title: DG, MeOH-fixed

city: Jena

first: Anja

last: Urbach

address: Am Klinikum 1

department: Neurology

institute: Universitätsklinikum Jena

description: droplet-baesd scRNAseq

data_processing:
Pre-processing of droplet-based datasets was conducted using R (v4.2.0) and the Seurat package v4.1.0. Briefly, for the MeOH-fixed sample, the raw count matrix was decontaminated using DecontX (Yang et al., 2020) and barcodes were considered high-quality cells when their total transcript counts were between 1000 and 35000, total genes more than 1000, mitochondrial genes less than 15% and a transcript to gene ratio greater than 1.2. Doublets were removed by applying scDblFinder algorithm (Germain et al., 2021) obtaining 5122 high-quality singlets. After Seurat integration and PCA, the first 15 PCs were selected to describe the merged dataset, utilized for UMAP representation and graph-based clustering. The seurat function ‘FindAllMarkers’ was applied (adjusted p-value < 0.05 (FDR correction), log-fold change ≥ 0.5 and ratio of the detection fraction between the cluster and the rest (pct.1/pct.2) > 2.5) in order to find markers differentially expressed in each cluster to match the clusters to cell types.
Assembly: GRCm38 mouse reference genome
Supplementary files format and content: Filtered_raw_count_matrix.csv (comma-separated files including expression values for MeOH-fixed filtered cells)
Supplementary files format and content: Metadata_filtered.csv (comma-separated files including metadata for MeOH-fixed filtered cells)

source_name: Brain

extract_protocol:
DGs of 5 mice were dissected as whole mounts in HBSS with calcium, magnesium and 10 mM glucose. Each DG was individually subjected to enzymatic and mechanical dissociation according to manufacturer's protocols (Papain Dissociation System, Worthington kit). Single cells were obtained in HBSS with calcium, magnesium and 0.1 M D-(+)-Trehalose dihydrate at 4 °C and kept on ice. After evaluation of the density and viability of the cell suspensions they were pooled at equal ratios and MeOH-fixed. Cells were kept at -20°C for 30 min and then stored at -80°C for 3 weeks. For rehydration, suspensions were moved from -80°C to 4°C on ice and kept for 5 min to equilibrate the temperature. Cells were pelleted at 1000 rcf at 4°C for 5 min, and resuspended in 3X SSC Buffer with 0.04% BSA, 0.2 U/µl of RNase inhibitor and 1 mM DL-Dithiothreitol.
P28 mouse MeOH-fixed cells were shipped on dry ice to Single Cell Discoveries. Prior to loading the 10x Chromium chip, cells were rehydrated as described in section 2.3, filtered and counted. Cells were loaded in a concentration of 700-1200 cells/µl on a 10x Genomics chip aiming for 10000 cells, and the chip was run on a Chromium controller to initiate GEM formation. Library preparation was performed following standard 10x Genomics guidelines 3’ v3.1 workflow with feature barcoding (CG000317 guide) to generate gene expression libraries. The resulting cDNA libraries were paired-end sequenced on Illumina NovaSeq S4 Flow Cell chip on a NextSeq6000 platform (read 1: 28 cycles, index reads: 2×10 cycles, read 2: 90 cycles) to obtain an average of 70000 reads per cell   . FASTQ files were generated from BCL files with 10x Genomics Cell Ranger (Zheng et al., 2017), mkfastq 6.0. Read 1 was used for identification of cell barcode and UMI. Read 2 was used to map to the reference genome GRCm38 mouse. Filtering of empty barcodes was done following standard Cell Ranger procedures.
10x Genomics Kit 3’ v3.1 (CG000317 guide)

value: Brain

value: DG cells

tag: age

value: 4-5 weeks old

tag: treatment

value: MeOH-fixed


title: prostate cancer patient pre-treatment serum, ENACT3000

status: Public on Sep 22 2023

type: RNA

city: Chicago

first: Morgan

last: Zenner

state: IL

address: 909 South Wolcott Ave

department: Pathology

country: USA

institute: University of Illinois at Chicago College of Medicine

data_processing:
The raw data (raw CT) values were input into GeneGlobe with a CT cutoff value of 33. In the GeneGlobe preprocessing, all CTs greater than 33 were changed to a value of 33 and the CTs were adjusted for the interplate calibrator (UniSp3) according to the miRCURY LNA miRNA PCR Panels & Assays Data Analysis Handbook.
Normalization values for each sample were calculated using the NormFinder method in GeneGlobe. The microRNAs used for normalization of serum samples included: miR-107, miR-24-3p, let-7i-5p, miR-19b-3p, miR-16-5p, miR-320a, miR-23a-3p, miR-21-5p, let-7b-5p, and miR-25-3p. The microRNAs included for normalization of serum EV samples included: included hsa-miR-107, hsa-miR-24-3p, hsa-miR-30c-5p, hsa-miR-93-5p, hsa-let-7i-5p, hsa-miR-222-3p, hsa-miR-27a-3p, hsa-miR-23a-3p, hsa-miR-21-5p, and hsa-miR-27b-3p.
These normalized values were then used to make comparisons between groups (adverse pathology versus not adverse pathology) to determine significantly different microRNAs using p < 0.05
The significant microRNAs were then used to generate random forest models to predict adverse pathology
The Fold Change Template shows the p-values for each microRNA. The microRNAs with p<0.05 were included in the random forest model to predict adverse pathology.

