title: Day 4 PPCA

city: Cincinnati

first: Jonathan

middle: D

last: Katz

state: Ohio

address: 3333 Burnet Avenue

department: Division of Immunobiology

institute: Cincinnati Children's Hospital Medical Center

description: 10X Genomics

data_processing:
Single-cell RNA sequencing (scRNA-Seq) of 8 samples (1 active T1D, 1 onset T1D, 3 from PPCA, and 3 from vehicle treatment group) was performed by the University of Cincinnati Genomics, Epigenomics and Sequencing Core (GESC). To quantify gene expression at a single-cell level, FASTQ files obtained from GESC for each sample were individually aligned to pre-built mouse reference genome indices (GENCODE vM23 / Ensembl 98) using the 10x Genomics Cell Ranger 6.1.2 (PMCID: PMC5241818) command-line tool. The resulting feature-barcode matrices (one per sample), each containing Unique Molecular Identifier (UMI) counts per gene and cell combination, were merged with a custom R script for joint analysis in subsequent steps. Cell barcodes were updated to reflect their samples of origin. All single-cell data analysis steps described below were performed in SciDAP (https://SciDAP.com) following the instructions outlined by Kotliar et al. 2024 (https://doi.org/10.1101/2024.02.28.582604).
“Single-Cell RNA-Seq Filtering Analysis” pipeline was used for removing low-quality cells. The following Quality Control (QC) filtering thresholds were applied to all samples: minimum of 1000 reads per cell, maximum of 5% of reads mapped to mitochondrial genes, Additionally, the thresholds for the minimum and maximum number of genes per cell were selected independently for each sample as follows: 1,085 – 3,000 for active T1D, 890 – 2,575 for onset T1D, 960 – 2,800 for vehicle treatment on day 2, 850 – 2,450 for PPCA treatment on day 2, 820 – 2,600 for vehicle treatment on day 3, 760 – 2,550 for PPCA treatment on day 3, 840 – 2,500 for vehicle treatment on day 4, and 650 – 2.170 for PPCA treatment on day 4.
Dimensionality reduction and samples integration were conducted using “Single-Cell RNA-Seq Dimensionality Reduction Analysis” pipeline. The workflow was run with 40 dimensions and 3,000 highly variable genes. To match shared cell types across multiple samples, as well as to correct for technical differences, the integration method was set to “seurat”. Thus, the cross-dataset pairs of cells that were in a matched biological state were used as integration anchors (PMCID: PMC6687398). The percentage of reads mapped to mitochondrial genes, as well as the expression levels of Trbc1 and Trbc2 genes, were regressed out as the confounding sources of variation.
In the next step “Single-Cell RNA-Seq Cluster Analysis” pipeline was executed to group cells by gene expression similarities. Target dimensionality and clustering resolution parameters were set to 30 and 0.3, respectively. Using the known hallmark genes, the following cell types were identified and excluded from the subsequent data analysis steps: NK cells (Klra1, Ncr1), dendritic cells (Myb, Gpr183), exocrine cells (Ctrb1, Prss2, Cela2a), monocytes (Lgals3, Tmem176a, Tmem176b), and B cells (Cd19, Cr2, Ms4a1). Additionally, a cluster with both Cd4+ and Cd8a+ cells and without any other distinct gene markers was removed as doublets.
After removing cell types of not particular interest, the “Single-Cell RNA-Seq Dimensionality Reduction Analysis” and “Single-Cell RNA-Seq Cluster Analysis” pipelines were rerun with 30 and 15 dimensions, respectively. Clustering resolution was set to 0.22 to achieve optimal separation between the expected cell types. Cluster annotation was made on the basis of the following marker genes: CD4 Naïve (Cd4, Ifngr2, Foxp1), CD8 TCM (Cd8a, Ccr7, Sell), CD8 TRM TEM (Cd8a, Ccl5, Itga1), CD4 Th1 (Cd4, Ifi27l2a, Ifit1, Ifit3, Igtp, Iigp1, Stat1), CD4 Treg (Cd4, Foxp3, Ctla4), CD4 Th17 (Cd4, Tbx21, Rora, Rorc, Ifng), and CD4 Th0 (Cd4, Cd69, Nfkbid, Nfkb1).
Assembly: GENCODE vM23 / Ensembl 98
Supplementary files format and content: [sample]_barcodes.tsv.gz - gzip-compressed TAB-delimited file with the cell barcodes represented in the sparse matrix file.
Supplementary files format and content: [sample]_features.tsv.gz - gzip-compressed TAB-delimited file with the gene names represented in the sparse matrix file.
Supplementary files format and content: [sample]_matrix.mtx.gz - gzip-compressed sparse matrix file with the UMI counts per gene and cell barcode combination.
Supplementary files format and content: merged_data.rds - analysis results saved in RDS (R Data Serialization) format. The origin of cells can be tracked through the "new.ident" metadata column.
Supplementary files format and content: merged_data.h5ad - analysis results saved in AnnData (H5AD) format. The origin of cells can be tracked through the "new.ident" metadata at the observation (obs) level.
Supplementary files format and content: merged_gene_markers.tsv - gzip-compressed TAB-delimited file with the identified gene markers for each cell type.

source_name: pancreas

extract_protocol:
Pancreas was removed, placed on ice and dissociated using a GentleMACS for 60 seconds, tissue was strained, debris removed using Miltenyi Debris Removal solution per manufacture's protocol. Cells were underlaid with Lympholyte-M and seperated per manufacture's protocol. CD45+ CD3+ TcR-beta+ cells were isolated by flow sorting on a Sony MA-900. Cells were frozen in 90% FBS, 10% DMSO and then all samples were subjected to RNA isolation at the same time using RNAeasy Kit (Qiagen) using manufacture's protocol.
Libraries were produced using the manufacture's protocol (single cell, 3', version 2, 10x Genomics) after passing quality control using the Agilent 2100 Bioanalyzer.

treatment_protocol: New onset diabetic female NOD mice (200-300 mg/dl blood glucose, 3-5 months of age) were treated with either PPCA (50 mg/kg Nutlin-3, Cayman Chemical; MK-1775 25 mg/kg, Cayman Chemical) on day 1, day 2 and day 3 or Vehicle control (30% EtOH - HPLC grade, 5% Tween 20, 65% PEG300). New onset (250 mg/dl blood glucose) and active T1D NOD control ( > 600 mg/dl blood glucose) were harvested on day 1. PPCA and Vehicle treated mice were treated daily and harvested the following day after indicated number of days of treatment.

value: pancreas

value: CD4+ and CD8+ primary lymphocytes

value: spontaneous new onset diabetic female NOD mice (3-4 months of age)

value: Day 4 PPCA


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_110

status: Public on Sep 11 2024

type: SRA

city: Ithaca

first: Conor

last: Loy

state: NY

address: 237 Tower Rd, Room 314

country: USA

institute: Cornell University

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_110

library_source: transcriptomic

data_processing:
Sequencing data was processed using a custom bioinformatics pipeline. Since pools sequenced on the Illumina NextSeq 2000 were optimized to produce paired-end, 61 bp reads, matched sequencing data from the Illumina NextSeq 500 were trimmed using Seqtk (v1.2).
Samples were then quality filtered and trimmed using BBDuk (v38.90), aligned to the Gencode GRCh38 human reference genome (v38, primary assembly) using STAR (v2.7.0f, default parameters).
Prior to feature quantification using featureCounts (v2.0.0), samples were deduplicated using Picard MarkDuplicates (v2.19.2). Mitochondrial, ribosomal, X, and Y chromosome genes were bioinformatically removed prior to analysis.
Samples were filtered on the basis of DNA contamination, rRNA contamination, total counts, and RNA degradation. DNA contamination was estimated by calculating the ratio of reads mapping to introns and exons. rRNA contamination was measured using SAMtools (v1.14). Total counts were calculated using featureCounts (v2.0.0). Degradation was estimated by calculating the 5’-3’ bias using Qualimap (v2.2.1).
Samples were removed from analysis if either the intron to exon ratio was greater than 4, if a sample had less than 90,000 total feature counts, or if the rRNA contamination, total counts, or 5’-3’ bias was greater than 4 standard deviations from the mean.
Assembly: Gencode GRCh38 human reference genome (v38, primary assembly)
Supplementary files format and content: comma-delimited .csf file includes the gene counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Plasma, extracted cell-free RNA

extract_protocol:
Plasma samples were received on dry ice and stored at -80°C until processed. Prior to cfRNA extraction, plasma samples were thawed at room temperature and centrifuged at 1300 x g for 10 minutes at 4°C. cfRNA was extracted from plasma using the Norgen Plasma/Serum Circulating and Exosomal RNA Purification Mini Kit (Norgen, 51000). Extracted RNA was DNase treated with 14 µl of 10 µl DNase Turbo Buffer (Invitrogen, AM2238), 3 µl DNase Turbo (Invitrogen, AM2238), and 1 µl Baseline Zero DNase (Lucigen-Epicenter, DB0715K) for 30 minutes at 37°C, then concentrated into 12 µl using the Zymo RNA Clean and Concentrated Kit (Zymo, R1015).
Sequencing libraries were prepared from 8 µl of concentrated RNA using the Takara SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian (Takara, 634485) and barcoded using the SMARTer® RNA Unique Dual Index Kit (Takara, 634451). Library concentration was quantified using the Qubit™ 3.0 Fluorometer (Invitrogen, Q33216) with the dsDNA HS Assay Kit (Invitrogen, Q32854). Libraries were quality-controlled using the Agilent Fragment Analyzer 5200 (Agilent, M5310AA) with the HS NGS Fragment Kit (Agilent, DNF-474-0500) and pooled to equal concentrations. Each pool was sequenced using both the Illumina NextSeq 500/550 platform (paired-end, 150 bp) and the Illumina NextSeq 2000 platform (paired-end, 100 bp).

