title: NSACB2_78_+S9_2

value: Spleen

tag: cell line

value: Lymphoblast

tag: chemical

tag: dose

tag: batch

tag: i5 index_id

value: ACAACCATC

tag: cas-rn


title: 4N-12

status: Public on Nov 15 2022

type: SRA

city: Rochester

first: Naba

last: Farooqui

state: MN

address: 200 1st St SW

country: USA

institute: Mayo Clinic

description: Mesenchymal stem cells harvested from the abdominal fat pad of domestic pigs 3 weeks after   induction of renal artery stenosis in pigs that were fed a high cholesterol diet, cultured in normoxic conditions (20% oxygen concentration)

library_source: genomic

data_processing:
Sequencing Reads were aligned to the Sus Scrofa 11.1 reference genome using Bowtie-2
Peaks were called using MACS2 narrow peak calling against the input sample
Reads were filtered using in house scripts to only those read pairs properly paired and mapped uniquely
duplicate reads were removed using PICARD
Wig files were generated with in-house scripts, step 20 and total base normalized
TDF files were generated from normalized WIGs using igvTools toTDF
Gene-body counts were calculated agaisnt the Ensembl SusScrofa11.1 gtf using htseq-count
Gene-body counts of sample group comparisons were performed using edgeR TMM normalization differentiation
Assembly: Sus Scrofa 11.1
Supplementary files format and content: BED/peak; TDF visualization; Counts non-normalized gene body read counts

molecule: genomic DNA

organism: Sus scrofa

source_name: Adipose derived Mesenchymal Stem Cells

growth_protocol: Adipose derived Mesenchymal Stem Cells were isolated and expanded from porcine abdominal adipose tissue. The harvested fat was processed under sterile conditions using the collagenase-H enzyme at 37°C for 45 minutes. Fetal bovine serum was added to the suspension to neutralize the digesting enzyme. The suspension was filtered through 100 µm cell strainers and the fluid collected was centrifuged at 100rpm for 5 minutes. The cell pellet obtained was resuspended in advanced minimum essential medium supplemented with 5% platelet lysate (PLTmax, Mill Creek Life Sciences Rochester, MN, USA), and expanded in culture for 2-4 passages. Where applicable, the flasks in P3 passage were preconditioned with hypoxia for 48 hrs.

extract_protocol:
Genomic DNAs were prepared from swine mesenchymal stem using the PureLink™ Genomic DNA Mini Kit according to the kit protocol (ThermoFisher Scientific, Cat# K182001) with RNase treatment following manufacturer’s instructions.   DNA was quantified with an ultraviolet spectrophotometer (NanoDrop) and diluted into a concentration of 100 ng/μl with TE buffer. The aliquot (100 ul) of diluted gDNA was sonicated using the Bioruptor® Pico (Diagenode, Seraing, Belgium) for 7 to 10 cycles with 30 sec on and 30 sec off. The size of fragmented DNA was analyzed by the Fragment analyzer (Advanced Analytical Technologies, Ankeny, IA) using the High Sensitivity NGS Fragment Analysis Kit (Cat. DNF-486). Fragmented DNA with an average size of 200 bp was denatured at 95oC for 10 minutes. 5 µg of DNA in 1X DIP buffer (10 mM sodium phosphate, pH7.0, 140 mM NaCl, 0.05% Triton X-100) was incubated with 1 µg of anti-5hmC antibody generated from the hybridoma clone EDL HMC 1A (equivalent to the antibody (Millipore, Cat. MABE1093)) for 3 hours at 4°C on a rotator. Protein G Dynabeads (Thermo Fisher, Cat. 10003D) were added, and the reactions were further incubated at 4°C on a rotator overnight. Beads-antibody-DNA complexes were extensively washed by DIP buffer and TE buffer. And enriched DNA fragments were eluted from the beads, purified with the ssDNA/RNA Clean & Concentrator Kit (Zymo Research, Cat. D7010) and quantified using the Qubit ssDNA High Sensitivity assay (Thermo Scientific, Cat. Q10212).
Libraries were prepared from input and enriched DIP DNAs by the ACCEL-NGS® 1S Plus DNA Library kit (Swift Bioscience, Cat. 10024) following the manufacturer’s instructions and were sequenced to 51 base pairs from both ends on an Illumina HiSeq4000 instrument in the Mayo Clinic Medical Genomics Facility.

treatment_protocol: Twenty domestic female pigs were studied during 16 weeks of observation after approval by the Institutional Animal Care and Use Committee (IACUC). At baseline, pigs were randomized into 4 groups, which were fed either a 2% high-cholesterol diet (n=15), as a surrogate for early atherosclerosis, or normal/healthy pig chow (n=5). Six weeks later, 0.5g of intramuscular ketamine and xylazine was used to anaesthetize all the pigs, and anaesthesia was then maintained with intravenous ketamine (0.2mg/kg/min) and xylazine (0.03mg/kg/min). Renal artery stenosis (RAS) was induced in high-cholesterol diet fed animals by placing a local-irritant coil in the main renal artery, leading to a gradual development of unilateral RAS and hypertension within 1-2 weeks, as described previously. The rationale for initiating diet before RAS was to reproduce the clinical scenario in ARAS in which early atherosclerosis precedes stenosis. A sham procedure, which involved cannulating the renal artery (without placement of irritant coil), was performed in normal animals. In addition, mean arterial pressure (MAP) was directly measured through a catheter inside the carotid artery using a pressure transducer sensor during multidetector computed tomography (MDCT) studies. Three weeks after induction of RAS, 5–10 g of subcutaneous abdominal adipose tissue was excised in order to harvest MSCs. These cells were grown till 80-90% confluency, passaged to P2-P3, and subjected to hypoxia or normoxia. Six weeks after RAS induction, the animals were similarly anesthetized, and the degree of stenosis determined by angiography (Siemens® Arcadis Avantic C-arm fluoroscope). Twelve weeks after starting the high cholesterol diet/10 weeks after induction of RAS, 10 x106 autologous MSC, which had been cultured under HPC (1% O2,  n=5) or AMSC cultured under normoxia (20% O2, n=5) were injected into renal arteries of ARAS pigs in the treatment groups, as described before. A vehicle (saline) was administered in 5 other untreated ARAS pigs. Four weeks after the intervention, the pigs were again similarly anesthetized, and the degree of stenosis determined by angiography. Blood samples were collected from the inferior vena cava for total cholesterol, triglycerides, high-density lipoprotein (HDL), low-density lipoprotein (LDL), and creatinine measurements, which were assessed by standard methods.   Two days after completion of all studies, pigs were euthanized with a lethal intravenous dose of 100mg/kg of sodium pentobarbital (Sleepaway, Fort Dodge Laboratories, Inc., Fort Dodge, Iowa). The kidneys were removed using a retroperitoneal incision and immediately dissected, and sections were frozen in liquid nitrogen (and maintained at −80°C) or preserved in formalin for in vitro studies.

tag: treatment

value: Normoxia

tag: antibody

value: anti-5hmC antibody

tag: cell type

value: Adipose derived Mesenchymal Stem Cells


title: 4H-11

description: Mesenchymal stem cells harvested from the abdominal fat pad of domestic pigs 3 weeks after induction of renal artery stenosis in pigs that were fed a high cholesterol diet, cultured and subjected to 48 hours of hypoxia preconditioning (1% oxygen concentration)

value: Hypoxia


title: NSACB4_39_+S9_1

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

library_source: transcriptomic

data_processing:
Base calling was performed by bcl2fastq v 2.20.422
Quality trimming was performed using fastp v0.20.0
Alignment was performed using STAR v2.7.8a
Gene counts were performed with qCount in the QuasR R package v1.30.0
Normalization was performed with DESeq2 v1.30.1
Assembly: Biospyder Human S1500+ v2.0
Supplementary files format and content: count_table.tsv is a genes by samples count matrix of raw counts from the TempO-Seq data alignments.
Library strategy: TempO-Seq

molecule: total RNA

organism: Homo sapiens

source_name: Spleen

growth_protocol: All experiments were performed with human lymphoblastoid TK6 (IVTG) cells (#13051501) purchased from Sigma-Aldrich (Oakville, ON). Cells were grown in RPMI1640 cell culture medium (ThermoFisher Scientific, Ottawa, ON) supplemented with 10% horse serum (ThermoFisher Scientific, Ottawa, ON), 2 mM L-Glutamine (ThermoFisher Scientific, Ottawa, ON), 1.8 mM sodium pyruvate (ThermoFisher Scientific, Ottawa, ON), and 100 U/mL of penicillin and streptomycin (ThermoFisher Scientific, Ottawa, ON). Cells were incubated at 37°C with 5% CO2 and maintained below 1x106/mL and >90% viability.

extract_protocol:
Cell lysates were used directly for TempO-Seq library building
The TempO-Seq® Human Surrogate+Tox Panel (S1500+) v2.0 (BioSpyder Technologies, Carlsbad, CA, USA) assay was completed following the manufacturer’s instructions in a 96-well plate format. Each 96-well plate included three assay controls in duplicate: a negative no-cell lysate (1X TempO-Seq® Enhanced Lysis buffer only), Human Reference Total RNA (Takara Bio, CA, USA), and Human Brain Reference Total RNA (Takara Bio, CA, USA). Briefly, for each treatment, 2 µL of cell lysate in 1X TempO-Seq® Enhanced Lysis buffer was hybridized to the Human S1500+ Surrogate detector oligo (DO) probe mix (V2.0), incubated at 70°C for 10 minutes, then ramped down to 45°C over 50 minutes (0.5°C/minute). A nuclease digestion followed to remove excess or incorrectly bound DOs at 37°C for 1 hour. The bound DO pairs were then ligated together at 37°C for 1 hour and 15 minutes at 80°C to generate templates for amplification. A 10 µL aliquot of amplification template was transferred to its respective well in the TempO-Seq® PCR Pre-Mix and Primers plate and amplified on the CFX96 thermocycler (Bio-Rad, Mississauga, ON, Canada) with the following program: 37°C for 10 min, 95°C for 1 min; 25 cycles of 95°C for 10 sec, 65°C for 30 sec, 68°C for 30 sec; 68°C for 2 min. For library building and purification, three 96-well plates (288 sample libraries) were pooled together (5 µL per sample) and purified using the Macherey-Nagel NucleoSpin® Gel and PCR Cleanup Kit (Clontech Laboratories Inc., Bethlehem, PA, USA) with the adjustments specified by the TempO-Seq® Assay User Guide. The pooled purified TempO-Seq® libraries were then diluted, quantified, and assessed for quality using the Agilent High Sensitivity D1000 TapeStation (Agilent Technologies, Santa Clara, CA, USA) and the qPCR KAPA Library Quantification Kit (Universal qPCR Master Mix) for Illumina NextSeq 500. Samples were sequenced on a total of two NextSeq® 500/550 High Output (75-cycle) flow cells using an Illumina NextSeq® 500 Sequencing Platform (Illumina, San Diego, CA, USA). A separate pool was completed for a fourth plate and an additional 96 sample libraries were added to the sequencing data for subsequent analysis.
The TempO-Seq® Human Surrogate+Tox Panel (S1500+) v2.0 - Index Sets F, G, H were used to index libraries (in two pools)

treatment_protocol: The cell density was adjusted to 1.5 x 105/mL, aliquoted in 96-well plates (100 µL/well), and exposed to 1% v/v solubilized test chemicals in DMSO in a six-point concentration range on a half-log distribution scale in duplicate. Six DMSO solvent controls were included per plate. For test chemicals requiring metabolic activation, the media were supplemented with 0.5% S9 Mix, Aroclor-1254 Induced Mutazyme® (Moltox, Boone, NC, USA). Treated cells were incubated at 37°C with 5% CO2 for 4H. Cells were collected via centrifugation at 300 x g for 5 minutes, washed with PBS, and resuspended in 1X TempO-Seq Enhanced Lysis buffer in PBS (40 µL/well) (BioSpyder Technologies, Carlsbad, CA, USA). If treated with 0.5% rat liver S9 fraction, cells were collected via centrifugation at 300 x g for 5 minutes, washed with PBS, resuspended in fresh media, and incubated at 37°C with 5% CO2 for a 3h recovery period. Following incubation, cells were collected, washed, and resuspended in 1X TempO-Seq® Enhanced Lysis buffer in PBS (40 µL/well) (BioSpyder Technologies, Carlsbad, CA, USA) and frozen at -80℃.