label: SYBR Green

molecule: total RNA

organism: Homo sapiens

source_name: peripheral venous source

label_protocol: PCR assay were performed using a miRCURY LNA miRNA Custom PCR Panel Catalog#YCA25430 (Qiagen) following the manufacturers instructions. Reverse transcription was performed from 5µ L total RNA using the miRCURY LNA RT Kit (Qiagen). Quantitative real-time PCR were performed (Applied Biosystems ViiA 7) with 40 cycles at 95C for 10 seconds and 56C for 60 seconds.

extract_protocol: Total RNA was extracted with the miRNeasy Serum/Plasma kit (Qiagen).

tag: patient id

tag: disease state

value: prostate cancer

tag: tissue

value: serum

tag: sample type

tag: grade of prostate cancer at biopsy

value: low-grade (0)

tag: capra risk

value: LOW

tag: capra score

tag: fraction

value: microRNA


title: P34_12wks_F_Input

type: SRA

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: Genomic DNA from placenta tissue

library_source: genomic

data_processing:
The ChIP-seq reads were aligned to the hg38 human reference genome using the Bowtie software package (Langmead et al, 2009) .
Mapped reads were further converted to “bed” files for later Metagene and read-density analyses by using the BEDTools software package  (Quinlan et al, 2010).
Assembly: hg38
Supplementary files format and content: peaks.txt

molecule: genomic DNA

source_name: placenta villous core

extract_protocol:
Frozen tissue was pulverized using a liquid nitrogen-chilled hammer mill, crosslinked with 1% formaldehyde in a volume of 10mL, quenched by addition of 5mL 2.5 M   glycine for 5 min at 4°C, washed generously in ice-cold PBS, and homogenized in Farnham Lysis Buffer [5 mM PIPES pH 8, 85 mM KCl, 0.5% NP-40, 1 mM DTT, 1x cOmplete protease inhibitor cocktail (Roche, 11697498001)], as described (Murakami et al., 2017).  The nuclei were collected by brief centrifugation and resuspended in SDS Lysis Buffer (50 mM Tris-HCl pH 7.9, 1% SDS, 10 mM EDTA, 1 mM DTT, 1x cOmplete protease inhibitor cocktail) by pipetting and incubating on ice for 10 min.
The chromatin was sheared to ~200 bp DNA fragments by sonication using a Bioruptor sonicator (Diagenode) for 24-28 cycles of 30 sec on and 30 sec off.  Fragment size was verified by agarose gel electrophoresis before quantification of protein concentrations using a BCA protein assay kit (Pierce, 23225). 100 µg of soluble chromatin was precleared with Protein A Dynabeads (Invitrogen, 10001D) before incubation overnight with 2.5 g of antibody: H3K4me1 (Abcam, ab8895) or H3K27ac (Abcam, ab4729).  ChIP-seq libraries were constructed as described previously (Franco et al., 2015)

tag: gestational age in weeks

tag: Sex

value: F

tag: trimester


title: PAX5-TSS-b del, viewpoint 1, rep 1

city: New York

first: Uttiya

last: Basu

address: 701 West 168 Street

institute: Columbia University

data_processing:
Adapter sequences and low-quality ends were trimmed using Cutadapt (version 3.3). Paired-end reads were mapped to viewpoint sequences to identify the valid capture sequences which were aligned to human reference genome (hg38) using Bowtie 2 (version 2.2.9) with default parameter to determine the interacting loci. RPM (reads per million)-normalized bedgraph files were then generated for visualization in IGV and circles plot based on the mapping of captured sequences.
Assembly: hg38
Supplementary files format and content: bedgraph files containing RPM normalized count of captured reads
Library strategy: 4C-Seq

source_name: Lymph node

growth_protocol: All PAX5-TSS2 point mutation clones, deletion clones or wild type clones of SU-DHL-10 were cultured in RPMI, 10 % fetal bovine serum, 1x NEAA, 1mM Sodium Pyruvate, 2mM glutamine, 10mM HEPES, 1x penicillin/streptomycin. Cells were cultured at 37℃ at 5% CO2.

extract_protocol:
Cells were fixed with 4% formaldehyde for 10 minutes. After quenching and cell lysis, cross-linked genomic DNA was digested with HindIII followed by ligation with T4 ligase. After reversion of cross-linking, second digestion with DpnII was performed, then ligate the DNA with T4 ligase to generate circulated DNA.
NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1) and NEBNext® Ultra™ II Q5® Master Mix were used to add index for Illumina sequencing after PCR with different viewpoint primer sets and circulated DNA.