tag: tissue

value: Plasma, extracted cell-free RNA

tag: diagnosis

value: KD

tag: site

value: UCSD


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_49

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_49


title: Hamster Toes, 3dpi, Mock #3

city: New York

first: Justin

middle: J

last: Frere

address: Alexandria Center for Life Sciences, West Tower, 430 E 29th St.

department: Microbiology

institute: NYU Langone Health

data_processing:
Samples were uplaoded to Illumina Basespace and aligned to either the Mesocricetus Auratus MesAur1.0 genome or Homo Sapiens GRCH38 as appropriate using the RNA Sequence Alignment application. The alignment was conducted using the Salmon alignment tool. The resulting quantifications of alignment were either utilized directly for analysis or were further processed using DESeq2.
Assembly: MesAur1.0; GRCH38
Supplementary files format and content: Salmon Files

molecule: polyA RNA

organism: Mesocricetus auratus

source_name: Toes

extract_protocol:
RNA was extracted from hamster toe specimens via trizol/phenol-chloroform extraction.
Libraries were poly-A enriched and constructed using TruSeq PolyA kits

value: Toes

tag: treatment

value: Hamster intranasally "infected" with 100 uL of PBS (Mock-treatment); toes harvested 3 days post-infection


title: KN tumors, replicate methyl-seq  3

city: Salt Lake City

first: Katherine

last: Gillis

state: UT

address: 2000 CIRCLE OF HOPE DR

institute: Snyder Lab at Huntsman Cancer Institute

library_source: genomic

data_processing:
Fastq reads were aligned to the mouse genome (build mm10) with Novocraft novoalign (version 4.03.01) in bisulfite mode (-b 4) with the following options: set penalty for unconverted CHG or CHH cytosines (option -u) to 12, hard clip 3’ bases to quality 20 (option -H), adapter trimming (option -a), and performance tuning set to ‘NOVOSEQ’.
Extreme coverage regions were identified using depth-normalized (Reads Per Million) mean coverage of replicates and MACS2 bdgpeakcall with an absolute depth cutoff of 2 RPM (mean depth was < 0.1), length 200 bp, and gap 500 bp. Alignments overlapping extreme regions were excluded from further analysis. Duplicate alignments were removed using samtools (version 1.16) fixmate and markdup (mode -s).
Alignments were processed with USeq NovoalignBisulfiteParser (version 9.3.0) to collect converted and non-converted C counts with minimum mapping quality score (-q) of 13, maximum alignment score (-x) of 360, and minimum base quality score (options -b and -c) of 20. Methylation data over CpG dinucleotides were extracted using USeq ParsePointDataContexts with regular expression of "..CG." Statistics were generated over CpG data using USeq BisStat with a minimum read coverage (-o) of 4 and using included lambda phage DNA for conversion efficiency (option -l). BaseFractionNonConverted.useq files were converted to CpG_MethylFraction.bw bigWig files using the USeq USeq2UCSCBig application.
BisMark compatible coverage files were generated from the Converted and NonConverted .useq files using the useq2bismark_methylation_extractor application (https://github.com/tjparnell/HCI-Scripts/blob/master/Methylation/useq2bismark_methylation_extractor.pl).
Assembly: build mm10
Supplementary files format and content: Bismark compatible coverage files containing counts of coverted and non-coverted CpGs for each sample. BigWig CpG fraction methylation files for each sample.

molecule: genomic DNA

organism: Mus musculus

source_name: lung

growth_protocol: Organoid cultures grown in 50% L-WRN conditioned media (Miyoshi and Stappenbeck, 2013).

extract_protocol:
DNA was extracted using the Dneasy Blood and Tissue (Qiagen).
DNA libraries were prepped using the NEBNext® Enzymatic Methyl-seq Kit with at least 10 ng of genomic DNA

treatment_protocol: Organoid cultures treated with 4-OH tamoxifen or ethanol for 48hr to delete Foxa1/2 conditional alleles. Cell pellets were collected two weeks post-deletion for DNA extraction. Mice were treated with tamoxifen (Sigma) dissolved in corn oil at a dose of 120mg/kg. Mice received 4 injections over the course of 5 days. One day following injections, mice were given pellets supplemented with 500mg/kg (Envigo) tamoxifen for 7 days. Tumors were harvested 8 weeks post tamoxifen treatment and cells were sorted for GFP+ DAPI- population.

value: lung

tag: genotype

value: tamoxifen


title: Day 4 Vehicle

description: 10X Genomics

library_source: transcriptomic single cell

tag: cell type

value: Day 4 Vehicle


title: Hamster Toes, 3dpi, Mock #2


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_84

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_84

value: MISC


title: KN tumors, replicate methyl-seq  2


title: Day 3 PPCA

description: 10X Genomics

value: Day 3 PPCA


title: Day 2 PPCA

description: 10X Genomics

value: Day 2 PPCA


title: K tumors, replicate methyl-seq  2


title: KN tumors, replicate methyl-seq  1


title: Hamster Toes, 3dpi, Mock #1


title: Day 3 Vehicle

description: 10X Genomics

value: Day 3 Vehicle


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_158

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_158


title: CecumSPF3

city: Guangzhou

first: Xiaoyun

last: Wang

state: Guangdong

address: 190 Kaiyuan Avenue, Huangpu

department: Infection and Immunity

country: China

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

description: The cecum were dissected from eight-week-old mice

data_processing:
Raw reads were subjected to base calling using Guppy basecaller (version 6.3.8+d9e0f64) from fast5 raw files. The base calling process included setting a minimum quality score threshold of 7, utilizing the rna_r9.4.1_70bps_hac.cfg configuration file, and employing the --fast5_out parameter.
The "pass" reads were further aligned to a reference genome sequence (mm39) using Minimap2 (version 2.17-r941) with the following parameters: "-ax splice -uf -k14."
Samtools was utilized for bam file conversion and sorting.
Fast5 files were aligned to their corresponding fastq files using "Nanopolish index". The "Nanopolish eventalign" command was then applied to partition the signal values from fast5 files onto individual 5-mer sequences.
Using the m6Anet, m5Cnet and Nanopsu to detect and quantify the modified sites. Using NanoCount to quantify transcripts.
Assembly: mm39, hg38
Supplementary files format and content: tsv

source_name: cecum

extract_protocol:
Total RNA was extracted using Trizol reagent (#AG21102, Accurate Bioeng. Co., Ltd., Hunan, China) and the mRNA was purified using the Dynabeads® mRNA Purification Kit Dynabeads Oligo(dT)25 (#61002, Invitrogen). mRNA was treated by DNaseⅠ buffer (AM8170G, Thermo Fisher Scientific) and Turbo DNase (Thermo Fisher Scientific, AM2238) at 37 ℃ for 10 min and purified by ethanol precipitation to remove genomic DNA.
Nanopore direct RNA sequencing libraries were prepared using about 1000ng mRNA following the SQK-RNA002 kit protocol (version: DRS_9080_v2_revK_14Aug2019). DRS library was added to the flow cell for sequencing on the Mk1C and GridION platform.

value: cecum

value: Water


title: CecumSPF1


title: K tumors, replicate methyl-seq  1


title: CecumSPF2


title: Day 2 Vehicle

description: 10X Genomics

value: pancreas

value: CD4+ and CD8+ primary lymphocytes

value: Day 2 Vehicle


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_42

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_42

value: Plasma, extracted cell-free RNA


title: KG1A-FoxA1, replicate 2

data_processing:
Fastq reads were pre-processed by merging the third Fastq containing the Unique Molecular Index with Read1 and Read2 using the merge_umi_fastq application from the UMIScripts package (https://github.com/HuntsmanCancerInstitute/UMIScripts)
Reads were aligned using Bowtie2 version 2.4.4 to the standard chromosomes of the mouse genome (build mm10). Duplicate alignments based on the UMI code were removed using the bam_umi_dedup application (UMIScripts) allowing for 1 mismatch.
Peaks were called using MACS2 version 2.2.7 with a significance of q-value < 0.05. Coverage tracks were generated with MACS2 as Reads Per Million.
Assembly: build mm10
Supplementary files format and content: bigWig, BED files (except for Input samples)