tag: tissue

tag: chemical long_name

value: Plate 1_IndexF

tag: sequencing pool

tag: technical control

value: F

tag: reference rna

tag: solvent control

tag: well

tag: i7 index_id

tag: index

value: ATCGCGACT

value: AGCAAGGTC


title: T47D HIF2A ChIP rep2

city: Oxford

first: David

middle: Robert

last: Mole

address: Roosevelt Drive, Headington

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
Illumina adaptor sequences were trimmed using Trimgalore (0.3.3) and reads were aligned to Genome Reference Consortium GRCh37 (hg19) using BWA (0.7.5a-r405). Low quality mapping was removed (MapQ < 15) using SAMtools (0.1.19)
Low quality mapping was removed (MapQ < 15) using SAMtools (0.1.19) and reads mapping to Duke Encode black list regions (http://hgwdev.cse.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeMapability) were excluded using BEDTools (2.17.0)
Duplicate reads were marked for exclusion using Picard tools (2.0.1) (http://picard.sourceforge.net/).
ChIP-seq peaks were identified using T-PIC (Tree shape Peak Identification for ChIP-Seq) and MACS (Model-based analysis of ChIP-Seq) in control mode
Peaks detected by both peak callers were filtered quantitatively using the total count under the peak to include only peaks that were above the 99.99th percentile of random background regions selected from the ENCODE DNASE II cluster (p-value < 0.0001).
Assembly: GRCh37 (hg19)
Supplementary files format and content: bigwig and bed files of called peaks

source_name: T47D Breast cancer cell line

growth_protocol: Culture medium was supplemented with 10%FBS, L-glutamine and penicillin-streptomycin. Culture medium used was DMEM (for T47D), F12K (for A549 and PC-3) and McCoy's 5a (for HCT-116). Cells were plated on 15cm plates and harvested at approximately 60-80% confluency.

extract_protocol:
Chromatin immunoprecipitation (ChIP) experiments were performed using antibodies directed against HIF-1a (rabbit polyclonal, PM14), HIF-2a (rabbit polyclonal, PM9), or HIF-1b (rabbit polyclonal, Novus Biologicals, NB100-110).
Automated library preparation was performed using the Apollo prep system (Takara, PrepX Comp ILMN 32i DNA Lib 96).

treatment_protocol: Hypoxia incubations were performed at 0.5% O2 for 16 hours in a hypoxia chamber (In Vivo2 400 Hypoxia Work Station, Ruskinn Technology).

tag: cell line

tag: ambient o2 concentration

tag: duration of hypoxia

value: 16 hours

tag: chip antibody

value: HIF-2a (rabbit polyclonal, PM9)


title: NSACB5_3536_+S9_1

tag: chemical

tag: dose

tag: batch

tag: i5 index_id

value: TAACGCGTC

tag: cas-rn


title: NSACB3_46_+S9_2

tag: tissue

tag: cell type

tag: chemical long_name

tag: treatment

value: TTCCGAATT


title: 49N-10

tag: antibody


title: DRXT18s02_1_P13

type: RNA

city: Kyoto

first: Masayoshi

last: Tsukahara

state: Kyoto

address: Shogoin kawahara-cho, sakyo-ku,

department: Research and Develpoment center

country: Japan

institute: CiRA foundation

description: SAMPLE 60

hyb_protocol: Gene expression hybridizatoin kits (Agilent) were used for hybridization.

scan_protocol: Slides were scanned on the SureScan microarray scanner system (Agilent).

data_processing: Fluorescent intensities were loaded and processed for backgroud correction by limma package of R software. Values were log-transformed and normalized by quantile normalization.

source_name: HLA homozygous iPSC

label_protocol: Low input quick amp labeling kits (Agilent) were used for cRNA labeling.

growth_protocol: Human iPSCs were maintained on iMatrix-511 (Nippi) coated plate with StemFit (AK03N, Ajinomoto).

extract_protocol: RNA was extracted by using TRIzol reagent (Thermo Fisher) and purifed by using RNA easy mini kit (QIAGEN).

treatment_protocol: Differentiation into three germ layers were conducted by using STEMDiff Trilineage differentiation kit (STEMCELL Technologies).

value: iPSC

tag: gender

value: Male

tag: source cell

value: PBMC

tag: generation method

value: pCE episomal vector


title: T47D HIF2A ChIP rep1

tag: cell line


title: NSACB3_46_+S9_1

value: Spleen

value: Lymphoblast

tag: sequencing pool

tag: technical control

tag: reference rna

tag: solvent control

tag: well

tag: i7 index_id

tag: index

value: AAACACCTT


title: DRXT18s01_3_P13

description: SAMPLE 59


title: 49H-9

value: anti-5hmC antibody

value: Adipose derived Mesenchymal Stem Cells


title: 33N-8

value: Normoxia


title: NSACB2_110_+S9_2

tag: chemical

tag: dose

tag: batch

value: Plate 1_IndexF

value: F

tag: i5 index_id

value: ACAACCATC

tag: cas-rn


title: DRXT18s01_1_P13

description: SAMPLE 57

tag: cell type


title: 33H-7

tag: treatment

value: Hypoxia

tag: antibody


title: PC3 HIF2A ChIP rep2

source_name: PC3 Prostate cancer cell line

tag: ambient o2 concentration

tag: duration of hypoxia

value: 16 hours

tag: chip antibody

value: HIF-2a (rabbit polyclonal, PM9)


title: NSACB5_5000_+S9_2

tag: tissue

tag: cell line

tag: chemical long_name

tag: sequencing pool

tag: technical control

value: TGGAACGCT

value: AAGTAGGCT


title: PC3 HIF2A ChIP rep1


title: NSACB2_110_+S9_1

tag: reference rna

tag: solvent control

tag: well

tag: i7 index_id

tag: index

value: ATCGCGACT

value: GTGCATTAG


title: Input_N-13

tag: sample type

value: input


title: DRXT07s15_2_P13

description: SAMPLE 55

tag: cell type

value: iPSC

tag: gender

value: Male

tag: source cell

value: PBMC

tag: generation method

value: pCE episomal vector


title: NSACB5_5000_+S9_1

value: Spleen

value: Lymphoblast

tag: chemical

tag: dose

tag: treatment

tag: batch

tag: i5 index_id

value: TAACGCGTC

tag: cas-rn


title: 21H-5

tag: antibody

value: anti-5hmC antibody

value: Adipose derived Mesenchymal Stem Cells


title: 21N-6

value: Normoxia


title: skin and hair follicle, minox 1

city: Tsukuba,

first: Meriem

last: Bejaoui

state: Ibaraki

address: 1 Chome-1-1 Tennodai

institute: University of Tsukuba

description: Gene expression data after 20 days topical application

hyb_protocol: Following fragmentation, 250 ng of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse. GeneChips were washed and stained in the Gene Atlas Fluidics Station 400

scan_protocol: GeneChips were scanned using the GeneAtlas Imaging Station

data_processing:
The raw data were normalized using Expression Console Software provided by the Affymetrix following robust multichip average (RMA) algorithm (http://www.affymetrix.com). Subsequent analysis of the gene expression data was carried out in the freely available Transcriptome Analysis Console (TAC) version 4 (Thermofisher inc.). Further analysis was conducted using an online data mining tool DAVID (Database for Annotation, Visualization and Integrated Discovery, ver. 6.8). We used 'Functional Annotation' tool of DAVID to identify the most relevant biological terms, including gene ontology (GO) terms, biological pathways, tissue expression, and disease associations (Huang da et al., 2009). We also performed gene set enrichment analysis (GSEA) for the top DEGs.
Expression console signal intensity. For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, we used freely available Transcriptome Analysis Console software (CEL files ).
RMA signal

label: biotin

organism: Mus

source_name: skin treated with minoxidil

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 9.4 ug total RNA

growth_protocol: C57BL6 mice (seven-weeks-old) was used in this experiment.

extract_protocol: The treated skin from all groups were collected cut into pieces and RNA was extracted using ISOGEN solution (Nippon Gene Co. Ltd., Toyama, Japan).

treatment_protocol: Six-weeks-old male C57BL/6 mice. An acclimatization period of seven days was granted to the mice, and four groups (n = 5) were randomly formed before proceeding with the hair growth experiment. We distinguish, untreatedgroup (MilliQ water), 1% minoxidil (minox, positive control), 1% keratin, and 1% microsphere (sphere keratin). The hair was trimmed and depleted and the treatments were applied topically for 20 day before sacrifice by cervical spine dislocation. We collected then the treated skin for further molecular analysis

tag: strain

tag: tissue

value: skin and hair follicle

value: minoxidil

tag: time

value: after 20 days topical application


title: PC3 HIF1A ChIP rep2

tag: cell line

tag: ambient o2 concentration

tag: duration of hypoxia

value: 16 hours

tag: chip antibody

value: HIF-1a (rabbit polyclonal, PM14)


title: DRXT18s01_2_P13

description: SAMPLE 58

tag: cell type

tag: gender


title: NSACB4_55_+S9_2

tag: chemical long_name

value: Plate 1_IndexF

tag: sequencing pool

tag: technical control

value: F

tag: reference rna

tag: solvent control

tag: well

tag: i7 index_id

tag: index

value: TGGAACGCT

value: GCAGATGCA


title: PC3 HIF1A ChIP rep1


title: 16N-4

tag: treatment

tag: antibody


title: NSACB4_55_+S9_1

tag: tissue

tag: chemical

tag: dose

tag: batch

tag: i5 index_id

value: AGCAAGGTC

tag: cas-rn


title: DRXT07s10_3_P13

description: SAMPLE 53

tag: cell type

value: iPSC

tag: gender

value: Male

tag: source cell

value: PBMC

tag: generation method

value: pCE episomal vector


title: T47D HIF1A ChIP rep1

tag: cell line

tag: ambient o2 concentration

tag: duration of hypoxia

tag: chip antibody


title: 16H-3

value: Hypoxia

value: anti-5hmC antibody


title: T47D HIF1A ChIP rep2


title: HCT-116 HIF2A ChIP rep3

source_name: HCT116 Colorectal cancer cell line

value: HIF-2a (rabbit polyclonal, PM9)


title: NSACB3_65_+S9_2

value: Spleen

value: Lymphoblast

tag: chemical long_name

tag: sequencing pool

tag: technical control

tag: reference rna

tag: solvent control

tag: well

tag: i7 index_id

tag: index

value: TTCCGAATT


title: HCT-116 HIF2A ChIP rep2

value: 16 hours


title: DRXT07s10_2_P13

description: SAMPLE 52


title: 110H-1

tag: treatment

tag: antibody

value: Adipose derived Mesenchymal Stem Cells


title: NSACB3_65_+S9_1

tag: tissue

tag: cell type

tag: chemical

tag: dose

tag: batch

value: Plate 1_IndexF

tag: i5 index_id

value: AAACACCTT

tag: cas-rn


title: NSACB2_156_+S9_2

tag: cell line

tag: chemical long_name

value: F

value: TGGAACGCT

value: ACAACCATC


title: DRXT07s10_1_P13

description: SAMPLE 51

value: iPSC

tag: gender

tag: source cell

tag: generation method


title: skin and hair follicle, no treat 1

source_name: skin treated with milliQ

tag: strain

value: skin and hair follicle

value: milliQ

tag: time

value: after 20 days topical application


title: DRXT07s09_3_P13

description: SAMPLE 50

value: Male

value: PBMC

value: pCE episomal vector


title: 110N-2

value: Normoxia

value: anti-5hmC antibody


title: DRXT07s15_1_P13

description: SAMPLE 54


title: HCT-116 HIF1A ChIP rep3

tag: ambient o2 concentration

tag: duration of hypoxia

tag: chip antibody

value: HIF-1a (rabbit polyclonal, PM14)


title: HCT-116 HIF1A ChIP rep2

value: 16 hours


title: A549 HIF2A ChIP rep3

source_name: A549 Lung cancer cell line

value: HIF-2a (rabbit polyclonal, PM9)


title: KO_13

city: Houston

first: Mark

last: Herman

state: Texas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
FASTQ files were uploaded to usegalaxy.org and paired-end reads from 2 lanes of sinlge flow cell were combined
Sequencing reads were aligned with HISTAT2 (2.1.0) to mm10
Transcript levels were quantified using FeatureCounts 1.6.3
Transcript counts were uploaded to BioJupies server and analyzed for differential gene expression and KEGG pathway enrichment
Assembly: mm10
Supplementary files format and content: A count matrix, with genes as rows and samples are columns supplied in excel format

organism: Mus musculus

source_name: Liver, HF/HS, 7

extract_protocol:
total RNA was extracted from previously snap-frozen liver tissues using TRI  reagent, RNA integrity check was performed using Fragment Analyzer (Advanced Analytical).
mRNA capture, fragmentation and cDNA library construction were conducted using a stranded mRNA-Seq Kit (Kapa biosystems, KR0960 – v6.17) according to manufacturer's protocol.

