title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_313

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_313


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_307

status: Public on Sep 11 2024

type: SRA

city: Ithaca

first: Conor

last: Loy

state: NY

address: 237 Tower Rd, Room 314

country: USA

institute: Cornell University

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
prevail_cu_cfrna_307

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: Plasma, extracted cell-free RNA

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

tag: tissue

value: Plasma, extracted cell-free RNA

tag: diagnosis

value: MISC

tag: site

value: EMORY


title: DRS_W303_+_thiolutin_6min_25°C_repB

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, grown at 25°C, treated with thiolutin for 6 minutes, experiment B

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

molecule: polyA RNA

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: genotype

value: WT

tag: strain

tag: treatment

value: 25degC + thiolutin for 6 min


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_108

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
prevail_cu_cfrna_108


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_321

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_321


title: B cells from Spleen, Zbtb24 B-CKO 3, D2

city: 苏州

first: He

last: Gao

address: 苏州市工业园区仁爱路199号

country: China

institute: Soochow University

description:
BKO3_D2
SPC_B_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

organism: Mus musculus

source_name: Spleen

growth_protocol: purified splenic B 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 B cells were stimulated with LPS for different periods before RNA extraction and RNA-Seq.

value: Spleen

tag: cell line

value: primary cell

tag: cell type

value: B cells

value: Zbtb24 B-CKO

value: total splenic B cells and activated them in vitro by LPS


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_260

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_260


title: B cells from Spleen, Zbtb24 B-CKO 3, D1

address: 苏州市工业园区仁爱路199号

description:
BKO3_D1
SPC_B_FPKM.txt


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_83

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
prevail_cu_cfrna_83


title: DRS_W303_+_thiolutin_0min_25°C_repB

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

value: 25degC + thiolutin for 0 min


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_81

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
prevail_cu_cfrna_81


title: B cells from Spleen, Zbtb24 B-CKO 2, D2

address: 苏州市工业园区仁爱路199号

description:
BKO2_D2
SPC_B_FPKM.txt


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_305

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_305


title: B1 cells, Cd19cre/+, CON 1

address: 苏州市工业园区仁爱路199号

description:
CON1
PERC_B1_FPKM.txt

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.

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: B1 cells

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


title: DRS_W303_+_thiolutin_2min_25°C_repB

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, grown at 25°C, treated with thiolutin for 2 minutes, experiment B

value: 25degC + thiolutin for 2 min


title: DRS_W303_–_heatstress_16min_25°C_to_37°C_repB

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, heatstressed by shifting from 25°C to 37°C for 16 minutes, experiment B

value: 37degC for 16 min


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_263

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_263


title: DRS_W303_–_heatstress_20min_25°C_to_37°C_repB

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, heatstressed by shifting from 25°C to 37°C for 20 minutes, experiment B

value: 37degC for 20 min


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_304

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_304

value: Plasma, extracted cell-free RNA


title: B cells from Spleen, Zbtb24 B-CKO 2, D1

address: 苏州市工业园区仁爱路199号

description:
BKO2_D1
SPC_B_FPKM.txt


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_258

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_258

value: MISC


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_308

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_308

value: EMORY


title: DRS_W303_–_heatstress_8min_25°C_to_37°C_repB

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, heatstressed by shifting from 25°C to 37°C for 8 minutes, experiment B

value: WT

value: 37degC for 8 min


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_82

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
prevail_cu_cfrna_82


title: B cells from Spleen, Zbtb24 B-CKO 3, D0

address: 苏州市工业园区仁爱路199号

description:
BKO3_D0
SPC_B_FPKM.txt

value: Spleen


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_301

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_301


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_319

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_319

value: other


title: B cells from Spleen, Zbtb24 B-CKO 1, D2

address: 苏州市工业园区仁爱路199号

description:
BKO1_D2
SPC_B_FPKM.txt

value: primary cell

value: B cells


title: DRS_W303_–_heatstress_4min_25°C_to_37°C_repB

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, heatstressed by shifting from 25°C to 37°C for 4 minutes, experiment B

value: 37degC for 4 min


title: DRS_W303_–_heatstress_0min_25°C_to_37°C_repB

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, heatstres control sample, experiment B

