-10 leave rosette


title: Rcb2


title: Nip_H2O_36_2

value: 36h with H2O


title: high lipid Huh-7 cells, Control01

value: Huh-7 cell line

value: high lipid Huh-7 cells

value: DMSO


title: F2_D1 individual, grown at 16C [T16_P5.G12_F2_D1]


title: F2_D2 individual, grown at 16C [T16_P5.G10_F2_D2]


title: P_6046 individual, grown at 16C [T16_P5.F9_P_6046]


title: Nip_H2O_36_3


title: Rcb1


title: F2_D2 individual, grown at 16C [T16_P5.G11_F2_D2]


title: F2_D1 individual, grown at 16C [T16_P5.G1_F2_D1]


title: Rca12

value: Before NAC


title: U937 Control PMA+Z-VAD-fmk+Cyclohexamide+TNF, replicate 1

description: Human monocyte

source_name: U937, PMA, Z-VAD-fmk, CHX, TNF, replicate 1

value: Macrophage

value: WT

value: PMA+Z-VAD+CHX+TNF


title: Nip_H2O_36_1

value: leaves

value: 14 days

value: Nipponbare


title: U937 Control PMA, replicate 3

description: Human monocyte

source_name: U937, PMA, replicate 3

value: PMA


title: Rca11

value: PBMC

value: CD14+ Monocytes

value: Rectal cancer


title: Nip_H2O_24_3

value: 24h with H2O


title: U937 Control PMA+LPS, replicate 2

description: Human monocyte

source_name: U937, PMA, LPS, replicate 2

value: PMA+LPS


title: U937 Control PMA, replicate 2

description: Human monocyte

source_name: U937, PMA, replicate 2


title: F2_D2 individual, grown at 16C [T16_P5.F8_F2_D2]

value: leaf

value: 7-10 leave rosette


title: Rca10


title: F2_D1 individual, grown at 16C [T16_P5.F7_F2_D1]


title: Nip_H2O_24_2


title: F2_D1 individual, grown at 16C [T16_P5.F6_F2_D1]


title: Rca9


title: U937 Control PMA, replicate 1

description: Human monocyte

source_name: U937, PMA, replicate 1


title: Nip_H2O_24_1


title: U937 Control PMA+LPS, replicate 1

description: Human monocyte

source_name: U937, PMA, LPS, replicate 1


title: U937 Control Media, replicate 2

description: Human monocyte

source_name: U937, Media, replicate 2

value: Media


title: U937 Control Media, replicate 1

description: Human monocyte

source_name: U937, Media, replicate 1


title: F2_D1 individual, grown at 16C [T16_P5.F3_F2_D1]

source_name: leaf


title: U937 C8KO PMA+Z-VAD-fmk+Cyclohexamide+TNF, replicate 2

description: Human monocyte


title: Rca6


title: Rca7


title: Rca8


title: F2_D1 individual, grown at 16C [T16_P5.F2_F2_D1]


title: U937 C8KO PMA+Z-VAD-fmk+Cyclohexamide+TNF, replicate 1

description: Human monocyte


title: Rca5


title: Rca4


title: U937 C8KO PMA+TNF, replicate 2

description: Human monocyte

value: PMA+TNF


title: U937 C8KO PMA+TNF, replicate 1

description: Human monocyte


title: Rca3

value: Before NAC


title: F2_D2 individual, grown at 16C [T16_P5.F12_F2_D2]


title: F2_D2 individual, grown at 16C [T16_P5.F11_F2_D2]


title: F2_D2 individual, grown at 16C [T16_P5.F5_F2_D2]


title: Nip_G11_48_2

value: 48h with Guy11


title: Nip_H2O_12_3

value: 12h with H2O


title: Nip_H2O_12_2


title: Nip_H2O_12_1


title: Rca2


title: F2_D2 individual, grown at 16C [T16_P5.F4_F2_D2]


title: Nip_G11_36_3

value: 36h with Guy11


title: Nip_G11_48_3

value: leaves


title: Nip_G11_48_1

value: 14 days


title: F2_D1 individual, grown at 16C [T16_P5.F10_F2_D1]


title: Rca1


title: Nip_G11_36_2

value: Nipponbare


title: F2_D1 individual, grown at 16C [T16_P5.E9_F2_D1]


title: U937 C8KO PMA, replicate 3

description: Human monocyte

value: Macrophage

value: PMA


title: U937 C8KO PMA+LPS, replicate 1

description: Human monocyte


title: Nip_G11_36_1


title: Dn19

value: PBMC

value: CD14+ Monocytes

value: Healthy control

value: HC

value: No NAC


title: F2_D1 individual, grown at 16C [T16_P5.E8_F2_D1]

value: leaf

value: 7-10 leave rosette


title: Dn18


title: F2_D2 individual, grown at 16C [T16_P5.E7_F2_D2]


title: Nip_G11_24_3

value: 24h with Guy11


title: U937 C8KO PMA+LPS, replicate 2

description: Human monocyte

value: PMA+LPS


title: Dn17


title: U937 C8KO PMA, replicate 2

description: Human monocyte


title: F2_D1 individual, grown at 16C [T16_P5.E6_F2_D1]


title: U937 C8KO PMA, replicate 1

description: Human monocyte


title: Nip_G11_24_1


title: U937 C10KO PMA+Z-VAD-fmk+Cyclohexamide+TNF, replicate 1

description: Human monocyte

value: PMA+Z-VAD+CHX+TNF


title: F2_D2 individual, grown at 16C [T16_P5.E3_F2_D2]


title: Dn16


title: U937 C8KO Media, replicate 1

description: Human monocyte

value: Media


title: Nip_G11_12_2

value: 12h with Guy11


title: Nip_G11_12_1

value: leaves


title: F2_D2 individual, grown at 16C [T16_P5.E4_F2_D2]


title: Dn12


title: U937 C10KO PMA+TNF, replicate 2

description: Human monocyte

value: PMA+TNF


title: Dn14


title: F2_D1 individual, grown at 16C [T16_P5.E5_F2_D1]


title: F1_D2 individual, grown at 16C [T16_P5.E2_F1_D2]


title: F2_D2 individual, grown at 16C [T16_P5.E1_F2_D2]


title: N3_H2O_48_2

value: 14 days

value: 48h with H2O


title: Dn13


title: N3_H2O_48_3


title: F2_D2 individual, grown at 16C [T16_P5.F1_F2_D2]


title: U937 C8KO Media, replicate 2

description: Human monocyte

value: Macrophage


title: F2_D2 individual, grown at 16C [T16_P5.E12_F2_D2]


title: N3_H2O_48_1


title: F2_D1 individual, grown at 16C [T16_P5.E11_F2_D1]


title: Dn15

value: PBMC


title: Nip_G11_24_2

value: Nipponbare


title: Nip_G11_12_3


title: U937 C10KO PMA+LPS, replicate 2

description: Human monocyte


title: Dn10

value: CD14+ Monocytes

value: Healthy control


title: U937 C10KO PMA+TNF, replicate 1

description: Human monocyte


title: U937 C10KO PMA+Z-VAD-fmk+Cyclohexamide+TNF, replicate 2

description: Human monocyte


title: Dn9

value: HC

value: No NAC


title: N3_H2O_36_3

value: 36h with H2O


title: U937 C10KO PMA, replicate 3

description: Human monocyte

value: PMA


title: U937 C10KO PMA+LPS, replicate 1

description: Human monocyte

value: PMA+LPS


title: F2_D1 individual, grown at 16C [T16_P5.E10_F2_D1]

value: leaf

value: 7-10 leave rosette


title: Dn8


title: Dn11


title: N3_H2O_36_2


title: U937 C10KO PMA, replicate 2

description: Human monocyte


title: F2_D1 individual, grown at 16C [T16_P5.D9_F2_D1]


title: N3_H2O_36_1


title: F2_D1 individual, grown at 16C [T16_P5.D8_F2_D1]


title: Dn7


title: U937 C10KO PMA, replicate 1

description: Human monocyte


title: N3_H2O_24_3

value: 24h with H2O


title: U937 C10KO Media, replicate 2

description: Human monocyte

value: Media


title: Dn5


title: N3_H2O_24_2

value: leaves


title: F2_D1 individual, grown at 16C [T16_P5.D5_F2_D1]


title: F2_D2 individual, grown at 16C [T16_P5.D7_F2_D2]


title: Huh_7_input (m6A-RIP)

city: shanghai

first: CHEN

last: HONG

address: 800 Dongchuan Road

institute: shanghai jiao tong university

data_processing:
fastp software (https://github.com/OpenGene/fastp) was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. And sequence quality of IP and Input samples were verified using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and RseQC (http://rseqc.sourceforge.net/).
Then we used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference genome Homo sapiens (Version: v101). Peak calling and diff peak analysis were performed by R package exomePeak2 (https://bioconductor.org/packages/release/bioc/html/exomePeak2.html), and peaks were annotated by intersection with gene architecture using R package ANNOVAR (http://www.openbioinformatics.org/annovar/).
MEME (http://meme-suite.org) and HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo and known motif finding followed by localization of the motif with respect to peak summit. And StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all transcripts and genes from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)).
The differentially expressed transcripts and genes were selected with log2 (fold change) ≥ 1 or log2 (fold change) ≤ -1 and p value < 0.05 by R package edgeR (https://bioconductor.org/packages/edgeR).
Assembly: homo sapiens Ensembl release-101
Supplementary files format and content: gene expression and methylation level

source_name: Homo sapiens

growth_protocol: Huh-7 cells were cultured in DMEM medium (Corning, USA) by adding 10% fetal bovine serum (FBS) (Excel, China) and 1% penicillin-streptomycin (Invitrogen, USA) at 37℃ in a 5% CO2 incubator. During passaging, cells were digested with 0.25% trypsin and passaged by 1:3~1:5 and cultured for 2-3 days