tag: tissue

value: Liver

value: male

tag: genotype

value: HGFAC KO

tag: treatment

value: HF/HS


title: NSACB2_156_+S9_1

value: Spleen

tag: cell type

value: Lymphoblast

tag: chemical

tag: dose

value: Plate 1_IndexF

tag: sequencing pool

tag: technical control

value: F

tag: reference rna

tag: solvent control

tag: well

tag: i7 index_id

tag: index

value: TGGAACGCT

value: GTGCATTAG


title: KO_11

source_name: Liver, HF/HS, 5

tag: gender

tag: strain


title: H9 cells, INDUCE-seq, rep 1

city: Cambridge

first: Julian

middle: E

last: Sale

address: Francis Crick Avenue

institute: MRC Laboratory of Molecular Biology

data_processing:
Demultiplexed FASTQ files were obtained and passed through Trim Galore to remove the adapter sequence at the 3’ end of reads using the default settings. Following read alignment to the human reference genome (hg38) using BWA-mem, alignments mapped with a low alignment score (MAPQ<30) were removed using SAMtools and soft-clipped reads were filtered using a custom AWK script to ensure accurate DSB assignment. The resulting BAM files were converted into BED files using bedtools bam2bed function, after which the list of read coordinates were filtered using regions of poor mappability, chromosome ends, and incomplete reference genome contigs, to remove these features from the data. DSB positions were assigned as the first 5’ nucleotide upstream of the read relative to strand orientation and were output as a ‘breakends’ BED file. By maintaining each read ID, flow cell X and Y positional information was used to filter out optical duplicates using a custom AWK script. The final output was a BED file containing a list of quantified single nucleotide break positions.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files reporting the position and of all mapped DSBs

growth_protocol: Human H9 embryonic stem cells were cultured at 37°C, 5% CO2 in Essential 8 Flex medium on Vitronectin-XF coated plates. Cells were passaged every 3-4 days based on cell density. Cells tested negative for mycoplasma contamination throughout the study.

extract_protocol:
Cells were harvested using Accutase to obtain a single cell suspension and counted, followed by two washes in DPBS. ~ 100,000 cells were deposited into a well of a Poly-D-lysine coated 96 well plate. Once sedimented, cells were crosslinked in 4% PFA for 10 min followed by two washes with PBS. Plates were tightly sealed, and cells kept in PBS at 4°C until downstream library preparation.
Cells were permeabilised by incubation in Lysis buffer 1 (10 mM Tris-HCL pH 8, 10 mM NaCl, 1 mM EDTA, 0.2% Triton X-100, pH 8 at 4˚C) for one hour at rt, followed by incubation in Lysis buffer 2 (10 mM Tris-HCL, 150 mM NaCl, 1 mM EDTA, 0.3% SDS, pH 8 at 25˚C) for one hour at 37˚C. Permeabilised cells were washed three times in 1x CutSmart Buffer (NEB) and blunt-end repaired using NEB Quick Blunting Kit +100 µg/mL BSA in a final volume of 50 µL at rt for one hour. Cells were then washed three times in 1x CutSmart Buffer and A-tailed using NEBNext dA-Tailing Module in a final volume of 50 µL at 37˚C for 30 mins. A-tailed cells were washed three times in 1x CutSmart buffer then incubated in 1x T4 DNA Ligase Buffer (NEB) for 5 mins at rt. A-tailed ends were labelled by ligation using T4 DNA ligase (NEB) + 0.4 µM Modified P5 adapter in a final volume of 50 µL at 16˚C for 16-20 h. Following ligation, excess P5 adapter was removed by washing cells 10 times in wash buffer at rt (10 mM Tris-HCL, 2 M NaCl, 2 mM EDTA, 0.5% Triton X-100, pH 8 at 25˚C), incubating for 2 mins each wash step. Cells were washed once in PBS and then once in nuclease free H2O. Genomic DNA was extracted by incubating cells in DNA extraction buffer (10 mM Tris-HCL, 100 mM NaCl, 50 mM EDTA, 1.0% SDS, pH 8 at 25˚C) + 1 mg/mL Proteinase K in a final volume of 100 µL for 5 mins at rt. The cell lysates were transferred to 1.5 mL Eppendorf RNA/DNA LoBind tubes and incubated at 65˚C for 1 hour, shaking at 800rpm. DNA was purified using Genomic DNA Clean & Concentrator-10 (Zymo Research), and eluted using 100 µL Elution Buffer. Genomic DNA was fragmented to 300-500bp using a Bioruptor Sonicator, and size selected using SPRI beads (GC Biotech) to remove fragments <150bp.  Fragmented and size-selected DNA was end-repaired using NEBNext Ultra II DNA Module. Fragmented and end-repaired DNA was added directly to the ligation reaction using NEBNext Ultra II Ligation Module according to the manufacturer’s instructions using 7.5 µM Modified half-functional P7 adapter and omitting USER enzyme addition. The ligated sequencing libraries were purified using SPRI beads. Libraries were purified twice more using SPRI beads, and size selected to remove fragments <200bp to remove residual adapter DNA. Final clean libraries were quantified by qPCR using the KAPA Library Quantification Kit for Illumina Platforms.
INDUCE-seq

tag: cell line

value: hESC

value: WT


title: DRXT18s02_2_P13

description: SAMPLE 61

value: iPSC

value: Male

tag: source cell

value: PBMC

tag: generation method

value: pCE episomal vector


title: H9 cells, INDUCE-seq, rep 2

tag: genotype


title: A549 HIF1A ChIP rep3

tag: ambient o2 concentration

tag: duration of hypoxia

value: 16 hours

tag: chip antibody

value: HIF-1a (rabbit polyclonal, PM14)


title: A549 HIF2A ChIP rep2

value: HIF-2a (rabbit polyclonal, PM9)


title: DRXT07s06_3_P13

description: SAMPLE 47

tag: cell type


title: DRXT07s06_2_P13

description: SAMPLE 46


title: AB46

city: Copenhagen

first: Josh

middle: M

last: Brickman

address: 3B Blegdamsvej

department: reNEW

country: Denmark

institute: Copenhagen University

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
read2 concatenated to R1 header separated to plate barcode - cell barcode - UMI
Genome_build: Hg38
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

molecule: polyA RNA

source_name: in vitro ESC-derived definitive endoderm

extract_protocol:
Cells were dissociated in 1 volume of trypsin-EDTA [0.25%] (Thermo Fisher) for 5 minutes at 37°C, and then the enzyme was inactivated with 0.5 volume of fetal bovine serum (FBS; Sigma). Single cells suspension was obtained by repeatedly washing with 10 volume of ice-cold washing buffer (PBS-/- 3% FBS).
Samples were flow sorted using AriaIII (BD Biosciences, BD Diva Software) cell sorter.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)
single cell RNA-seq for gene expression quantitation

tag: Stage

value: ADE

value: anterior definitive endoderm cells


title: KO_10

source_name: Liver, HF/HS, 4

tag: tissue

value: Liver

value: male

value: HGFAC KO

tag: treatment

value: HF/HS


title: KO_9

source_name: Liver, HF/HS, 3


title: A549 HIF1A ChIP rep2


title: DRXT07s06_1_P13

description: SAMPLE 45


title: AB45


title: KO_8

source_name: Liver, HF/HS, 2


title: KO_7

source_name: Liver, HF/HS, 1


title: DRXT07s01_3_P13

description: SAMPLE 44


title: KO_12

source_name: Liver, HF/HS, 6


title: DRXT07s01_2_P13

description: SAMPLE 43


title: DRXT07s09_1_P13

description: SAMPLE 48


title: AB44

value: ventral foregut progenitor cells


title: Patient 1991, convalescent sample

city: Chicago

first: Yan

last: Che

state: Illinois

address: 303 E Superior St

institute: Northwestern University

description:
1991x9q1
DENV_gene_count_matrix.csv

data_processing:
Sequencer-generated base call (BCL) files were converted to FASTQ files and the multiplexed samples were separated using bcl2fastq
Demultiplexed fastq were assessed for sequencing quality using FastQC (version 0.11.4, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
The fastq files were quality filtered by using FASTAX Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) with the invocation fastq_quality_filter -q 30 -p 50 -v -Q 33
Sequencing reads that met all quality control requirements were aligned to the latest human reference genome (GRCh38) using HISAT2 (version 2.0.4)
Gene expression in units of overlapping read counts per million were obtained by using the script from ballgown on gtf files of preprocessed RNA-seq alignments.
Counts per million were normalized using the voom methodology and expression profiles were modeled using mixed-effect models in limma (version 3.30.6)
Genome_build: GRCh38
Supplementary_files_format_and_content: DENV_gene_count_matrix.csv

source_name: Whole blood

extract_protocol:
Total RNA was extracted from PAXgene RNA blood solution with the MagNA Pure96 Cellular RNA Large Volume Kit on Roche MagNA Pure96 (MP96) Automated Nucleic Acid Isolator  by following manufacturers’ instructions and an additional clean-up using RNAClean XP beads from Beckman Coulter. Purified RNA samples were quantified by Qubit 3.0 fluorometer with RNA High Sensitivity Assay kit. Quality of the RNA samples was confirmed with the RNA High Sensitivity ScreenTape using the TapeStation 2200.
Sample libraries were then prepared from the 136 samples’ libraries (from two time points of 68 paired patient samples). First, ribosomal RNA (rRNA) and globin mRNA were removed from 200 ng total RNA, and the remaining RNA was fragmented and primed for cDNA synthesis using TruSeq Total Stranded RNA HT kit with Ribo-Zero Globin on a Microlab STAR automated liquid handling system. The libraries were barcoded with TruSeq HT indices to allow for multiplexing, and ligation-mediated PCR was performed to enrich barcoded libraries for 15 cycles, then purified with the Agencourt AMPure XP beads system. The libraries were assessed for quality with the high-sensitivity DNA chip in a TapeStation 2200 and quantified with KAPA Library Quantification Kits for Illumina platforms. The libraries were diluted to 2nM and combined equimolarly in pools of 12. These pools were then clustered using a cBot with a HiSeq 3000/4000 paired-end cluster kit on a patterned flow cell over 8 lanes. The flow cell was sequenced on a HiSeq4000 using a HiSeq 3000/4000 SBS kit.

tag: timepoint

value: 30d post symptom onset

tag: age (years)

tag: Sex

value: F

tag: infection

value: Secondary

tag: symptom

value: Dengue Fever

tag: virus type


title: AB43


title: Patient 1987, convalescent sample

description:
1987x9q1
DENV_gene_count_matrix.csv

value: 19d post symptom onset


title: AB42


title: DRXT07s01_1_P13

description: SAMPLE 42

value: iPSC

tag: gender

value: Male

value: PBMC


title: KO_6

source_name: Liver, Chow, 6

tag: strain

value: Chow


title: Patient 1987, acute sample

description:
1987x1q1
DENV_gene_count_matrix.csv

value: 5d post symptom onset


title: KO_5

source_name: Liver, Chow, 5


title: DRXT30

description: SAMPLE 41

source_name: HLA homozygous iPSC

tag: source cell

tag: generation method

value: pCE episomal vector


title: AB41


title: DRXT28

description: SAMPLE 40


title: skin and hair follicle, no treat 2

value: skin and hair follicle

value: milliQ

tag: time

value: after 20 days topical application


title: AB40


title: DRXT27

description: SAMPLE 39


title: Patient 1991, acute sample

description:
1991x1q1
DENV_gene_count_matrix.csv

value: 4d post symptom onset


title: Patient 1969, acute sample

description:
1969x1q1
DENV_gene_count_matrix.csv

value: Dengue Hemorrhagic Fever/Dengue Shock Syndrome


title: KO_3

source_name: Liver, Chow, 3

value: Liver

value: male

tag: genotype

value: HGFAC KO


title: AB39

value: ventral foregut progenitor cells


title: KO_4

source_name: Liver, Chow, 4


title: KO_2

source_name: Liver, Chow, 2


title: DRXT07s09_2_P13

description: SAMPLE 49


title: DRXT25

description: SAMPLE 38


title: KO_1

source_name: Liver, Chow, 1


title: HCT116 miR-24 inhibitor leChRO-seq sample #3

city: Ithaca

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

department: Biomedical Science

institute: Cornell University

description:
JV9_24i
leChRO-seq. Batch 1. HCT116 cells treated with 100 nM miR-24-3p inhibitor locked nucleic acid (LNA)
ChRO_DESeq_normalized_counts27SEP21.csv