value: 37degC for 0 min


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_298

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_298


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_293

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_293


title: B cells from Spleen, Zbtb24 B-CKO 1, D0

address: 苏州市工业园区仁爱路199号

description:
BKO1_D0
SPC_B_FPKM.txt

value: Zbtb24 B-CKO

value: total splenic B cells and activated them in vitro by LPS


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_315

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_315


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_320

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_320


title: DRS_W303_–_heatstress_18min_25°C_to_37°C_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, heatstressed by shifting from 25°C to 37°C for 18 minutes, experiment A

value: 37degC for 18 min


title: B cells from Spleen, CON 3, D2

address: 苏州市工业园区仁爱路199号

description:
CON3_D2
SPC_B_FPKM.txt

value: CON


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_252

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_252


title: DRS_W303_–_heatstress_14min_25°C_to_37°C_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, heatstressed by shifting from 25°C to 37°C for 14 minutes, experiment A

value: 37degC for 14 min


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_300

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_300


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_370

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_370

value: CNH


title: DRS_W303_–_heatstress_12min_25°C_to_37°C_repB

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, heatstressed by shifting from 25°C to 37°C for 12 minutes, experiment B

value: 37degC for 12 min


title: B cells from Spleen, CON 3, D1

address: 苏州市工业园区仁爱路199号

description:
CON3_D1
SPC_B_FPKM.txt


title: DRS_W303_–_heatstress_10min_25°C_to_37°C_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, heatstressed by shifting from 25°C to 37°C for 10 minutes, experiment A

value: 37degC for 10 min


title: B cells from Spleen, Zbtb24 B-CKO 2, D0

address: 苏州市工业园区仁爱路199号

description:
BKO2_D0
SPC_B_FPKM.txt


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_382

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_382

value: Plasma, extracted cell-free RNA


title: B cells from Spleen, CON 3, D0

address: 苏州市工业园区仁爱路199号

description:
CON3_D0
SPC_B_FPKM.txt


title: B cells from Spleen, Zbtb24 B-CKO 1, D1

address: 苏州市工业园区仁爱路199号

description:
BKO1_D1
SPC_B_FPKM.txt


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_381

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_381


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_297

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_297

value: MISC

value: EMORY


title: DRS_W303_–_heatstress_6min_25°C_to_37°C_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, heatstressed by shifting from 25°C to 37°C for 6 minutes, experiment A

value: WT

value: 37degC for 6 min


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_380

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_380

value: other


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_379

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_379


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_390

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_390


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_392

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_392


title: DRS_W303_–_heatstress_2min_25°C_to_37°C_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, heatstressed by shifting from 25°C to 37°C for 2 minutes, experiment A

value: 37degC for 2 min


title: B cells from Spleen, CON 2, D2

address: 苏州市工业园区仁爱路199号

description:
CON2_D2
SPC_B_FPKM.txt

value: Spleen

value: primary cell

value: B cells


title: B cells from Spleen, CON 2, D1

address: 苏州市工业园区仁爱路199号

description:
CON2_D1
SPC_B_FPKM.txt

value: total splenic B cells and activated them in vitro by LPS


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_378

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_378

value: KD


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_391

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_391


title: DRS_W303_–_heatstress_0min_25°C_to_37°C_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, heatstres control sample, experiment A

value: 37degC for 0 min


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_374

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_374


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_377

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_377


title: B cells from Spleen, CON 2, D0

address: 苏州市工业园区仁爱路199号

description:
CON2_D0
SPC_B_FPKM.txt

value: CON


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_385

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_385

value: CNH


title: DRS_W303_–_heatstress_20min_25°C_to_37°C_repD

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, heatstressed by shifting from 25°C to 37°C for 20 minutes, experiment D

value: 37degC for 20 min


title: DRS_W303_–_heatstress_16min_25°C_to_37°C_repD

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, heatstressed by shifting from 25°C to 37°C for 16 minutes, experiment D