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Approximately more than 25 μg of total RNA representing a specific adipose type was used to deplete ribosomal RNA according to the manuscript of the Epicentre Ribo-Zero Gold Kit (Illumina, San Diego, USA). Following purification, the ribosomal-depleted RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. Then the cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). Then the IP RNA was reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.
MeRIP-seq

treatment_protocol: none treatment

value: Homo sapiens

value: cancer

value: WT


title: F2_D2 individual, grown at 16C [T16_P5.D6_F2_D2]


title: N3_H2O_12_3

value: 14 days

value: 12h with H2O


title: Dn6

value: PBMC

value: CD14+ Monocytes


title: N3_H2O_24_1


title: Dn4

value: Healthy control

value: HC


title: U937 C10KO Media, replicate 1

description: Human monocyte

value: Macrophage


title: Dn3

value: No NAC


title: F2_D1 individual, grown at 16C [T16_P5.D4_F2_D1]


title: Huh_7_IP (m6A-RIP)

value: m6A antibody IP


title: Dn2


title: N3_H2O_12_2


title: F2_D2 individual, grown at 16C [T16_P5.D3_F2_D2]

value: leaf


title: Dn1


title: N3_H2O_12_1


title: F2_D2 individual, grown at 16C [T16_P5.D2_F2_D2]

value: 7-10 leave rosette


title: Ccb8

value: Colon cancer

value: XELOX (Capecitabine plus Oxaliplatin) or FOLFOX-4 (oxaliplatin, L-leucovorin and fluorouracil) NAC


title: F2_D2 individual, grown at 16C [T16_P5.D1_F2_D2]


title: Huh_7_IP (RIP-Seq)

data_processing:
Illumina Casava1.8 software used for basecalling.
Trimmomatic was used to filter raw reads, and then clean reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing
The de-duplicated consensus sequences were mapped to the reference genome using STAR software (version 2.5.3a) with default parameters.
The exomePeak (Version 3.8) software was used for peak calling.
Assembly: homo sapiens Ensembl release-101
Supplementary files format and content: gene expression and IP level

source_name: Liver

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0.
Poly(A) RNA was purified from total RNA using Dynabeads Oligo (dT) by two rounds of purification. The poly(A) RNA used in immunoprecipitation reactions with anti-YTHDF2 (abcam,ab220163) as IP. The IP/input RNA were reverse-transcribed to create the final cDNA library by using Stranded mRNA Library Prep Kit for Illumina following the manufacturer’s instruction.

value: Liver


title: F2_D1 individual, grown at 16C [T16_P5.D12_F2_D1]


title: N3_G11_48_3

value: leaves

value: 48h with Guy11


title: Cca17


title: WsRNA2_2

city: Callaghan

first: Ting

last: La

state: NSW

address: University Drive

country: Australia

institute: UON

data_processing:
NovaSeq PE150 (6 G raw data per sample).
Original image data file from NovaSeq PE150 is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling).
Raw data are stored in FASTQ (fq) format files, which contain sequences of reads and corresponding base quality. Each read has four descriptive lines: (1) Line 1: begins with the at sign (@) followed by sequence identifiers and optional description (such as FASTA header); (2) Line 2: base sequences (raw read, A, G, C, and T); (3) Line 3: begins with the plus sign (+) optionally followed by the same Illumina sequence identifiers and description information as in Line 1; (4) Line 4: the quality values for each base, corresponding to the data in Line 2.
(1) Remove reads with adaptor contamination.
(2) Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%).
(3) Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read.
Mapping clean reads to the reference genome: Homo sapiens (GRCh38/hg38).
Assembly: GRCh38/hg38
Supplementary files format and content: *.txt: Matrix tables with raw gene counts and FPKM for every gene.

source_name: WiDr

growth_protocol: WiDr (ATCC® CCL-218™) were cultured in DMEM with 10% FBS.

extract_protocol:
Total cellular RNA isolated using an ISOLATE II RNA Mini Kit (Bioline).
Eukaryotic Strand-Specific Transcriptome Library.

treatment_protocol: Transfected with 100 nM siRNAs for 24 hours.

value: WiDr

value: colon adenocarcinoma

tag: sirna

value: LIMp27 siRNA2


title: Cca16

source_name: PBMC

value: PBMC


title: WsRNA2_3


title: WsRNA2_1


title: F2_D2 individual, grown at 16C [T16_P5.D11_F2_D2]


title: WsRNA1_3

value: LIMp27 siRNA1


title: Cca15

value: CD14+ Monocytes


title: N3_G11_36_3

value: 14 days

value: 36h with Guy11


title: N3_G11_36_2


title: N3_G11_48_1


title: F2_D2 individual, grown at 16C [T16_P5.D10_F2_D2]


title: F2_D2 individual, grown at 16C [T16_P5.C9_F2_D2]


title: N3_G11_36_1


title: Cca14

value: No NAC


title: Cca13


title: WsRNA1_1


title: Cca12


title: F2_D1 individual, grown at 16C [T16_P5.C8_F2_D1]


title: N3_G11_48_2


title: N3_G11_24_3

value: 24h with Guy11


title: F2_D2 individual, grown at 16C [T16_P5.C7_F2_D2]

value: leaf


title: Huh_7_input  (RIP-Seq)

value: cancer

value: WT


title: N3_G11_24_2


title: WsCtrl_3

value: siCtrl


title: F2_D2 individual, grown at 16C [T16_P5.C6_F2_D2]

value: 7-10 leave rosette


title: Cca11

value: Colon cancer


title: WsCtrl_2


title: Cca10


title: N3_G11_24_1

value: leaves


title: WsCtrl_1

value: WiDr


title: P_6046 individual, grown at 16C [T16_P5.C4_P_6046]


title: N3_G11_12_3

value: 12h with Guy11


title: Cca8

value: Before NAC


title: N3_G11_12_2


title: Cca7

value: PBMC


title: WsRNA1_2

value: colon adenocarcinoma

value: LIMp27 siRNA1


title: F2_D2 individual, grown at 16C [T16_P5.C2_F2_D2]


title: Cca9

value: CD14+ Monocytes


title: Cca6


title: Cervical adenosquamous carcinoma tissue [AS_1]

city: Beijing

first: Hongxue

last: Luo

state: China

address: Department of Ob/Gyn, Peking University People's Hospital, Beijing, PR China

institute: Peking university people's hospital

data_processing:
Clean reads for subsequent analysis were obtained through raw data filtering, sequencing error rate check and GC content distribution check.
The clean reads were then compared and mapped to the reference genome.
Find_circ and CIRI2 were both used to detect and identify circRNAs
Following identification of circRNAs, the length distribution and sources of known or novel circRNAs were counted.
Normalization of readcount by TPM was conducted before expression analysis.
Assembly: hg19
Supplementary files format and content: Normalized readcount data by TPM

source_name: Cervical adenosquamous carcinoma tissue

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad,CA, USA) following the manufacturer’s protocol. The integrity of RNA was evaluated by standard denaturing agarose gel electrophoresis and using the Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). The purity and concentration, as well as the preliminary quantification were determined in a Nano Drop spectrophotometer (Nano Drop, Wilmington, DE, USA).  The minimum concentration of total RNA used for the construction of sequencing libraries exceed 3nM.
After removal of ribosomal RNA and building a special library, RNA-seq data collection were conducted using Illumina PE150 platform by Novogene Bioinformatics Technology Co. Ltd. (Beijing, China).

tag: tumor stage

tag: hpv types_infected

tag: disease

value: cervical cancer

tag: Sex

value: female

value: Cervical adenosquamous carcinoma tissue


title: Adjacent normal tissue of cervical adenosquamous carcinoma [AS_2]

tag: tissue


title: Adjacent normal tissue of cervical adenocarcinoma [A_2]


title: F2_D2 individual, grown at 16C [T16_P5.C1_F2_D2]

value: leaf

tag: treatment


title: osrdr2-3_pistil_sRNA

city: Nanjing

first: Lili

address: Weigang No.1

institute: Nanjing Agricultural University

description: fem1-3_pistil sRNA-seq

data_processing:
Adapter sequences were trimed and clean reads with sizes ranging from 18 to 45 were mapped to MSU7.0 using Bowtie with parameter -v 0.
Annotated structure RNAs were excluded.
Read counts were normalized to RPTM.
Genome_build: MSU 7.0

source_name: pistil

growth_protocol: Rice plants grown in soil in jiangsu province

extract_protocol:
RNA was extrated using TRIzol method.
18-45nt small RNA was cut from PAGE gel.

tag: cultivar

value: Japponica


title: Cca5

tag: cell type

value: No NAC


title: Cca4


title: Nip_pistil_sRNA

description: Nip_pistil sRNA-seq


title: P_6191 individual, grown at 16C [T16_P5.C5_P_6191]

tag: developmental stage

tag: genotype


title: Adjacent normal tissue of cervical squamous carcinoma [S_2]


title: Cervical squamous carcinoma tissue [S_1]

source_name: Cervical squamous carcinoma tissue

value: Cervical squamous carcinoma tissue


title: Cca3


title: F2_D2 individual, grown at 16C [T16_P5.C11_F2_D2]

value: 7-10 leave rosette


title: osrdr2-6_stamen_sRNA

description: fem1-6_stamen sRNA-seq

source_name: stamen


title: F2_D1 individual, grown at 16C [T16_P5.C10_F2_D1]


title: F2_D2 individual, grown at 16C [T16_P5.C3_F2_D2]


title: Human brain organoids, CHO

first: Yan

last: Liu

state: JiangSu

address: 101Longmian Avenue

department: Institute for Stem Cell and Neural Regeneration

institute: Nanjing Medical University

data_processing:
Reads were aligned to the hg38 human reference genome, and gene-level unique molecular identifier (UMI) counts were obtained using Cell Ranger (version 3.1.0).
Assembly: hg38
Supplementary files format and content: h5 file includes barcodes, gene features and expression matrix for each sample

source_name: Human brain organoids

extract_protocol:
To obtain a single-cell suspension,  5-7 organoids at D30 were randomly selected into a 1.5 ml EP tube with 1 ml of TrypLE (Life Technologies) and incubated in a 37 degrees Celsius incubator for 40 min with gentle agitation every 5-8 min. The organoids were then washed with DPBS (Life Technologies) 3 times and gently dissociated into single cells with a 200 microliter pipette.
The organoids were dissociated by trypLE (Life technology) into single cells. The cell debris and other aggregates were removed by an additional low-speed centrifugation. About 5,000 cells were captured and the released RNA were barcoded through reverse transcription in individual GEMs. Droplet-based single-cell RNA sequencing was performed using the 10X Genomics Chromium Single Cell 3 platform, version 3, according to manufacturers instructions.