data_processing:
Library strategy: leChRO-seq
Sequencing was aligned and quantiitated using miRquant2.0 (small RNAseq), aligned and quantified using STAR/Salmon (RNA-seq), or proseq2.0 (leChRO).
RNA- and leChRO-seq HCT116 data was normalized using DESeq2. Mutant enteroid RNA- and smRNA-seq data was rlog transformed followed by limma batch correction.
Genome_build: Mouse enteroids: mm9 (small RNAseq) or vM10 (RNAseq). HCT116: hg19 for both RNA- and leChRO-seq datasets.
Supplementary_files_format_and_content: Normalized counts

source_name: Colon

extract_protocol:
Libraries were prepared according to the protocol outlined in Chu, T. et al. Nature Genetics (2018)
RNA was isolated according to the leChRO-seq protocol described in Chu, T. et al. Nature Genetics (2018)

value: Colon

tag: cell line

value: miR-24 inhibitor


title: HCT116 miR-24 inhibitor leChRO-seq sample #2

description:
JV8_24i
leChRO-seq. Batch 1. HCT116 cells treated with 100 nM miR-24-3p inhibitor locked nucleic acid (LNA)
ChRO_DESeq_normalized_counts27SEP21.csv


title: Patient 1942, acute sample

description:
1942x1q1
DENV_gene_count_matrix.csv

value: F

value: Secondary

value: Dengue Fever


title: WT_14

source_name: Liver, HF/HS, 7

value: Control

value: HF/HS


title: DRXT24

description: SAMPLE 37

tag: cell type

value: iPSC

value: Male

value: PBMC

value: pCE episomal vector


title: Patient 1932, convalescent sample

description:
1932x9q1
DENV_gene_count_matrix.csv

value: 16d post symptom onset


title: HCT116 miR-24 inhibitor leChRO-seq sample #1

description:
JV7_24i
leChRO-seq. Batch 1. HCT116 cells treated with 100 nM miR-24-3p inhibitor locked nucleic acid (LNA)
ChRO_DESeq_normalized_counts27SEP21.csv


title: Patient 1969, convalescent sample

description:
1969x9q1
DENV_gene_count_matrix.csv

value: 15d post symptom onset

value: Dengue Hemorrhagic Fever/Dengue Shock Syndrome


title: HCT116 Scramble leChRO-seq sample #3

description:
JV6_Scramble
leChRO-seq. Batch 1. HCT116 cells treated with 100 nM scramble locked nucleic acid (LNA)
ChRO_DESeq_normalized_counts27SEP21.csv

value: scramble


title: DRXT18

description: SAMPLE 35


title: WT_13

value: Liver

value: male


title: Patient 1932, acute sample

description:
1932x1q1
DENV_gene_count_matrix.csv

value: 4d post symptom onset


title: Patient 1942, convalescent sample

description:
1942x9q1
DENV_gene_count_matrix.csv

value: 17d post symptom onset


title: HCT116 Scramble leChRO-seq sample #2

description:
JV5_Scramble
leChRO-seq. Batch 1. HCT116 cells treated with 100 nM scramble locked nucleic acid (LNA)
ChRO_DESeq_normalized_counts27SEP21.csv

value: Colon


title: DRXT11

description: SAMPLE 34


title: Patient 1911, convalescent sample

description:
1911x9q1
DENV_gene_count_matrix.csv

value: M

value: Secondary


title: WT_12

source_name: Liver, HF/HS, 5

value: Control


title: WT_11

value: HF/HS


title: Patient 1911, acute sample

description:
1911x1q1
DENV_gene_count_matrix.csv


title: DRXT01

description: SAMPLE 32

value: iPSC


title: HCT116 Scramble leChRO-seq sample #1

description:
JV4_Scramble
leChRO-seq. Batch 1. HCT116 cells treated with 100 nM scramble locked nucleic acid (LNA)
ChRO_DESeq_normalized_counts27SEP21.csv


title: HCT116 miR-24 inhibitor RNA-seq sample #3

description:
JV9_24i
RNA-seq. Batch 1. HCT116 cells treated with 100 nM miR-24-3p inhibitor locked nucleic acid (LNA)
DESeq_normalized_counts_nMk.csv

data_processing:
Sequencing was aligned and quantiitated using miRquant2.0 (small RNAseq), aligned and quantified using STAR/Salmon (RNA-seq), or proseq2.0 (leChRO).
RNA- and leChRO-seq HCT116 data was normalized using DESeq2. Mutant enteroid RNA- and smRNA-seq data was rlog transformed followed by limma batch correction.
Genome_build: Mouse enteroids: mm9 (small RNAseq) or vM10 (RNAseq). HCT116: hg19 for both RNA- and leChRO-seq datasets.
Supplementary_files_format_and_content: Normalized counts

extract_protocol:
Libraries were prepared according to the NEBNext Ultra II Directional RNA kit protocol following PolyA enrichment
RNA was isolated using the the Norgen Total RNA Purification Kit according to the manufacturer's protocol.

value: miR-24 inhibitor


title: Patient 1894, convalescent sample

description:
1894x9q1
DENV_gene_count_matrix.csv

value: Dengue Fever


title: Patient 1894, acute sample

description:
1894x1q1
DENV_gene_count_matrix.csv


title: DRXT07

description: SAMPLE 33

value: Male

value: PBMC

value: pCE episomal vector


title: WT_8


title: DRXT07s15_3_P13

description: SAMPLE 56


title: DEMSs11_P11

description: SAMPLE 30


title: DEMSs16_P11

description: SAMPLE 31


title: HCT116 miR-24 inhibitor RNA-seq sample #1

description:
JV7_24i
RNA-seq. Batch 1. HCT116 cells treated with 100 nM miR-24-3p inhibitor locked nucleic acid (LNA)
DESeq_normalized_counts_nMk.csv


title: Patient 1554, acute sample

description:
1554x1q1
DENV_gene_count_matrix.csv

value: 3d post symptom onset

value: Primary


title: DRXT22

description: SAMPLE 36


title: Patient 1554, convalescent sample

description:
1554x9q1
DENV_gene_count_matrix.csv

value: 14d post symptom onset


title: WT_7

source_name: Liver, Chow, 7

value: Liver

value: male

value: Chow


title: HCT116 Scramble RNA-seq sample #3

description:
JV6_Scramble
RNA-seq. Batch 1. HCT116 cells treated with 100 nM scramble locked nucleic acid (LNA)
DESeq_normalized_counts_nMk.csv

value: Colon

value: scramble


title: DEMSs08_P11

description: SAMPLE 29


title: Patient 1551, convalescent sample

description:
1551x9q1
DENV_gene_count_matrix.csv

value: 15d post symptom onset

value: F

value: Secondary


title: WT_6

value: Control


title: HCT116 Scramble RNA-seq sample #2

description:
JV5_Scramble
RNA-seq. Batch 1. HCT116 cells treated with 100 nM scramble locked nucleic acid (LNA)
DESeq_normalized_counts_nMk.csv


title: 409B2 P70_3_2

description: SAMPLE 27

source_name: Technical replicates

value: iPSC

value: Female

value: pCXLE episomal vector


title: DEMSs04_P11

description: SAMPLE 28

value: Male

value: PBMC


title: WT_10

source_name: Liver, HF/HS, 3

value: HF/HS


title: WT_5


title: HCT116 Scramble RNA-seq sample #1

description:
JV4_Scramble
RNA-seq. Batch 1. HCT116 cells treated with 100 nM scramble locked nucleic acid (LNA)
DESeq_normalized_counts_nMk.csv


title: Patient 1551, acute sample

description:
1551x1q1
DENV_gene_count_matrix.csv

value: 5d post symptom onset

value: Dengue Fever


title: WT_4

value: Liver


title: Patient 1385, convalescent sample

description:
1385x9q1
DENV_gene_count_matrix.csv

value: 14d post symptom onset

value: M

value: Primary


title: Patient 1385, acute sample

description:
1385x1q1
DENV_gene_count_matrix.csv


title: WT_9

source_name: Liver, HF/HS, 2

value: male


title: HCT116 miR-24 inhibitor RNA-seq sample #2

description:
JV8_24i
RNA-seq. Batch 1. HCT116 cells treated with 100 nM miR-24-3p inhibitor locked nucleic acid (LNA)
DESeq_normalized_counts_nMk.csv

value: Colon

value: miR-24 inhibitor


title: 409B2 P70_3_1

description: SAMPLE 26


title: 409B2 P70_2_1

description: SAMPLE 24


title: Patient 1372, convalescent sample

description:
1372x9q1
DENV_gene_count_matrix.csv

value: 15d post symptom onset

value: F

value: Secondary


title: RNA-seq for HUES4 170-3 VFG passage 6, BMP4 withdrawal and FGF10 stimulation, GFP low, rep2

data_processing:
Fastq files were aligned to the hg38/GRCh38 genome using STAR v2.5.3a32. Transcript expression levels were estimated with the --quantMode GeneCounts option and GRCh38p10.v27 annotations.
Genome_build: hg38
Supplementary_files_format_and_content: tab separated matrix file with raw read counts and a rowname column with ensembl IDs

source_name: ventral foregut progenitor cells

growth_protocol:
growth protocol for H9 WT ESC cells H9_WT_ESC_A  H9_WT_ESC_B  H9_WT_ESC_C: Undifferentiated hESCs H9 (WA09, WiCell Madison, WI) were maintained on tissue culture plates pre-coated with 0.1% gelatine with irradiated C57BL6 mouse embryonic fibroblast (MEF) feeder cells (25,000 cells/cm2) in H9 hESC media: DMEM/F12 GlutaMAX medium (Thermo Fisher) supplemented KnockOut Serum Replacement (KSR) (Thermo Fisher Scientific), MEM Non-Essential Amino Acids (NEAA), beta-mercaptoethanol (Sigma), and 10ng/mL FGF2 (Peprotech). Cells were passaged as clusters with collagenase IV (Thermo Fisher Scientific) and maintained in 20% O2/5% CO2/37°C. H9 WT ESC line was routinely screened for mycoplasma, and was negative.
growth protocol for HUES4 WT and 170-3 ESC cells (HUES4_1703_ESC_A  HUES4_1703_ESC_B  HUES4_1703_ESC_C): Undifferentiated hESC HUES4 WT and PDXeG clone 170-3 (Ameri et al., 2017) were adapted and maintained in DEF-CS (Takara). Cells were dissociated with TrypLE (Thermo Fisher) and maintained in 20% O2/5% CO2/37°C. HUES4 WT and 170-3 ESC lines were routinely screened for mycoplasma, and both are negative.
growth protocol for VFG cells H9_WT_VFGp8_A  H9_WT_VFGp8_B  H9_WT_VFGp8_C  HUES4_1703_VFGp3_A  HUES4_1703_VFGp3_B  HUES4_1703_VFGp3_C  HUES4_1703_VFGp6_A  HUES4_1703_VFGp6_B  HUES4_1703_VFGp6_C  HUES4_1703_VFGp18_A  HUES4_1703_VFGp18_B: Production and maintenance of VFG culture was based on a protocol from the Gadue’s lab (Cheng et al., 2012) with slight modifications. VFG was maintained on polystyrene cell culture plates pre-coated with un-diluted growth factor reduced Matrigel (GRF-Matrigel; Corning) pre-seeded with low density (8,000 cells/cm2) irradiated DR4 mouse embryonic fibroblast (MEF) feeder cells (Lonza). Cells were cultured in complete VFG media (SFD medium supplemented with BMP4 [50ng/ml], FGF2 [10ng/ml], VEGF [10ng/ml], EGF [10ng/ml], 0.5 mM ascorbic acid (Wako), and 4.5x10-4 M Monothioglycerol (Sigma)) and maintained under hypoxic conditions (5% O2/5% CO2/37°C). All VFG cell lines were routinely screened for mycoplasma, and all are negative.

extract_protocol:
Two hundred thousand cells were collected for total mRNA isolated with QIAGEN RNeasy Micro kit. Total mRNA amount and RNA integrity were assessed using a Fragment Analyzer (AATI). Ribosomal RNA was removed from the samples using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB).
Sequencing libraries were prepared from 100ng of purified total mRNA using NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions. Single-read RNA-sequencing was performed using the NextSeq 500 (Illumina) with 75 High Output Kit (Illumina, FC-404-2005).

