title: OB_pat_LuC_79

description: Sample collection timepoint: nan; Tissue type: nan; Current site: Lung; Sex: female; Age of onset: 56

source_name: lung cancer (adenocarcinoma)

extract_protocol:
To isolate RNA, 10 µM - thick paraffin slices were trimmed from each FFPE tissue block using a microtome. RNA was extracted from FFPE slices using QIAGEN RNeasy FFPE Kit following the manufacturer’s protocol. RNA 6000 Nano or Qubit RNA Assay kits were used to measure RNA concentration.
RNA was processed and  subjected to isolation of generation of sequencing libraries according to Suntsova et al., 2019 [PMID: 31015567].

value: lung cancer (adenocarcinoma)


title: Vehicle_day7_4

status: Public on Sep 11 2024

type: SRA

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

country: USA

institute: LSUHSC

library_source: transcriptomic

data_processing:
BaseCall performed with CASAVA v1.8.2
Reads were aligned to the mm10 version of the mouse genome as reference using STAR v2.7.8a after removal of contaminants  (rDNA, tRNA, mtrDNA) using Bowtie2 (version 2.2.5)
Reads aligned to STAR were quantified to the mm10-RefSeq Transcripts 96 and normalized by TMM (+0.0001 / TMM / log2 transformation)
Normalized counts were used to determine differential gene expression between tumor and non-tumor (control) with limma-trend
All analyses were done at p < 0.05 and fold change 2
Assembly: mm10
Supplementary files format and content: RawCounts
Supplementary files format and content: TMM_Normalized_counts

molecule: total RNA

organism: Mus musculus

source_name: lung

growth_protocol: The virus was propagated from Stanley Perlman’s MA30 stock virus in TMPRSS2 expressing Vero cells. The TMPRSS2 Vero cells were grown in Dulbecco’s modified Eagle’s medium DMEM, supplemented with 10% FBS

extract_protocol:
Total RNA was extracted from FFPE tissue samples using the AllPrep DNA/RNA FFPE kit (Qiagen) following the manufacturer's protocol
Paired-end libraries (2 x 76) were prepared (600ng per sample) using the TruSeq RNA exome library preparation kit

treatment_protocol: Mice were intraperitoneally injected with 10 mg/kg compound prior to infection and the treatment was continued daily for the duration of the experiment.

tag: treatment

value: vehicle

tag: time point

tag: tissue

value: lung


title: siSTAMBPL1_1

city: beijing

first: hongli

last: zhang

state: beijing

address: Beijing University of Chemical Technology

country: China

data_processing:
The low-quality raw data was removed using SMRTlink (minLength = 50, minReadScore = 0.75). The SUPPA2 (https://github.com/comprna/SUPPA) was used to determine differential splicing events and all genes with intron retention events were used for KEGG analysis.
Assembly: hg38
Supplementary files format and content: consensus sequence
Library strategy: Long-read Iso-seq

organism: Homo sapiens

source_name: Liver

growth_protocol: Huh7 cell lines cultured in DMEM with 10% FBS

extract_protocol:
PacBio single-molecule real-time (SMRT) sequencing was conducted at Grandomics Biosciences Co., Ltd. (Beijing, China) according to standard procedures. Briefly, the full-length cDNA was synthesized from the total RNA using a SMART PCR cDNA Synthesis Kit.
Average 20-kb-insert-size libraries were constructed using an SMRTbell template prep kit 1.0 and then sequenced on a PacBio Sequel instrument.

treatment_protocol: siRNA transfected by lipo 2000（Thermofisher）

value: Liver

tag: cell line

tag: cell type

value: HCC

tag: genotype

value: Transfection


title: siSTAMBPL1_2

institute: Beijing University of Chemical Technology


title: B73_TRM-sRNA-seq_Rep2

city: Shanghai

first: Susu

last: Chen

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

institute: Shanghai University of Traditional Chinese Medicine

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: Zea mays

source_name: inflorescences, leaves, roots, fruits

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 seperated 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 seperated 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 seperated 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 seperated 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: inflorescences, leaves, roots, fruits

tag: ecotype

value: WT

tag: library type

value: TRM-sRNA-seq


title: siNC_1

value: NC


title: Vehicle_day4_4


title: CecumGF2

city: Guangzhou

first: Xiaoyun

last: Wang

state: Guangdong

address: 190 Kaiyuan Avenue, Huangpu

department: Infection and Immunity

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

molecule: polyA RNA

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: Germ-free


title: B73_TRM-sRNA-seq_Rep1


title: CecumGF3


title: Auricular Cartilage, M5

type: RNA

first: Run

last: Yang

address: No.83 Fenyang Rd.

institute: Eye&ENT Hospital of Fudan University

description: Gene expression of microtia

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 15 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

source_name: Auricular Cartilage

label_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: The isolated cartilage tissues were rapidly immersed in TRIzol reagent (Invitrogen). RNA was extracted by adding chloroform and then precipitated with isopropyl alcohol. The RNA precipitates were washed twice with 70% ethanol, dried, and resolved in water without RNase. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis or Agilent 2100 Bioanalyzer.