treatment_protocol: The brain organoids were treated with 15μg/ml cholesterol (MβCD-cholesterol,sigma C4951) from day 1 to day 30.

value: Human brain organoids

tag: cell line

value: brain organoids

value: cultured with additional cholesterol


title: N3_G11_12_1

source_name: leaves

value: leaves

value: 14 days

value: 12h with Guy11


title: F2_D2 individual, grown at 16C [T16_P5.B9_F2_D2]


title: Cca1

value: PBMC

value: Colon cancer


title: 20_Gy_4h

data_processing:
Basecalls were performed using bcl2fastq v2.20.0.422 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 15, using Trimmomatic v0.36, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the NCBI GRCh38_p13 genome using BWA version 0.7.15-r1140.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to Reads Per Kilobase per Million mapped reads, rkpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.2 with the significance cut-off q-value <=0.05
bigWig files were generated using the subcommand(bamCoverage) of Deeptools v3.2.1. narrowPeak files were generated using MACS v2 with default settings.
Assembly: GRCh38_p13
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: SKIN

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the NEXTflex® Rapid DNA-Seq Library Prep Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for ip samples. Libraries were amplified using 15 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Q-Sep400.

treatment_protocol: Cells were exposed to 20Gy of ionizing radiation using X-ray linear accelerator (Rad Source, Suwanee, GA) at a fixed dose rate of 1.15 Gy/min

value: SKIN

value: HaCaT

tag: antibody

value: 20 Gy X ray irradiation


title: Nip_stamen_sRNA

description: Nip_stamen sRNA-seq


title: Cca2

value: CD14+ Monocytes


title: osrdr2-3_stamen_sRNA

description: fem1-3_stamen sRNA-seq


title: 0_Gy

value: non


title: F2_D2 individual, grown at 16C [T16_P5.B8_F2_D2]

value: leaf


title: osrdr2-6_pistil_sRNA

description: fem1-6_pistil sRNA-seq

value: Japponica


title: Cervical adenocarcinoma tissue [A_1]

source_name: Cervical adenocarcinoma tissue

value: cervical cancer

value: female

value: Cervical adenocarcinoma tissue


title: F2_D2 individual, grown at 16C [T16_P5.B7_F2_D2]

value: 7-10 leave rosette


title: F2_D1 individual, grown at 16C [T16_P5.C12_F2_D1]


title: DSP-1001660008975-G-H11

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: No Neoadjuvant chemotherapy

tag: segment

value: CK

tag: tissue site

value: Internal

tag: slide

tag: roi number

tag: roi x_coordinate

tag: roi y_coordinate


title: F2_D2 individual, grown at 16C [T16_P5.B6_F2_D2]


title: DSP-1001660008975-G-H12

tag: disease state

tag: patient


title: DSP-1001660008975-G-H10

value: Bordered


title: spASCs-ECs coculture-DSCM, scRNAseq

city: Guangzhou

first: Sheng

last: Zhang

state: None Selected

address: 132 Waihuan West Road, Guangzhou Science Park, Luogang District

institute: School of Materials Science and Engineering, Sun Yat-sen University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCm38 and GRCh38 respectively for the Rattus norvegicus and Homo sapiens data
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Astrocyte cells and Endothelial cells

extract_protocol:
Spinal cord slice culture system: After 12 days of cultivation, the organotypic was removed from  the hydrogel, and hydrogel with cells was digested by collagenaseand  trypsin. Digestion was neutralized with DMEM supplemented with  10% FBS. After concentration (300g, 5min), The cell pellet was washed and resuspension with  PBS supplemented with 0.04% BSA. The cell numbers and viability (>75%) were confirmed  using TC20 Automated Cell Counter. In hspASC-HUVEC co-culture system: After  five days of cultivation, the approaches used for cell digestion and suspension preparation were  identical to the Spinal cord slice culture system
The cell suspension was loaded into Chromium microfluidic chips with 30  chemistry and barcoded with a 10× Chromium Controller  (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed  and sequencing libraries constructed with reagents from a Chromium Single Cell 30   reagent kit (10X Genomics) according to the  manufacturer’s instructions. Sequencing was performed with Illumina  NovaSeq 6000.

value: Astrocyte cells and Endothelial cells

tag: growth protocol

value: hspASCs and ECs cocultured on DSCM

tag: model

value: human hspASC-hEC co-culture model


title: spASCs-ECs coculture-COL+SRGN, scRNAseq

description: 10x Genomics

value: hspASCs and ECs cocultured on SRGN added COLI


title: 105-gfp-O1

city: Basel

first: Panagiotis

last: Papasaikas

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute

data_processing:
Final libraries were sequenced on a HiSeq2500 (50cycles single-end) and demultiplexing performed using a standard Illumina bcl2fastq2 pipeline.
Reads were aligned against the hydra vulgaris NCBI genome guided by transcriptome annotation (NCBI Hydra vulgaris assembly Hydra_RP_1.0, NCBI  Hydra vulgaris annotation release 102).
Alignments were performed using STAR version 2.5.0 with the following command line parameters: --outSJfilterReads Unique --outFilterType BySJout --outFilterMultimapNmax 5 --alignSJoverhangMin 8 --alignSJDBoverhangMin 4 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --seedSearchStartLmax 50 --twopassMode Basic --genomeChrBinNbits 12 --genomeSAsparseD 2 --quantMode GeneCounts.
Raw (exonic) gene counts as determined by the STAR GeneCounts quantification mode
Genome_build: NCBI Hydra_RP_1.0
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Hydra vulgaris

source_name: tentacles

growth_protocol: standard Hydra culture conditions

extract_protocol:
Original and ectopic tentacles were collected 7 days after the third electroporation from mock, Zic4, Sp5, and Zic4/Sp5 RNAi animals. When possible, the proximal and distal tentacle halves were separated (original tentacles of Zic4 RNAi and Sp5 RNAi). Corresponding samples were pooled in the lysis buffer, frozen on dry ice and stored at -80 °C for RNA extraction. The RNA was extracted with the Single Cell RNA Purification Kit (Norgen), according to the manufacturer’s instructions.
cDNA amplification was performed using the SmartSeq2 approach as per the original protocol (31). Full length cDNA was processed for Illumina sequencing using Tagmentation with an in-house purified Tn5 transposase (32): 1ng of amplified cDNA was tagmented in TAPS-DMF buffer (10mM TAPS pH8.5, 5mM MgCl2, 10% DMF), at 55C for 7min. Tn5 was then stripped using SDS (0.04% final) and tagmented DNA was amplified using Phusion High-Fidelity DNA Polymerase (ThermoFisher). PCR was performed in the Phusion HF buffer, with a first extension at 72 °C for 3min, followed by 10 cycles of amplification (95 °C – 30 s, 55 °C –30 s, 72 °C – 30s). Commercial Nextera XT indexes were used for the PCR amplification (1/5 dilution).

treatment_protocol: 20-30 animals per RNAi treatment were incubated at 4 °C for 1 hour and then transferred into an electroporation cuvette (Gene Pulser / Micro Pulser Electroporation Cuvette 0.4 cm gap; Bio-Rad or electroporation cuvettes 4 mm gap; VWR) and washed twice with chilled MiliQ water. Residual water was removed and 200 μL of the siRNA (siRNAs were ordered as 20 bp RNA duplexes from Integrated DNA Technologies (IDT)) solution was added to each cuvette. Each siRNA was diluted in ddH2O to a final concentration of 1.35 μM per treatment. Animals were incubated with the siRNA solution for 5 minutes. After relaxation of the animals, two pulses (150 V range) were applied for 50 ms (Gene Pulser II with RF module; Bio-Rad). After electroporation, 500 μL of ice-cold recovery medium (80 % HM, 20 % v/v dissociation medium) was added to the animals. Animals were carefully transferred into a new Petri dish filled with pre-chilled recovery medium. The next day, the animals were transferred into fresh HM. Three electroporations were performed in this manner with 1 day for recovery in between successive rounds.

tag: strain

tag: tissue

value: original tentacles

value: wild type

tag: treatment

value: mock RNAi


title: 105-double-N4

value: ectopic tentacles

value: Zic4/Sp5 RNAi


title: 105-double-O4


title: F2_D1 individual, grown at 16C [T16_P5.B5_F2_D1]

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

value: leaf

tag: developmental stage

tag: cell type


title: DSP-1001660008975-G-H09

value: Colon cancer


title: F2_D2 individual, grown at 16C [T16_P5.B4_F2_D2]

value: 7-10 leave rosette

tag: genotype


title: DSP-1001660008975-G-H08

value: Colorectal cancer


title: F2_D1 individual, grown at 16C [T16_P5.B3_F2_D1]


title: X512, dscm, tnfa, 24h, asc.4 biol rep 4

description: X512_dscm_tnfa_24h_asc.4 biol rep 4

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house  Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
The bulk RNA-seq raw sequences were cleaned using fastp (version 0.21.0)
Cleaned sequence reads were mapped to hg38 by HISAT2 (version 2.0.4), and sorted using Samtools (version 1.13).
After assembling and quantification by StringTie (version 2.1.4), the comma separated values file containing the gene-level raw count data matrix was produced.
Assembly: hg38
Supplementary files format and content: comma separated values file including gene expression raw count data

source_name: hspASC

growth_protocol:
cultured on DSCM
human spinal cord astrocyte cells were maintained in AM medium in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol (Invitrogen, 15596018).
Libraries for RNA-seq were prepared using NEBNext® UltraTM RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: human spinal cord astrocyte cells  were cultured on COLI/DSCM hydrogel for 5days, and then treated with TNF-alpha (designated 0min and 24 hours) with 20ng/ml TNF-alpha.