treatment_protocol:
treatment protocol for ADE differentiation H9_WT_ADE_A  H9_WT_ADE_B  H9_WT_ADE_C  HUES4_1703_ADE_A  HUES4_1703_ADE_B  HUES4_1703_ADE_C: Transient ADE cells were generated from wild type H9 and HUES4 WT hESCs, as well as HUES4 PDX1-eGFP reporter (PDXeG clone 170-3) hESC cell line (Ameri et al., 2017) using the protocol as specified from the Gadue’s lab (Cheng et al., 2012). In brief, the hESC cells at 70-80% confluence were collected with Accutase (00455556, Thermo Fisher Scientific), re-plated at a density of 50,000 cells/cm2 on a polystyrene cell culture plates (Corning, 353047) pre-coated with un-diluted growth factor reduced Matrigel (GRF-Matrigel; Corning), cultured in either H9 hESC or DEF-CS media for 48 hours with 10µM ROCKi (Y-27632, STEMCELL Technologies) for first 24 hours and maintained in 20% O2/5% CO2/37°C. The hESC clusters were used to generate transient ADE cells in three-dimension differentiation culture under hypoxic conditions (5% O2/5% CO2/37°C) for 5 days. In day 1, the cell clusters were cultured in RPMI 1640 GlutaMAX (61870044, Gibco) with 10% SFD media (Gouon-Evans et al., 2006) supplemented with Activin A [100ng/mL], CHIR99021 [3µM] and 4.5x10-4 M Monothioglycerol (Sigma). In day 2, medium was changed to RPMI 1640 GlutaMAX supplemented with Activin A [100ng/mL], BMP4 [0.5ng/mL], FGF2 [10ng/mL], VEGF [10ng/mL], 0.5 mM ascorbic acid [Wako], and 4.5x10-4 M Monothioglycerol (Sigma). The same media was applied at day 3. In day 4, differentiation media was changed to SFD media supplemented with Activin A [100ng/mL], BMP4 [0.5ng/mL], FGF2 [10ng/mL], VEGF [10ng/mL], 0.5 mM ascorbic acid (Wako), and 4.5x10-4 M Monothioglycerol (Sigma).
treatment protocol for PE differentiation HUES4_1703_PE_A  HUES4_1703_PE_B  HUES4_1703_PE_C: Protocol adapted from Nostro et al., 2015 was used for Pancreatic Endoderm (PE) differentiation. VFG cells generated from HUES4 PDX1-eGFP reporter (PDXeG clone 170-3) hESC cell line (Ameri et al., 2017) at passage 6 were plated at 25,000 cells/cm2 on polystyrene cell culture plates pre-coated with un-diluted growth factor reduced Matrigel (GRF-Matrigel; Corning) and pre-seeded with 8000 per cm2 irradiated DR4 mouse embryonic fibroblast (MEF) in the VFG medium. Day 5 expanding VFG cells were used for pancreatic differentiations under hypoxic conditions (5% O2/5% CO2/37°C). In brief, cells were fed SFD media supplemented with 50 ng/ml of hFGF10, 3 ng/ml mWnt3a and 0.75 μM dorsomorphin (Sigma) for 3 days with the medium changed every day. Then, the medium was changed to DMEM GlutaMAX medium (Thermo Fisher) with 1% vol/vol B27 e (Life Technologies), 50 ng/ml hFGF10 (RnD), 50 ng/ml hNOGGIN (RnD), 50μg/ml ascorbic acid (Sigma), 2 µM retinoic acid (Sigma), with or without 0.25 μM KAAD-cyclopamine (Sigma) for one day. Finally, the medium was changed to DMEM GlutaMAX medium (Thermo Fisher) with 1% vol/vol B27 supplement (Life Technologies), 50 ng/ml hNOGGIN (RnD), 50 ng/ml hEGF (Peprotech), 10 mM nicotinamide (Sigma), and 50 μg/ml ascorbic acid (Sigma) for 4 days with the medium changed every day.
treatment protocol for BMP4 withdrawal and FGF10 treatment HUES4_1703_VFGp6_BMPminus_A  HUES4_1703_VFGp6_BMPminus_B  HUES4_1703_VFGp6_BMPminus_C  HUES4_1703_VFGp6_BMPminus_FGFstimulation_GFPhigh_A  HUES4_1703_VFGp6_BMPminus_FGFstimulation_GFPhigh_B  HUES4_1703_VFGp6_BMPminus_FGFstimulation_GFPhigh_C  HUES4_1703_VFGp6_BMPminus_FGFstimulation_GFPlow_A  HUES4_1703_VFGp6_BMPminus_FGFstimulation_GFPlow_B: PDX1-eGFP reporter VFG cells at passage 6 was plated at 20x103 cells/cm2 on polystyrene cell culture plates pre-coated with un-diluted growth factor reduced Matrigel (GRF-Matrigel; Corning) and pre-seeded with 8x103 per cm2 irradiated DR4 mouse embryonic fibroblast (MEF). The cells were cultured in BMP4 withdrawal VFG media (SFD medium supplemented with FGF2 [10ng/ml], VEGF [10ng/ml], EGF [10ng/ml], 0.5 mM ascorbic acid (Wako), and 4.5x10-4 M Monothioglycerol (Sigma)) and maintained under hypoxic conditions (5% O2/5% CO2/37°C) for 5 days with medium changing every other day. For generating PDX1-eGFP positive and negative fractions, cells were further differentiated in DMEM GlutaMAX (Thermo Fisher), 1% vol/vol B27 supplement (Life Technologies), with or without FGF10 [10ng/ml] for 5 days with medium changing every day. Both BMP4 withdrawal and FGFs stimulations were under hypoxic conditions (5% O2/5% CO2/37°C).

value: 170-3 PDX1-eGFP reporter

tag: facs sorted population

value: PDX1-eGFP low cells


title: WT_1

tag: tissue

value: Control

value: Chow


title: WT_2

tag: treatment


title: RNA-seq for HUES4 170-3 VFG passage 6, BMP4 withdrawal and FGF10 stimulation, GFP low, rep1


title: RNA-seq for HUES4 170-3 VFG passage 6, BMP4 withdrawal and FGF10 stimulation, GFP high, rep3

value: PDX1-eGFP high cells


title: 409B2 P70_1_2

description: SAMPLE 23

value: iPSC

value: Female

value: PBMC

value: pCXLE episomal vector


title: RNA-seq for HUES4 170-3 VFG passage 6, BMP4 withdrawal and FGF10 stimulation, GFP high, rep2


title: Patient 1367, convalescent sample

description:
1367x9q1
DENV_gene_count_matrix.csv

tag: timepoint

value: 16d post symptom onset

value: Dengue Fever


title: 409B2 P70_1_1

description: SAMPLE 22


title: Patient 1367, acute sample

description:
1367x1q1
DENV_gene_count_matrix.csv

value: 5d post symptom onset

tag: age (years)


title: RNA-seq for HUES4 170-3 VFG passage 6, BMP4 withdrawal and FGF10 stimulation, GFP high, rep1


title: WCE, C57, Liver, Water

data_processing:
The sequencing ChIP-seq reads were demultiplexed using bcl2fastq and aligned to the GRCm38 mouse genome using Bowtie2. PCR duplicates and low-quality reads were removed by Picard. Reads were processed using SAMtools and subjected to peak-calling with MACS2. SAMtools was also used to obtain 2 pseudoreplicates per sample. Only the peaks present in both pseudoreplicates were included for further downstream analysis. The coverage for peaks was obtained using BEDtools multicov. Normalization and differential analysis were performed using edgeR between fructose and water gavage conditions. To visualize ChIP-seq signals, reads were converted to the BigWig file format using BEDtools and bedGraphToBigWig. Peaks were tied to genes based on the nearest gene and transcription start site (TSS) within a radius of 200kb distance. The gtf file from GENCODE version M24 is filtered to include only processed transcript and protein coding transcript types as well as filtered for well supported transcripts (using only transcript support levels 1 and 2).
Assembly: GENCODE version M24
Supplementary files format and content: bigWig

source_name: Liver

extract_protocol:
25-30 mg of frozen liver tissue were quickly minced with razor blades in PBS at room temperature. Tissue was crosslinked with 0.5 M disuccinimidyl glutarate in PBS for 45 min at room temperature, followed by second fixation with 1% formaldehyde in Fixing Buffer A (Covaris) for 5 min at room temperature. Crosslinking was stopped by Quenching Buffer E (Covaris). After washing, nuclei were isolated by Dounce homogenization followed by centrifugation. After washing and centrifugation, the nuclear pellet was resuspended in cold 0.25% SDS Shearing Buffer (Covaris). Chromatin was sheared in 1 ml AFA milliTUBEs (Covaris) using Covaris S220X focused ultrasonicator with the following parameters: peak incident power 140W, duty factor 5%, cycles per burst 200 for 12 min. The sheared chromatin was centrifuged at 13,000rpm for 10min at 4°C to remove debris, and a 10 ul aliquot was de-crosslinked and used for quantification with Qubit (Thermo Fisher Scientific). Sheared chromatin (1.5 – 3 μg) was diluted in ChIP dilution buffer (16.7 mM Tris [pH8], 1.2 mM EDTA, 25 mM NaCl, 1.1% Triton X-100, 0.01% SDS), and 1 μg of  ChREBP antibody (Novus, NB400-135) or control rabbit IgG was added, followed by overnight incubation at 4°C. The reactions were then incubated for 1h at 4°C with protein A/G dynabeads (Invitrogen) pre-blocked in PBS/0.5% BSA/0.5% Tween. Beads were then washed in low salt wash buffer (20 mM Tris [pH8], 1 mM EDTA, 140 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS), high salt wash buffer (20 mM Tris [pH8], 1 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS), LiCl wash buffer (10 mM Tris [pH8], 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate, 250 mM LiCl) and TE buffer (10 mM Tris [pH8], 1 mM EDTA) and eluted and reverse cross-linked in elution buffer (10 mM Tris [pH8], 5 mM EDTA, 0.1% SDS, 300 mM NaCl, 0.8 mg/ml proteinase K, 10 μg/ml RNase A) by incubating at 65°C for 10 hours. Next, DNA was extracted using AMPure XP beads following the manufacturer’s manual and quantified by Qubit (Thermo Fisher Scientific). Immunoprecipitated chromatin was pooled by genotype and gavage condition for further analysis.
Sequencing libraries were constructed using the “on-bead” preparation method as previously described (Kang, S., Tsai, L.T., Zhou, Y., Evertts, A., Xu, S., Griffin, M.J., Issner, R., Whitton, H.J., Garcia, B.A., Epstein, C.B., et al. (2015)). Briefly, either 5ng (ChREBP) or 10ng (WCE input) of immunopreciptated chromatin were used as input for library construction. We performed end repair/ phosphorylation using the End-It DNA End-Repair Kit (Epicentre), A-tailing using the Klenow Fragment (NEB M0212) and index adaptor ligation using Quick Ligase (NEB M2200). AMPure XP beads were used for isolation of DNA per manufacturer protocol. After ligation, DNA was eluted and amplified by PCR for 12 (WCE) or 16 (ChREBP) cycles using the PfuUltra II Hotstart PCR Master Mix (Agilent 600850). DNA sized between 250 and 600bp was selected by gel electrophoresis and extraction using E-Gel EX Agarose Gels (Invitrogen) and MinElute Gel Extraction kits (Qiagen). Libraries were analyzed using the Qubit and Agilent Bioanalyzer, pooled at a final concentration of 12pM for sequencing.