value: Lymph node

tag: cell line

tag: cell type

value: B lymphocyte

tag: genotype

tag: bait


title: prostate cancer patient pre-treatment serum, ENACT2009

value: high-grade (1)


title: P42_10wks_M_H3K27ac

description: H3K27 ChIP-enriched DNA from placenta tissue

value: M


title: prostate cancer patient pre-treatment serum, ENACT2008

value: INTERMEDIATE


title: PAX5-TSS-a WT, viewpoint 1, rep 3

value: WT


title: P34_12wks_F_H3K4me1

description: H3K4me1 ChIP-enriched DNA from placenta tissue


title: Mdx_NSG_Pax7ko_8dpi

city: Irvine

first: Michael

last: Hicks

state: CA

address: 845 Health Sciences Road, Room 3101

institute: University of California, Irvine

description:
AP4
All Nuclei

library_source: transcriptomic single cell

data_processing:
Bioanalyzer/tape station for RIN values.
CellRanger
Assembly: mm10
Supplementary files format and content: Summary metrics data of processed reads, Cloupe file for use in Loupe Browser, matrix.H5 file for use in R Studio, .rds file is processed in R Studio and Seurat for unique genes and PCA.
Supplementary files format and content: Combined Summary of Sequencing Reads. Combined .rds file is processed in R Studio and Seurat for unique genes and PCA, Differential Gene Expression by Population, DotPlot of key myogenic genes by population, Featureplot of key myofiber type IIB identifier genes, R script used for analysis of combined RDS files.

organism: Mus musculus

source_name: Skeletal Muscle, Tibialis Anterior

extract_protocol:
10X Genomics Frankenstine protocol using freshly dissected mouse skeletal muscle.
10X Genomics single nucleus RNA seq.
Paired End 2x50 bp reads.

value: Skeletal Muscle, Tibialis Anterior


title: P34_12wks_F_H3K27ac


title: PAX5-TSS-a WT, viewpoint 1, rep 2


title: prostate cancer patient pre-treatment serum, ENACT2007


title: Mdx_NSG_8dpi

description:
AP3
All Nuclei


title: P32_39wks_F_Input

description: Genomic DNA from placenta tissue


title: PAX5-TSS-a WT, viewpoint 1, rep 1


title: Asyn_ESRRB_rep2

city: Memphis

first: Xiaolong

last: Chen

state: TN

address: 262 Danny Thomas Pl

institute: St Jude Children's Research Hospital

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were aligned to mouse genome assembly mm10 by BWA(0.7.17） by internal automatically mapping pipeline.
Uniquely mapped reads for ChIP-seq were obtained using samtools (V1,10), with parameter “-q 10 -F1024".
Stringent peaks for each replicate were called by MACS2 (V 2.1.1.20160309, with default parameters using Input (for ChIP-seq) as control and filtered with fold enrichment cutoff: 5 and p-value threshold: 1e-9.
RPM was applied to the normalized read counts to generatebigwigtracks
Assembly: mm10
Supplementary files format and content: bigwig files of normalized read counts.
Supplementary files format and content: narrowPeak from MACS2

source_name: embryonic stem cells

growth_protocol: mESCs were cultured in Knockout DMEM supplemented with 15% ES-qualified FBS, 1% NEAA, 1% GlutaMAX, 0.5 mM beta-mercaptoethanol, and 10 ng/ml mLIF on 0.1% gelatin-coated tissue culture dishes.

extract_protocol:
truChIP® Chromatin Shearing Kit (https://www.covaris.com/products-services/kits-reagents/truchip)
KAPA Hyper Prep Kit (KK8504)

treatment_protocol: For mitotic synchronization, mESCs were treated with 100 ng/ml nocodazole for 6 hours, and then mitotic cells were collected by gently shake-off.

value: mouse embryonic stem cells

tag: strain

value: untreatment

tag: antibody

value: Rabbit (DA1E) mAb IgG XP® Isotype Control (CST#3900S)


title: P32_39wks_F_H3K4me1


title: Mdx_NSG

description:
AP1
All Nuclei

tag: treatment


title: prostate cancer patient pre-treatment serum, ENACT2006

tag: patient id

tag: disease state

tag: ap


title: Tfe3-ERT2_Tamoxifen_3

first: Lydia

last: Finley

state: NY

address: 430 E 67th St

department: Cell Biology Program

institute: Memorial Sloan Kettering Cancer Center

library_source: transcriptomic

data_processing:
Quality control and filtering of raw fastq files was performed using fastp.
Sequencing reads were aligned to mm10 using STAR.
Raw counts were generated using featurecounts.
Assembly: mm10
Supplementary files format and content: Processed data files include raw counts for each sample in CSV format.