tag: cell line

value: hspASC

value: human spinal cord astrocyte cells

value: WT

value: cultured on DSCM

value: TNF-alpha

tag: time

value: 24 hours


title: 105-double-O3


title: F2_D1 individual, grown at 16C [T16_P5.B2_F2_D1]

source_name: leaf


title: DSP-1001660008975-G-H07

value: No Neoadjuvant chemotherapy

tag: segment

value: CK

tag: tissue site

value: Internal


title: X512, col, tnfa, 24h, asc.2 biol rep 4

description: X512_col_tnfa_24h_asc.2 biol rep 4

growth_protocol:
cultured on COLI
human spinal cord astrocyte cells were maintained in AM medium in humidified atmosphere with 5% CO2 at 37C

value: cultured on COLI


title: 105-double-N2

value: wild type


title: X426, dscm, tnfa, 24h, asc.4 biol rep 3

description: X426_dscm_tnfa_24h_asc.4 biol rep 3


title: DSP-1001660008975-G-H06

tag: slide

tag: roi number


title: X426, col, tnfa, 24h, asc.2 biol rep 3

description: X426_col_tnfa_24h_asc.2 biol rep 3


title: F2_D2 individual, grown at 16C [T16_P5.B1_F2_D2]


title: 105-double-N1

value: ectopic tentacles


title: F2_D1 individual, grown at 16C [T16_P5.B12_F2_D1]


title: DSP-1001660008975-G-H05

tag: roi x_coordinate

tag: roi y_coordinate


title: DSP-1001660008975-G-H04

tag: disease state

tag: patient

value: External


title: 105-gfp-O3

value: original tentacles

value: mock RNAi


title: X423, dscm, tnfa, 24h, asc.16 biol rep 2

description: X423_dscm_tnfa_24h_asc.16 biol rep 2

tag: growth protocol


title: spASCs-ECs coculture-COL, scRNAseq

description: 10x Genomics

value: Astrocyte cells and Endothelial cells

value: hspASCs and ECs cocultured on COLI

tag: model

value: human hspASC-hEC co-culture model


title: X420, dscm, tnfa, 24h, asc.4 biol rep 1

description: X420_dscm_tnfa_24h_asc.4 biol rep 1

value: hspASC

value: human spinal cord astrocyte cells


title: DSP-1001660008975-G-H03

tag: tissue

value: Colorectal cancer

value: Colon cancer


title: P_6191 individual, grown at 16C [T16_P5.B11_P_6191]

value: leaf

value: 7-10 leave rosette

tag: treatment


title: 105-double-N3

tag: strain

value: Zic4/Sp5 RNAi


title: 105-gfp-O2


title: F2_D2 individual, grown at 16C [T16_P5.B10_F2_D2]

tag: developmental stage

tag: cell type


title: DSP-1001660008975-G-H02

value: No Neoadjuvant chemotherapy

value: Bordered


title: 105-double-O1

tag: genotype

value: wild type


title: X420, col, tnfa, 24h, asc.2 biol rep 1

description: X420_col_tnfa_24h_asc.2 biol rep 1

tag: cell line

value: WT

value: cultured on COLI

value: TNF-alpha

tag: time

value: 24 hours


title: DSP-1001660008975-G-H01

tag: segment

value: CK

tag: tissue site


title: F2_D1 individual, grown at 16C [T16_P5.A9_F2_D1]


title: 105-G-Tb-4

value: original tentacle proximal halves

value: mock RNAi


title: 105-double-O2

value: original tentacles


title: F2_D1 individual, grown at 16C [T16_P5.A8_F2_D1]


title: DSP-1001660008975-G-G12

tag: slide

tag: roi number


title: X512, col, 0min, asc.1 biol rep 4

description: X512_col_0min_asc.1 biol rep 4

value: hspASC

value: human spinal cord astrocyte cells


title: 105-Sp-Tb-O-1

value: Sp5 RNAi


title: DSP-1001660008975-G-G11

value: Colorectal cancer

value: Colon cancer

tag: roi x_coordinate

tag: roi y_coordinate


title: X512, dscm, 0min, asc.3 biol rep 4

description: X512_dscm_0min_asc.3 biol rep 4

value: cultured on DSCM


title: F2_D2 individual, grown at 16C [T16_P5.A7_F2_D2]

value: leaf

value: 7-10 leave rosette


title: F2_D2 individual, grown at 16C [T16_P5.A6_F2_D2]


title: 105-Sp-N-1

value: ectopic tentacles

value: wild type


title: X426, dscm, 0min, asc.3 biol rep 3

description: X426_dscm_0min_asc.3 biol rep 3

value: WT


title: X423, col, tnfa, 24h, asc.14 biol rep 2

description: X423_col_tnfa_24h_asc.14 biol rep 2

value: cultured on COLI

value: TNF-alpha


title: F2_D1 individual, grown at 16C [T16_P5.A5_F2_D1]


title: 105-G-Tb-2


title: 105-G-Tb-3


title: F2_D1 individual, grown at 16C [T16_P5.A4_F2_D1]


title: X423, dscm, 0min, asc.15 biol rep 2

description: X423_dscm_0min_asc.15 biol rep 2


title: DSP-1001660008975-G-G09

tag: disease state

tag: patient

value: No Neoadjuvant chemotherapy

value: CK

value: Bordered


title: F2_D1 individual, grown at 16C [T16_P5.A3_F2_D1]


title: DSP-1001660008975-G-G10


title: DSP-1001660008975-G-G08

value: Rectal cancer

value: Neoadjuvant chemotherapy

value: External


title: X426, col, 0min, asc.1 biol rep 3

description: X426_col_0min_asc.1 biol rep 3

value: hspASC

value: human spinal cord astrocyte cells

tag: growth protocol


title: 105-G-Tb-1

tag: tissue

value: original tentacle proximal halves

value: mock RNAi


title: X423, col, 0min, asc.13 biol rep 2

description: X423_col_0min_asc.13 biol rep 2

tag: treatment


title: DSP-1001660008975-G-G07

value: Colorectal cancer


title: X420, dscm, 0min, asc.3 biol rep 1

description: X420_dscm_0min_asc.3 biol rep 1

value: cultured on DSCM


title: 105-G-Tp-3

tag: strain

value: original tentacle distal halves


title: F2_D1 individual, grown at 16C [T16_P5.A2_F2_D1]

value: leaf

tag: developmental stage

value: 7-10 leave rosette


title: DSP-1001660008975-G-G06


title: 105-Z-Tb-2

value: wild type

value: Zic4 RNAi


title: F2_D1 individual, grown at 16C [T16_P5.A1_F2_D1]

tag: cell type


title: X420, col, 0min, asc.1 biol rep 1

description: X420_col_0min_asc.1 biol rep 1

tag: genotype

value: WT

value: cultured on COLI


title: DSP-1001660008975-G-G05

value: CK

value: Internal


title: 105-Z-Tp-3


title: 105-Z-Tp-4


title: F2_D1 individual, grown at 16C [T16_P5.A12_F2_D1]


title: F2_D2 individual, grown at 16C [T16_P5.A11_F2_D2]


title: DSP-1001660008975-G-G04

value: Rectal cancer

value: Neoadjuvant chemotherapy


title: Sample 6 (P15 - RS02098409)

city: Buffalo

first: Jianmin

state: NY

address: Elm and Carlton Streets

department: Bioinformatics and Biostatistics

institute: Roswell Park Comprehensive Cancer Center

data_processing:
Raw sequencing data were processed using Cellranger v6.0.0 software
Filtered gene-barcode matrices were used for further analyses with Seurat single cell data analysis R package.
Assembly: GRCh38
Supplementary files format and content: gene expression count matrix

source_name: Renal cell carcinoma

extract_protocol:
tissue dissociation to prepare single cell suspension
Single cell libraries are generated using the 10X Genomics Chromium Single Cell 3’ Reagent V3 Kit according to manufacturer’s protocol.  Cell suspensions are first assessed with Trypan Blue using a Countess FL automated cell counter (ThermoFisher), to determine concentration, viability and the absence of clumps and debris that could interfere with single cell capture.  Cells are loaded into the Chromium Controller (10X Genomics) where they are partitioned into nanoliter-scale Gel Beads-in-emulsion with a single barcode per cell.  Reverse transcription is performed and the resulting cDNA is amplified.  The full-length amplified cDNA is used to generate gene expression libraries by enzymatic fragmentation, end-repair, a-tailing, adapter ligation, and PCR to add Illumina compatible sequencing adapters.  The resulting libraries are evaluated on D1000 screentape using a TapeStation 4200 (Agilent Technologies), and quantitated using Kapa Biosystems qPCR quantitation kit for Illumina. They are then pooled, denatured, and diluted to 300pM with 1% PhiX control library added.  The resulting pool is then loaded into the appropriate NovaSeq Reagent cartridge and sequenced on a NovaSeq6000 following the manufacturer’s recommended protocol (Illumina Inc.).
10X Genomics Chromium Single Cell 3’ Reagent V3 Kit

treatment_protocol: RCC patients were treated with a 15Gy radiation dose. 4 weeks post radiation tumors were resected, processed to single cell suspension and cryopreserved. Prior to performing single cell RNA seq, tumor samples were thawed and sorted for viability. Viable tumor cells were sent for scRNA sequencing.

tag: gender

value: Female

value: Tumor - single cell suspension

value: 15 Gy radiation dose


title: Sample 5 (P14 - RS02065737)

value: Male


title: P_6191 individual, grown at 16C [T16_P5.A10_P_6191]


title: 105-Z-Tb-1

value: original tentacle proximal halves


title: DSP-1001660008975-G-G03

value: Colorectal cancer


title: Sample 4 (P10 - RS01985670)


title: DSP-1001660008975-G-G02


title: F2_D1 individual, grown at 16C [T16_P4.H9_F2_D1]


title: 105-Z-Tp-1

value: original tentacle distal halves


title: DSP-1001660008975-G-G01


title: 105-Z-Tp-2


title: DSP-1001660008975-G-F12

value: External


title: 105-G-Tp-2

value: mock RNAi


title: F2_D1 individual, grown at 16C [T16_P4.H6_F2_D1]

value: leaf

value: 7-10 leave rosette


title: F2_D1 individual, grown at 16C [T16_P4.H7_F2_D1]


title: 105-Sp-Tp-O-1

value: wild type

value: Sp5 RNAi


title: F2_D1 individual, grown at 16C [T16_P4.H8_F2_D1]


title: 105-Z-Tb-4

value: Zic4 RNAi


title: Sample 1 (C1 - RS00123497)


title: DSP-1001660008975-G-F09

value: CK

value: Internal


title: 105-Z-Tb-3


title: E2013 [miRNA-seq]

city: Atlanta

first: Michael

last: Davis

state: GA

address: 2015 Uppergate Dr

institute: Emory University

description: small RNA

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.