extract_protocol:
For all organoid experiments, two 24-well plates (approximately 4 – 8 million cells) were collected in Cell Recovery Solution (500 µl per dome). Organoids were submerged in ice for 30 min before centrifugation at 4°C (300G). Cells were washed three times in cold PBS. On the second wash, PBS was supplemented with DNase solution (containing a final concentration of 200U/ml DNase [Worthington], 2.5 mM MgCl2, 500 mM CaCl2). After the third wash, organoids were resuspended in 2 mM DSG buffer (1X PBS, 1 mM MgCl2) and rotated at room temperature for 35 min. Formaldehyde was then added to a final concentration of 1% and cells were crosslinked for 10 min. The cross-linking reaction was stopped with the addition of glycine to a final concentration of 125 mM. Cells were washed with cold PBS, then frozen at -80. Cell pellets were thawed on ice for 5 min then lysed in 1 ml of Farnham lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP40) for all TF experiments or 400 ul of Chromatrap Hypotonic buffer (catalog #100007) for all histone experiments. Samples were centrifuged at 4°C (1000G) then resuspended in 1ml of RIPA lysis buffer (1X PBS, 1% NP40, 0.5% sodium deoxycholate, 0.1% sodium dodecyl sulfate) or 100 µl of Chromatrap Lysis buffer (catalog #100005) for TF and histone ChIPs respectively. Chromatin extract was sonicated with QSonica Q800R (pulse: 30 s on/30 s off; sonication time: 20 min; amplitude: 70%) then was brought up to a volume of 1 ml with RIPA lysis buffer. Chromatin from all samples was immunoprecipitated with antibodies premixed with Protein A Dynabeads: FoxA1 (Abcam, ab170933, rabbit monoclonal, 5 µg/ChIP).
For in vivo experiments, KN and KNF1F2 tumor-bearing mice were euthanized at 14 weeks post tumor initiation and the rib-cage was dissected to reveal the trachea and heart. Lungs were perfused with cold PBS, removed, and snap frozen in liquid nitrogen. Flash-frozen lungs were minced on ice in 2 ml of ice-cold PBS for 3 – 5 min. Minced lungs were dounced 10 times with a large 7 ml homogenizer (Wheaton) and centrifuged for 5 min at 4°C (300G). Tissue was crosslinked in 2 mM DSG buffer and 1% Formaldehyde as previously described (In vitro organoid ChIP-seq). After fixation, lung samples were resuspended in 2 – 3 ml of TST buffer (Slyper et al. 2020) with protease inhibitors for 5 min. During this time, samples were dounced an additional 5 times in a small 2 ml homogenizer (Wheaton) to extract nuclei. Lysis was quenched with 5 ml of 1X ST buffer (Slyper et al. 2020) plus protease inhibitors. Nuclei were washed in cold PBS and resuspended in 5 – 10 ml cold PBS supplemented with DAPI and protease inhibitors. Nuclei suspension was then sequentially filtered through a 70 μm and 35 μm cell strainer. Nuclei were sorted using BD FACSAria with the 85 μm nozzle for GFP-positive, DAPI-positive nuclei. Samples were sorted into 1 ml of cold PBS with 1% BSA and 10X protease inhibitor. Approximately 3 million nuclei were sorted for histone ChIP-seq and 10 million for TF ChIP-seq experiments.  After sorting, nuclei were pelleted for 10 min at 4°C (500G) then resuspended in Chromatrap Hypotonic and Lysis buffers and sonicated as previously described (In vitro organoid ChIP-seq). Chromatin was immunoprecipitated with antibodies premixed with Protein A Dynabeads: FoxA1 (Abcam, ab170933, rabbit monoclonal, 5 µg/ChIP), TET3 (Sigma, ABE290, rabbit polyclonal, 5 µg/ChIP) and H3K27ac (Active Motif, 39133, rabbit polyclonal, 5 µg/ChIP).
ChIP-seq libraries were prepared using the ChIP-Seq with NEBNext Ultra II DNA Library Prep Kit. 10ng of DNA was used as strating material for input and IP samples.

treatment_protocol: For in vitro experiments, organoid cultures treated with ethanol for 48hr, then collected two weeks post treatment for ChIP. Mice were treated with tamoxifen (Sigma) dissolved in corn oil at a dose of 120mg/kg. For in vivo experiments, mice received 4 injections over the course of 5 days. One day following injections, mice were given pellets supplemented with 500mg/kg (Envigo) tamoxifen for 7 days. Tumors were harvested 8 weeks post tamoxifen treatment and nuclei were sorted for GFP+ DAPI+ population.

tag: cell line

value: lung tumors

tag: chip-antibody

value: FoxA1 (Abcam, ab170933)

value: KrasFSF-G12D/+; Rosa26FSF-CreERT2/Sun1; Nkx2-1F/F; FoxA1F/F; FoxA2F/F

value: ethanol


title: Active T1D

description: 10X Genomics

value: spontaneous new onset diabetic female NOD mice (3-4 months of age)

value: Active T1D


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_170

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_170

value: UCSD


title: NCI-H1299 (p53Y220C) cells, MS78 [Y220C-78-4]

first: Tiphaine

middle: Christiane

last: Martin

address: 1470 Madison Ave

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute

data_processing:
We first assessed the quality of paired-end reads with FASTQC (v0.11.8).
we filtered reads with BBDUK from BBTOOLS (v37.53) to remove adapters, known artefacts, and quality trimmed (PHRED quality score <10).
Reads that became too short after trimming (N<60 bp) were discarded. Singleton reads (i.e., reads whose mate has been discarded) were not retained.
We estimated the transcript-level quantification of cleaned RNA-seq data using SALMON (v1.0.0) by a quasi-mapping on Homo sapien sapien hg38.
Assembly: Human hg38
Supplementary files format and content: SALMON - format - .sf - TMM and read counts

growth_protocol: NCI-H1299 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and 1% Penicilin-Streptomycin. NCI-H1299 (p53Y220C) stable cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS), 1% Penicilin-Streptomycin and 500µg/mL G418. Both cell lines were cultured in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Cells were washed with ice-cold PBS and pelleted. The flash frozen samples were sent to Azenta Life Sciences where RNA was harvested.
RNA-seq libraries were constructed from the PolyA selected mRNA (prepared by Azenta Life Sciences)

treatment_protocol: Vehicle or 10µM of MS78 treated for 24h

value: non-small cell lung carcinoma cell


title: Onset T1D

description: 10X Genomics

value: Onset T1D


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_109

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_109

value: KD


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_41

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_41


title: NCI-H1299 (p53Y220C) cells, MS78 [Y220C-78-3]


title: HUES8 hESCs, Day 6, CK666, Rep 4

city: San Francisco

first: Nathaniel

middle: Paul

last: Meyer

state: California

address: 513 Parnassus Ave

department: Cell and Tissue Biology

institute: University of California, San Francisco

data_processing:
Raw data (raw reads) were processed through fastp to remove adapters, poly-N sequences, and reads with low quality. Q20, Q30 and GC content of the clean data were calculated and found to be within the normal range. All the downstream analyses were based on the clean data with high quality. Reference genome (ID: 51) and gene model annotation files were downloaded from genome website browser (NCBI) directly. Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software. FeatureCounts was used to count the read numbers mapped of each gene. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis was performed using DESeq2 R package. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR). Genes with a padj < 0.05 found by DESeq2 were assigned as differentially expressed. The R package clusterProfiler was used to test the statistical enrichment of differential expression genes in KEGG pathways. KEGG terms with padj < 0.05 were considered significant enrichment. Transcription factor binding motif analysis was performed using Enrichr.
Assembly: hg38; NCBI Genome ID: 51; Genome Reference Consortium Human GRCh38.p14 (GCA_000001405.29)
Supplementary files format and content: csv file includes raw counts for each sample
Supplementary files format and content: csv file includes fpkm for each sample

growth_protocol: Primed human embryonic stem cell lines HUES8 (RRID: CVCL_B207) were maintained on Matrigel (Corning Life Science #354277) in feeder-free mTeSR-1 medium (STEMCELL Technologies # 85850) at 37°C with 5% CO2 with daily medium changes. Cells were passaged approximately every 3 days, by dissociating with Accutase (STEMCELL Technologies #07920) and including the Rho-associated coiled-coil kinase (ROCKi) inhibitor Y-276932 (10 µM; Selleckchem #S1049) in the plating medium to facilitate survival.

extract_protocol:
RNA was extracted with the RNeasy Mini Plus kit (Qiagen, #74104) according to the manufacturer’s instructions and sample concentrations were determined by NanoDrop. RNA degradation and contamination were monitored on 1% agarose gels, RNA purity was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA), and RNA integrity and quantitation were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure was ligated to prepare for hybridization. To select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor- ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated with >20 million reads per sample. The above protocol, with the exception of RNA extraction, was performed externally by Novogene Co. Ltd (USA).

treatment_protocol: For control primed samples, cells were maintained in feeder-free mTeSR-1 medium (STEMCELL Technologies # 85850) on Matrigel (Corning Life Science #354277) at 37°C with 5% CO2 with daily medium changes for the duration of the experiment. Cells were passaged approximately every 3 days, by dissociating with Accutase (STEMCELL Technologies #07920) and including the Rho-associated coiled-coil kinase (ROCKi) inhibitor Y-276932 (10 µM; Selleckchem #S1049) in the plating medium to facilitate survival. To induce naive dedifferentiation, cells were plated at a density of 10,000 cells per cm2 in the presence of ROCKi (10µM). After 24 h, cells were washed 3 times with PBS and incubated in naïve dedifferentiation medium of mTeSR-1 supplemented with 12 ng/mL bFGF (Peprotech #AF-100-18B), 1 µM PD0325901 (MEKi, Selleckchem #S1036), 3 µM CHIR99021 (GSK3βi, Selleckchem # S2924), 10 µM Forskolin (StemCell Technologies #72112), 50 ng/mL ascorbic acid (Sigma # A92902), and 1000 U recombinant human LIF (StemCell Technologies #78055). Medium was replaced daily, and cells were passaged every 3 days with Accutase. To investigate the role of actin nucleators on naive dedifferentiation, the above media was supplemented with 80 μM CK666 (EMD Millipore #182515) throughout the entire dedifferentiation process. When passaging, media was supplemented with both ROCKi (10µM) and the appropriate inhibitor.