value: elastic cartilage

tag: gender

value: Male

tag: age

tag: diagnosis

value: Microtia


title: CecumGF1


title: Auricular Cartilage, C4

description: Gene expression of control

value: Tympanitis


title: Auricular Cartilage, C5

description: Gene expression of control

value: Female


title: Auricular Cartilage, M3

description: Gene expression of microtia


title: Auricular Cartilage, C1

description: Gene expression of control

value: Acquired external auditory canal stenosis


title: BrainSPF3

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

source_name: brain

value: brain

value: Water


title: BrainSPF1


title: Auricular Cartilage, M2

description: Gene expression of microtia


title: Auricular Cartilage, M1

description: Gene expression of microtia


title: Auricular Cartilage, M7

description: Gene expression of microtia


title: BrainGF3


title: Auricular Cartilage, C3

description: Gene expression of control

value: Cholesteatoma of middle ear


title: Auricular Cartilage, M8

description: Gene expression of microtia


title: Auricular Cartilage, M4

description: Gene expression of microtia


title: Auricular Cartilage, M6

description: Gene expression of microtia


title: siNC_2

value: Liver

value: HCC


title: BrainGF2


title: Auricular Cartilage, M9

description: Gene expression of microtia


title: shPHF82

city: Chongqing

first: Li

middle: qiu

last: Liu

address: No. 10, Changjiang Road, Daping, Yuzhong District, Chongqing

institute: Chongqing Daping Hospital

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Assembly: GRCh38
Supplementary files format and content: TXT file contain counts for each sample

growth_protocol: 1640  medium with 10% FBS

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
mRNA libraries were prepared for sequencing using standard Illumina protocols

value: Prostate cancer cell line

value: PHF8 knockdown


title: shControl3

value: WT


title: shPHF81


title: BrainSPF2


title: shPHF83


title: shControl2


title: BCR of 20 NPC samples

city: GuangZhou

first: Dong-Mei

last: Chi

address: 651 Dongfeng Road East

institute: SYSUCC

data_processing:
BCR reads were aligned to human reference VDJ dataset (http://cf.10Xgenomics.com/supp/cell-vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-2.0.0.tar.gz) using CellRanger (“vdj” option; version 3.0.1; 10x Genomics).
Sequencing data in FASTQ files and manually aligned histological images were analysed with Space Ranger (version 1.3.0) and the probe set for alignment provided by 10X Genomics (Visium Human Transcriptome Probe Set v1.0 GRCh38-2020-A).
Assembly: hg38
Supplementary files format and content: BCR information were respectively represented by comma-separated text files including 20 samples.
Supplementary files format and content: 10X Genomics standard output format of spatial transcriptomics

source_name: Nasopharynx

extract_protocol:
Viable single cells were prepared from the PBMC and tumor of 10 nasopharyngeal carcinoma patients; formalin-fixed paraffin-embedded (FFPE) biopsy sections were prepared from 12 nasopharyngeal carcinoma patients
10X Genomics protocol CG000086 and CG000407

value: Nasopharynx

tag: disease state

value: Nasopharyngeal carcinoma


title: BrainGF1

value: Germ-free


title: shControl1


title: g7NHC_shNT-2_3

city: Austin

first: Sergio

last: Gradilone

address: 801 16th Avenue NE

department: The Hormel Institute

institute: University of Minnesota

data_processing:
The University of Minnesota Research Informatics at MSI  analyzed the RNA Seq output. 2 x 75bp FastQ paired-end reads for 6 samples  were trimmed using Trimmomatic (v 0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30.
Quality control on raw sequence data for each sample was performed with FastQC
Sequencing reads were mapped to the human reference genome (hg38, UCSC) using Hisat2.
Genes differentially expressed between NHC-NT and NHC-IFT88   were calculated using edgeR software package with an Absolute fold-change cutoff set at >2 and FDR < 0.05
Assembly: Homo_sapiens (hg38)
Supplementary files format and content: RawReadsGradilone008.txt

source_name: NHC

growth_protocol: The NHC cell lines were cultured cultured in plastic flasks with media at 37°C and 5% CO2.

extract_protocol:
The analysis of differential gene expression between the NHC-NT and NHC-IFT88 cell lines was conducted using the RNA-seq technique. Total RNA was obtained using the Qiagen RNeasy kit, following the manufacturer's instructions.
RNA libraries were prepared for sequencing using Illumina TruSeq stranded mRNA Protocols at the University of Minnesota Genomic Center (UMGC)

value: NHC

value: shNT


title: g8NHC_shIFT88_5198-4_1


title: g8NHC_shIFT88_5198-4_4


title: g8NHC_shIFT88_5198-4_3


title: g8NHC_shIFT88_5198-4_2


title: g7NHC_shNT-2_2


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_401.trimmed

city: Ithaca

first: Conor

last: Loy

state: NY

address: 237 Tower Rd, Room 314

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.
prevail_cu_cfrna_401.trimmed