value: 37degC for 16 min


title: B cells from Spleen, CON 1, D2

address: 苏州市工业园区仁爱路199号

description:
CON1_D2
SPC_B_FPKM.txt


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_386

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_386

value: Plasma, extracted cell-free RNA


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_364

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_364


title: B cells from Spleen, CON 1, D1

address: 苏州市工业园区仁爱路199号

description:
CON1_D1
SPC_B_FPKM.txt


title: DRS_W303_–_heatstress_12min_25°C_to_37°C_repD

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, heatstressed by shifting from 25°C to 37°C for 12 minutes, experiment D

value: 37degC for 12 min


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_376

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_376


title: B cells from Spleen, CON 1, D0

address: 苏州市工业园区仁爱路199号

description:
CON1_D0
SPC_B_FPKM.txt


title: NPC_ST3

city: GuangZhou

first: Dong-Mei

last: Chi

address: 651 Dongfeng Road East

institute: SYSUCC

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

source_name: Nasopharynx

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

value: Nasopharynx

tag: tissue type

value: Nasopharyngeal carcinoma


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_387

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_387


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_393

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_393


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_366

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_366


title: DRS_W303_–_heatstress_8min_25°C_to_37°C_repD

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, heatstressed by shifting from 25°C to 37°C for 8 minutes, experiment D

value: WT

value: 37degC for 8 min


title: DRS_W303_–_heatstress_4min_25°C_to_37°C_repD

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303, heatstressed by shifting from 25°C to 37°C for 4 minutes, experiment D

value: 37degC for 4 min


title: NPC_ST2


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_342

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_342

value: MISC


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_341

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_341


title: DRS_W303_–_heatstress_0min_25°C_to_37°C_repD

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


title: NPC_ST1


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_222

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_222


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_203

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_203


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_223

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_223


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_212

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_212


title: cerebral cortex, Eed-cKO

city: Brisbane

first: Michael

last: Piper

state: QLD

address: The University of Queensland, St Lucia

department: School of Biomedical Sciences

country: Australia

institute: The University of Queensland

library_source: transcriptomic single cell

data_processing:
Remapping to a pre-mRNA genome, barcode processing, gene counting, and aggregation was made using the Cell Ranger 7.0.1.
Datasets of the three samples were merged. Cells with <2% mitochondrial RNA were removed. Using the Seurat toolkit, the data was normalised with both SCTransform and NormaliseData and clustered with the standard Seurat workflow (RunPCA, RunUMAP, FindNeighbors, FindClusters) (dims = 1:30, resolution = 0.2). Clusters with unusual nFeature, nCount, or abnormal gene expression were filtered out as these were likely to be doublets or abnormal cells.
Assembly: mm10
Supplementary files format and content: Output from CellRanger (tab seperated values and matrix files)
Supplementary files format and content: Seurat object (R Data Serialization)

source_name: cerebral cortex

extract_protocol:
Tissue was dissected and immediately homogenised in a Dounce homogenizer, filled with 1 ml of homogenisation buffer [250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris buffer (pH 8), 1 µM DTT, 1x protease inhibitor (cOmplete Protease Inhibitor Cocktail Tablets, Roche), 0.1% (v/v) Triton X-100 10%, and 40 U/mL RNase (RNasIn, Promega), diluted in nuclease-free water]. The homogenate was then incubated in 4 ml of homogenisation buffer for 5 minutes on ice. The homogenate was then strained through a 40 µm cell strainer prewetted with 0.5 ml homogenisation buffer. The strainer was washed with 0.5 ml homogenisation buffer. The homogenate was centrifuged for 5 minutes at 500 g in a swing bucket. The cell pellet was resuspended in 2ml wash media [1% BSA and 100 U/mL RNasIn, diluted in PBS], and DAPI was added at 1:5000 concentration in 1 ml wash media. The cell suspension was submitted for FACS sorting, using DAPI to filter nuclei from debris and to avoid collection of doublet nuclei.
The library was prepared with the 10x Genomics Chromium platform using a 3’ v3.1 kit.
snRNA-Seq

value: cerebral cortex

value: Eed-cKO


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_221

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_221


title: DRS_pan2_ccr4_W303_37C_repB

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303 pan2Δ ccr4Δ, grown at 37°C, experiment B

value: pan2{delta} ccr4{delta}


title: cerebral cortex, Eed-cHet

value: Eed-cHet


title: DRS_pan2_ccr4_W303_25C_repD

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303 pan2Δ ccr4Δ, grown at 25°C, experiment D