source_name: mESC

growth_protocol: ES cells were maintained on gelatin-coated plates in serum/LIF media. Serum/LIF medium contained knockout DMEM (10829018; Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (FBS; Gemini), 0.1 mM 2-mercaptoethanol, 2 mM l-glutamine and 1,000 U ml−1 LIF (Gemini).

extract_protocol:
RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions. 500 ng of total RNA was used as input for sequencing library construction.
RNA libraries were prepared using the TruSeq Stranded mRNA LT Kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: Tfe3 nuclear translocation was induced by treating cells with 4-hydroxytamoxifen (1µg/mL, Sigma Aldrich) for 48 hours. Ethanol was used as a vehicle control.

value: mESC


title: prostate cancer patient pre-treatment serum, ENACT2005

value: prostate cancer

tag: tissue

tag: sample type

tag: grade of prostate cancer at biopsy


title: Tfe3-ERT2_Tamoxifen_2


title: prostate cancer patient pre-treatment serum, ENACT2003

value: serum

tag: capra risk

tag: capra score

tag: fraction


title: P32_39wks_F_H3K27ac

tag: gestational age in weeks

tag: Sex

tag: trimester


title: prostate cancer patient pre-treatment serum, ENACT2002


title: Tfe3-ERT2_Tamoxifen_1

tag: cell type


title: PAX5-TSS-a mut, viewpoint 1, rep 2

tag: cell line

tag: genotype

tag: bait


title: PAX5-TSS-a mut, viewpoint 1, rep 1


title: Mdx_NSG_Pax7ko

description:
AP2
All Nuclei

tag: treatment

value: Tamoxifen


title: Tfe3-ERT2_EtOH_3

value: Ethanol (vehicle)


title: prostate cancer patient pre-treatment serum, ENACT1023

tag: patient id

value: low-grade (0)

value: LOW

value: microRNA


title: P29_10wks_M_H3K4me1


title: Tfe3-ERT2_EtOH_2


title: P28_12wks_F_Input

description: Genomic DNA from placenta tissue

value: F


title: PAX5-TSS-a mut, viewpoint 1, rep 3

value: Lymph node

value: B lymphocyte


title: P29_10wks_M_H3K27ac

value: M


title: P28_12wks_F_H3K4me1


title: prostate cancer patient pre-treatment serum, ENACT1022

tag: disease state


title: Tfe3-ERT2_EtOH_1


title: PBMCs, WARS1, 24h, 3

city: Incheon

first: Mirim

last: Jin

address: 155, Gaetbeol-ro

country: South Korea

institute: Gachon University

data_processing:
Paired end sequence files from eleven samples (Fastq: R1, R2) were obtained and processed using Trimmomatic-0.36 with the following parameter settings: leading: 5, trailing: 5, sliding window: 4:15, and minlen: 36. After quality scoring and assessing the read lengths, RNA-Seq reads were mapped to the human reference genome GRCh38 (Gencode release 12) using STAR with default parameters.
Accurately quantifying the expression level of a gene from RNASeq reads was achieved using RSEM, which assembles individual transcripts from RNA-Seq reads that have been aligned to the genome sequences. Next, TPM was calculated for each transcribed fragment in the sample to quantify the expression level. To compare each sample, TPM underwent global normalization and was used for further analysis. Principal component analysis (PCA) was applied to the obtained gene expression profiles using the R package stats.
The normalized expression profiles of DEGs expressing more than 0.3 TPM and five read counts were used for DEGs analysis using EdgeR. The expression profile of each gene was scaled to a z-score and hierarchically clustered using a complete linkage method. Visualization was achieved using the ggplot2 library in R packages.
Assembly: GRCh38 (Gencode release 12)
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Peripheral blood mononuclear cells

growth_protocol: PBMCs were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% streptomycin & penicillin with 5% CO2 at 37 ℃

extract_protocol:
Total RNA was extracted from individual samples and controls using Trizol reagent (Invitrogen) according to the manufacturer’s protocol. Total RNA was then quantitated using a Nanodrop spectrophotometer (Thermo Scientific) and quality assessed using the RNA 6000 Nano assay kit (Agilent) and Bioanalyser 2100 (Agilent).
NGS sequencing libraries were generated from 1 µg of total RNA using a TruSeq RNA Sample Prep Kit (Illumina) according to the manufacturer's protocol.
The resulting cDNA libraries were then paired-end sequenced (2 × 101 bp) for samples with the Novaseq 6000 system (Illumina).