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).

value: Plasma, extracted cell-free RNA

value: Healthy

tag: site

value: EMORY


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_402.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.
prevail_cu_cfrna_402.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_403.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.
prevail_cu_cfrna_403.trimmed


title: g7NHC_shNT-2_1


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_424.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.
prevail_cu_cfrna_424.trimmed


title: Auricular Cartilage, C2

description: Gene expression of control

value: elastic cartilage

value: Male


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_400.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.
prevail_cu_cfrna_400.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_412.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.
prevail_cu_cfrna_412.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_410.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.
prevail_cu_cfrna_410.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_414.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.
prevail_cu_cfrna_414.trimmed

value: KD


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_415.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.
prevail_cu_cfrna_415.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_417.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.
prevail_cu_cfrna_417.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_413.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.
prevail_cu_cfrna_413.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_418.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.
prevail_cu_cfrna_418.trimmed


title: Auricular Cartilage, M10

description: Gene expression of microtia

value: Microtia


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_422.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.
prevail_cu_cfrna_422.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_293.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_293.trimmed

value: UCSF


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_286.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_286.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_313.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_313.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_285.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_285.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_251.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_251.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_250.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_250.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_292.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_292.trimmed


title: g7NHC_shNT-2_4


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_281.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_281.trimmed

value: UCSD


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_241.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_241.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_312.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_312.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_277.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_277.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_256.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_256.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_273.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_273.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_260.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_260.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_314.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_314.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_278.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_278.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_276.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_276.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_299.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_299.trimmed


title: VP25-TCR

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: TCR V(D)J segments

library_source: transcriptomic single cell

data_processing:
Sequencing was performed on MGISEQ-2000 platform in a 28+100 or 100+100 base paired-end mode.
The MGISEQ-2000 control software operated base calling analysis software and delivered raw sequencing data.
Generated reads were input into the cellranger pipeline (Cell Ranger v.6.0.0, 10x Genomics) for UMI counting for each gene (or tag sequence)-cell (barcode) combination and B cell and T cell receptor repertoire profiling.
Supplementary files format and content: genematrix.h5: HDF5 format files including counts data for each gene and cell (barcode) combination
Supplementary files format and content: airr_rearrangement.tsv: tab-delimited text file including detected clonotypes for each cell (barcode)
Supplementary files format and content: clonotypes.csv: comma-delimited text file including the BCR or TCR clonotype information

source_name: PBMC

extract_protocol:
PBMCs were isolated using a Ficoll gradient, frozen in CellBanker (Takara), and stored in liquid nitrogen vapor phase, while plasma samples were stored at -80°C until use. Frozen PBMCs were thawed quickly in a water bath at 37 °C.
Droplet-based single-cell RNAseq was performed according to the protocol of the Chromium Single Cell V(D)J Reagent Kits v1.1 (10x Genomics). Gene expression, TCR and BCR V(D)J libraries were prepared for each sample according to the manufacturer’s protocol (10x Genomics).

value: PBMC

tag: subject status

value: patients who were vaccinated COVID-19 vaccine


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_320.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_320.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_307.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_307.trimmed


title: VP25-BCR

description: BCR V(D)J segments


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_263.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_263.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_306.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_306.trimmed


title: VP25-RNA

description: poly A RNA


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_239.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_239.trimmed


title: VP12-TCR

description: TCR V(D)J segments


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_238.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_238.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_261.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_261.trimmed


title: VP12-BCR

description: BCR V(D)J segments


title: VP10-BCR

description: BCR V(D)J segments


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_275.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_275.trimmed


title: VP12-RNA

description: poly A RNA


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_325.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_325.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_301.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_301.trimmed


title: VP10-TCR

description: TCR V(D)J segments


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_246.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_246.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_258.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_258.trimmed


title: VP10-RNA

description: poly A RNA


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_319.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_319.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_247.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_247.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_279.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_279.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_257.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_257.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_318.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_318.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_245.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_245.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_310.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_310.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_294.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_294.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_282.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_282.trimmed


title: sca1-pos-cre-pos2

first: Qi

last: Lou

address: 74 Zhongshan 2nd road

institute: Sun Yat Sen University

description:
sca1-pos-cre-pos2 (sca1pos_cpos2_count)
sca1pos_cneg_vs_sca1pos_cpos_lfc

data_processing:
The raw reads were trimmed using Trimmomatic 0.32 with recommmended settings. Trimmed reads were mapped and quantified using Salmon1.4.0. Get the DEGs by Deseq2.
Assembly: mm10
Supplementary files format and content: Raw counts
Supplementary files format and content: TPM

source_name: Bone marrow

extract_protocol:
RNA were havested by Commerial RNA isolate kit
DNA library was parpared by Vanzyme commerial DNA library Kit