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_205

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_205


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_226

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_226


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_375

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_375


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_220

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_220


title: cerebral cortex, CTRL

value: CTRL


title: DRS_pan2_ccr4_W303_37C_repE

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303 pan2Δ ccr4Δ, grown at 37°C, experiment E


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_219

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_219


title: DRS_pan2_ccr4_W303_25C_repA

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303 pan2Δ ccr4Δ, grown at 25°C, experiment A


title: UT_3

city: Lansing

first: Kayla

middle: N

last: Conner

state: Michigan

address: 4125 Beaumont Rd

institute: Michigan State University

data_processing:
Base calling was performed with Illumina Real Time Analysis (RTA; Version 3.4.4), and the output of RTA was demultiplexed and converted to the FastQ format with Illumina Bcl2fastq (Version 2.20.0).
FastQC (Version 0.11.7) was used to assess read quality.
Bowtie2 (Version 2.4.1) with default settings was used to map reads with the GRCm39 mouse reference genome.
Aligned reads counts were assessed using FeatureCounts from the Subread package (Version 2.0.0)
Differential gene expression analysis was conducted using the DESeq2 package (Version 1.36.0) in R (Version 4.2.1).
Assembly: GRCm39
Supplementary files format and content: raw_counts.csv - raw read count matrix for all samples as produced by FeatureCounts
Supplementary files format and content: normalized_counts.csv - normalized read count matrix for all samples as produced by DESeq2

source_name: Fetal Liver Alveolar-Like Macrophages

growth_protocol: FLAMs were isolated and cultured in complete RPMI (Thermo Fisher Scientific) containing 10% FBS (R&D Systems), 1% penicillin-streptomycin (Thermo Fisher Scientific), 30 ng/ml recombinant mouse GM-CSF (PeproTech), and 20 ng/ml recombinant human TGFβ1 (PeproTech) included where indicated. Media were refreshed every 2–3 d. When cells reached 70–90% confluency, they were lifted by incubating for 10 min with 37°C PBS containing 10 mM EDTA, followed by gentle scraping.

extract_protocol:
FLAMs with and without TGFβ were plated in 6-well plates at 1 x 106 cells/well and treated with Pam3  for 18 hours. We used the Direct-zol RNA Extraction Kit (Zymo Research, Cat no. R2072) to extract RNA according to the manufacturer’s protocol.
Quality was assessed by the MSU Genomics Core using an Agilent 4200 TapeStation System. The Illumina Stranded mRNA Library Prep kit (Illumina, Cat no. 20040534) with IDT for Illumina RNA Unique Dual Index adapters was used for library preparation following the manufacturer’s recommendations but using half-volume reactions. Qubit™ dsDNA HS (ThermoFischer Scientific, Cat no. Q32851) and Agilent 4200 TapeStation HS DNA1000 assays (Agilent, Cat no. 5067-5584) were used to measure quality and quantity of the generated libraries. The libraries were pooled in equimolar amounts, and the Invitrogen Collibri Quantification qPCR kit (Invitrogen, Cat no. A38524100) was used to quantify the pooled library.

treatment_protocol: Cells were seeded in 24-well or 48-well treated culture plates cells/well and allowed to settle overnight then treated with Pam3CSK4 25ng/ml (Invivogen, Cat no. tlrl-pms) where indicated.

value: Fetal Liver Alveolar-Like Macrophages

value: Untreated


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_199

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_199

value: CNH


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_37

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_37

value: UCSD


title: UT_2


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_19

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_19

value: Plasma, extracted cell-free RNA


title: DRS_pan2_ccr4_W303_25C_repC

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303 pan2Δ ccr4Δ, grown at 25°C, experiment C


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_98

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_98


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_13

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_13


title: Tobacco leaf tissue -GDH94×TN90_rep3

city: Guiyang

first: Renxiang

last: Liu

state: Guizhou

address: Huaxi

institute: Guizhou University

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

organism: Nicotiana tabacum

source_name: hybrid GDH94×TN90

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

value: mature leaf

tag: line


title: UT_1


title: DRS_pan2_ccr4_W303_37C_repF

description: Nanopore Direct RNA Sequencing of S. cerevisaie W303 pan2Δ ccr4Δ, grown at 37°C, experiment F