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

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: Yerkes Nonhuman Primate Genomics Core

tag: heart chamber

value: Atrium

tag: age

value: 3 months

tag: Sex

tag: diagnosis

value: Ventricular septal defect


title: E2016 [miRNA-seq]

description:
small RNA
sRNA_processed.csv

value: 1-2 week

value: Female

value: Coarctation, atrial septal defect, ventricular septal defect

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


title: E1100 [miRNA-seq]

description:
small RNA
sRNA_processed.csv

value: < 1 week

value: Hypoplastic left heart syndrome


title: DSP-1001660008975-G-F10

value: Colorectal cancer

value: Rectal cancer

value: Neoadjuvant chemotherapy

tag: segment

tag: tissue site

tag: slide

tag: roi number

tag: roi x_coordinate

tag: roi y_coordinate


title: F2_D2 individual, grown at 16C [T16_P4.H4_F2_D2]

tag: tissue

value: leaf

value: 7-10 leave rosette

tag: treatment


title: 105-Sp-Tp-O-2

tag: strain

value: original tentacle distal halves

value: wild type

value: Sp5 RNAi


title: Sample 3 (P6 - RS01813260)

tag: cell type

value: Tumor - single cell suspension

value: 15 Gy radiation dose


title: F2_D2 individual, grown at 16C [T16_P4.H2_F2_D2]

tag: developmental stage

tag: genotype


title: 105-Sp-N-2

value: ectopic tentacles


title: E1097 [miRNA-seq]

description:
small RNA
sRNA_processed.csv

tag: patient id

tag: sequence facility

value: Yerkes Nonhuman Primate Genomics Core

value: Atrium

value: 3 months

value: Male

value: Tetralogy of Fallot


title: E1099 [miRNA-seq]

description: small RNA

tag: heart chamber

tag: age

value: 5 months

value: Female

value: Complete atrioventricular canal defect, Downs syndrome

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


title: F2_D1 individual, grown at 16C [T16_P4.H3_F2_D1]

value: leaf


title: DSP-1001660008975-G-F11

value: Colorectal cancer

tag: disease state

value: Rectal cancer

tag: patient

value: Neoadjuvant chemotherapy

value: External


title: F2_D2 individual, grown at 16C [T16_P4.H1_F2_D2]

value: 7-10 leave rosette


title: Sample 2 (C23 - RS01519713)

tag: gender

value: Tumor - single cell suspension


title: E1095 [miRNA-seq]

description: small RNA

value: Novogene

tag: Sex

tag: diagnosis

value: Double outlet right ventricle


title: 105-Sp-Tp-O-3

value: original tentacle distal halves

value: wild type

value: Sp5 RNAi


title: 105-Sp-Tb-O-3

value: original tentacle proximal halves


title: DSP-1001660008975-G-F04

tag: segment

tag: tissue site

value: Bordered

tag: slide

tag: roi number

tag: roi x_coordinate


title: F2_D2 individual, grown at 16C [T16_P4.H12_F2_D2]

tag: tissue

tag: cell type

tag: treatment


title: DSP-1001660008975-G-F06

tag: roi y_coordinate


title: P_6046 individual, grown at 16C [T16_P4.H5_P_6046]

tag: developmental stage

tag: genotype


title: P_6191 individual, grown at 16C [T16_P4.H11_P_6191]


title: DSP-1001660008975-G-F05

value: CK


title: E1083 [miRNA-seq]

description:
small RNA
sRNA_processed.csv

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-1001660008975-G-F08

value: Colorectal cancer

tag: disease state

value: Rectal cancer

tag: patient

value: Neoadjuvant chemotherapy


title: DSP-1001660008975-G-F03

tag: segment


title: 105-Sp-Tb-O-2

tag: strain


title: 105-Sp-N-3

value: ectopic tentacles


title: E1066 [miRNA-seq]

description:
small RNA
sRNA_processed.csv

value: 6 months

tag: Sex

tag: diagnosis

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

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


title: E1063 [miRNA-seq]

description:
small RNA
sRNA_processed.csv

value: 3 years

value: Male

value: Ventricular septal defect


title: DSP-1001660008975-G-F07

tag: tissue site

value: Internal

tag: slide

tag: roi number

tag: roi x_coordinate


title: 105-G-Tp-4

tag: tissue

value: original tentacle distal halves

value: wild type

tag: treatment

value: mock RNAi


title: DSP-1001660008975-G-F02

tag: roi y_coordinate


title: F2_D2 individual, grown at 16C [T16_P4.G9_F2_D2]

value: leaf

tag: developmental stage

value: 7-10 leave rosette

tag: cell type

tag: genotype


title: E1050 [miRNA-seq]

description: small RNA

tag: patient id

tag: sequence facility

value: Novogene

tag: heart chamber

value: Atrium

tag: age

value: 1 week

value: Female

value: Hypoplastic left heart syndrome


title: 105-G-Tp-1

tag: strain


title: E1045 [miRNA-seq]

description: small RNA

value: Yerkes Nonhuman Primate Genomics Core

value: < 1 week

tag: Sex

value: Coarctation of the aorta, ventricular septal defect


title: DSP-1001660008975-G-F01

value: Colorectal cancer

tag: disease state

value: Rectal cancer

tag: patient

value: Neoadjuvant chemotherapy

tag: segment

value: CK


title: F2_D1 individual, grown at 16C [T16_P4.G8_F2_D1]


title: DSP-1001660008975-G-E12

tag: tissue site

value: External

tag: slide

tag: roi number


title: F2_D2 individual, grown at 16C [T16_P4.G6_F2_D2]

tag: tissue

tag: treatment


title: DSP-1001660008975-G-E11

tag: roi x_coordinate

tag: roi y_coordinate


title: F2_D2 individual, grown at 16C [T16_P4.G5_F2_D2]

tag: developmental stage

tag: cell type

tag: genotype


title: E1007 [miRNA-seq]

description:
small RNA
sRNA_processed.csv

tag: patient id

tag: sequence facility

tag: heart chamber

value: 6 months

value: Male

tag: diagnosis

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

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


title: E1010 [miRNA-seq]

description:
small RNA
sRNA_processed.csv

tag: age

value: 9 weeks

tag: Sex

value: Tetralogy of Fallot


title: F2_D1 individual, grown at 16C [T16_P4.G4_F2_D1]

value: leaf

value: 7-10 leave rosette


title: F2_D2 individual, grown at 16C [T16_P4.H10_F2_D2]


title: DSP-1001660008975-G-E09

tag: disease state

tag: patient

tag: segment

value: Internal


title: F2_D1 individual, grown at 16C [T16_P4.G3_F2_D1]


title: E1006 [miRNA-seq]

description: small RNA

value: Yerkes Nonhuman Primate Genomics Core

value: Atrium

value: Female

value: Complete atrioventricular canal defect


title: E1004 [miRNA-seq]

description: small RNA

value: 12 months

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


title: E985 [miRNA-seq]

description:
small RNA
sRNA_processed.csv

value: 2 weeks

value: Interrupted aortic arch


title: F2_D1 individual, grown at 16C [T16_P4.G2_F2_D1]


title: E975 [miRNA-seq]

description:
small RNA
sRNA_processed.csv

value: 6 months


title: DSP-1001660008975-G-E07

value: Colorectal cancer

value: Rectal cancer

value: Neoadjuvant chemotherapy

value: CK

tag: tissue site

tag: slide

tag: roi number


title: DSP-1001660008975-G-E06

tag: tissue

tag: treatment

tag: roi x_coordinate


title: F2_D2 individual, grown at 16C [T16_P4.G12_F2_D2]

tag: developmental stage

tag: cell type


title: E957 [miRNA-seq]

description:
small RNA
sRNA_processed.csv

tag: patient id

value: 7 months

value: Male

value: Partial anomalous pulmonary venous return

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


title: RNA-seq, TBX5 haplo, rep 3

city: Nashville

first: Kevin

last: Bersell

state: TN

address: 2215 Garland Ave

institute: Vanderbilt University

description:
Total RNA-seq
human_3491_3604_gene.count
TBX5_vs_Brugada_min5_DESeq2.csv
TBX5_vs_Isogenic_min5_DESeq2.csv
TBX5_vs_Control_min5_DESeq2.csv
TBX5_Haplo_S18

data_processing:
Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files. The short-read sequence files generated by Illumina's CASAVA pipeline were processed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to validate the quality of sequencing data, such as adapter contamination, base quality and sequence quality. STAR (v2.5.2b) was used to map reads to the GENCODE hg19 genome (GRCh37.p13) with option (--twopassMode Basic--outSAMprimaryFlag AllBestScore). Gene annotation file from GENCODE (v19) was used in STAR index preparation. FeatureCounts (v1.5.0-p2) was used to counting the reads mapped to genes.The gene expression differential analysis was performed using DESeq2 (v1.12.4). Cluster at sample and gene levels was illustrated by Heatmap3 (v1.1.1). NGSPERL framework was used to pileup and perform those tasks in cluster system.
Assembly: GRCh37.p13
Supplementary files format and content: csv - contains read counts per gene for the Bulk RNA-seq data
Supplementary files format and content: txt - contains the normalized reads per gene for the Bulk RNA-seq data

source_name: iPSC-derived cardiomyocytes

extract_protocol:
Total RNA was isolated from iPSC-CM on day 35-38 of differentiation using the RNeasy Mini Kit with DNase treatment (Qiagen) from 3-4 unique clones per group.
rRNA-depleted libraries were generated using TruSeq Total RNA sample kits with indexed adaptors (Illumina). Library quality was assessed using the 2100 Bioanalyzer (Agilent) and libraries were quantitated using KAPA Library Quantification Kits (KAPA Biosystems).