tag: time

value: Day 6

value: Human embryonic stem cells

value: WT

value: Naïve dedifferentiation media +  80 uM CK666


title: KG1A-FoxA1-Input, replicate 2


title: HUES8 hESCs, Day 6, CK666, Rep 3


title: K tumors, replicate methyl-seq  3

value: lung

value: tamoxifen


title: NCI-H1299 (p53Y220C) cells, MS78 [Y220C-78-2]


title: KG1A-FoxA1, replicate 1


title: HUES8 hESCs, Day 6, CK666, Rep 2


title: HUES8 hESCs, Day 6, CK666, Rep 1


title: KG1A-FoxA1-Input, replicate 1


title: 22E-FoxA1, replicate 2

value: KrasFSF-G12D/+; p53FSF/+;Rosa26FSF-CreERT2/Sun1; Nkx2-1F/F; FoxA1F/F; FoxA2F/F


title: HUES8 hESCs, Day 6, Naïve, Rep 4

value: Naïve dedifferentiation media


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_48

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_48

value: Plasma, extracted cell-free RNA


title: 22E-FoxA1-Input, replicate 2

value: lung tumors

value: FoxA1 (Abcam, ab170933)


title: NCI-H1299 (p53Y220C) cells, MS78 [Y220C-78-1]


title: HUES8 hESCs, Day 6, Naïve, Rep 3


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_226_trimmed

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_226_trimmed


title: NCI-H1299 (p53Y220C) cells, DMSO [Y220C-DMSO-4]

source_name: NCI-H1299 (p53Y220C) cells, DMSO

value: DMSO


title: NCI-H1299 (p53Y220C) cells, DMSO [Y220C-DMSO-3]


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_8

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_8


title: 22E-FoxA1-Input, replicate 1

value: ethanol


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_108

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_108

value: UCSD


title: HUES8 hESCs, Day 6, Naïve, Rep 1


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_157

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_157

value: MISC


title: HUES8 hESCs, Day 6, Primed, Rep 4

value: Control


title: NCI-H1299 (p53Y220C) cells, DMSO [Y220C-DMSO-1]

value: non-small cell lung carcinoma cell


title: NCI-H1299 (p53Y220C) cells, DMSO [Y220C-DMSO-2]


title: KNF1F2-H3K27ac-Input, replicate 2

value: H3K27ac (Active Motif, 39133)

value: KrasFSF-G12D/+; Rosa26FSF-CreERT2/Sun1; Nkx2-1F/F; FoxA1F/F; FoxA2F/F


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_82

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_82


title: KNF1F2-H3K27ac, replicate 2


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_107

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_107

value: KD


title: NCI-H1299 cells, MS78 [Null-78-4]

source_name: NCI-H1299 cells, MS78


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_83

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_83


title: KNF1F2-H3K27ac-Input, replicate 1


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_146

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_146


title: NCI-H1299 cells, MS78 [Null-78-3]


title: Tobacco leaf tissue -GDH94×TN90_rep1

city: Guiyang

first: Renxiang

last: Liu

state: Guizhou

address: Huaxi

institute: Guizhou University

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep(https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters.
Then clean reads were separately aligned to reference genome（https://solgenomics.net/organism/Nicotiana_tabacum/genome） with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml)software.
The mapped reads of each sample were assembled by StringTie(https://ccb.jhu.edu/software/stringtie/index.shtml?t=example) .
RSEM （http://deweylab.github.io/RSEM/）establishes the maximum likelihood abundance estimation model based on the maximum expectation algorithm, and considers the paid end reads, the length of reads, the length distribution of fragments, and the quality value to distinguish which transcripts are different subtypes of the same gene. The results of expression quantification are expressed in TPM/FPKM. The homogenization process of TPM/FPKM makes the total expression amount in different samples consistent.
Assembly: Nitab-v4.5
Supplementary files format and content: TPM

organism: Nicotiana tabacum

source_name: hybrid GDH94×TN90

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent (Plant RNA Purification Reagent for plant tissue) according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) andquantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA-seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA. After quantified by TBS380, paired-end RNA-seq sequencing library was sequenced with the Illumina HiSeq xten/NovaSeq 6000 sequencer (2 × 150bp read length)

value: mature leaf

tag: line


title: NCI-H1299 cells, MS78 [Null-78-2]


title: HUES8 hESCs, Day 6, Primed, Rep 3

value: Day 6

value: Human embryonic stem cells

value: WT


title: 22E-FoxA1, replicate 1

value: KrasFSF-G12D/+; p53FSF/+;Rosa26FSF-CreERT2/Sun1; Nkx2-1F/F; FoxA1F/F; FoxA2F/F


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_169

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_169

value: Plasma, extracted cell-free RNA


title: KN-H3K27ac, replicate 2

value: lung

value: tamoxifen


title: HUES8 hESCs, Day 6, Primed, Rep 1


title: HUES8 hESCs, Day 6, Naïve, Rep 2

value: Naïve dedifferentiation media


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_206_trimmed

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_206_trimmed


title: NCI-H1299 cells, MS78 [Null-78-1]


title: KN-H3K27ac-Input, replicate 2


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_81

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_81


title: NCI-H1299 cells, DMSO [Null-DMSO-4]

source_name: NCI-H1299 cells, DMSO

value: DMSO


title: Total RNA from PBMC of FM6  patient post MT treatment

first: Elisa

middle: Elisa

last: Oltra

state: VALÈNCIA

address: C/ Quevedo 2

department: Pathology

country: Spain

institute: Universidad Catolica de Valencia San Vicente Martir

data_processing:
Quality of RNA-seq reads was assessed with FastQC tool
RNA sequences were mapped to the human reference genome (GRCh38/hg38) using STAR aligner tool
Read count extraction was perfomed with htseq-count
Expression levels are summarized as transcripts per million (TPM)
Assembly: GRCh38/hg38
Supplementary files format and content: Excel (xls) Post/Pre DEA (Differential Expression Analysis)

source_name: PBMC

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen, MD, USA) according to the manufacturer's instructions. RNA quality was assessed using Agilent TapeStation 2100 (Agilent). All RNA samples had an RNA Integrity number (RIN) above 7.
Libraries generated with NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations, after removing rRNA using the Epicentre Ribo-zeroTM rRNA Removal Kit (Epicentre, USA) kit.

value: PBMC


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_162

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_162

value: MISC

value: UCSD


title: NCI-H1299 cells, DMSO [Null-DMSO-3]

value: non-small cell lung carcinoma cell


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_80

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_80


title: KN-H3K27ac-Input, replicate 1

value: H3K27ac (Active Motif, 39133)


title: HUES8 hESCs, Day 6, Primed, Rep 2

value: Control


title: KNF1F2-TET3, replicate 2

value: TET3 (Sigma, ABE290)

value: KrasFSF-G12D/+; Rosa26FSF-CreERT2/Sun1; Nkx2-1F/F; FoxA1F/F; FoxA2F/F


title: KNF1F2-H3K27ac, replicate 1


title: Total RNA from PBMC of FM5 patient post MT treatment


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_198_trimmed

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_198_trimmed

value: KD


title: NCI-H1299 cells, DMSO [Null-DMSO-2]


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_154

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_154


title: KNF1F2-TET3-Input, replicate 2


title: Total RNA from PBMC of FM4 patient pre MT treatment


title: NCI-H1299 cells, DMSO [Null-DMSO-1]


title: Total RNA from PBMC of FM6 patient pre MT treatment


title: Total RNA from PBMC of FM4 patient post MT treatment


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_78

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_78


title: plt_4

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

institute: CIC bioGUNE

description: smallRNA

data_processing:
FASTQs were trimmed for the adapters following the recommendations of the NEXTflex™ Small RNA-Seq Kit manufacturers.
We used Bowtie 1.0.1 to align the reads against the human genome (GRCh38), with a mismatch 0, to avoid false positives employing Partek Flow application, software version 7.0. Only the miRNAs with 10 or more reads were considered for differential expression analysis.
Mapped reads were quantified to mirbase v22 using Partek E/M method, so the processed data file contains counts values normalized by Partek E/M method
Genome_build: GRCh38
Supplementary_files_format_and_content: read count table

source_name: platelets

extract_protocol:
Total RNA from extracellular vesicles and platelets from surplus platelet concentrates obtained from Finnish Red Cross Blood Services was extracted using RNA Qiagen miRNeasy micro kit
Sequencing libraries were prepared following the protocol included with the kit “NEXTflex™ Small RNA-Seq Kit v3,” (©Bioo Scientific Corp. Catalog #5132-05).
Small RNA-Seq

treatment_protocol: Platelets were isolated from surplus platelet concentrates by size exclusion chromatography (platelet sample), and diluted to 250 x 10E6 per mL concentration. Platelets were then activated through 1) CLEC-2, 2) GPVI receptor, or 3) thrombin and collagen co-activation. Non-activated platelets were used as control. After 30 minute incubation platelets were removed by centrifugation, and platelet-derived EVs (PEVs) were isolated from the platelet-free supernatant by cushioned-density ultracentrifugation.