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_15

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_15


title: TGF_3

value: TGF-B


title: Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna_187

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_187

value: EMORY


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_92

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_92


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_27

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_27


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_36

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_36


title: TGF_2


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_31

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_31


title: TGF_1


title: Tobacco leaf tissue -GDH94×TN90_rep2


title: PAM_TGF_3

value: Pam3 + TGF-B


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_20

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_20


title: Tobacco leaf tissue - K326×TN90_rep3

source_name: hybrid K326×TN90


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_26

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_26


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_35

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_35


title: Tobacco leaf tissue - K326×TN90_rep2


title: PAM_TGF_2


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_14

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_14


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_17

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_17


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_89

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_89


title: PAM_3


title: Tobacco leaf tissue - TN90_rep2

source_name: male parent TN90 of hybrid GDH94×TN90


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_25

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_25


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_30

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_30


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_38

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_38


title: PAM_2


title: Tobacco leaf tissue - TN90_rep1


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_34

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_34


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_1

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_1


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_101

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_101


title: Tobacco leaf tissue - GDH94_rep3

source_name: female parent GDH94 of hybrid GDH94×TN90


title: PAM_1


title: Tobacco leaf tissue - GDH94_rep2


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_32

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_32


title: PAM_TGF_1


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_102

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_102


title: Tobacco leaf tissue - GDH94_rep1


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_3

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_3


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_2

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_2


title: Tobacco leaf tissue - G70×Basma_rep3

source_name: hybrid G70×Basma


title: Tobacco leaf tissue - K326×TN90_rep1


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_100

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_100


title: Tobacco leaf tissue - TN90_rep3


title: Tobacco leaf tissue - G70×Basma_rep2


title: DRS_WT_W_303_AID_control_25°C_repA

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

value: WT

value: 25degC + 1-NAA for 2h


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_22

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_22


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_6

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_6


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_16

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_16


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_4

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_4


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_29

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_29


title: Tobacco leaf tissue - G70×Basma_rep1


title: RNA_bisulfite-seq_CecumSPF2

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

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.
1 μg of poly(A) RNA was fragmented into ~200 nt nucleotide fragments. According to the EZ RNA Methylation Kit protocol (#R5001, ZYMO RESEARCH), the poly(A) RNA fragments underwent sodium bisulfite treatment, desalting, and desulfonation reactions, leading to the construction of a strand-specific Bisulfit-seq library. The bisulfite-converted library was initiated with random hexamers (ACT) to reverse transcribe RNA samples. The first strand cDNA of the bisulfite-converted library was synthesized using 5× first-strand buffer (#18080044, Invitrogen), 10 mM DTT (#18080044, Invitrogen), 10 mM dNTP mix (#N0447L, NEB), 40 U/μl RNase Inhibitor (#M0307L, NEB), and reverse transcriptase III (#18080044, Invitrogen). The second strand cDNA synthesis was performed using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (#NR604-02, VAHTS), and the necessary adapters for library preparation were provided by the VAHTS® RNA Adapters set3 for Illumina.

value: cecum

value: tissue

value: Water


title: Tobacco leaf tissue - G70×Qinggeng_rep3

source_name: hybrid G70×Qinggeng


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_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.
cfrna_kd_95


title: RNA_bisulfite-seq_CecumSPF1


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_97

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_97


title: Tobacco leaf tissue - G70×Qinggeng_rep2


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_172

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_172

value: MISC


title: RNA_bisulfite-seq_CecumGF3

value: Germ-free


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_160

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_160


title: Tobacco leaf tissue - G70×Qinggeng_rep1


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_182_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_182_trimmed

value: KD


title: RNA_bisulfite-seq_CecumGF2


title: Tobacco leaf tissue -Basma_rep3

source_name: male parent Basma of hybrid G70×Basma

value: Basma


title: RNA_bisulfite-seq_CecumGF1


title: Tobacco leaf tissue -Basma_rep2


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_221_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_221_trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_181_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_181_trimmed


title: RNA_bisulfite-seq_CecumSPF3


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_228_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_228_trimmed


title: RNA_bisulfite-seq_BrainSPF3

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

source_name: brain

value: brain


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_115

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_115


title: Tobacco leaf tissue -Basma_rep1


title: RNA_bisulfite-seq_BrainSPF2


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_179_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_179_trimmed


title: Tobacco leaf tissue - Qing_rep3

source_name: male parent Qinggeng of hybrid G70×Qinggeng

value: Qing


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_5

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_5

value: UCSD


title: RNA_bisulfite-seq_BrainSPF1


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_45

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_45

value: Plasma, extracted cell-free RNA


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_201_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_201_trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_114