value: BMMSCs

tag: sorted cell type

value: Sorted IGF1R knockout PDGFRa+Sca1+ BMMSC

value: IGF1R Knockout


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_244.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_244.trimmed


title: sca1-pos-cre-pos1

description:
sca1-pos-cre-pos1 (sca1pos_cpos1_count)
sca1pos_cneg_vs_sca1pos_cpos_lfc


title: sca1-neg2

description:
sca1-neg2 (sca1Neg2_count)
sca1neg_vs_sca1pos_tpmcount_lfc_2rd.csv

value: Sorted postnatal PDGFRa+Sca1-

value: wild type


title: sca1-pos-cre-neg3

description:
sca1-pos-cre-neg3 (neo3_count)/ (sca1pos_cneg3_count)/ (sca1Pos3_count)
sca1pos_cneg_vs_sca1pos_cpos_lfc / adu_vs_neo_tpmcount_lfc / sca1neg_vs_sca1pos_tpmcount_lfc_2rd.csv

value: Sorted postnatal PDGFRa+Sca1+ BMMSC


title: sca1-pos-cre-neg1

description:
sca1-pos-cre-neg1 (neo1_count)/ (sca1pos_cneg5_count)
sca1pos_cneg_vs_sca1pos_cpos_lfc / adu_vs_neo_tpmcount_lfc


title: sca1-neg3

description:
sca1-neg3 (sca1Neg3_count)
sca1neg_vs_sca1pos_tpmcount_lfc_2rd.csv


title: neg-3

description:
neg-3 (ps6wt3_count)
adu_vs_neo_tpmcount_lfc

value: Sorted adult PDGFRa+CD51+


title: sca1-pos-cre-neg2

description:
sca1-pos-cre-neg2 (neo2_count)/ (sca1pos_cneg2_count)/ (sca1Pos2_count)
sca1pos_cneg_vs_sca1pos_cpos_lfc / adu_vs_neo_tpmcount_lfc / sca1neg_vs_sca1pos_tpmcount_lfc_2rd.csv


title: neg-1

description:
neg-1 (ps6wt1_count)
adu_vs_neo_tpmcount_lfc


title: neg-2

description:
neg-2 (ps6wt2_count)
adu_vs_neo_tpmcount_lfc


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_295.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_295.trimmed

value: Plasma, extracted cell-free RNA


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_243.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_243.trimmed


title: sca1-pos-cre-pos3

description:
sca1-pos-cre-pos3 (sca1pos_cpos3_count)
sca1pos_cneg_vs_sca1pos_cpos_lfc


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_255.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_255.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_308.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_308.trimmed


title: DRS_pop2Δ_W303_1_repA

city: Warsaw

first: Andrzej

last: Dziembowski

address: 4 Ks. Trojdena Street

country: Poland

institute: International Institute Of Molecular And Cell Biology In Warsaw

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303 pop2Δ, grown at 25°C

data_processing:
Sequencing was performed with the MinION device, followed by basecalling with Guppy (ONT), mapping to custom S. cerevisiae transcriptome described in Tudek et al (2021) using Minimap2 2.17 with options -k 14 -ax map-ont –secondary = no, and processing with samtools 1.9 to filter out supplementary alignments and reads mapping to the reverse strand (samtools view -b -F 2320). Lengths of poly(A) tails were estimated with Nanopolish-polya (v0.13.2).
Assembly: SacCer3
Supplementary files format and content: CSV files with the experiment-related information on nanopolish-polya derived poly(A) lengths (including mean, meadina values and quantiles of distribution) and counts attributed to each transcript

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cultures were prepared in YPDA media and grown in 25 °C unless stated othwerwise

extract_protocol:
RNA extraction was performed using the hot acid phenol method. Cell pellets were resuspended in 400 μl phenol solution saturated with 0.1 M citrate at pH 4.3 (Sigma; P4682), followed by the addition of 400μl of TES buffer (10 mM Tris pH 7.5, 5 mM EDTA, 1 % SDS). Samples were vortexed for 45 min at 65 °C, then centrifuged at 4 °C for 10 min. The supernatant was transferred to a fresh tube, and 400 μl phenol solution saturated with 0.1 M citrate at pH 4.3 was added. The samples were again vortexed for 20 min at 65 °C and then centrifuged at 4 °C for 10 min. The supernatant was transferred to a fresh tube and 400 μl of chloroform was added (C2432; Sigma). The samples were briefly vortexed at room temperature to remove phenol, and centrifuged at 4 °C for 10 min. The supernatant was transferred to a fresh tube; 45 μl of 2 M LiCl was added and 1 ml of 95 % ethanol. Samples were precipitated at – 80 °C for at least 30 min, then centrifuged at 4 °C for 25 min, washed with 400 μl of 80 % ethanol, and dried at 37 °C after removing the supernatant. Pellets were resuspended in nuclease-free water, and RNA concentration was measured using a Nanodrop apparatus.
The pA+ fraction was prepared using magnetic beads coupled to oligo-dT from LifeTechnologies (61005). 35 μg of total RNA was resuspended in 50 μl of nuclease-free water. The RNA was mixed with 50 μl of binding buffer (20 mM Tris-HCl, ph 7.5, 1 M LiCl, 2 mM EDTA) and denatured for 2 min at 65 °C before cooling on ice. 100 μl of slurry beads per 35 μg of total RNA was pre-washed 3 times in 1 ml of binding buffer and resuspended in 50 μl of binding buffer per sample. The beads were added to the denatured RNA and incubated at room temperature with occasional shaking for 20 min. The supernatant was removed, and beads were washed twice with 100 μl of wash buffer (10 mM Tris-HCl pH 7.5, 150 mM LiCl, 1 mM EDTA) and after removing any remnants of wash buffer, resuspended in 12 μl of nuclease-free water. The beads were then incubated for 2 min at 80 °C, and the supernatant removed from the beads was utilized for sequencing library preparation and/or qPCR analyses as the pA+ fraction. Sequencing libraries were prepared using the Direct RNA Sequencing Kit (Oxford Nanopore Technologies, SQK- RNA002) according to the manufacturer’s protocol, using 50–200 ng oligo-dT(25)-enriched mRNA from Saccharomyces cerevisiae yeast mixed with cap-enriched or total RNA from other organisms (human, mouse, A. thaliana, or C. elegans)
RNA-seq (Nanopore Direct RNA Sequencing)