treatment_protocol: WARS1 (50 nM) for 24 h

tag: time

value: 24 hours

value: Peripheral blood mononuclear cells

value: WT


title: PBMCs, saline, 24h, 2

value: PBS


title: PBMCs, WARS1, 24h, 2


title: PBMCs, WARS1, 24h, 1


title: prostate cancer patient pre-treatment serum, ENACT1021

tag: tissue


title: prostate cancer patient pre-treatment serum, ENACT1020

tag: sample type


title: P29_10wks_M_Input

description: Genomic DNA from placenta tissue


title: PBMCs, saline, 24h, 1


title: P28_12wks_F_H3K27ac


title: P26_19wks_M_Input

description: Genomic DNA from placenta tissue


title: prostate cancer patient pre-treatment serum, ENACT1017

tag: grade of prostate cancer at biopsy


title: prostate cancer patient pre-treatment serum, ENACT2000

tag: ap

value: high-grade (1)

tag: capra risk


title: P26_19wks_M_H3K4me1


title: 396InputoxBS

city: Oklahoma City

first: Kyla

last: Tooley

state: OK

address: 825 NE 13th St

department: Genes and Human Disease

institute: Oklahoma Medical Research Foundation

data_processing:
Sequencing reads were trimmed using trimmomatic 0.35 with the follwing settings: ILLUMINACLIP: TruSeq3-PE-2.fa:2:30:10 SLIDINGWINDOW:5:30 LEADING:25 TRAILING:25 HEADCROP:4 MINLEN:25 AVGQUAL:25
mm10 genome was prepared with in silico bisulfite conversion using Bismark 0.16.3-intel-2016a "bismark_genome_preparation" with Bowtie2/2.3.41-foss-2017b
Paired, trimmed fastqs were aligned to mm10 using Bismark 0.16.3-intel-2016a with the following settings: -p 6 -N 1 --bowtie2 --non_bs_mm --un
Bams were deduplicated using Bismark 0.16.3-intel-2016a "deduplicate_bam" function
Deduplicated BAM files were run through methylKit 1.10.0 to generate context-specific (CpG/CHG/CHH) coverage text files
Assembly: mm10
Supplementary files format and content: Tab-delimited text files containing CpG/CHG/CHH methylation

source_name: Hippocampus

extract_protocol:
The purification of viable, neuronal-specific nuclei from brain tissue of Tam-induced Camk2a-cre/ERT2+; NuTRAP+ mice was achieved by the INTACT isolation method. For each mouse, the hippocampus from one hemisphere was minced into small pieces and homogenized in 1 ml ice-cold nuclei EZ lysis buffer (#NUC-101, Millipore Sigma) supplemented with 1X HaltTM protease inhibitor cocktail (ThermoFisher Scientific) using a glass dounce tissue grinder set (#D9063; Millipore Sigma: 20 times with pestle A and 15 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 HaltTM protease inhibitor cocktail), and subjected to the INTACT protocol. Briefly, 30 µl of resuspended M-280 Streptavidin Dynabeads (#11205, ThermoFisher Scientific) were added into a fresh 2 ml microcentrifuge tube and washed with 1ml of NPB using a DynaMag-2 magnet (#12321; ThermoFisher 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 neuronal-specific, biotinylated nuclei. After incubation, the streptavidin-bound nuclei were magnetically separated with the DynaMag-2 magnet for a period of 3 min and the unbound nuclei collected in a fresh 2 ml microcentrifuge tube, centrifuged at 4°C (1,000 x g, 3 min), resuspended in 100 µl of NPB and reserved as the negative nuclei fraction. 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 each nuclear fraction (input, negative, and positive), a 3 µl aliquot was mixed with equal volume of DAPI counterstain and used for confocal microscopy visualization and calculation of purity percentage. The AllPrep DNA/RNA kit Micro (#80284, Qiagen, Germantown, MD) was used to extract gDNA from each sample. gDNA was quantified with a Nanodrop 2000c spectrophotometer (Thermofisher Scientific) and its quality assessed by genomic DNA D1000 (#5067-5582) with a 2200 Tapestation analyzer (Agilent Technologies, Santa Clara, CA).
For each input, negative, and positive INTACT-isolated sample 400ng 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 (QubitTM dsDNA, Thermofisher Scientific). Two aliquots of 200 ng gDNA fragments were prepared in a 12 µl volume to which 1µl of spike-in control DNA (0.08 ng/ul) with known levels of specific mC, hmC, and fC at individual sites was added. Whole genome oxidative bisulfite (WGoxBS) libraries were constructed with NuGen Ovation Ultra-low Methyl Seq Library System with True-Methyl OXBS module.

value: Hippocampus

value: Neuron

tag: fraction

value: Input

tag: library prep_kit

value: Nugen Ovation Ultra-Low Methyl Seq with True-Methyl OxBS module


title: CIS treatment - Donor 13

city: Cambridge

first: Madison

middle: R

last: Mack

state: Massachusetts

address: 350 Water St

department: Immunology & Inflammation Research

institute: Sanofi

description:
S31A_FIS
gene_count.txt
gene_fpkm.txt

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count to reads numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: hg38
Supplementary files format and content: Transcript counts per gene from Hisat2 featureCounts
Supplementary files format and content: Fragments per kilobase per million reads (FPKM)