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_114


title: Tobacco leaf tissue - Qing_rep2

value: mature leaf


title: Tobacco leaf tissue - Qing_rep1


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_211_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_211_trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_192_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_192_trimmed


title: RNA_bisulfite-seq_BrainGF2


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_86

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_86


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_85

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_85


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_127

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_127


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_210_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_210_trimmed


title: Tobacco leaf tissue - G70_rep2

source_name: female parent G70 of hybrid G70×Qinggeng/G70×Basma


title: RNA_bisulfite-seq_BrainGF1


title: Tobacco leaf tissue - G70_rep3


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_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.
cfrna_kd_159

source_name: Plasma, extracted cell-free RNA


title: Tobacco leaf tissue - G70_rep1


title: KNF1F2-H3K27ac, replicate HiChIP 1

city: Salt Lake City

first: Katherine

last: Gillis

state: UT

address: 2000 CIRCLE OF HOPE DR

institute: Snyder Lab at Huntsman Cancer Institute

library_source: genomic

data_processing:
The paired-end HiChIP sequencing reads were aligned to the mouse genome mm10 with the HiC-Pro pipeline (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0831-x ).
HiC-DC+ was used to call chromatin loops by binning the genome into 5kb bins (https://www.nature.com/articles/s41467-021-23749-x#citeas).
Chromatin loops were removed if the qvalue < 0.05 or anchors overlapped with ENCODE blacklist regions (https://www.nature.com/articles/s41598-019-45839-z ).
Assembly: build mm10
Supplementary files format and content: allValidPairs file containing H3K27ac interactions for all samples.
Library strategy: HiChIP

molecule: genomic DNA

source_name: lung

extract_protocol:
KN and KNF1F2 tumor-bearing mice were euthanized at 14 weeks post tumor initiation and the rib-cage was dissected to reveal the trachea and heart. Lungs were perfused with cold PBS, removed, and snap frozen in liquid nitrogen. Flash-frozen lungs were minced on ice in 2 ml of ice-cold PBS for 3 – 5 min. Minced lungs were dounced 10 times with a large 7 ml homogenizer (Wheaton) and centrifuged for 5 min at 4°C (300G). Tissue was crosslinked in 2 mM DSG buffer (1X PBS, 1 mM MgCl2) for 35min, then formaldehyde was added to final concentration of 1% and incubated for 10min. The cross-linking reaction was stopped with the addition of glycine to a final concentration of 125 mM. After fixation, lung samples were resuspended in 2 – 3 ml of TST buffer (Slyper et al. 2020) with protease inhibitors for 5 min. During this time, samples were dounced an additional 5 times in a small 2 ml homogenizer (Wheaton) to extract nuclei. Lysis was quenched with 5 ml of 1X ST buffer (Slyper et al. 2020) plus protease inhibitors. Nuclei were washed in cold PBS and resuspended in 5 – 10 ml cold PBS supplemented with DAPI and protease inhibitors. Nuclei suspension was then sequentially filtered through a 70 μm and 35 μm cell strainer. Nuclei were sorted using BD FACSAria with the 85 μm nozzle for GFP-positive, DAPI-positive nuclei. Samples were sorted into 1 ml of cold PBS with 1% BSA and 10X protease inhibitor. Approximately 10 million nuclei were sorted for HiChIP experiments.
HiChIP protocol based on Mumbach et al., 2016, Nature Methods. Cross-linked chromatin was digested with the MboI restriction enzyme followed by end-repair with dNTPs including biotin labeled dATP, ligation using T4 DNA ligase, and sonication to obtain 1kb chromatin fragments using Qsonica (Q800). To enrich for chromatin interactions occurring at active regulatory elements, an anti-H3K27ac antibody (Abcam, ab4729, rabbit polyclonal, 7.5ug/HiChIP) was used for DNA fragment capture. Streptavidin magnetic beads were used to pull down ligated DNA fragments and HiChIP libraries were prepared using Illumina Tagment DNA Enzyme and Buffer Kit. Sequencing was performed with the Illumina Nextera Library preparation.