value: platelets

tag: sample type

tag: individual

value: healthy volunteers

tag: platelet activation

value: no activation


title: Total RNA from PBMC of FM3 patient pre MT treatment


title: KNF1F2-TET3-Input, replicate 1


title: plt_3

description: smallRNA


title: KNF1F2-TET3, replicate 1


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_79

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_79

value: Plasma, extracted cell-free RNA


title: Total RNA from PBMC of FM3 patient post MT treatment


title: plt_2

description: smallRNA


title: KN-TET3, replicate 2

value: lung


title: plt_1

description: smallRNA


title: Total RNA from PBMC of FM2 patient pre MT treatment


title: KN-H3K27ac, replicate 1

value: tamoxifen


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_145

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_145


title: KN-TET3-Input, replicate 2


title: Total RNA from PBMC of FM2 patient post MT treatment


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_173

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_173


title: Total RNA from PBMC of FM1 patient pre MT treatment


title: KN-TET3, replicate 1


title: RH_EV3

description: smallRNA

source_name: extracellular vesicles from platelets

value: extracellular vesicles from platelets

value: CLEC-2 activation


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_74

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_74


title: RH_EV4

description: smallRNA


title: KN-TET3-Input, replicate 1


title: Total RNA from PBMC of FM1 patient post MT treatment

value: PBMC


title: RH_EV2

description: smallRNA


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_144

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_144

value: MISC


title: KN-FoxA1, replicate 2

value: FoxA1 (Abcam, ab170933)


title: RH_EV1

description: smallRNA


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_73

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_73

value: UCSD


title: SNU-4713S3-TO under normal gravity

city: Seoul

first: JA-LOK

last: KU

address: 101 Daehak-ro, Jongno-gu

department: Cancer Research Institute

country: South Korea

institute: Seoul National University College of Medicine

data_processing:
Paired end sequencing reads of cDNA libraries (101bp) generated from a NovaSeq6000 instrument were verified its sequence quality with FastQC v 0.11.7. For data preprocessing, low quality bases and adapter sequences in reads were trimmed using Trimmomatic v 0.38. The trimmed reads were aligned to the human genome (UCSC hg19) using HISAT v2.1.0, a splice-aware aligner. Then, transcript assembly of known transcripts, novel transcripts, and alternative splicing transcripts was processed by StringTie v1.3.4d. Based on the result of that, expression abundance of transcript and gene were calculated as read count or FPKM value (Fragments Per Kilobase of exon per Million fragments mapped) per sample. For each program, transcriptome reads were mapped to the human genome (Ensmebl database).
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw read-counts for each sample

extract_protocol:
Total RNA was isolated from cell lysate using TRIzol (Qiagen) and Qiagen RNeasy kit (Qiagen, Cat# 74104).
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA LT Sample Prep Kit using manufacturer's protocols.

value: Colorecal Cancer Organoids

value: WT


title: CR_EV4

description: smallRNA

value: GPVI activation


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_171

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_171


title: KN-FoxA1-Input, replicate 2


title: KN-FoxA1, replicate 1


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_77

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_77


title: SNU-4713S3-TO under microgravity

value: Microgravity


title: SNU-4631AS4-TO under normal gravity

value: Control


title: KN-FoxA1-Input, replicate 1


title: CR_EV3

description: smallRNA

value: platelets


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_72

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_72


title: SNU-4631AS4-TO under microgravity


title: CR_EV2

description: smallRNA

value: healthy volunteers


title: KG1A-4OHT replicate 2

description:
19847X4
KG1A_rawcounts.txt

data_processing:
Optical duplicates were removed from Fastq files using Clumpify (BBMap, v38.34) with a pixel distance of 10000.
Adapters were removed using Cutadapt (v 3.5) with a minimum overlap of 6 bp and minimum trimmed read length of 20. Reads were aligned to the reference  using STAR version 2.7.6a in two-pass basic mode.
Alignments were counted over gene annotation using Subread featureCounts  (v1.6.3) in paired-end mode, assigning to the gene with the largest overlap.
Raw counts were filtered to remove features with zero counts and features with five or fewer reads in every sample
Assembly: build mm39; ensembl release 104 for in vivo and KG1A samples
Assembly: build mm10; ensembl release 102 for 22E samples
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
RNA was extracted using the PureLink RNA Mini Kit (Thermo).
RNA libraries for in vivo tumors were prepped using the NEBNext Ultra II Directional RNA Library Prep with rRNA Depletion Kit (mouse) with at least 10ng of total RNA per sample. RNA libraries for in vitro 3D organoid samples were prepped with the NEBNext Ultra II Directional RNA Library Prep with poly(A) mRNA Isolation with at least 100ng of total RNA per sample.

treatment_protocol: For in vitro experiments, organoid cultures treated with 4-OH tamoxifen or ethanol for 48hr to delete Foxa1/2 conditional alleles. Cultures collected in TRIzol two weeks post-deletion. Mice were treated with tamoxifen (Sigma) dissolved in corn oil at a dose of 120mg/kg. For in vivo experiments, mice received 4 injections over the course of 5 days. One day following injections, mice were given pellets supplemented with 500mg/kg (Envigo) tamoxifen for 7 days. Tumors were harvested 8 weeks post tamoxifen treatment and cells were sorted for GFP+ DAPI- population before resuspension in TRIzol.

value: lung tumors

value: KrasFSF-G12D/+; Rosa26FSF-CreERT2/Sun1; Nkx2-1F/F; FoxA1F/F; FoxA2F/F

value: 4-OH tamoxifen


title: SNU-4146S1-TO under normal gravity


title: Total RNA from PBMC of FM5 patient pre MT treatment


title: CR_EV1

description: smallRNA


title: KG1A-4OHT replicate 1

description:
19847X3
KG1A_rawcounts.txt


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_71

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_71

value: Plasma, extracted cell-free RNA


title: SNU-4146S1-TO under microgravity


title: TC_EV4

description: smallRNA

value: extracellular vesicles from platelets

value: thrombin collagen co-activation


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_166

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_166


title: SNU-4139S3-TO under normal gravity


title: KG1A-EtOH replicate 2

description:
19847X2
KG1A_rawcounts.txt

value: ethanol


title: SNU-4139S3-TO under microgravity


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_165

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_165

value: MISC


title: KG1A-EtOH replicate 1

description:
19847X1
KG1A_rawcounts.txt


title: TC_EV3

description: smallRNA


title: GaC_M55

city: GuangZhou

first: Dong-Mei

last: Chi

address: 651 Dongfeng Road East

institute: SYSUCC

data_processing:
*library strategy: Spatial Transcriptomics
spaceranger and SAW
Assembly: GRCh38
Supplementary files format and content: matrix and location files

source_name: stomach

extract_protocol:
Fresh frozen tissue were OCT embedded, and 10um frozen sections were cut with cryostat
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatial Gene Expression Slides & Reagent and BGI stereo-seq kit according to manufacturer's construction

value: stomach

tag: tissue type

value: Gastric cancer


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_70

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_70

value: UCSD


title: TC_EV2

description: smallRNA


title: GaC_M39


title: 22E-4OHT replicate 1

description:
18994X5
22E_rawcounts.txt

value: KrasFSF-G12D/+; p53FSF/+;Rosa26FSF-CreERT2/Sun1; Nkx2-1F/F; FoxA1F/F; FoxA2F/F


title: TC_EV1

description: smallRNA


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_150

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_150


title: 22E-EtOH replicate 2

description:
18994X3
22E_rawcounts.txt


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_153

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_153


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_69

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_69


title: c_EV4

description: smallRNA

value: no activation


title: c_EV3

description: smallRNA


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_148

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_148


title: 22E-EtOH replicate 1

description:
18994X1
22E_rawcounts.txt


title: c_EV2

description: smallRNA


title: NeoBCC18

city: Vienna

first: Florian

last: Halbritter

address: Zimmermannplatz 10

country: Austria

institute: St. Anna Children's Cancer Research Institute (CCRI)

data_processing:
Raw sequence data were processed using cellranger-7.0.0 (10x Genomics)
Assembly: refdata-gex-GRCh38_HSV-2020-A-
Supplementary files format and content: compressed matrix files of CellRanger outputs

source_name: BCC

extract_protocol:
3-5 mm skin punch biopsies were digested for 1 hour at 37 °C using the Miltenyi Skin Dissociation Kit (#130-101-540) and filtered through a 40µm strainer. Red blood cells were lysed for 1 min at RT with ACK buffer (Gibco #A10492-01). After washing, cells were stained with CD45 PerCP-Cy5.5 (Biolegend #304027), EpCAM APC (Biolegend #324207) and DAPI (Invitrogen #D1306) and sorted with FACSaria (BD). 40,000 CD45+ immune cells and 4,000 CD45- EpCAM+ tumor cells were sorted into PBS+0.2% BSA and loaded into a 10x Genomics 5´ V1.1 reaction for further processing with the 10x Genomics pipeline with a relative centrifugal force (RFM) of 500 g at 4 °C.
RT, DNA synthesis and gene expression libraries preparation was performed according to the 10xGenomics 5’ V1.1 protocol, using the Single Cell 5' PE chemistry. Qubit dsDNA HS kit (Invitrogen #Q33231) and Tapestation (Agilent) were used for quality control. Libraries were sequenced on a NovaSeq SP flow cell.