treatment_protocol: Wild-type, male 8-week old C3H/HeJ and C57BL/6J mice were fasted for 5 hours and gavaged with fructose (4 g /kg BW) versus water control (n=6 / group).  Mice were euthanized 90 min after gavage and tissues were harvested and snap-frozen in liquid nitrogen for further analysis

value: Liver

tag: Sex

value: male

value: Wild-type

value: Water

tag: age

value: 8-week old


title: WCE, C57, Liver, Fructose

value: Fructose


title: RNA-seq for HUES4 170-3 VFG passage 6, BMP4 withdrawal, rep3

value: 170-3 PDX1-eGFP reporter

value: CD184-PeCy7 and CD117-APC double positive cells


title: 201B P32_21

description: SAMPLE 21

value: pMX retrovirus


title: 201B P32_20

description: SAMPLE 20


title: RNA-seq for HUES4 170-3 VFG passage 6, BMP4 withdrawal, rep2


title: WCE, C3H, Liver, Water


title: Patient 1363, convalescent sample

description:
1363x9q1
DENV_gene_count_matrix.csv

source_name: Whole blood

value: 15d post symptom onset

value: F

tag: infection

value: Secondary

tag: symptom


title: WT_3

tag: gender

value: Control

value: Chow


title: RNA-seq for HUES4 170-3 VFG passage 6, BMP4 withdrawal, rep1


title: Patient 1372, acute sample

description:
1372x1q2
DENV_gene_count_matrix.csv

value: 4d post symptom onset

tag: virus type


title: Patient 1354, convalescent sample

description:
1354x9q1
DENV_gene_count_matrix.csv

value: 17d post symptom onset

value: M

value: Dengue Hemorrhagic Fever/Dengue Shock Syndrome


title: 409B2 P70_2_2

description: SAMPLE 25

value: iPSC

value: Female

tag: source cell

value: PBMC

value: pCXLE episomal vector


title: 201B P32_19

description: SAMPLE 19

tag: generation method


title: 201B P32_18

description: SAMPLE 18


title: 201B P32_17

description: SAMPLE 17


title: ChREBP, C57, Liver, Water

value: Liver

tag: strain

value: male

value: Wild-type

value: Water

value: 8-week old


title: RNA-seq for HUES4 170-3 VFG-derived PE rep3

source_name: pancreatic endoderm progenitor cells

tag: genotype

value: 170-3 PDX1-eGFP reporter

value: PDX1-eGFP positive cells


title: Patient 1351, convalescent sample

description:
1351x9q1
DENV_gene_count_matrix.csv

value: 18d post symptom onset

value: Secondary


title: WCE, C3H, Liver, Fructose

value: Fructose


title: ChREBP, C57, Liver, Fructose


title: ChREBP, C3H, Liver, Water


title: RNA-seq for HUES4 170-3 VFG-derived PE rep2

tag: cell line


title: RNA-seq for HUES4 170-3 VFG-derived PE rep1


title: 201B P32_16

description: SAMPLE 16

tag: cell type

value: pMX retrovirus


title: Patient 1351, acute sample

description:
1351x1q1
DENV_gene_count_matrix.csv

value: 3d post symptom onset

value: M


title: RNA-seq for HUES4 170-3 hESC-derived VFG passage 18 rep2

tag: facs sorted population

value: CD184-PeCy7 and CD117-APC double positive cells


title: 201B P32_15

description: SAMPLE 15

value: iPSC

value: Female


title: ChREBP, C3H, Liver, Fructose

tag: tissue


title: Patient 1363, acute sample

description:
1363x1q1
DENV_gene_count_matrix.csv

value: 5d post symptom onset

value: F

value: Dengue Fever


title: 201B P32_14

description: SAMPLE 14

value: PBMC


title: RNA-seq for HUES4 170-3 hESC-derived VFG passage 18 rep1


title: Patient 1342, acute sample

description:
1342x1q1
DENV_gene_count_matrix.csv

value: Primary


title: RNA-seq for HUES4 170-3 hESC-derived VFG passage 6 rep3


title: 201B P32_13

description: SAMPLE 13


title: Nanoparticle-treated, scRNAseq

city: Ann Arbor

first: Jeffrey

last: Ma

state: Michigan

address: 1600 Huron Parkway

department: Biomedical Engineering

institute: University of Michigan

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.
Raw reads were processed, counted, and mapped to individual cells by Cell Ranger software v6.0 (Illumina).
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files

source_name: lung

extract_protocol:
Female BALB/c mice were inoculated with 100,000 4T1 tumor cells and treated with either saline or PLG nanoparticles every 3 days starting 1 day after tumor inoculation. 14 days after inoculation, lungs were collected and pooled from n=4 mice per condition. Lungs were physically and chemically processed into a single cell suspension, treated with ACK buffer to remove red blood cells, and resuspended in DPBS supplemented with 2 mM EDTA and 0.5% BSA.
Library preparation was performed by the University of Michigan Advanced Genomics Core following manufacturer instructions (Illumina NovaSeq 6000).

value: lung

value: BALB/cJ

value: 12 weeks

tag: tumor stage

value: 14 day 4T1 tumor

tag: treatment

value: intravenous PLG nanoparticles


title: Saline control, scRNAseq

description: 10x Genomics

value: intravenous saline


title: Patient 1336, convalescent sample

description:
1336x9q1
DENV_gene_count_matrix.csv

tag: timepoint

value: 15d post symptom onset

tag: age (years)

value: Secondary


title: Patient 1336, acute sample

description:
1336x1q1
DENV_gene_count_matrix.csv

value: 3d post symptom onset

tag: Sex


title: RNA-seq for HUES4 170-3 hESC-derived VFG passage 6 rep2

value: 170-3 PDX1-eGFP reporter

value: CD184-PeCy7 and CD117-APC double positive cells


title: 201B P32_12

description: SAMPLE 12

value: iPSC

value: Female

value: pMX retrovirus


title: Patient 1354, acute sample

description:
1354x1q1
DENV_gene_count_matrix.csv

value: 5d post symptom onset

value: M

tag: infection

value: Dengue Hemorrhagic Fever/Dengue Shock Syndrome


title: brain of C57BL/6, wild type, ICH+P7C3-A203

city: Xi’an

first: Yang

last: Wu

state: Shaanxi

address: 569 Xinsi Road

department: Department of Neurosurgery

country: China

institute: Tangdu Hospital, Air Force Medical University,

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
We aligned reads of all samples to the reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: build_3.00
Supplementary files format and content: count and FPKM

source_name: Brain

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp.

value: Brain

value: wild type

value: 72 hours after ICH+P7C3-A20 treatment


title: 201B P32_11

description: SAMPLE 11

value: PBMC


title: brain of C57BL/6, wild type, ICH+P7C3-A202


title: 201B P32_10

description: SAMPLE 10


title: Patient 1335, acute sample

description:
1335x1q1
DENV_gene_count_matrix.csv

value: Primary

tag: symptom

value: Dengue Fever


title: RNA-seq for HUES4 170-3 hESC-derived VFG passage 3 rep2


title: RNA-seq for HUES4 170-3 hESC-derived VFG passage 3 rep3


title: Patient 1342, convalescent sample

description:
1342x9q1
DENV_gene_count_matrix.csv

value: 15d post symptom onset


title: 201B P32_9

description: SAMPLE 9

tag: gender


title: Patient 1335, convalescent sample

description:
1335x9q1
DENV_gene_count_matrix.csv

value: 14d post symptom onset

tag: virus type


title: brain of C57BL/6, wild type, ICH3

value: 72 hours after ICH


title: RNA-seq for HUES4 170-3 hESC-derived VFG passage 3 rep1

value: 170-3 PDX1-eGFP reporter


title: brain of C57BL/6, wild type, ICH2


title: Patient 1332, convalescent sample

description:
1332x9q1
DENV_gene_count_matrix.csv

value: 18d post symptom onset


title: Patient 1332, acute sample

description:
1332x1q1
DENV_gene_count_matrix.csv


title: Patient 1329, convalescent sample

description:
1329x9q1
DENV_gene_count_matrix.csv

value: 17d post symptom onset

value: F

value: Secondary


title: RNA-seq for HUES4 170-3 hESC-derived ADE rep3

source_name: anterior definitive endoderm cells

value: CD184-PeCy7 and CD117-APC double positive cells


title: 201B P32_6

description: SAMPLE 6

value: iPSC

value: Female

tag: source cell

value: pMX retrovirus


title: RNA-seq for HUES4 170-3 hESC-derived ADE rep2


title: brain of C57BL/6, wild type, sham3

value: Brain

value: wild type

value: 72 hours after control treament


title: Patient 1329, acute sample

description:
1329x1q1
DENV_gene_count_matrix.csv

value: 5d post symptom onset


title: Patient 1327, convalescent sample

description:
1327x9q1
DENV_gene_count_matrix.csv

value: M

value: Dengue Fever


title: brain of C57BL/6, wild type, ICH+P7C3-A201

value: 72 hours after ICH+P7C3-A20 treatment


title: brain of C57BL/6, wild type, sham2


title: RNA-seq for HUES4 170-3 hESC-derived ADE rep1


title: RNA-seq for HUES4 170-3 hESC-derived VFG passage 6 rep1


title: 201B P32_5

description: SAMPLE 5

value: PBMC

tag: generation method


title: brain of C57BL/6, wild type, sham1

tag: strain


title: RNA-seq for HUES4 170-3 hESC rep3

source_name: embryonic stem cells

tag: genotype

value: 170-3 PDX1-eGFP reporter

value: unsorted


title: 201B P32_4

description: SAMPLE 4


title: 201B P32_3

description: SAMPLE 3


title: Patient 1325, convalescent sample

description:
1325x9q1
DENV_gene_count_matrix.csv

value: 17d post symptom onset

value: Primary


title: 201B P32_2

description: SAMPLE 2


title: brain of C57BL/6, wild type, ICH1

value: 72 hours after ICH


title: 201B P32_8

description: SAMPLE 8


title: 9_oxBS

city: Oklahoma City

first: Michael

last: Stout

state: OK

address: 825 N.E. 13th Street

department: Aging and Metabolism

institute: Oklahoma Medical Research Foundation

data_processing:
Prior to alignment, paired-end reads were adaptor-trimmed and filtered using Trimmomatic 0.35. End-trimming removed leading and trailing bases with Q-score<25, cropped 6 bases from the start of the read and 5 bases from the 3’ end, dropped reads less than 30 bases long, and dropped reads with an average Q-score<25.
Alignment of trimmed bisulfite converted sequences was carried out using Bismark 0.22.3 with Bowtie 2.3.1 against the mouse reference genome (GRCm38/mm10). Bams were de-duplicated using Bismark. Methylation call percentages for each CpG and non-CpG (CH) site within the genome were calculated by dividing the methylated counts over the total counts for that site in the oxidative bisulfite converted libraries (OXBS). Genome-wide CpG and CH methylation levels were calculated separately. Hydroxymethylation levels in CpG (hmCG) and CH (hmCH) contexts were calculated by subtracting methylation call levels from the oxidative bisulfite-converted (OXBS) libraries from the bisulfite converted (BS) libraries.
Deduplicated bam files generated by Bismark were run through MethylKit in R to generate context-specific (CpG/CH) coverage text files. Bisulfite conversion efficiency for C, mC, and hmC was estimated using CEGX spike-in control sequences. Untrimmed fastq files were run through CEGX QC v0.2, which output a fastqc_data.txt file containing the conversion mean for C, mC, and hmC.
Analysis of methylation levels in the proximity of the promoter region was performed on a list of all expressed genes as follows. The R package Enriched Heatmap40 was used to intersect site-specific methylation call files with genomic coordinates of gene lists. Flanking regions of 4,000 nucleotides were constructed upstream of the transcription start site (TSS) and downstream of the transcription end site (TES) and then split into 20 bins of 200 nucleotides each. The gene body was split into 27 equal bins, depending on the gene length.
Assembly: mm10
Supplementary files format and content: txt file, site-specific CpG methylation