treatment_protocol: To deplete Mex67 using the Anchor Away tag (Haruki et al, 2008), rapamycin (Cayman Chemicals cat. no. 13346) was added to a final concentration of 1 μg/ml. The heat-stress chase experiment was performed by pre-culturing cells at 25 °C and adding an equal volume of media pre-heated to 51 °C, resulting in a final temperature of 37 °C. Treatment with thiolutin (Sigma; T3450) was performed by adding the compound to a final concentration of 4 ug/ml. Samples for all chase experiments were collected by mixing the cell culture with an equal volume of ice-cold ethanol, which inactivates cellular metabolism. To deplete Xrn1 and Dcp2 using AID tags (Nishimura et al, 2009; Morawska and Ulrich, 2013), 1-Naphthaleneacetic acid (1-NAA; N0640-25G, Merck) was added to a final concentration of 1 mM. Pab1 depletion using the AID system involved adding auxin sodium salt (I5148-2G; Merck) to a final concentration of 1-3 mM

tag: strain


title: DRS_ccr4Δ_W303_4_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303 ccr4Δ, grown at 25°C, experiment 4


title: DRS_pan2Δ_W303_1_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303 ccr4Δ, grown at 25°C, experiment 1


title: DRS_pan2Δ_W303_2_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303 ccr4Δ, grown at 25°C, experiment 2


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_242.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_242.trimmed


title: DRS_ccr4Δ_W303_3_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303 ccr4Δ, grown at 25°C, experiment 3


title: DRS_ccr4Δ_W303_2_repB

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303 ccr4Δ, grown at 25°C, experiment 2, biological replicate B


title: DRS_pan2Δ_W303_3_repA


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_322.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_322.trimmed


title: DRS_ccr4Δ_W303_2_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303 ccr4Δ, grown at 25°C, experiment 2, biological replicate A


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_311.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_311.trimmed


title: DRS_ccr4Δ_W303_1_repB

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303 ccr4Δ, grown at 25°C, experiment 1, biological replicate B


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_254.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_254.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_305.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_305.trimmed


title: DRS_ccr4Δ_W303_1_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303 ccr4Δ, grown at 25°C, experiment 1, biological replicate A


title: DRS_WT_30_5_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, WT, grown at 25°C, experiment 5 biological replicate A

value: WT


title: DRS_WT_30_4_repB

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, WT, grown at 25°C, experiment 4 biological replicate B


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_297.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_297.trimmed


title: DRS_WT_30_3_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, WT, grown at 25°C, experiment 3 biological replicate A


title: DRS_WT_30_2_repB

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, WT, grown at 25°C, experiment 2 biological replicate B


title: DRS_WT_30_4_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, WT, grown at 25°C, experiment 4 biological replicate A


title: DRS_WT_30_5_repB


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_298.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_298.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_240.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_240.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_321.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_321.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_300.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_300.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_259.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_259.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_283.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_283.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_296.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_296.trimmed


title: DRS_Mex67_AA_0_min_25°C_control_(-_rapamycin)_repB

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, Mex67 Anchor Away system, grown at 25°C, control without rapamycin, experiment B

value: 25degC - rapamycin for 0 min


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_266.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_266.trimmed


title: DRS_Mex67_AA_16_min_37°C_(+_rapamycin)_repB

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, Mex67 Anchor Away system, grown at 37°C, treated with rapamycin for 16 minutes, experiment B

value: 37degC + rapamycin for 16 min


title: DRS_Mex67_AA_16_min_37°C_(+_rapamycin)_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, Mex67 Anchor Away system, grown at 37°C, treated with rapamycin for 16 minutes, experiment A


title: DRS_WT_30_1_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, WT, grown at 25°C, experiment 1 biological replicate A