molecule: polyA RNA

source_name: dorsal root ganglia

extract_protocol:
After removing culture medium, dissociated DRG cultured neurons were immersed in RNAlater (Thermo Fisher Scientific, Waltham, MA, USA), scraped off the plate and stored in Eppendorf Tubes at 0 ºC. After spinning down RNAlater tubes with 3,000 x g for 5 minutes, RNAlater was removed and resuspend in 350 µL RLT buffer containing 2-mercaptoethanol (Acros Organics, Fair Lawn, NJ, USA). Samples were mixed thoroughly by shaking for 15–30 secs. Total RNA was extracted using the RNeasy Mini Kit (QIAGEN, Valencia, CA, USA) and quantified using the Nanodrop ND-1000 (Thermo Fischer Scientific, Waltham, MA, USA).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP for non-directional library. Following end repair, A-tailing, adapter ligation, size selection, amplification and purification, the libraries were checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution. Quantified libraries were pooled and sequenced on Illumina Novaseq 6000. Clustering of the index-coded samples was performed according to manufacturer's instructions.

treatment_protocol: Cultures were stimulated with 500 nM IL-4, IL-13, IL-33 (R&D Systems, Minneapolis MN) or the combination of IL-4 and IL-13 for 24 hours. A cocktail of inflammatory mediators – histamine (Sigma-Aldrich, St-Louis, MO), serotonin (Sigma-Aldrich, St-Louis, MO), bradykinin (Sigma-Aldrich, St-Louis, MO), Allyl isothiocyanate (AITC; Sigma-Aldrich, St-Louis, MO) and prostaglandin E2 (Tocris Bioscience, Bristol, UK) was used as a Control Inflammatory Stimuli (CIS).

tag: individual

value: Donor 13

value: dorsal root ganglia

value: primary cells

value: CIS


title: prostate cancer patient pre-treatment serum, ENACT1015

value: prostate cancer

value: serum

value: low-grade (0)

value: LOW

tag: capra score

value: microRNA


title: 396InputBS

tag: cell type


title: P23_16wks_F_Input

description: Genomic DNA from placenta tissue

tag: gestational age in weeks

tag: Sex

value: F

tag: trimester


title: P26_19wks_M_H3K27ac

value: M


title: IL-4 + IL-13 treatment - Donor 12

description:
S29B_4_13
gene_count.txt
gene_fpkm.txt

value: Donor 12

tag: cell line

tag: treatment


title: 396PosoxBS

tag: genotype

value: Positive


title: IL-4 + IL-13 treatment - Donor 13

description:
S31A_4_13
gene_count.txt
gene_fpkm.txt


title: 392PosoxBS

value: Hippocampus


title: P23_16wks_F_H3K4me1


title: prostate cancer patient pre-treatment serum, ENACT1014

tag: patient id

tag: disease state

value: INTERMEDIATE


title: IL-4 + IL-13 treatment - Donor 11

description:
S29A_4_13
gene_count.txt
gene_fpkm.txt

value: Donor 11

tag: tissue


title: IL-33 treatment - Donor 13

description:
S31A_33
gene_count.txt
gene_fpkm.txt


title: 392PosBS

value: Neuron

value: Nugen Ovation Ultra-Low Methyl Seq with True-Methyl OxBS module


title: 392InputoxBS

value: Input


title: 396PosBS


title: 392InputBS


title: IL-33 treatment - Donor 12

description:
S29B_33
gene_count.txt
gene_fpkm.txt

value: dorsal root ganglia

value: primary cells


title: prostate cancer patient pre-treatment serum, ENACT1009

value: prostate cancer

tag: sample type

tag: grade of prostate cancer at biopsy


title: prostate cancer patient pre-treatment serum, ENACT1012

value: serum

tag: capra risk


title: prostate cancer patient pre-treatment serum, ENACT1011

tag: ap

value: low-grade (0)