source_name: retina

extract_protocol:
The purification of viable, cell-specific nuclei from brain tissue from Tam-induced Aldh1l1-cre/ERT2+; NuTRAP+ mice was achieved by combining two previously published protocols, with modifications. For each sample, two retinae were homogenized in 1 ml ice-cold nuclei EZ lysis buffer (#NUC-101, Millipore Sigma) supplemented with 1X Halt protease inhibitor cocktail (Thermo Fisher Scientific) and 1 mM DTT using a glass dounce tissue grinder set (20 times with pestle A and 20 times with pestle B). Undissociated tissue, largely composed of blood vessels, was removed by centrifugation at 200 x g for 1.5 min at 4°C, and the supernatant containing the nuclear material filtered through a 30 µm strainer and centrifuged at 500 x g for 5 min at 4°C. The resulting nuclear pellet was resuspended in nuclei lysis EZ buffer, incubated on ice for 5 min, washed by centrifugation, and resuspended in 200 µl nuclei EZ storage buffer by gentle trituration with a micropipette. From the total resuspended pellet volume, 10% was reserved as input nuclei fraction and the rest was diluted with 1.6 ml nuclei purification buffer (NPB: 20 mM HEPES, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 1X Halt protease inhibitor cocktail, 1mM DTT), and subjected to the INTACT protocol. Briefly, 30 µl of resuspended M-280 Streptavidin Dynabeads (#11205, Thermo Fisher Scientific) were added into a fresh 2 ml microcentrifuge tube and washed with 1 ml of NPB using a DynaMag-2 magnet (#12321; Thermo Fisher Scientific) for a total of three washes (1 min incubation/each). The washed beads were reconstituted to their initial volume (30 µl) with NPB and gently mixed with the nuclear suspension. The mixture of nuclei and magnetic beads was incubated at 4°C for 40 min under gentle rotation settings to allow the affinity binding of streptavidin beads to the cell-specific, biotinylated nuclei. After incubation, the streptavidin-bound nuclei were magnetically separated with the DynaMag-2 magnet for a period of 3 min. The nuclei bound to the beads were washed in the magnet for three washes (1 min/each), resuspended in 30 µl of NPB, and reserved as the positive nuclei fraction. From the nuclear fraction [input and positive (enriched in biotinylated nuclei)], an aliquot was mixed with equal volume of DAPI counterstain and used for confocal microscopy visualization. The AllPrep DNA/RNA kit Micro (#80284, Qiagen, Germantown, MD) was used to extract gDNA and nuclear RNA from each sample. gDNA and nuclear RNA were quantified with a Nanodrop One spectrophotometer (Thermo Fisher Scientific) and its quality assessed by genomic DNA D1000 (#5067-5582) and HSRNA ScreenTape, respectively, with a 4150 TapeStation analyzer.
For each input and positive INTACT-isolated sample 400 ng of gDNA was brought up to 50 µl volume with 1X low-EDTA TE buffer and sheared with a Covaris E220 sonicator (Covaris, Inc., Woburn, MA) to an average 200 base pair size using the following settings: intensity of 5, duty cycle of 10%, 200 cycles per burst, 2 cycles of 60 seconds, at 7°C. The size of sheared products was confirmed by capillary electrophoresis (DNA D1000, Agilent).  gDNA fragments were cleaned by an Agencourt bead-based purification protocol, after which gDNA was quantified (Qubit dsDNA, Thermo Fisher Scientific). Two aliquots of 62.2 ng DNA fragments were prepared in a 12 µl volume to which 1 µl of spike-in control DNA (0.08 ng/ul) with known levels of specific mC, hmC, and fC at individual sites was added.  End repair, ligation of methylated adaptors (#L2V11DR-BC 1-96 adaptor plate, NuGEN, Tecan Genomics, Inc., Redwood City, CA) and final repair were performed according to manufacturer’s instructions (Ovation Ultralow Methyl-Seq Library System, NuGEN).

value: retina

value: Aldhl1l-Cre/Ert2+; NuTRAP+

tag: fraction

value: oxBS

tag: animal number

tag: library type

value: WGoxBS

tag: library prep kit

value: Tecan Ultralow Methyl-Seq with TrueMethyl oxBS


title: Patient 1327, acute sample

description:
1327x1q1
DENV_gene_count_matrix.csv

value: 3d post symptom onset

value: Secondary


title: RNA-seq for HUES4 170-3 hESC rep2

tag: cell line

tag: facs sorted population


title: RNA-seq for HUES4 170-3 hESC rep1


title: 201B P32_7

description: SAMPLE 7

tag: cell type

value: iPSC

value: Female

value: pMX retrovirus


title: 9_BS

tag: tissue

value: BS


title: Patient 1325, acute sample

description:
1325x1q1
DENV_gene_count_matrix.csv

tag: timepoint

value: 4d post symptom onset

tag: age (years)

tag: Sex

value: M

value: Dengue Fever


title: Patient 1323, convalescent sample

description:
1323x9q1
DENV_gene_count_matrix.csv

value: 17d post symptom onset

tag: infection

tag: symptom


title: 201B P32_1

description: SAMPLE 1

tag: gender

tag: source cell

value: PBMC


title: RNA-seq for H9 wild type hESC-derived VFG passage 8 rep2

value: WT

value: CD184-PeCy7 and CD117-APC double positive cells


title: 7_BS

value: retina

value: Aldhl1l-Cre/Ert2+; NuTRAP+


title: H9_2_Endoderm

description: SAMPLE 390

source_name: Differentiated cells from ESC (WiCell institute)

value: ESC

tag: generation method


title: Patient 1323, acute sample

description:
1323x1q1
DENV_gene_count_matrix.csv

value: 2d post symptom onset

value: Primary

tag: virus type


title: H9_2_Ectoderm

description: SAMPLE 389


title: Patient 1322, convalescent sample

description:
1322x9q1
DENV_gene_count_matrix.csv

value: 16d post symptom onset

value: Secondary


title: 6_oxBS

tag: genotype

tag: fraction

value: oxBS

value: WGoxBS

value: Tecan Ultralow Methyl-Seq with TrueMethyl oxBS


title: 6_BS

value: BS

tag: animal number

tag: library type


title: H9_Mesoderm

description: SAMPLE 388

value: Female


title: RNA-seq for H9 wild type hESC-derived ADE rep2

tag: cell line


title: RNA-seq for H9 wild type hESC-derived VFG passage 8 rep1

tag: facs sorted population


title: RNA-seq for H9 wild type hESC-derived ADE rep3


title: 4_oxBS

tag: library prep kit


title: Patient 1322, acute sample

description:
1322x1q1
DENV_gene_count_matrix.csv

value: 4d post symptom onset

value: M

value: Dengue Fever


title: 7_oxBS

tag: tissue


title: Patient 1321, convalescent sample

description:
1321x9q1
DENV_gene_count_matrix.csv

tag: timepoint

value: 23d post symptom onset

value: Dengue Hemorrhagic Fever/Dengue Shock Syndrome


title: H9_Ectoderm

description: SAMPLE 386

tag: cell type


title: RNA-seq for H9 wild type hESC-derived ADE rep1

value: WT

value: CD184-PeCy7 and CD117-APC double positive cells


title: 4_BS

value: retina

value: Aldhl1l-Cre/Ert2+; NuTRAP+


title: H9_Endoderm

description: SAMPLE 387

value: ESC


title: RNA-seq for H9 wild type hESC-derived VFG passage 8 rep3


title: 3_oxBS


title: Patient 1312, convalescent sample

description:
1312x9q1
DENV_gene_count_matrix.csv

value: 18d post symptom onset

tag: age (years)

tag: Sex


title: Patient 1321, acute sample

description:
1321x1q1
DENV_gene_count_matrix.csv

value: 5d post symptom onset

tag: infection

value: Secondary

tag: symptom


title: H9_2_Mesoderm

description: SAMPLE 391

tag: gender

tag: source cell


title: RNA-seq for H9 wild type hESC rep2

value: unsorted


title: RNA-seq for H9 wild type hESC rep3


title: KthES14_Mesoderm

description: SAMPLE 385

source_name: Differentiated cells from ESC (Kyoto university)

tag: generation method


title: Patient 1312, acute sample

description:
1312x1q1
DENV_gene_count_matrix.csv

value: 3d post symptom onset

tag: virus type


title: 1_oxBS

tag: genotype

tag: fraction

value: oxBS

value: WGoxBS

value: Tecan Ultralow Methyl-Seq with TrueMethyl oxBS


title: RNA-seq for H9 wild type hESC rep1


title: KthES14_Endoderm

description: SAMPLE 384

value: Female


title: KthES14_Ectoderm

description: SAMPLE 383


title: Patient 1310, convalescent sample

description:
1310x9q1
DENV_gene_count_matrix.csv

value: 17d post symptom onset

value: M

value: Primary

value: Dengue Fever


title: 1_BS

value: BS

tag: animal number

tag: library type


title: CCR2+ TREM2KO Macrophages KO3

city: Boston

first: Ming

last: Zhai

state: Massachusetts

address: Avenue Louis Pasteur

department: Cardiovascular Division, Department of Medicine

institute: Brigham and Women's Hospital

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: Macrophage

growth_protocol: C3H 10T1/2 mesenchymal cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Adipogenic differentiation was induced by treatment of 2-day post confluent cells (designated day 0, D0) with 10ug/ml insulin (Sigma),

value: Macrophage

tag: disease state

value: post Myocardial infarction


title: Patient 1310, acute sample

description:
1310x1q1
DENV_gene_count_matrix.csv


title: CCR2+ TREM2KO Macrophages KO2


title: KthES13_Mesoderm

description: SAMPLE 382

value: ESC


title: Patient 1309, convalescent sample

description:
1309x9q1
DENV_gene_count_matrix.csv

value: 19d post symptom onset

value: F


title: KthES13_Endoderm

description: SAMPLE 381


title: CCR2+ TREM2KO Macrophages KO1


title: In vitro Effector-Polarized (IL-2) CD8 T Cells

city: Leuven

first: Juan

last: Fernández-García

address: Campus Gasthuisberg, O&N4, Herestraat 49, box 912

department: VIB-KU Leuven Center for Cancer Biology

country: Belgium

institute: VIB/KU Leuven

description: 10x Genomics Single-Cell Gene Expression 3' v2

data_processing:
Single-cell libraries were sequenced on an Illumina NovaSeq 6000 System. Sequenced reads were then mapped to the mouse genome (mm10 build GRCm38.p4) using the 10x Genomics Cell Ranger software, and the resulting single-cell gene expression data was analyzed within the R/Bioconductor framework. Specifically, raw UMI count matrices for each sample were first imported using Seurat v2.3.4, and then converted for further processing with Monocle3-alpha v2.99.3.
Low-quality cells were first filtered based on standard quality-control metrics, with sample-specific thresholds chosen based on evaluating quality-control histograms for each sample independently. In particular, cells were filtered based on their mitochondrial RNA content (allowing for a maximum of 5% in all cases), library size (removing cells with total UMI counts below 1000/2500/2000 for the Activated/Effector/Memory samples, respectively), and number of detected genes (removing cells expressing less than 350/800/700 genes for the Activated/Effector/Memory samples, respectively). Genes expressed in less than 10 cells were additionally ignored in all subsequent analyses.
Size-factor and variance-stabilizing normalization (based on fitting to a negative binomial distribution) were applied to the filtered data sets, and highly-variable genes (HVGs) were identified for each of them based on their departure from the average normalized dispersion versus expression trend observed among all genes. After excluding mitochondrial, ribosomal-protein, and cell cycle-associated genes, the top 1000 HVGs with size-factor normalized expressions above 0.005 were selected for each sample. Principal component analysis (PCA) was then performed on the size factor-normalized and variance-stabilized count matrix restricted to these HVGs only, followed by 2D UMAP dimensional reduction based on the resulting top 50 principal components (with correlation distance metric, number of neighbors = 15, and minimum distance = 0.05, and without further PCA scaling). Cells were then clustered in the UMAP plane by applying the Louvain graph-based algorithm at high resolution (kNN = 5/10/5 for the Activated/Effector/Memory samples, respectively), in order to attain a fine-grained cluster structure for each sample (69/66/40 clusters for the activation/effector/memory samples, respectively).
Fine-grained clusters displaying features indicative of low quality (e.g. elevated Actb content and/or low number of detected genes relative to neighboring clusters, or markedly high expression of apoptosis and/or exhaustion markers) were removed for all subsequent analyses at this point. The remaining fine-grained clusters were manually annotated to specific cell states, based on evaluating the cluster-averaged normalized expression profiles of a number of cell state-specific markers.
UMAP dimensional reduction was also performed on a merged differentiation sample, consisting of both the Effector/Memory-polarized samples put together. The latter was processed analogously as described above for the single samples, with some particularities. First, cell filtering was performed simply by removing all cells previously filtered out from the corresponding Effector/Memory-polarized single-sample data sets. Second, UMAP dimensional reduction was performed using cosine distance metric and increased number of neighbors (30) and minimum distance (0.2) parameters, to account for the increased cell numbers. Finally, formal clustering was not performed on this merged differentiation sample, but instead the cell-state annotations derived from the corresponding Effector/Memory-polarized single-sample data sets were transferred to their merged counterpart.
Assembly: mm10 build GRCm38.p4
Supplementary files format and content: For each sample, the raw-count output of the 10x Genomics CellRanger pipeline is provided in the form of a MatrixMarket sparse matrix with gene|barcode|counts triplets (matrix_SID.mtx, where SID = ACT/EFF/MEM for the Activated/Effector-polarized/Memory-Polarized samples, respectively), together with the corresponding gene (genes_SID.tsv) and barcode (barcodes_SID.tsv) index files. In addition, analogous supplementary files are provided containing a merged gene|barcode|counts sparse matrix for the combination of all three samples (matrix_AllSamples.mtx, genes_AllSamples.tsv, barcodes_AllSamples.tsv), after removing cells based on standard quality-control metrics (mitochondrial RNA content, library size, and number of detected genes), but before filtering out low-quality fine-grained clusters within each sample. The latter are accompanied by text-based tables (GeneMetaData_AllSamples.txt, CellMetaData_AllSamples.txt) with all the relevant gene/cell meta data needed to reproduce the results of our final analysis, including quality-control metrics, cell-state annotations, single-sample fine-grained cluster assignments, and single-sample (or merged-sample) UMAP coordinates. A description of the full contents of these meta data tables is provided in a separate text file (MetaDataDescription_AllSamples.txt).