value: BCC

value: Talimogene laherparepvec (T-VEC)


title: NeoBCC17


title: N neoplasias, replicate 2

description:
20274X1
invivo_rawcounts.txt

value: lung

value: Rosa26FSF-CreERT2/Sun1; Nkx2-1F/F

value: tamoxifen


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_164

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_164


title: N neoplasias, replicate 3

description:
20274X2
invivo_rawcounts.txt


title: 22E-4OHT replicate 2

description:
18994X7
22E_rawcounts.txt

value: lung tumors


title: c_EV1

description: smallRNA

value: platelets

value: healthy volunteers


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_143

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_143

value: Plasma, extracted cell-free RNA


title: MPP_DKO (pooled from 5 mice transplanted with DKO BM, same no. of MPP per mouse used in the pool)

city: Barcelona

first: Cristina

last: Lopez-Rodriguez

address: Carrer Dr. Aiguader, 88

department: Medicine and Life Sciences

institute: Universitat Pompeu Fabra

description:
AS5943_3369AF
COUNTS_genes_ARAMBURUJOS_12

data_processing:
RNA-seq reads were mapped with STAR/2.7.8a against the Mus musculus reference genome (GRCm39)
Gene quantification was performed with RSEM/1.3.0 with default options
The gene annotation used was gencode.M26
Assembly: GRCm39
Supplementary files format and content: raw counts (tsv)

source_name: Bone marrow

growth_protocol: CD45.2+ HSC (CD48-CD150+ within LSK) and CD45.2+ MPP (LSK CD48+CD150- within LSK) populations of the respective donor genotypes were FACS-sorted from the bone marrow of transplated CD45.1+ wild-type mice 13 weeks after transplantation

extract_protocol:
RNeasy Microkit (Qiagen, Cat# 74004)
cDNA libraries were prepared from poly A RNA (mRNA) using the Smart-Seq2 single-cell protocol

treatment_protocol: Bone marrow was isolated from the respective mouse genotypes (CD45.2 background) and transplanted into irradiated wild-type CD45.1 recipient mice

value: Bone marrow

value: primary cells

value: hematopoietic multipotent progenitor (MPP), CD48+ CD150- cells within LSK cell population in bone marrow

value: NFAT5-deficient (Nfat5 fl/fl Vav-Cre) and IFNAR1-deficient (DKO)


title: NeoBCC12


title: NeoBCC14


title: NeoBCC15


title: MPP_IFNAR (pooled from 5 mice transplanted with IFNAR1-deficient BM, same no. of MPP per mouse used in the pool)

description:
AS5942_3368AF
COUNTS_genes_ARAMBURUJOS_12

value: IFNAR1-deficient (IFNAR)

value: Bone marrow was isolated from the respective mouse genotypes (CD45.2 background) and transplanted into irradiated wild-type CD45.1 recipient mice


title: NeoBCC11


title: N neoplasias, replicate 1

description:
20040X8
invivo_rawcounts.txt


title: KNF1F2 tumors, replicate 3

description:
20040X6
invivo_rawcounts.txt

value: KrasFSF-G12D/+; Rosa26FSF-CreERT2/Sun1; Nkx2-1F/F; FoxA1F/F; FoxA2F/F


title: KNF1F2 tumors, replicate 2

description:
20040X5
invivo_rawcounts.txt


title: MPP_N5 (pooled from 5 mice transplanted with Nfat5 fl/fl Vav-Cre BM, same no. of MPP per mouse used in the pool)

description:
AS5941_3367AF
COUNTS_genes_ARAMBURUJOS_12

value: NFAT5-deficient (Nfat5 fl/fl Vav-Cre, N5)


title: NeoBCC10

value: BCC


title: KNF1F2 tumors, replicate 1

description:
20040X4
invivo_rawcounts.txt


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_142

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_142

value: MISC

value: UCSD


title: MPP_WT (pooled from 5 mice transplanted with WT BM, same no. of MPP per mouse used in the pool)

description:
AS5940_3366AF
COUNTS_genes_ARAMBURUJOS_12

value: wild-type (Nfat5 +/+ Vav-Cre, WT)


title: NeoBCC08

value: Talimogene laherparepvec (T-VEC)


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_141

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_141


title: HSC_DKO (pooled from 5 mice transplanted with DKO BM, same no. of HSC per mouse used in the pool)

description:
AS5939_3365AF
COUNTS_genes_ARAMBURUJOS_12

value: hematopoietic stem cell (HSC), CD48- CD150+ cells within LSK cell population in bone marrow


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_68

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_68


title: NeoBCC07


title: HSC_IFNAR (pooled from 5 mice transplanted with IFNAR1-deficient BM, same no. of HSC per mouse used in the pool)

description:
AS5938_3364AF
COUNTS_genes_ARAMBURUJOS_12


title: KN tumors, replicate 2

description:
20040X2
invivo_rawcounts.txt

value: lung

value: tamoxifen


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_66

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_66

value: Plasma, extracted cell-free RNA


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_65

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_65


title: HSC_N5 (pooled from 5 mice transplanted with Nfat5 fl/fl Vav-Cre BM, same no. of HSC per mouse used in the pool)

description:
AS5937_3363AF
COUNTS_genes_ARAMBURUJOS_12

value: Bone marrow


title: KN tumors, replicate 1

description:
20040X1
invivo_rawcounts.txt


title: NeoBCC06


title: HSC_WT (pooled from 5 mice transplanted with WT BM, same no. of HSC per mouse used in the pool)

description:
AS5936_3362AF
COUNTS_genes_ARAMBURUJOS_12

value: primary cells


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_105

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_105


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_147

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_147


title: K tumors, replicate 3

description:
20346X2
invivo_rawcounts.txt


title: NeoBCC04


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_219_trimmed

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_219_trimmed

value: KD


title: NeoBCC05


title: RNA_bisulfite-seq_NSUN2

description: The cells were collected after transfecting the plasmids for 48h

data_processing:
The adapter sequences were removed using cutadapt (version 1.18), and low-quality bases were filtered using fastqc (version 0.11.9).
The clean reads were then aligned and m5C sites were called using meRanTK (version 1.3.0).
The meRanGh was employed to map the clean reads to the reference genome sequence (hg38 or mm39), and m5C sites were called using meRanCall.
Assembly: mm39, hg38
Supplementary files format and content: BED files include four columns, which means chromosome, start position, end position, methylation ratio. BS-seq generates the m5C sites at the single-base resolution, so the 'end position' represent the m5C sites.
Library strategy: RNA Bisulfite-seq

extract_protocol:
Total RNA was extracted using Trizol reagent (#AG21102, Accurate Bioeng. Co., Ltd., Hunan, China) and the mRNA was purified using the Dynabeads® mRNA Purification Kit Dynabeads Oligo(dT)25 (#61002, Invitrogen). mRNA was treated by DNaseⅠ buffer (AM8170G, Thermo Fisher Scientific) and Turbo DNase (Thermo Fisher Scientific, AM2238) at 37 ℃ for 10 min and purified by ethanol precipitation to remove genomic DNA.
1 μg of poly(A) RNA was fragmented into ~200 nt nucleotide fragments. According to the EZ RNA Methylation Kit protocol (#R5001, ZYMO RESEARCH), the poly(A) RNA fragments underwent sodium bisulfite treatment, desalting, and desulfonation reactions, leading to the construction of a strand-specific Bisulfit-seq library. The bisulfite-converted library was initiated with random hexamers (ACT) to reverse transcribe RNA samples. The first strand cDNA of the bisulfite-converted library was synthesized using 5× first-strand buffer (#18080044, Invitrogen), 10 mM DTT (#18080044, Invitrogen), 10 mM dNTP mix (#N0447L, NEB), 40 U/μl RNase Inhibitor (#M0307L, NEB), and reverse transcriptase III (#18080044, Invitrogen). The second strand cDNA synthesis was performed using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (#NR604-02, VAHTS), and the necessary adapters for library preparation were provided by the VAHTS® RNA Adapters set3 for Illumina.

value: Overexpression NSUN2 plasmids


title: K tumors, replicate 2

description:
20346X1
invivo_rawcounts.txt


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_230_trimmed

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_230_trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_9

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_9


title: KN tumors, replicate 3

description:
20040X3
invivo_rawcounts.txt


title: RNA_bisulfite-seq_pcDNA3

value: Empty pcDNA3 plasmids


title: Col-0_ inflorescence_TRM-sRNA-seq

city: Shanghai

first: Susu

last: Chen

address: 1200 Cailun Road, Pudong New District, Shanghai, China

institute: Shanghai University of Traditional Chinese Medicine

description: Col-0 PBA+OX

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim_galore (version 0.6.6).
Trimmed sequence reads were mapped to TAIR10 using ShortStack (version- 3.8.5 parameters- --align_only –nohp --mmap u --bowtie_m 1000 --ranmax 50 --mismatches 0).
Reads count extraction was performed using featureCounts (version- v2.0.1 parameters- -O --largestOverlap -fraction).
Reads count normalization was performed using DESeq2 and custom R scripts.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text files include sequence counts for each Sample.