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_309.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_309.trimmed


title: DRS_Mex67_AA_0_min_25°C_control_(-_rapamycin)_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, Mex67 Anchor Away system, grown at 25°C, control without rapamycin, experiment A


title: DRS_Mex67_AA_60_min_25°C_repC

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, Mex67 Anchor Away system, grown at 25°C, treated with rapamycin for 60 minutes, experiment C

value: 25degC + rapamycin for 60 min


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_317.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_317.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_274.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_274.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_262.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_262.trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_236

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.
prevail_cu_cfrna_236

value: MISC

value: EMORY


title: DRS_Mex67_AA_30_min_25°C_repC

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, Mex67 Anchor Away system, grown at 25°C, treated with rapamycin for 30 minutes, experiment C

value: 25degC + rapamycin for 30 min


title: DRS_WT_30_2_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, WT, grown at 25°C, experiment 2 biological replicate A


title: DRS_Mex67_AA_8_min_25°C_repC

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, Mex67 Anchor Away system, grown at 25°C, treated with rapamycin for 8 minutes, experiment C

value: 25degC + rapamycin for 8 min


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_269

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.
prevail_cu_cfrna_269


title: DRS_Mex67_AA_16_min_25°C_repC

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, Mex67 Anchor Away system, grown at 25°C, treated with rapamycin for 16 minutes, experiment C

value: 25degC + rapamycin for 16 min


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_235

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.
prevail_cu_cfrna_235


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_270

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.
prevail_cu_cfrna_270


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_271

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.
prevail_cu_cfrna_271


title: DRS_Mex67_AA_0_min_25°C_repC

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, Mex67 Anchor Away system, grown at 25°C, control sample, experiment C

value: 25degC + rapamycin for 0 min


title: DRS_Mex67_AA_14_min_25°C_repB

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, Mex67 Anchor Away system, grown at 25°C, treated with rapamycin for 14 minutes, experiment B

value: 25degC + rapamycin for 14 min


title: DRS_Mex67_AA_20_min_25°C_repB

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, Mex67 Anchor Away system, grown at 25°C, treated with rapamycin for 20 minutes, experiment B

value: 25degC + rapamycin for 20 min


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_269.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_269.trimmed

value: UCSD


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_278

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.
prevail_cu_cfrna_278


title: DRS_Mex67_AA_4_min_25°C_repC

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, Mex67 Anchor Away system, grown at 25°C, treated with rapamycin for 4 minutes, experiment C

value: 25degC + rapamycin for 4 min


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_196

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.
prevail_cu_cfrna_196


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_195

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.
prevail_cu_cfrna_195


title: DRS_Mex67_AA_10_min_25°C_repB

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, Mex67 Anchor Away system, grown at 25°C, treated with rapamycin for 10 minutes, experiment B

value: 25degC + rapamycin for 10 min


title: DRS_Mex67_AA_4_min_25°C_repB

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, Mex67 Anchor Away system, grown at 25°C, treated with rapamycin for 4 minutes, experiment B


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_192

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.
prevail_cu_cfrna_192


title: DRS_Mex67_AA_0_min_25°C_repB

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, Mex67 Anchor Away system, grown at 25°C, control sample, experiment B


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_191

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.
prevail_cu_cfrna_191


title: DRS_Mex67_AA_12_min_25°C_repB

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, Mex67 Anchor Away system, grown at 25°C, treated with rapamycin for 12 minutes, experiment B

value: 25degC + rapamycin for 12 min


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_193

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.
prevail_cu_cfrna_193

value: Plasma, extracted cell-free RNA


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_194

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.
prevail_cu_cfrna_194


title: DRS_Mex67_AA_16_min_25°C_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, Mex67 Anchor Away system, grown at 25°C, treated with rapamycin for 16 minutes, experiment A


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_183

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.
prevail_cu_cfrna_183


title: DRS_Mex67_AA_14_min_25°C_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, Mex67 Anchor Away system, grown at 25°C, treated with rapamycin for 14 minutes, experiment A


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_182

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.
prevail_cu_cfrna_182


title: DRS_Mex67_AA_12_min_25°C_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, Mex67 Anchor Away system, grown at 25°C, treated with rapamycin for 12 minutes, experiment A


title: DRS_Mex67_AA_8_min_25°C_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, Mex67 Anchor Away system, grown at 25°C, treated with rapamycin for 8 minutes, experiment A


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_179

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.
prevail_cu_cfrna_179


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_177

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.
prevail_cu_cfrna_177


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_174

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.
prevail_cu_cfrna_174


title: DRS_Mex67_AA_0_min_25°C_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, Mex67 Anchor Away system, grown at 25°C, control sample, experiment A