value: iPSC-derived cardiomyocytes

tag: genotype

value: TBX5 -/WT


title: RNA-seq, Isogenic control, rep 4

description:
Total RNA-seq
human_3491_3604_gene.count
Isogenic_vs_Brugada_min5_DESeq2.csv
TBX5_vs_Isogenic_min5_DESeq2.csv
Isogenic_vs_Control_min5_DESeq2.csv
Isogenic_S17

value: WT


title: RNA-seq, TBX5 haplo, rep 1

description:
Total RNA-seq
human_3491_3604_gene.count
TBX5_vs_Brugada_min5_DESeq2.csv
TBX5_vs_Isogenic_min5_DESeq2.csv
TBX5_vs_Control_min5_DESeq2.csv
TBX5_Haplo_Z


title: E956 [miRNA-seq]

description: small RNA

tag: sequence facility

value: Novogene

tag: heart chamber

value: Atrium

value: 5 months

value: Female

value: Complete atrioventricular canal defect


title: DSP-1001660008975-G-E04

value: Internal

tag: roi y_coordinate


title: RNA-seq, TBX5 haplo, rep 2

description:
Total RNA-seq
human_3491_3604_gene.count
TBX5_vs_Brugada_min5_DESeq2.csv
TBX5_vs_Isogenic_min5_DESeq2.csv
TBX5_vs_Control_min5_DESeq2.csv
TBX5_Haplo_PP


title: DSP-1001660008975-G-E05

value: Colorectal cancer


title: E930 [miRNA-seq]

description:
small RNA
sRNA_processed.csv

value: Yerkes Nonhuman Primate Genomics Core

tag: age

value: < 1 week

tag: Sex

tag: diagnosis

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


title: F2_D2 individual, grown at 16C [T16_P4.G10_F2_D2]

first: Rahul

address: Dr. Bohrgasse 3

institute: Gregor Mendel Institute

value: leaf

value: 7-10 leave rosette


title: F2_D2 individual, grown at 16C [T16_P4.G11_F2_D2]


title: RNA-seq, Isogenic control, rep 2

description:
Total RNA-seq
human_3491_3604_gene.count
Isogenic_vs_Brugada_min5_DESeq2.csv
TBX5_vs_Isogenic_min5_DESeq2.csv
Isogenic_vs_Control_min5_DESeq2.csv
Isogenic_CR_37


title: DSP-1001660008975-G-E08

tag: disease state

value: Rectal cancer

tag: patient

value: Neoadjuvant chemotherapy

tag: segment

value: CK


title: DSP-1001660008975-G-E10

tag: tissue site

tag: slide

tag: roi number


title: RNA-seq, Isogenic control, rep 3

description:
Total RNA-seq
human_3491_3604_gene.count
Isogenic_vs_Brugada_min5_DESeq2.csv
TBX5_vs_Isogenic_min5_DESeq2.csv
Isogenic_vs_Control_min5_DESeq2.csv
Isogenic_S16

value: iPSC-derived cardiomyocytes


title: DSP-1001660008975-G-E03

tag: tissue

tag: treatment

tag: roi x_coordinate


title: E926 [miRNA-seq]

description:
small RNA
sRNA_processed.csv

tag: patient id

value: 14 months

value: Male

value: Ventricular septal defect

tag: cell type

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


title: F2_D1 individual, grown at 16C [T16_P4.G1_F2_D1]

tag: developmental stage

tag: genotype


title: F2_D2 individual, grown at 16C [T16_P4.F9_F2_D2]


title: F2_D1 individual, grown at 16C [T16_P4.F7_F2_D1]


title: E925 [miRNA-seq]

description:
small RNA
sRNA_processed.csv

tag: sequence facility

tag: heart chamber

value: Atrium

value: Female

value: Total anomalous pulmonary venous return


title: DSP-1001660008975-G-E01

value: Colorectal cancer

value: Bordered

tag: roi y_coordinate


title: DSP-1001660008975-G-E02


title: F2_D2 individual, grown at 16C [T16_P4.F6_F2_D2]


title: RNA-seq, Isogenic control, rep 1

description:
Total RNA-seq
human_3491_3604_gene.count
Isogenic_vs_Brugada_min5_DESeq2.csv
TBX5_vs_Isogenic_min5_DESeq2.csv
Isogenic_vs_Control_min5_DESeq2.csv
Isogenic_CR_Y

value: WT


title: E924 [miRNA-seq]

description:
small RNA
sRNA_processed.csv

value: Yerkes Nonhuman Primate Genomics Core

tag: age

value: 2 months

tag: Sex

tag: diagnosis


title: E903 [miRNA-seq]

description: small RNA

value: Novogene

value: < 1 week

value: Hypoplastic left heart syndrome


title: RNA-seq,  BrS, rep 3

description:
Total RNA-seq
human_3491_3604_gene.count
Brugada_vs_Control_min5_DESeq2.csv
Isogenic_vs_Brugada_min5_DESeq2.csv
TBX5_vs_Brugada_min5_DESeq2.csv
BrS026_10

value: TBX5 G145R/WT


title: F2_D2 individual, grown at 16C [T16_P4.F5_F2_D2]

value: leaf

value: 7-10 leave rosette


title: RNA-seq,  BrS, rep 2

description:
Total RNA-seq
human_3491_3604_gene.count
Brugada_vs_Control_min5_DESeq2.csv
Isogenic_vs_Brugada_min5_DESeq2.csv
TBX5_vs_Brugada_min5_DESeq2.csv
BrS026_05

value: iPSC-derived cardiomyocytes


title: F2_D2 individual, grown at 16C [T16_P4.F3_F2_D2]


title: E902 [miRNA-seq]

description:
small RNA
sRNA_processed.csv

value: 4 years

value: Male

value: Atrial septal defect


title: E896 [miRNA-seq]

description:
small RNA
sRNA_processed.csv

value: Atrium

value: 12 months

value: Female

value: Ventricular septal defect

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


title: DSP-1001660008975-G-D11

value: Colorectal cancer

tag: disease state

value: Rectal cancer

tag: patient

value: Neoadjuvant chemotherapy

tag: segment

value: CK

value: Internal


title: DSP-1001660008975-G-D08

tag: tissue site

tag: slide

tag: roi number


title: DSP-1001660008975-G-D09

tag: tissue

tag: treatment

tag: roi x_coordinate


title: E894 [miRNA-seq]

description:
small RNA
sRNA_processed.csv

tag: patient id

value: Yerkes Nonhuman Primate Genomics Core

value: Ventricle

value: 6 months

value: Not determined

value: Not known

tag: cell type


title: RNA-seq, Population control, rep 3

description:
Total RNA-seq
human_3491_3604_gene.count
Brugada_vs_Control_min5_DESeq2.csv
TBX5_vs_Control_min5_DESeq2.csv
Isogenic_vs_Control_min5_DESeq2.csv
C4_3

value: iPSC-derived cardiomyocytes

tag: genotype

value: WT


title: RNA-seq, Population control, rep 2

description:
Total RNA-seq
human_3491_3604_gene.count
Brugada_vs_Control_min5_DESeq2.csv
TBX5_vs_Control_min5_DESeq2.csv
Isogenic_vs_Control_min5_DESeq2.csv
C2_1


title: DSP-1001660008975-G-D07


title: F1_D1 individual, grown at 16C [T16_P4.F11_F1_D1]

value: leaf

tag: developmental stage

value: 7-10 leave rosette


title: F2_D1 individual, grown at 16C [T16_P4.F12_F2_D1]


title: C2013 [miRNA-seq]

description: small RNA

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

tag: sequence facility

value: Novogene

tag: heart chamber

value: Atrium

value: 3 months

value: Male


title: DSP-1001660008975-G-D12

value: Colorectal cancer

value: Rectal cancer

value: External

tag: roi y_coordinate


title: RNA-seq,  BrS, rep 4

description:
Total RNA-seq
human_3491_3604_gene.count
Brugada_vs_Control_min5_DESeq2.csv
Isogenic_vs_Brugada_min5_DESeq2.csv
TBX5_vs_Brugada_min5_DESeq2.csv
BrS026_11

value: TBX5 G145R/WT


title: RNA-seq, Population control, rep 4

description:
Total RNA-seq
human_3491_3604_gene.count
Brugada_vs_Control_min5_DESeq2.csv
TBX5_vs_Control_min5_DESeq2.csv
Isogenic_vs_Control_min5_DESeq2.csv
C6_1


title: RNA-seq, Population control, rep 1

description:
Total RNA-seq
human_3491_3604_gene.count
Brugada_vs_Control_min5_DESeq2.csv
TBX5_vs_Control_min5_DESeq2.csv
Isogenic_vs_Control_min5_DESeq2.csv
C1_4


title: DSP-1001660008975-G-D06

value: Neoadjuvant chemotherapy

value: Bordered


title: C1100 [miRNA-seq]