tag: fraction


title: CIS treatment - Donor 11

description:
S29A_FIS
gene_count.txt
gene_fpkm.txt

tag: individual

value: CIS


title: P22_21wks_F_Input

description: Genomic DNA from placenta tissue


title: P22_21wks_F_H3K4me1


title: prostate cancer patient pre-treatment serum, ENACT1008

value: LOW

tag: capra score

value: microRNA


title: IL-33 treatment - Donor 11

description:
S29A_33
gene_count.txt
gene_fpkm.txt


title: prostate cancer patient pre-treatment serum, ENACT1013


title: 391PosBS

tag: cell type

tag: library prep_kit


title: P22_21wks_F_H3K27ac

tag: gestational age in weeks

tag: Sex

value: F


title: IL-13 treatment - Donor 13

description:
S31A_13
gene_count.txt
gene_fpkm.txt

value: Donor 13

tag: cell line


title: prostate cancer patient pre-treatment serum, ENACT1006


title: 391InputoxBS


title: P23_16wks_F_H3K27ac

tag: trimester


title: IL-13 treatment - Donor 11

description:
S29A_13
gene_count.txt
gene_fpkm.txt

tag: treatment


title: P10_39wks_F_Input

description: Genomic DNA from placenta tissue


title: 391InputBS

tag: genotype


title: P10_39wks_F_H3K4me1


title: prostate cancer patient pre-treatment serum, ENACT1005

tag: patient id

tag: disease state


title: prostate cancer patient pre-treatment serum, ENACT1004

tag: tissue

tag: sample type


title: IL-4 treatment - Donor 12

description:
S29B_4
gene_count.txt
gene_fpkm.txt

value: Donor 12


title: 389PosoxBS

value: Hippocampus

value: Positive


title: IL-4 treatment - Donor 13

description:
S31A_4
gene_count.txt
gene_fpkm.txt


title: 389PosBS


title: P09_39wks_M_Input

description: Genomic DNA from placenta tissue

value: M


title: 391PosoxBS

value: Neuron


title: prostate cancer patient pre-treatment serum, ENACT1002

tag: grade of prostate cancer at biopsy

tag: capra risk


title: prostate cancer patient pre-treatment serum, ENACT1003

tag: fraction


title: P10_39wks_F_H3K27ac


title: IL-4 treatment - Donor 11

description:
S29A_4
gene_count.txt
gene_fpkm.txt

tag: individual

value: Donor 11


title: P09_39wks_M_H3K4me1


title: prostate cancer patient pre-treatment serum, DOD62

tag: ap

value: high-grade (1)

value: INTERMEDIATE

tag: capra score


title: 389InputoxBS

tag: cell type

value: Input

tag: library prep_kit

value: Nugen Ovation Ultra-Low Methyl Seq with True-Methyl OxBS module


title: P09_39wks_M_H3K27ac

tag: gestational age in weeks

tag: Sex


title: 389InputBS


title: Vehicle treatment - Donor 12

description:
S29B_Veh
gene_count.txt
gene_fpkm.txt

value: dorsal root ganglia

tag: cell line

value: primary cells

value: Vehicle


title: prostate cancer patient pre-treatment serum, DOD61

value: prostate cancer

value: serum

value: HIGH


title: Vehicle treatment - Donor 11

description:
S29A_Veh
gene_count.txt
gene_fpkm.txt

tag: treatment


title: input DNA for TRIM28_ChIPSeq

city: Minhang

first: bing

last: zhang

state: Shanghai

address: 800 Dong Chuan Road

department: Shanghai Center for Systems Biomedicine

country: China

institute: Shanghai Jiao Tong University

data_processing:
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2.
ChiP-seq peaks were called using MACS version 1.4 with default parameters.
ChiP-seq peaks were annotated by Homer.
ChiP-seq peaks were compared by bedtools.
bigWig files were generated by deeptools.
Genome_build: hg38
Supplementary_files_format_and_content: bed,bigWig

source_name: Human umbilical endothelial cells

growth_protocol: Human umbilical endothelial cells were routinely cultured in EGM2 medium(CC-2530, Lonza)

extract_protocol:
The nucleis were extracted with hypotonic buffer. The chromatin was sonicated in Qsonica Sonicator in nuclei dilution buffer.  ChIP-DNA was immunoprecipitated with LARP7 or TRIM28 antibody, and protein G Dynabeads were loaded the reaction to further purify  antibody-bound chromatin DNA.
ChIP-seq Libraries were prepared using TIANSeq Fast DNA Library Kit (TianGen, NG102).

value: Primary human umbilical endothelial cells

tag: passages

tag: antibody


title: MERS, 4dpì, rep3 [E93_12_6]

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

description: Infected with SARS-CoV carrying PBM variant "MERS". Collected at 4dpi. Replicate 3

data_processing:
Alignment: Illumina reads were aligned against mouse genome with RNA-STAR with default parameters for paired-end sequences. Results in SAM format were compressed (BAM), sorted and indexed with commands "samtools view", "samtools sort" and "samtools index"
Labelling duplicated reads: Putative PCR and optical duplicates, in BAM files, were marked using MarkDuplicates function of Picard package
Gene quantification: Aligned reads were assigned to mouse genes using featureCounts function of Rsubread package. PCR and optical duplicates were ignored (ignoreDup=TRUE). Only primary alignments were considered (primaryOnly=TRUE)
Assembly: GRCm38.101
Supplementary files format and content: Text-tabulated file containinf the number of aligned reads per gene in all samples

source_name: Lung

extract_protocol:
To extract total RNA, lungs were homogenized in 2 ml of RLT lysis buffer (QIAGEN) supplemented with 1% β-mercaptoethanol using the GentleMACS Dissociator system (Miltenyi Biotec) following the protocol proposed by the manufacturer. Samples were centrifuged at 3000xg for 10 minutes, and RNA was purified from supernatants using the RNeasy mini kit reagent (QIAGEN) as previously described.
rRNA is removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs(dUTP, dATP, dGTP and dCTP), RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Then followed by purification by AMPure XP beads, terminal repair, polyadenylation, sequencing adapter ligation, size selection and degradation of second-strand U-contained cDNA by the USER enzyme. The strand-specific cDNA library was generated after the final PCR enrichment.