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_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.
prevail_cu_cfrna_171


title: DRS_Pab1_AID_25°C_2h_repB

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, Pab1-AID degron, grown at 25°C, treated with auxin for 2h, experiment B

value: 25degC + auxin for 2h


title: DRS_Pab1_AID_25°C_1h_repB

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, Pab1-AID degron, grown at 25°C, treated with auxin for 1h, experiment B

value: 25degC + auxin for 1h


title: DRS_Pab1_AID_25°C_1h_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, Pab1-AID degron, grown at 25°C, treated with auxin for 1h, experiment A


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_152

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.
prevail_cu_cfrna_152


title: DRS_Pab1_AID_25°C_2h_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, Pab1-AID degron, grown at 25°C, treated with auxin for 2h, experiment A


title: DRS_WT_W_303_AID_control_for_Pab1_experiment_25°C_repB

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, Pab1-AID degron, grown at 25°C, without auxin treatment (control), experiment B


title: DRS_Mex67_AA_30_min_25°C_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, Mex67 Anchor Away system, grown at 25°C, treated with rapamycin for 30 minutes, experiment A


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_149

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.
prevail_cu_cfrna_149

value: Healthy


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_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.
prevail_cu_cfrna_164


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_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.
prevail_cu_cfrna_148


title: DRS_Xrn1_AID_25°C_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, Xrn1-AID degron, grown at 25°C, treated with 1-NAA for 2h, experiment A

value: 25degC + 1-NAA for 2h


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_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.
prevail_cu_cfrna_170


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_185

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.
prevail_cu_cfrna_185


title: DRS_Xrn1_AID_25°C_repB

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, Xrn1-AID degron, grown at 25°C, treated with 1-NAA for 2h, experiment B


title: DRS_WT_W_303_AID_control_25°C_repB

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, WT, grown at 25°C, treated with 1-NAA for 2h, experiment B

value: WT


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_151

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.
prevail_cu_cfrna_151

value: EMORY


title: DRS_Dcp2_AID_25°C_repB

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, Dcp2-AID degron, grown at 25°C, treated with 1-NAA for 2h, experiment B


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_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.
prevail_cu_cfrna_162


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_175

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.
prevail_cu_cfrna_175


title: DRS_Dcp2_AID_25°C_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, Dcp2-AID degron, grown at 25°C, treated with 1-NAA for 2h, experiment A


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_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.
prevail_cu_cfrna_150


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_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.
prevail_cu_cfrna_165


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_159

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.
prevail_cu_cfrna_159


title: Total RNA-seq of XCHT-H2

first: Yao

state: Shanghai

address: No. 528, Zhangheng Road

department: Department of Medical Oncology, Shuguang Hospital

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include Genecount, FPKM and tpm values for each Sample

source_name: Subcutaneous tumor tissue of colorectal cancer

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: Intervention group:XCHT-H rep2


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_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.
prevail_cu_cfrna_166


title: DRS_total_mRNA_WT_W303_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, WT, grown at 25°C, poly(A)+ fraction - control for digestion with the recombinant Xrn1


title: DRS_W303_+_thiolutin_60min_25°C_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, grown at 25°C, treated with thiolutin for 60 minutes, experiment A

value: 25degC + thiolutin for 60 min


title: DRS_WT_W_303_AID_control_for_Pab1_experiment_25°C_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, Pab1-AID degron, grown at 25°C, without auxin treatment (control), experiment A


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_110

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.
prevail_cu_cfrna_110

value: MISC


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_106

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.
prevail_cu_cfrna_106

value: other


title: Total RNA-seq of XCHT-H1

value: Subcutaneous tumor tissue of colorectal cancer

value: Intervention group:XCHT-H rep1


title: Total RNA-seq of XCHT-L3

value: Intervention group:XCHT-L rep3


title: DRS_W303_+_thiolutin_30min_25°C_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, grown at 25°C, treated with thiolutin for 30 minutes, experiment A

value: 25degC + thiolutin for 30 min


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_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.
prevail_cu_cfrna_169


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_131

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.
prevail_cu_cfrna_131


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_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.
prevail_cu_cfrna_144


title: DRS_W303_+_thiolutin_20min_25°C_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, grown at 25°C, treated with thiolutin for 20 minutes, experiment A

value: 25degC + thiolutin for 20 min


title: Total RNA-seq of XCHT-L1

value: Intervention group:XCHT-L rep1


title: DRS_total_mRNA_WT_W303_digested_xrn1_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, WT, grown at 25°C, poly(A)+ fraction digested with the recombinant Xrn1 for 1h


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_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.
prevail_cu_cfrna_145

value: Plasma, extracted cell-free RNA


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_167

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.
prevail_cu_cfrna_167


title: Total RNA-seq of XCHT-L2

value: Intervention group:XCHT-L rep2


title: Total RNA-seq of XCHT-H3

value: Intervention group:XCHT-H rep3


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_286

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.
prevail_cu_cfrna_286


title: DRS_W303_+_thiolutin_16min_25°C_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, grown at 25°C, treated with thiolutin for 16 minutes, experiment A

value: 25degC + thiolutin for 16 min


title: Total RNA-seq of Stress3

value: Model group Stress rep3


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_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.
prevail_cu_cfrna_42