organism: Arabidopsis thaliana

source_name: inflorescence

growth_protocol: The seeds were grown in soil. After cultivated in 4 ℃ for three days, the seeds were transferred to 16/8 h (light/dark) greenhouse.

extract_protocol:
Total RNAs were extracted from inflorescence tissues using TRIzol reagent (Invitrogen, USA) following standard protocols. For "conventional sRNA-seq" library, total RNA was separated in 16% denaturing PAGE gel to excise 18-30 nt, and gel purified RNA was treated by NaCl solution. For "NaIO4 treatment" library, total RNA was separated in 16% denaturing PAGE gel to excise 18-30 nt, and gel purified RNA was treated by NaIO4 solution. For "PBA-PAGE" library, total RNA was separated in 16% denaturing PAGE gel supplemented with 2% PBA to excise 18-30 nt, and gel purified RNA was treated by NaCl solution. For "TRM-sRNA-seq" library, total RNA was separated in 16% denaturing PAGE gel supplemented with 2% PBA to excise 18-30 nt, and gel purified RNA was treated by NaIO4 solution. For AGO1-RIP samples, protein was extracted from Col-0 inflorescence. After immunoprecipitation, AGO1-bound RNAs were isolated by phenol-chloroform extraction and ethanol precipitation.
All types of small RNA libraries were constructed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, USA) following manufacturer's instructions and purified using Monarch PCR & DNA kit (NEB, USA).

value: inflorescence

tag: ecotype

tag: library type

value: TRM-sRNA-seq


title: Retina D91,Myrf fl/fl

city: Portland

first: Gregory

last: Duncan

state: Oregon

address: 3181 SW Sam Jackson Park Road, BRB 453

institute: OHSU

data_processing:
Raw reads were sorted based on barcodes and FASTQC files were produced
Reads were aligned to Mus musculus (GRCm38/Mm10)
Expression counts were performed using STAR.
DeSeq2 was run using Basepair software to determine differentially expressed genes between whole retina and the ganglion cell layer
DeSeq2 was run using Basepair software to determine differentially expressed genes between the ganglion cell layer of Myrf fl/fl and Myrf fl/fl Sox10 CreERT
Assembly: mm10
Supplementary files format and content: .csv containing STAR expression counts
Supplementary files format and content: .csv containing DeSeq2 comparisons

source_name: Retina

extract_protocol:
Eyes were dissected and snap frozen in OCT, then sectioned on a cryostat at 20 µm thickness and mounted onto Poly-L-Lysine (P1524, Sigma) coated membrane slides (414190-9041-000, Zeiss). Sections were fixed in 70% ethanol for two minutes before staining in Harris Modified Hematoxylin (HHS32, Sigma) with 0.2% glacial acetic acid for 30s. Sections were then immersed in 70% ethanol twice and 100% ethanol twice for 30s each and stored at -80°C in a sealed container until LCM was performed. A Zeiss Palm Microbeam microscope was used to conduct LCM with cut segments extracted onto the lid of adhesive cap tubes (415190-9181-000, Zeiss). The ganglion cell layer was identified and sectioned—at least 20 sections per animal. For sampling of the whole retina, laser incisions were made through each retinal layer. Samples were treated with RLT lysis buffer and RNA isolated using the MicroRNAeasy kit (74004, Qiagen) as per the manufacturer’s instructions.
RNA quantity and quality were evaluated on an Agilent 2100 Bioanalyzer using the Eukaryote Total RNA Pico. cDNA libraries were produced by loading 15ng of RNA for use with the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit and sequenced with a NovaSeq 6000 at 50 million reads per sample.

value: Retina

tag: strain

value: Myrf fl/fl

value: 18 weeks old

tag: Sex

value: Male

value: Neurons


title: K tumors, replicate 1

description:
20040X7
invivo_rawcounts.txt

tag: tissue


title: ntp7-1_ inflorescence_TRM-sRNA-seq

description: ntp7-1 PBA+OX


title: GCL D102, Myrf fl/fl Sox10 CreERT

source_name: Ganglion cell layer

value: Ganglion cell layer

value: Myrf fl/fl Sox10 CreERT


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_140

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_140

data_processing:
Sequencing data was processed using a custom bioinformatics pipeline. Since pools sequenced on the Illumina NextSeq 2000 were optimized to produce paired-end, 61 bp reads, matched sequencing data from the Illumina NextSeq 500 were trimmed using Seqtk (v1.2).
Samples were then quality filtered and trimmed using BBDuk (v38.90), aligned to the Gencode GRCh38 human reference genome (v38, primary assembly) using STAR (v2.7.0f, default parameters).
Prior to feature quantification using featureCounts (v2.0.0), samples were deduplicated using Picard MarkDuplicates (v2.19.2). Mitochondrial, ribosomal, X, and Y chromosome genes were bioinformatically removed prior to analysis.
Samples were filtered on the basis of DNA contamination, rRNA contamination, total counts, and RNA degradation. DNA contamination was estimated by calculating the ratio of reads mapping to introns and exons. rRNA contamination was measured using SAMtools (v1.14). Total counts were calculated using featureCounts (v2.0.0). Degradation was estimated by calculating the 5’-3’ bias using Qualimap (v2.2.1).
Samples were removed from analysis if either the intron to exon ratio was greater than 4, if a sample had less than 90,000 total feature counts, or if the rRNA contamination, total counts, or 5’-3’ bias was greater than 4 standard deviations from the mean.
Assembly: Gencode GRCh38 human reference genome (v38, primary assembly)
Supplementary files format and content: comma-delimited .csf file includes the gene counts for each sample

source_name: Plasma, extracted cell-free RNA

extract_protocol:
Plasma samples were received on dry ice and stored at -80°C until processed. Prior to cfRNA extraction, plasma samples were thawed at room temperature and centrifuged at 1300 x g for 10 minutes at 4°C. cfRNA was extracted from plasma using the Norgen Plasma/Serum Circulating and Exosomal RNA Purification Mini Kit (Norgen, 51000). Extracted RNA was DNase treated with 14 µl of 10 µl DNase Turbo Buffer (Invitrogen, AM2238), 3 µl DNase Turbo (Invitrogen, AM2238), and 1 µl Baseline Zero DNase (Lucigen-Epicenter, DB0715K) for 30 minutes at 37°C, then concentrated into 12 µl using the Zymo RNA Clean and Concentrated Kit (Zymo, R1015).
Sequencing libraries were prepared from 8 µl of concentrated RNA using the Takara SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian (Takara, 634485) and barcoded using the SMARTer® RNA Unique Dual Index Kit (Takara, 634451). Library concentration was quantified using the Qubit™ 3.0 Fluorometer (Invitrogen, Q33216) with the dsDNA HS Assay Kit (Invitrogen, Q32854). Libraries were quality-controlled using the Agilent Fragment Analyzer 5200 (Agilent, M5310AA) with the HS NGS Fragment Kit (Agilent, DNF-474-0500) and pooled to equal concentrations. Each pool was sequenced using both the Illumina NextSeq 500/550 platform (paired-end, 150 bp) and the Illumina NextSeq 2000 platform (paired-end, 100 bp).

tag: diagnosis

tag: site

value: UCSD


title: HCT116 cells, siJOSD1_3

city: Xinxiang

first: Zhongbo

last: li

state: Henan

institute: Xinxiang medical university

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using ClC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to reference genome using CLc genomc benchwok (parameters-mismath cost: 2 insenion cost: 3 deletion cost. 3 lendh fracion: 0.8 similanity fraction: 0.8
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg19
Supplementary files format and content: Excel files include RPKM values for each Sample

source_name: colon

growth_protocol: HCT116 cells were plated in 12-well plates at 30% fusion per well

extract_protocol:
Lysis of cells with Trizol reagent and harvesting of RNA
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols

treatment_protocol: HCT116 cells were transfected with Control or siJOSD1.

value: colon

value: Colorectal cancer

tag: treatment


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_139

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_139

value: Plasma, extracted cell-free RNA


title: Col-0_inflorescence_high RI_AGO1-RIP-TRM-sRNA-seq_Rep2

description:
AGO1 RIP high quality PBA+OX R2
immunoprecipitated RNA

tag: genotype

value: TRM-RIP-sRNA-seq


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_189_trimmed

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_189_trimmed

value: KD


title: ntp6-1 ntp7-1_ inflorescence_TRM-sRNA-seq

description: ntp6-1 ntp7-1 PBA+OX

value: ntp6-1 ntp7-1


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_138

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_138


title: GCL D90, Myrf fl/fl Sox10 CreERT

tag: cell type


title: GCL D91, Myrf fl/fl


title: HCT116 cells, siJOSD1_1

tag: cell line


title: Retina D89, Myrf fl/fl

tag: time


title: Col-0_inflorescence_high RI_AGO1-RIP-sRNA-seq_Rep2

description:
AGO1 RIP high quality CK R2
immunoprecipitated RNA

value: conventional RIP-sRNA-seq


title: HCT116 cells, Control_3

value: Control


title: Col-0_inflorescence_high RI_AGO1-RIP-sRNA-seq_Rep1

description:
AGO1 RIP high quality CK R1
immunoprecipitated RNA

value: inflorescence


title: GCL D89, Myrf fl/fl


title: Col-0_inflorescence_high RI_AGO1-RIP-TRM-sRNA-seq_Rep1

description:
AGO1 RIP high quality PBA+OX R1
immunoprecipitated RNA


title: heso1-1_ inflorescence_TRM-sRNA-seq

description: heso1-1 PBA+OX

value: TRM-sRNA-seq


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_223_trimmed

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_223_trimmed


title: HCT116 cells, Control_1


title: GCL C94, Myrf fl/fl Sox10 CreERT


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_62

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_62


title: HCT116 cells, siJOSD1_2


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_18

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_18


title: B16_16h, replicate 4

city: Helsinki

first: Niina

last: Santio

address: Haartmaninkatu 8

department: Research Program Unit, CAN-PRO

country: Finland

institute: University of Helsinki

data_processing:
Reads were aligned to GRCh38.p12 using HISAT2 v 2.2.1, default settings with soft clipping turned on.
Mapped reads were counted using HTSeq v 2.0, reference genome GRCh38.109, default settings.
Assembly: GRCh38.p12
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

source_name: vascular

growth_protocol: The Mus musculus skin melanoma cell line B16-F10 (American Type Culture Collection, ATCC®CRL-6475TM ) and Human Umbilical Vein ECs (HUVEC) (Cell Applications, Inc., San Diego, CA, USA) were maintained in EBMTM-2 EC Growth Basal Medium-2 supplemented with EGMTM-2 MV Microvascular Endothelial SingleQuotsTM Kit (Lonza, Basel, Switzerland).