source_name: Isolated from Spleen

growth_protocol: Naïve CD8+ T cells were isolated from the spleens of 11-week-old OT-I transgenic mice by negative selection using the MojoSort™ Mouse CD8 Naïve T Cell Isolation Kit. Flat-bottom 96-well plates were coated overnight at 4°C with 50 µL/well of 10 µg/mL anti-mouse CD3ε in PBS. Freshly isolated naïve CD8+ T cells were then seeded at ~0.5 x 10^6 cells/mL in culture medium supplemented with 0.5 µg/mL soluble anti-mouse CD28 and 10 ng/mL (~50 U/mL) recombinant murine Interleukin-2 (IL-2), and activated for 24h (Activated sample) or 54h (Effector/Memory-polarized samples). For Effector/Memory-polarized samples, cells were harvested after 54h activation and re-plated in round-bottom 96-well plates at ~0.25 x 10^6 cells/mL in fresh culture medium supplemented with either 10 ng/mL IL-2 (Effector-polarized) or 50 ng/mL (~10 U/mL) recombinant murine Interleukin-15 (IL-15; Memory-polarized). Cells were then differentiated for 144h in either condition, subject to daily harvesting and re-plating in new round-bottom 96-well plates at ~0.5 x 10^6 cells/mL in fresh culture media supplemented with either cytokine (IL-2/15 for Effector/Memory-polarized, respectively). All experiments were performed in humidified temperature/CO2-controlled (37°C, 5% CO2) incubators, and using a custom home-made blood-like medium (BLM), whose formulation/preparation has been described elsewhere (see DOI: 10.1007/978-1-4939-8769-6_14). BLM was in all cases supplemented with 10% fetal bovine serum, 100 U/mL penicillin, 100 µg/mL streptomycin, and 50 µM β-mercaptoethanol.

extract_protocol:
For the Activated sample, CD8+ T cells were collected after 24h in vitro stimulation and subject to dead-cell removal using a MACS® Dead Cell Removal Kit. In brief, ~2 x 10^6 cells were pooled from 24 culture wells and resuspended in 100 µL Dead Cell Removal MicroBeads suspension, following the manufacturer’s guidelines thereafter. The purified live-cell suspension (~90% viability) was then washed once with fresh culture medium, and resuspended at ~10^6 cells/mL in fresh culture medium supplemented with 10 ng/mL IL-2. Dead cell removal was not necessary for the 144h Effector-polarized (~90% viability) or Memory-polarized (~70% viability) samples, in which case ~10^6 cells/sample were pooled from 6 culture wells each, washed once with fresh culture media, and resuspended at ~10^6 cells/mL in fresh culture media supplemented with either 10 ng/mL IL-2 (Effector-polarized) or 50 ng/mL IL-15 (Memory-polarized). Cell suspensions were kept on ice and immediately processed for single-cell library preparation.
Cell suspensions for each sample were converted to barcoded single-cell cDNA libraries using the Chromium Single Cell 3’ v2 Library, Gel Bead, Chip, and Multiplex Kit, following the manufacturer’s guidelines, and aiming for a total of 10000 cells per library.

value: CD8 T Cells

value: Isolated from Spleen

tag: strain

value: C57BL/6-Tg(TcraTcrb)1100Mjb/Crl (OT-I)

value: Male

tag: age

value: 11 weeks old

tag: treatment


title: 3_BS

tag: tissue

value: retina

value: Aldhl1l-Cre/Ert2+; NuTRAP+

value: WGoxBS

tag: library prep kit

value: Tecan Ultralow Methyl-Seq with TrueMethyl oxBS


title: Patient 1309, acute sample

description:
1309x1q1
DENV_gene_count_matrix.csv

tag: timepoint

value: 4d post symptom onset

tag: age (years)

tag: Sex

value: Secondary


title: CCR2+ Macrophages Control3

tag: cell type

value: WT


title: KthES12_2_Mesoderm

description: SAMPLE 379

tag: gender

value: Female

tag: source cell


title: CCR2+ Macrophages Control2

value: Macrophage

value: post Myocardial infarction


title: In vitro Activated CD8 T Cells

value: anti-CD3/28 + IL-2 + Dead-Cell Removal


title: Patient 1308, convalescent sample

description:
1308x9q2
DENV_gene_count_matrix.csv

value: 17d post symptom onset

value: F

tag: infection

tag: symptom

value: Dengue Fever

tag: virus type


title: Patient 1308, acute sample

description:
1308x1q2
DENV_gene_count_matrix.csv


title: Patient 1306, convalescent sample

description:
1306x9q1
DENV_gene_count_matrix.csv

value: 26d post symptom onset

value: Primary


title: CCR2+ Macrophages Control1

tag: genotype


title: KthES12_2_Ectoderm

description: SAMPLE 377

value: ESC

tag: generation method


title: KthES12_2_Endoderm

description: SAMPLE 378


title: GA 8

city: Amsterdam

first: Sara

last: Mainardi

address: Plesmanlaan 121

country: Netherlands

institute: The Netherlands Cancer Institute

data_processing:
Perform alignment against reference genome mm10 (BAM-files)
Default multiplexing - Index in separate read. Not barcoded
Assembly: mm10
Supplementary files format and content: csv file, matrix table with normalized abundance

source_name: pancreas

extract_protocol:
RNA was extracted using the RNeasy Mini Kit from Qiagen and analyzed using an Agilent 2100 Bioanalyzer system
[W17] polyA+ stranded RNA Library prep from tissue

value: pancreas

tag: cell line

value: KCPmut

value: epithelial pancreatic cancer cells

value: KrasG12D (Krastm4Tyj); Pdx1-Cre (Tg(Pdx1-cre)6Tuv); Trp53mut/+(Trp53tm1Tyj)


title: Patient 1306, acute sample

description:
1306x1q1
DENV_gene_count_matrix.csv

value: 3d post symptom onset


title: EtOH Brain, E2, Sample 3, Batch 2

city: Rockville

first: Danielle

last: Sambo

state: MD

address: 5625 Fishers Lane

institute: National Institute on Alcohol Abuse and Alcoholism

data_processing:
10X Genomics Cell Ranger Single Cell pipeline was used to demultiplex samples, process and align barcodes, and integrate samples using the default and recommended parameters.
Assembly: Cellranger’s default mm10 reference dataset was used for alignment.
Supplementary files format and content: Data files contain the raw counts per cell for each sample and cluster. No processed data is included for Sal5 because this sample was excluded from downstream analysis.

source_name: Brain, cortex

extract_protocol:
Nuclei were isolated. RNA was extracted during library preparation using the Single Cell 3’ V3.1 Reagent Kit.
Nuclei were isolated and library preparation was completed using the 10X Single Cell Version 3.1 chemistry per the manufacturer’s instructions.

value: Brain, cortex

value: Embrynoic day 14

tag: pregnant dam

value: EtOH


title: EtOH Brain, E2, Sample 4, Batch 2

tag: age


title: GA 4

tag: treatment


title: EtOH Brain, E2, Sample 2, Batch 2

tag: tissue


title: Patient 1304, convalescent sample

description:
1304x9q1
DENV_gene_count_matrix.csv

value: M

value: Secondary


title: KthES12_Endoderm

description: SAMPLE 376

data_processing: Fluorescent intensities were loaded and processed for backgroud correction by limma package of R software. Values were log-transformed and normalized by quantile normalization.

extract_protocol: RNA was extracted by using TRIzol reagent (Thermo Fisher) and purifed by using RNA easy mini kit (QIAGEN).

value: Female


title: In vitro Memory-Polarized (IL-15) CD8 T Cells

value: CD8 T Cells

value: Isolated from Spleen

tag: strain

value: C57BL/6-Tg(TcraTcrb)1100Mjb/Crl (OT-I)

value: Male

value: 11 weeks old


title: KthES12_Mesoderm

description: SAMPLE 375

value: ESC


title: Control 2

value: pancreas

value: Vehicle


title: Patient 1304, acute sample

description:
1304x1q1
DENV_gene_count_matrix.csv

tag: timepoint

value: 4d post symptom onset

value: Dengue Fever


title: KthES11_Mesoderm

description: SAMPLE 374


title: EtOH Brain, E1, Sample 2, Batch 1


title: EtOH Brain, E2, Sample 1, Batch 2


title: Control 1

value: KCPmut

value: epithelial pancreatic cancer cells

value: KrasG12D (Krastm4Tyj); Pdx1-Cre (Tg(Pdx1-cre)6Tuv); Trp53mut/+(Trp53tm1Tyj)


title: KthES13_Ectoderm

description: SAMPLE 380


title: Patient 1303, convalescent sample

description:
1303x9q1
DENV_gene_count_matrix.csv

value: 29d post symptom onset

tag: age (years)

value: F


title: EtOH Brain, E1, Sample 1, Batch 1

value: Brain, cortex

value: Embrynoic day 14

value: EtOH


title: KthES11_Endoderm

description: SAMPLE 373

value: Female


title: KthES11_Ectoderm

description: SAMPLE 372


title: Saline Brain, S2, Sample 4, Batch 2

value: Saline


title: Patient 1302, convalescent sample

description:
1302x9q1
DENV_gene_count_matrix.csv

value: 18d post symptom onset

tag: Sex

value: M

value: Secondary


title: SEc12-E3

first: Anna

last: Greka

state: MA

address: 415 Main St

department: Kidney Disease Initiative

institute: Broad Institute of MIT and Harvard

description: 10x Genomics

data_processing:
cellranger-6.0.2
Samples raw base calls demultiplexing, barcoded processing, sequence alignment and gene counting  were made using the Cell Ranger software 6.0.2 function. Raw sequence reads were aligned to the latest mouse reference genome (mm10).
Downstream analysis were performed in the R programming language for graphics and statistical computing version 4.0.3 (R-v4.0.3).
Data analysis and visualization were performed using Seurat within R.
Assembly: mm10_v3.0.0
Supplementary files format and content: h5 files from CellRanger

source_name: Whole kidney cell suspensions

extract_protocol: Each animal was perfused with 20 ml of cold PBS, and then 1/2 of the kidney was sampled and quicly placed in media with 2% FBS on ice. After micing with razor blade, the remainings were transferred to 1X Liberase TH (Millipore Sigma) dissociation medium and subjected to single cell dissociation.

treatment_protocol:
Mice were injected with either vehicle or PTH (1-34, 300 ug/kg) or SK-124 (40 mg/kg) and sacrified using CO2 inhalation, 90 minutes or 2.5 hours post injection, resectively.
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)

value: Whole kidney cell suspensions

tag: cell type

value: Kidney

value: PTH

tag: age (weeks)


title: SEc13-E4

description: 10x Genomics


title: DRXT28s05_Mesoderm

description: SAMPLE 371

source_name: Differentiated cells from HLA homozygous iPSC

tag: gender

value: Male

tag: source cell

value: PBMC

value: pCE episomal vector


title: Saline Brain, S2, Sample 3, Batch 2


title: SEc11-E2

description: 10x Genomics

value: VEH


title: DRXT28s05_Endoderm

description: SAMPLE 370


title: Patient 1302, acute sample

description:
1302x1q1
DENV_gene_count_matrix.csv

value: 5d post symptom onset

tag: infection

tag: symptom

value: Dengue Fever


title: SEc10-E1

description: 10x Genomics


title: DRXT28s05_Ectoderm

description: SAMPLE 369


title: SEc9-D12

description: 10x Genomics


title: SEc8-D11

description: 10x Genomics


title: YZWJs524_Mesoderm

description: SAMPLE 368

value: Cord blood


title: Saline Brain, S2, Sample 2, Batch 2

value: Brain, cortex

value: Embrynoic day 14


title: Patient 1298, convalescent sample

description:
1298x9q1
DENV_gene_count_matrix.csv

tag: virus type


title: Patient 1298, acute sample

description:
1298x1q1
DENV_gene_count_matrix.csv


title: Patient 1293, convalescent sample

description:
1293x9q1
DENV_gene_count_matrix.csv

value: 16d post symptom onset

value: Dengue Hemorrhagic Fever/Dengue Shock Syndrome


title: YZWJs524_Endoderm

description: SAMPLE 367

tag: generation method


title: Saline Brain, S2, Sample 1, Batch 2

value: Saline