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_299

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.
prevail_cu_cfrna_299


title: DRS_W303_+_thiolutin_12min_25°C_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, grown at 25°C, treated with thiolutin for 12 minutes, experiment A

value: WT

value: 25degC + thiolutin for 12 min


title: Total RNA-seq of Stress2

value: Model group Stress rep2


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_296

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.
prevail_cu_cfrna_296

value: EMORY


title: DRS_W303_+_thiolutin_8min_25°C_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, grown at 25°C, treated with thiolutin for 8 minutes, experiment A

value: 25degC + thiolutin for 8 min


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_292

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.
prevail_cu_cfrna_292

value: MISC


title: Total RNA-seq of Stress1

value: Subcutaneous tumor tissue of colorectal cancer

value: Model group Stress rep1


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_295

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.
prevail_cu_cfrna_295


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_285

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.
prevail_cu_cfrna_285


title: DRS_W303_+_thiolutin_4min_25°C_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, grown at 25°C, treated with thiolutin for 4 minutes, experiment A

value: 25degC + thiolutin for 4 min


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_12

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.
prevail_cu_cfrna_12


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_284

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.
prevail_cu_cfrna_284


title: Total RNA-seq of Ctrl3

value: The control group rep3


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_282

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.
prevail_cu_cfrna_282


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_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.
prevail_cu_cfrna_109


title: DRS_W303_+_thiolutin_0min_25°C_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, grown at 25°C, thiolutin treatment control sample, experiment A

value: 25degC + thiolutin for 0 min


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_294

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.
prevail_cu_cfrna_294


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_287

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.
prevail_cu_cfrna_287


title: Total RNA-seq of Ctrl1

value: The control group rep1


title: DRS_W303_+_thiolutin_30min_25°C_repB

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, grown at 25°C, treated with thiolutin for 30 minutes, experiment B

value: 25degC + thiolutin for 30 min


title: Total RNA-seq of Ctrl2

value: The control group rep2


title: DRS_W303_+_thiolutin_40min_25°C_repB

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, grown at 25°C, treated with thiolutin for 40 minutes, experiment B

value: 25degC + thiolutin for 40 min


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_309

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.
prevail_cu_cfrna_309

value: Plasma, extracted cell-free RNA


title: DRS_W303_+_thiolutin_18min_25°C_repB

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, grown at 25°C, treated with thiolutin for 18 minutes, experiment B

value: 25degC + thiolutin for 18 min


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_280

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.
prevail_cu_cfrna_280


title: B1 cells, Cd19cre/+, CON 2

city: 苏州

first: He

last: Gao

address: 苏州市工业园区仁爱路199号

institute: Soochow University

description:
CON2
PERC_B1_FPKM.txt

data_processing:
PE-end 2x150 bp sequencing was performed on the MGI2000
Raw data was filtered by SOAPnuke
Reads were mapped to human reference genome mm10 using BWA/Bowtie2 tool
Genes expression level is quantified by RSEM package.
The differentially expression was indentified by R package DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited tsv files including lengths, counts and Fragments per Kilobase Million(FPKM) for mRNA transcripts

source_name: Peritoneal cavity

growth_protocol: purified splenic B1 cells were cultured in RPMI-1640 supplemented with FBS, antibiotics, sodium pyruvate, HEPES and 2-ME.

extract_protocol:
total RNA were extracted by Omega RNA-isolation kit.
libraries with different indexs were multiplexed and loaded on an  MGI2000 instrument for sequencing using a 2x150 paired-end (PE) configuration

treatment_protocol: purified splenic B1 cells were stimulated with 0.1 ug/ml LPS overnight before RNA extraction and RNA-Seq.

value: Peritoneal cavity

value: primary cell

value: B1 cells

value: total peritoneal CD19+CD23- B1 cells and activated them in vitro by 0.1 ug/ml LPS


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_95

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.
prevail_cu_cfrna_95

value: EMORY


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_310

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.
prevail_cu_cfrna_310

value: MISC


title: DRS_W303_+_thiolutin_14min_25°C_repB

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, grown at 25°C, treated with thiolutin for 14 minutes, experiment B

value: WT

value: 25degC + thiolutin for 14 min


title: B1 cells, Zbtb24 B-CKO 2

address: 苏州市工业园区仁爱路199号

description:
BKO2
PERC_B1_FPKM.txt

value: Zbtb24 B-CKO


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_303

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.
prevail_cu_cfrna_303


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_318

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.
prevail_cu_cfrna_318


title: DRS_W303_+_thiolutin_10min_25°C_repB

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, grown at 25°C, treated with thiolutin for 10 minutes, experiment B

value: 25degC + thiolutin for 10 min


title: B1 cells, Zbtb24 B-CKO 1

address: 苏州市工业园区仁爱路199号

description:
BKO1
PERC_B1_FPKM.txt