extract_protocol:
RNAwas isolated by NucleoSpin RNA kit (Macherey-Nagel, Düren, Germany)
Goals: Total RNA c ≥ 200 ng, RNA integrity ≥ 4.0, with smooth base line, Purity A260/280 = 1.8-2.2, A260/230 ≥ 1.8

treatment_protocol: For collection of conditioned medium B16-F10 were cultured on 6 cm plates in 2 ml culture medium, which was collected after 48h and spinned. Ctrl medium was similarly cultured on empty plates. HUVEC cells were plated in 50 000 cells/ well density on 24 well plates o/n after which conditioned medium was used to replace the culture medium. After 16 h, RNAwas isolated for mRNA-Seq.

value: vascular

value: HUVEC

value: endothelial cell

value: B16 conditioned media, 16h


title: Col-0_inflorescence_low RI_AGO1-RIP-sRNA-seq

description:
AGO1 RIP low quality CK
immunoprecipitated RNA


title: GCL C93, Myrf fl/fl

value: Ganglion cell layer

value: Myrf fl/fl

value: 18 weeks old

value: Female

value: Neurons


title: hen1-5_inflorescence_TRM-sRNA-seq

description: hen1-5 PBA+OX


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_33

first: Conor

last: Loy

institute: Cornell University

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_33

value: Plasma, extracted cell-free RNA

value: UCSD


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_10

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_10


title: GCL C91, Myrf fl/fl


title: GCL C92, Myrf fl/fl Sox10 CreERT

value: Myrf fl/fl Sox10 CreERT


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_94

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_94


title: HCT116 cells, Control_2

value: colon

value: Colorectal cancer


title: hen1-5_inflorescence_sRNA-seq

description: hen1-5 CK

value: conventional sRNA-seq


title: hen1-1_inflorescence_TRM-sRNA-seq

description: hen1-1 PBA+OX

value: inflorescence


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_137

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_137

value: KD


title: B16_16h, replicate 1

value: vascular


title: Untreated, replicate 4

value: HUVEC

value: ctrl treatment


title: hen1-1_inflorescence_sRNA-seq

description: hen1-1 CK


title: GCL C90, Myrf fl/fl Sox10 CreERT


title: Col-0_T15_ inflorescence_TRM-sRNA-seq_Rep2

description: T15 PBA+OX R2

value: TRM-sRNA-seq


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_61

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_61


title: Untreated, replicate 3

value: endothelial cell


title: GCL C89, Myrf fl/fl

value: Ganglion cell layer

value: Myrf fl/fl

value: Male


title: Col-0_ T15_inflorescence_TRM-sRNA-seq_Rep1

description: T15 PBA+OX R1


title: B16_16h, replicate 3

value: B16 conditioned media, 16h


title: Untreated, replicate 2


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_183_trimmed

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_183_trimmed

value: Plasma, extracted cell-free RNA


title: Untreated, replicate 1


title: Col-0_T10_ inflorescence_TRM-sRNA-seq_Rep2

description: T10 PBA+OX R2


title: GCL C79, Myrf fl/fl Sox10 CreERT

value: 18 weeks old

value: Female

value: Neurons


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_133

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_133

value: UCSD


title: Retina C78, Myrf fl/fl

value: Retina


title: B16_16h, replicate 2


title: Col-0_ T10_inflorescence_TRM-sRNA-seq_Rep1

description: T10 PBA+OX R1

value: inflorescence


title: GCL C78, Myrf fl/fl


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_231_trimmed

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_231_trimmed

value: KD


title: CD4_CD8_GD_NKT_MAIT_Blood_I

city: Aurora

first: Tonya

last: Brunetti

state: CO

address: 12800 East 19th Avenue

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical Campus

description: BD Rhapsody

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation  were made by the BD Rhapsody WTA Analysis Pipeline software (revision 4)
Assembly: GRCh38
Supplementary files format and content: comma-separated raw count matrix
Supplementary files format and content: comma-separated VDJ

source_name: Blood

extract_protocol:
To extract thymocytes for both single-cell RNA sequencing (scRNAseq) and flow cytometry, the thymus tissue was placed in complete RPMI 1640 media (Gibco, #22400-071) (10% heat-inactivated fetal bovine serum (FBS, Sigma-Aldrich), 1% non-essential amino acids (Sigma-Aldrich), 1% Sodium Pyruvate (Sigma-Aldrich), 1X GlutaMAX (Gibco), 1% Penicillin/Streptomycin (Gibco), and 1X 2-mercaptoethanol (BME, Sigma-Aldrich)), cut into small pieces, and gently pressed with the back of a 10 ml syringe to release thymocytes. The resulting suspension was passed through a 70 µm filter. Thymocytes and PBMCs were isolated using a Ficoll-Paque density gradient provided by Cytiva. PBMCs were cryopreserved in FBS with 10% DMSO from Sigma-Aldrich and stored in liquid nitrogen. Tetramer staining for MAIT and iNKT cells was performed on freshly isolated thymocytes. For tetramer staining of MAIT and iNKT cells, freshly isolated thymocytes were used. To enrich for thymic MAIT and thymic/blood iNKT cells, up to 2x109 cells were incubated with MR1-5-OP-RU-PE-Tet or CD1d-PBS57-PE respectively in MACS buffer (0.5% BSA, 2mM ETDA, PBS), for 25 mins at room temperature. Cells were washed twice and incubated with anti-PE microbeads (Miltenyi), followed by separation using an autoMACS Pro Separator (Miltenyi) according to manufacturer’s instructions. Enriched MAIT and iNKT from thymus, enriched iNKT from PBMC, unenriched gd T ,CD4+ and CD8+ from thymus, and unenriched MAIT, gd T , CD4+ and CD8+ T cells from PBMC were stained with the following cell surface markers in MACS buffer at room temperature for 20 mins: CD3-AF488 (clone OKT3, Biolegend), CD14-eFluor450 (clone 61D3, ThermoFisher), CD19-eFluor450 (clone H1B19, ThermoFisher), Va7.2-BV785 (clone 3C10, Biolegend), Va24-PerCP-Cy5.5 (clone C15, Biolegend), CD4-AF710 (clone OKT4, Tonbo), CD8a-PE-Cy7 (clone SK1, Tonbo), TCR-BV650 (clone 11F2, BD Biosciences), FcgR block (Miltenyi). Cells were washed twice and resuspended in MACS buffer prior to cell sorting on the Aria 3 (BD Biosciences).
Single cell whole transcriptomes and TCR sequencing libraries were prepared using the BD Rhapsody Single-Cell Analysis System (BD Biosciences) according to the manufacturer's specifications. Prior to cell sorting on the Aria 3 (BD Biosciences) and during cell surface antibody staining, up to 2 x106 enriched or unenriched cells were labeled with an oligonucleotide-tagged antibody sample tag (BD Biosciences). From infant thymus and PBMC donors up to 5 populations were sorted after doublet, viability, B cell (CD19+CD3-) and monocyte (CD14+CD3-) discrimination: 1. MAIT cells (MR1-5-OP-RU-Tet+Va7.2+CD3+), 2. iNKT cells (CD1d-PBS57-Tet+Va24+CD3+), 3. gd T cells (CD3+TCRgd+), 4. CD4+ T cells (CD4+CD8-CD3+) and CD8+ T cells (CD8+CD4-CD3+). Prior to cDNA library preparation for the WTA and VDJ libraries, all cell subsets from the different donors were pooled, with up to 12 unique sample tags combined per library. Libraries were quantified and pooled according to equivalent molar concentrations and sequenced on the NovaSeq sequencing platform at the University of Colorado Genomics Core with the following read lengths: read 1 – 150 cycles; read 2 – 150 cycles; and i7 index - 8 cycles.

value: Blood

value: F/M/M

tag: age


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_123

address: 237 Tower Rd, Room 314

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_123


title: Col-0_T0_ inflorescence_TRM-sRNA-seq_Rep2

description: T0 PBA+OX R2