description:
small RNA
sRNA_processed.csv

value: Yerkes Nonhuman Primate Genomics Core

tag: age

value: < 1 week

tag: Sex

value: Female

tag: diagnosis

value: Hypoplastic left heart syndrome

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


title: F2_D2 individual, grown at 16C [T16_P4.F4_F2_D2]

value: leaf


title: DSP-1001660008975-G-D05

tag: disease state

tag: patient

tag: segment

value: CK


title: RNA-seq,  BrS, rep 1

description:
Total RNA-seq
human_3491_3604_gene.count
Brugada_vs_Control_min5_DESeq2.csv
Isogenic_vs_Brugada_min5_DESeq2.csv
TBX5_vs_Brugada_min5_DESeq2.csv
BrS026_03

value: iPSC-derived cardiomyocytes


title: PTB108-EVs

first: Wei

last: Ge

address: 5 Dong Dan San Tiao, Dongcheng District

department: Department of Immunology

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences

description: Column name in processed data files: 090-EVs

data_processing:
Sequencing libraries were prepared using Total RNA-seq Library Prep kit from Illumina.
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0
the gene expression level was estimated using RSEM v1.2.15
For lncRNA expression analysis, we used the transcript set from Lncipedia (http://www.lncipedia.org). TMM (trimmed mean of M-values) was used to normalize gene expression.
Differentially expressed genes were identified using the statistical R package edgeR.
For circRNA expression analysis, the reads were mapped to the human genome using STAR and DCC was used to annotate the circRNAs and to estimate expression levels. TMM was used for normalization.
Genome_build: hg38
Supplementary_files_format_and_content: Excel files include FPKM values for circRNAs, lncRNAs, genes for each Sample

source_name: brain frontal cortex

extract_protocol:
The frozen brain tissue was chopped on ice using a scalpel to generate 5 mm3 sections.EVs are extracted by using a SEC column (qEV original, Izon).Total RNA was extracted from isolated EVs using the RNeasy Micro Kit (74004, Qiagen) according to the manufacturer’s instructions. The RNA concentration and purity were measured with Qubit 3.0 (Thermo Scientific) and Agilent 2100 Bioanalyzer. RNA sequencing was performed using the Illumina HiSeq 3000 platform. Sequencing libraries were prepared using Total RNA-seq Library Prep kit from Illumina.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain frontal cortex

value: Alzheimer's disease

tag: fraction

value: extracellular vesicles (EVs)


title: F2_D1 individual, grown at 16C [T16_P4.E9_F2_D1]

tag: tissue

value: 7-10 leave rosette


title: F2_D2 individual, grown at 16C [T16_P4.F10_F2_D2]

tag: treatment


title: DSP-1001660008975-G-D04

value: Colorectal cancer

value: Rectal cancer

tag: tissue site

tag: slide

tag: roi number

tag: roi x_coordinate


title: F2_D1 individual, grown at 16C [T16_P4.F1_F2_D1]

tag: developmental stage

tag: cell type

tag: genotype


title: PTB050-EVs

description: Column name in processed data files: 050-EVs


title: DSP-1001660008975-G-D10

value: Internal

tag: roi y_coordinate


title: C1097 [miRNA-seq]

description: small RNA

tag: patient id

tag: sequence facility

value: Novogene

tag: heart chamber

value: Atrium

tag: age

value: 3 months

value: Male

value: Tetralogy of Fallot


title: F2_D1 individual, grown at 16C [T16_P4.E8_F2_D1]


title: C1099 [miRNA-seq]

description: small RNA

value: 5 months

tag: Sex

value: Female

tag: diagnosis

value: Complete atrioventricular canal defect, Downs syndrome


title: F2_D1 individual, grown at 16C [T16_P4.E7_F2_D1]

value: leaf


title: DSP-1001660008975-G-D03

tag: disease state

tag: patient

value: Neoadjuvant chemotherapy

tag: segment

value: CK

value: Bordered


title: C1095 [miRNA-seq]

description:
small RNA
sRNA_processed.csv

value: Yerkes Nonhuman Primate Genomics Core

value: Double outlet right ventricle

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


title: PTB051-EVs

description: Column name in processed data files: 051-EVs

tag: tissue

value: brain frontal cortex

value: Alzheimer's disease

tag: fraction

value: extracellular vesicles (EVs)


title: PTB104-EVs

description: Column name in processed data files: 104-EVs


title: DSP-1001660008975-G-D02

value: Colorectal cancer

value: Rectal cancer

tag: treatment

tag: tissue site

value: External

tag: slide

tag: roi number


title: F2_D1 individual, grown at 16C [T16_P4.E5_F2_D1]

tag: developmental stage

value: 7-10 leave rosette

tag: cell type

tag: genotype


title: C1092 [miRNA-seq]

description:
small RNA
sRNA_processed.csv

tag: patient id

tag: sequence facility

value: Atrium

value: 4 years

value: Atrial septal defect


title: PTB218-EVs

description: Column name in processed data files: 218-exo


title: DSP-1001660008975-G-C12

value: Colon cancer

value: No Neoadjuvant chemotherapy

value: Internal

tag: roi x_coordinate

tag: roi y_coordinate


title: F2_D2 individual, grown at 16C [T16_P4.E3_F2_D2]

value: leaf


title: DSP-1001660008975-G-D01

value: Neoadjuvant chemotherapy


title: F2_D2 individual, grown at 16C [T16_P4.E4_F2_D2]


title: PTB078-EVs

description: Column name in processed data files: 078-exo


title: C2016 [miRNA-seq]

description: small RNA

value: Novogene

tag: heart chamber

tag: age

value: 1-2 week

tag: Sex

value: Female

tag: diagnosis

value: Coarctation, atrial septal defect, ventricular septal defect


title: C1066 [miRNA-seq]

description:
small RNA
sRNA_processed.csv

value: Yerkes Nonhuman Primate Genomics Core

value: 6 months

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

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


title: C1083 [miRNA-seq]

description:
small RNA
sRNA_processed.csv

value: < 1 week

value: Interrupted aortic arch, ventricular septal defect


title: C1063 [miRNA-seq]

description: small RNA

value: Atrium

value: 3 years

value: Male

value: Ventricular septal defect


title: F2_D2 individual, grown at 16C [T16_P4.E2_F2_D2]

tag: tissue

value: 7-10 leave rosette


title: PTB215-EVs

description: Column name in processed data files: 215-exo

value: brain frontal cortex

tag: disease state

value: Alzheimer's disease

tag: fraction

value: extracellular vesicles (EVs)


title: DSP-1001660008975-G-C10

value: Colorectal cancer

value: Colon cancer

tag: patient

tag: treatment

value: No Neoadjuvant chemotherapy

tag: segment

tag: tissue site

value: Internal


title: PTB114-EVs

description: Column name in processed data files: 114-exo


title: DSP-1001660008975-G-C11

value: CK

tag: slide

tag: roi number


title: F2_D2 individual, grown at 16C [T16_P4.E1_F2_D2]

value: leaf

tag: developmental stage

tag: cell type

tag: genotype


title: DSP-1001660008975-G-C09

tag: roi x_coordinate

tag: roi y_coordinate


title: F2_D2 individual, grown at 16C [T16_P4.E12_F2_D2]


title: C1048 [miRNA-seq]

description:
small RNA
sRNA_processed.csv

tag: patient id

tag: sequence facility

value: Yerkes Nonhuman Primate Genomics Core

tag: heart chamber

tag: age

value: 6 years

value: Female

value: Atrial septal defect

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


title: PTB176-EVs

description: Column name in processed data files: 176-EVs

tag: tissue

tag: disease state

value: normal


title: DSP-1001660008975-G-C08

tag: patient


title: PTB190-EVs

description: Column name in processed data files: 190-EVs

tag: fraction


title: DSP-1001660008975-G-C07

tag: treatment

tag: segment


title: F2_D1 individual, grown at 16C [T16_P4.E11_F2_D1]


title: C1050 [miRNA-seq]

description:
small RNA
sRNA_processed.csv

value: Atrium

value: 1 week

tag: Sex

tag: diagnosis

value: Hypoplastic left heart syndrome


title: C1010 [miRNA-seq]

description:
small RNA
sRNA_processed.csv

value: 9 weeks

value: Male

value: Tetralogy of Fallot


title: DSP-1001660008975-G-C06

value: Colorectal cancer

value: Colon cancer

tag: tissue site

value: External

tag: slide

tag: roi number


title: PTB230-EVs

description: Column name in processed data files: 186-EVs

value: brain frontal cortex

value: extracellular vesicles (EVs)


title: F2_D2 individual, grown at 16C [T16_P4.D9_F2_D2]

value: leaf

tag: developmental stage

value: 7-10 leave rosette

tag: cell type

tag: genotype


title: C1045 [miRNA-seq]

description:
small RNA
sRNA_processed.csv

tag: patient id

tag: sequence facility

value: Yerkes Nonhuman Primate Genomics Core

value: < 1 week

value: Female

value: Coarctation of the aorta, ventricular septal defect


title: C1007 [miRNA-seq]

description: small RNA

value: Novogene

tag: heart chamber

value: Atrium

tag: age

value: 6 months

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

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


title: DSP-1001660008975-G-C05

tag: tissue

tag: disease state

value: No Neoadjuvant chemotherapy

value: Bordered

tag: roi x_coordinate

tag: roi y_coordinate


title: C1006 [miRNA-seq]

description: small RNA

value: Complete atrioventricular canal defect


title: PTB213-EVs

description: Column name in processed data files: 213-EVs

value: normal

tag: fraction


title: C1004 [miRNA-seq]

description: small RNA

value: 12 months

tag: Sex

value: Male

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


title: PTB214-EVs

description: Column name in processed data files: 214-exo

value: brain frontal cortex

value: extracellular vesicles (EVs)


title: F2_D2 individual, grown at 16C [T16_P4.D8_F2_D2]

value: leaf

value: 7-10 leave rosette

tag: treatment


title: PTB187-EVs

description: Column name in processed data files: 187-exo


title: C985 [miRNA-seq]