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

value: lung

tag: chip-antibody

value: H3K27ac (Active Motif, 39133)

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

value: tamoxifen


title: KN-H3K27ac, replicate HiChIP 1


title: KG1A-4OHT replicate methyl-seq  2

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

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

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

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

value: lung tumors

value: 4-OH tamoxifen


title: Tobacco leaf tissue - K326_rep3

source_name: female parent K326 of hybrid K326×TN90


title: Tobacco leaf tissue - K326_rep2


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_197_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_197_trimmed


title: RNA_bisulfite-seq_BrainGF3

value: tissue


title: KG1A-4OHT replicate methyl-seq  1


title: Tobacco leaf tissue - K326_rep1


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_217_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_217_trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_178_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_178_trimmed


title: KG1A-EtOH replicate methyl-seq  2

value: ethanol


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_216_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_216_trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_126

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_126


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_188_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_188_trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_187_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_187_trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_220_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_220_trimmed


title: Hamster Toes, 30dpi, SARS-CoV-2 #4

city: New York

first: Justin

middle: J

last: Frere

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

department: Microbiology

institute: NYU Langone Health

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

organism: Mesocricetus auratus

source_name: Toes

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

value: Toes

value: Hamster intranasally infected with 1000 PFU of SARS-CoV-2 (Washington Strain) in 100 uL of PBS; toes harvested 30 days post-infection


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_113

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_113

value: KD


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_234_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_234_trimmed


title: KG1A-EtOH replicate methyl-seq  1


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_233_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_233_trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_54

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_54


title: Hamster Toes, 30dpi, SARS-CoV-2 #3


title: 22E-4OHT replicate methyl-seq  2

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


title: Hamster Toes, 30dpi, SARS-CoV-2 #1


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_177_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_177_trimmed


title: 22E-4OHT replicate methyl-seq  1


title: Hamster Toes, 30dpi, SARS-CoV-2 #2


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_44

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_44


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_200_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_200_trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_112

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_112


title: 22E-EtOH replicate methyl-seq  2


title: Hamster Toes, 3dpi, SARS-CoV-2 #3

value: Hamster intranasally infected with 1000 PFU of SARS-CoV-2 (Washington Strain) in 100 uL of PBS; toes harvested 3 days post-infection


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_199_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_199_trimmed


title: 22E-EtOH replicate methyl-seq  1


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_209_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_209_trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_53

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_53


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_232_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_232_trimmed


title: Hamster Toes, 3dpi, SARS-CoV-2 #2


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_111

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_111


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_43

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_43


title: N neoplasias, replicate methyl-seq  3

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


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_227_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_227_trimmed

value: UCSD


title: N neoplasias, replicate methyl-seq  2


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_190_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_190_trimmed

value: Plasma, extracted cell-free RNA


title: Hamster Toes, 30dpi, Mock #4

value: Hamster intranasally "infected" with 100 uL of PBS (Mock-treatment); toes harvested 30 days post-infection


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_125

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_125


title: N neoplasias, replicate methyl-seq  1

value: lung


title: Hamster Toes, 30dpi, Mock #3


title: KNF1F2 tumors, replicate methyl-seq  3


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_176_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_176_trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_180_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_180_trimmed


title: Hamster Toes, 30dpi, Mock #2


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_196_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_196_trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_28

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_28


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_50

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_50


title: Hamster Toes, 30dpi, Mock #1


title: KNF1F2 tumors, replicate methyl-seq  2


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_124

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_124


title: KNF1F2 tumors, replicate methyl-seq  1


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_191_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_191_trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_186_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_186_trimmed


title: Hamster Toes, 3dpi, Mock #4

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


title: Hamster Toes, 3dpi, SARS-CoV-2 #1