description:
small RNA
sRNA_processed.csv

value: Yerkes Nonhuman Primate Genomics Core

value: 2 weeks

tag: diagnosis

value: Interrupted aortic arch


title: F2_D1 individual, grown at 16C [T16_P4.D6_F2_D1]


title: DSP-1001660008975-G-C04

value: Colorectal cancer

value: Colon cancer

tag: patient

tag: segment

value: CK

tag: tissue site

tag: slide


title: F2_D2 individual, grown at 16C [T16_P4.D7_F2_D2]

tag: developmental stage

tag: cell type

tag: genotype


title: DSP-1001660008975-G-C02

value: No Neoadjuvant chemotherapy

value: Internal

tag: roi number


title: PTB158-EVs

description: Column name in processed data files: 158-exo


title: F2_D1 individual, grown at 16C [T16_P4.D5_F2_D1]


title: C975 [miRNA-seq]

description:
small RNA
sRNA_processed.csv

tag: patient id

tag: sequence facility

tag: heart chamber

value: Atrium

tag: age

value: 6 months

value: Tetralogy of Fallot

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


title: DSP-1001660008975-G-C01

tag: tissue

tag: disease state

value: Bordered

tag: roi x_coordinate

tag: roi y_coordinate


title: F2_D1 individual, grown at 16C [T16_P4.E10_F2_D1]

tag: treatment


title: PTB207-EVs

description: Column name in processed data files: 207-EVs

value: brain frontal cortex

value: normal

tag: fraction


title: F2_D2 individual, grown at 16C [T16_P4.D4_F2_D2]

value: leaf


title: DSP-1001660008975-G-B12

tag: patient

tag: segment


title: PTB074-EVs

description: Column name in processed data files: 074-exo

value: extracellular vesicles (EVs)


title: F2_D2 individual, grown at 16C [T16_P4.D3_F2_D2]

value: 7-10 leave rosette


title: C956 [miRNA-seq]

description:
small RNA
sRNA_processed.csv

value: Yerkes Nonhuman Primate Genomics Core

value: 5 months

tag: Sex

value: Female

tag: diagnosis

value: Complete atrioventricular canal defect


title: F2_D1 individual, grown at 16C [T16_P4.D2_F2_D1]

tag: developmental stage

tag: cell type


title: PTB041-EVs

description: Column name in processed data files: 041-exo


title: DSP-1001660008975-G-B11

value: Colorectal cancer

value: Colon cancer

tag: tissue site

tag: slide

tag: roi number


title: DSP-1001660008975-G-C03

value: No Neoadjuvant chemotherapy

value: Internal


title: Day 7 Th17

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

description: Naïve T cells isolated from healthy donors treated under Th17 media conditions for 7 days.

data_processing:
Sequencing Reads were aligned to GRCh37 (hg19) build of the human genome using Burrows-Wheeler Alignment (BWA)
Peaks were called using MACS2 software.
Genome_build: hg19
Supplementary_files_format_and_content: BED Files (Peak calls)

source_name: PBMCs

growth_protocol: Following bead isolation, naïve T cells were cultured in a 24-well tissue culture plate for 7 days in cRPMI media (RPMI, 10% FCS, 10mM HEPES, 1mM Sodium Pyruvate, 1% Non-essential Amino Acids, 2mM L-Glutamine, Penicillin/Streptomycin, culture-grade 50uM 2-mercaptoethanol) with TCR activation [anti-CD28 (2µg/ml, BD BioSciences cat# 555725), plate-bound anti-CD3 (2µg/ml, BD BioSciences cat# 555329)] and : T regulatory inducing cytokines [IL-2 (10ng/ml, Peprotech Cat# 200-02), and TGFβ (5ng/ml, Peprotech cat# 100-21C)], or Th17 differentiation cytokines [IL-1β1 (20 ng/mL; Peprotech Cat# 200-01B-10ug), TGF-β1 (5 ng/mL),  IL-6  (50 ng/mL; Peprotech Cat# 200-06-20ug), IL-21 (100 ng/mL; Peprotech Cat# 200-21-10ug), IL-23 (20  ng/mL; Peprotech Cat# 200-23-10ug), mouse anti-human IFN-γ (10  µg/mL; BD Biosciences Cat#554698), anti-IL4 (2.5 µg/mL, Biolegend Cat#500702)], or UNC0642 2uM.. During the 7 day incubation, additional media with cytokines was added on day 3. On day 5, cells were harvested and washed once with DPBS. Cells were resuspended in fresh cRPMI media with only CD28 and replated on freshly coated anti-CD3 plates until day 7 harvest for ATAC-seq analysis.

extract_protocol:
ATAC-seq was performed from 50,000 Treg cells per a previously published protocol (Buenrostro, Nature Methods, 2013). Briefly, nuclei were prepared by washing cells with PBS, followed by lysis using cold lysis buffer. Nuclei were spun and the pellet was then resuspended in the transposase reaction mix for 30 min at 37 °C. The samples were then purified using a Qiagen Minelute kit.
Amplified libraries were purified, and the sizes of library DNA were determined by the Fragment Analyzer (Advanced Analytical Technologies, IA) using the High Sensitivity NGS Fragment Analysis Kit (Cat # DNF-486). The enrichment of accessible region was determined by the fold difference between positive and negative genomic loci using real-time PCR. The libraries were sequenced to 51 base pairs from both ends on an Illumina HiSeq instrument in the Mayo Clinic Center for Individualized Medicine Medical Genomics Facility.

treatment_protocol: UNC0642 was added to one of the conditions only as specified.

value: Naive T cells

tag: treatment 1

value: Anti-CD3 + Anti CD28 treatment

tag: treatment 2

tag: treatment 3

value: Anti-IL4, Anti-IFNg


title: C957 [miRNA-seq]

description:
small RNA
sRNA_processed.csv

tag: patient id

tag: sequence facility

tag: heart chamber

value: Atrium

tag: age

value: 7 months

value: Male

value: Partial anomalous pulmonary venous return

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


title: DSP-1001660008975-G-B10

tag: tissue

tag: disease state

tag: treatment

value: CK

tag: roi x_coordinate

tag: roi y_coordinate


title: C926 [miRNA-seq]

description:
small RNA
sRNA_processed.csv

value: Yerkes Nonhuman Primate Genomics Core

value: 14 months

tag: Sex

tag: diagnosis

value: Ventricular septal defect


title: C930 [miRNA-seq]

description: small RNA

value: Novogene

value: < 1 week

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

tag: cell type


title: C925 [miRNA-seq]

description: small RNA

value: Female

value: Total anomalous pulmonary venous return


title: DSP-1001660008975-G-B09

value: Colorectal cancer

value: Colon cancer

tag: patient

value: No Neoadjuvant chemotherapy

tag: segment

tag: tissue site

value: Internal

tag: slide


title: DSP-1001660008975-G-B07

tag: roi number


title: DSP-1001660008975-G-B06


title: DSP-1001660008975-G-B08


title: BMDM Ko3

city: Shanghai

first: Zhiqiang

last: Li

state: Shanghai

address: 301 Middle Yanchang Road

department: Department of Cardiology

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

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

tag: genotype

value: TRIM21 KO

value: LPS treatment


title: F2_D2 individual, grown at 16C [T16_P4.D12_F2_D2]

city: Vienna

last: Pisupati

value: leaf

tag: developmental stage

value: 7-10 leave rosette


title: BMDM Ko2


title: F2_D2 individual, grown at 16C [T16_P4.D1_F2_D2]


title: C924 [miRNA-seq]

description:
small RNA
sRNA_processed.csv

tag: patient id

tag: sequence facility

value: Yerkes Nonhuman Primate Genomics Core

tag: heart chamber

value: Atrium

tag: age

value: 2 months

value: Male

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


title: DSP-1001660008975-G-B05

first: Irina

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

institute: Tomsk State University

tag: tissue

tag: disease state

tag: treatment

value: External

tag: roi x_coordinate


title: Day 7 Treg

description: Naïve T cells isolated from healthy donors treated under Treg media conditions for 7 days.

tag: cell type

value: Naive T cells

tag: treatment 1

value: Anti-CD3 + Anti CD28 treatment

tag: treatment 2

value: IL2 and TGFβ1


title: F2_D1 individual, grown at 16C [T16_P4.C8_F2_D1]


title: BMDM Ko1


title: Day 0 - Naïve T Cell

description: Naïve T cells isolated from healthy donors and not treated.

value: no treatment


title: F2_D1 individual, grown at 16C [T16_P4.C9_F2_D1]


title: DSP-1001660008975-G-B04

value: Colorectal cancer

value: Colon cancer

tag: patient

value: No Neoadjuvant chemotherapy

tag: segment

tag: tissue site

value: Bordered

tag: roi y_coordinate


title: C902 [miRNA-seq]

description:
small RNA
sRNA_processed.csv

value: 4 years

tag: Sex

tag: diagnosis

value: Atrial septal defect


title: Day 7 Th0 + G9ai

description: Naïve T cells isolated from healthy donors treated with TCR stimulation (anti-CD3 and anti-CD28) and G9a-inhibitor (UNC0642) for 7 days.

value: Anti-CD3 treatment

value: Anti-CD28 treatment

tag: treatment 3

value: UNC0642 2uM


title: F2_D2 individual, grown at 16C [T16_P4.C7_F2_D2]

value: leaf

tag: developmental stage

value: 7-10 leave rosette

tag: genotype


title: C896 [miRNA-seq]

description:
small RNA
sRNA_processed.csv

tag: patient id

tag: sequence facility

value: Yerkes Nonhuman Primate Genomics Core

tag: heart chamber

value: Atrium

tag: age

value: 12 months

value: Female

value: Ventricular septal defect

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


title: BMDM Wt3

tag: cell line

value: BMDM

value: mouse bone marrow-derived macrophages

value: WT

tag: treatment

value: LPS treatment


title: BMDM Wt2

tag: cell type