treatment_protocol: Mice were anesthetized with isoflurane and inoculated intranasally using 100.000 or 10.000 PFUs of the corresponding virus in a 50 μl volume of DMEM supplemented with 2% FBS

value: Lung

tag: strain

value: BALB/c

tag: time


title: input DNA for LARP7_ChIPSeq


title: prostate cancer patient pre-treatment serum, DOD60

tag: patient id

tag: disease state

tag: tissue

tag: sample type

value: microRNA


title: prostate cancer patient pre-treatment serum, DOD59

tag: grade of prostate cancer at biopsy

value: low-grade (0)

tag: capra risk

tag: fraction


title: MERS, 4dpì, rep2 [E93_12_5]

description: Infected with SARS-CoV carrying PBM variant "MERS". Collected at 4dpi. Replicate 2


title: prostate cancer patient pre-treatment serum, DOD57

tag: ap

tag: capra score


title: TRIM28_ChIPSeq

tag: cell type


title: MERS, 4dpì, rep1 [E93_12_4]

description: Infected with SARS-CoV carrying PBM variant "MERS". Collected at 4dpi. Replicate 1


title: Vehicle treatment - Donor 13

description:
S31A_Veh
gene_count.txt
gene_fpkm.txt

tag: individual

value: Donor 13


title: LARP7_ChIPSeq

value: LARP7 (Bethyl laboratories,A303-723A, lot A303-723A-1 )


title: HEK293T cells, shNT, Rep1

city: La Jolla

first: Brian

last: Yee

address: 9500 Gilman Dr

department: Health

institute: UCSD

data_processing:
Reads were mapped using STAR 2.7.6a
Read count extraction was performed using featureCounts from the Subread package. Results were sorted into counts matrices
TPM was calculated manually from counts matrix
Differential splicing analysis was performed on STAR-aligned reads using rMATS 4.0.2.  For each condition, shRNA knockdown samples represent SAMPLE_1, while non-targeting controls (shNT_1, shNT_2, and shNT_3) represent SAMPLE_2.
Assembly: GRCh38
Supplementary files format and content: csv files include TPM values for each sample in comparison to non-targeting shRNA control, along with sample means and standard deviations
Supplementary files format and content: tab-delimited text files include differential skipped exon splicing analysis for each knockdown (SE.MATS.JC.txt from rMATS)

extract_protocol:
RNA was harvested using DirectZol RNA Miniprep Kit (Zymo)
RNA libraries for RNA-seq were prepared using Stranded mRNA Prep, Ligation kit (Illumina) following manufacturer's protocols.

treatment_protocol: Knockdown was performed through lentiviral transduction of target-specific shRNAs followed by puromycin selection

tag: cell line

value: Human Embryonic Kidney

tag: genotype

value: Non-targeting shRNA


title: HEK293T cells, shNT, Rep2


title: MERS, 2dpì, rep3 [E93_12_3]

description: Infected with SARS-CoV carrying PBM variant "MERS". Collected at 2dpi. Replicate 3

tag: treatment


title: prostate cancer patient pre-treatment serum, DOD56

value: high-grade (1)

value: INTERMEDIATE


title: HEK293T cells, shSTAU2, Rep3

description:
shSTAU2_TPM.csv
shSTAU2_SE.MATS.JC.txt

value: STAU2 knockdown


title: HEK293T cells, shSTAU2, Rep2

description:
shSTAU2_TPM.csv
shSTAU2_SE.MATS.JC.txt


title: Stage 8 Sox3 V5 rep 2

city: Pittsburgh

first: Miler

middle: T

last: Lee

state: PA

address: 4249 Fifth Ave

department: Biological Sciences

institute: University of Pittsburgh

data_processing:
Reads were mapped to the X. laevis v10.1 genome using bowtie2 2.4.2 (--no-mixed --no-discordant), discarding reads on the mitochondrial chromosome. High quality (MAPQ>=30) were retained for analysis, allowing at most 1 fragment per unique coordinate
Paired reads were joined and converted to bigWigs normalized to total number of retained fragments per million, using bedtools v2.30.0 genomecov and wigToBigWig
Assembly: X. laevis v10.1
Supplementary files format and content: bigWig files of coverage pooled across replicates
Library strategy: CUT&RUN

organism: Xenopus laevis

source_name: Whole embryos

extract_protocol:
CUT&RUN procedure was based on Hainer et al Cell 2019 and Skene et. al. Nature Protocols 2019. 12 embryos per sample were collected, devitellinized in 1mg/mL pronase, dissolved in MR/3, and cells were dissociated in 1 mL of NP2.0 buffer (Briggs et al Science 2018) with gentle agitation. Dissociated cells were lysed in NE buffer (20mM HEPES-KOH, pH 7.9, 10mM KCl, 500uM spermidine, 0.1% Triton X-100, 20% glycerol) with gentle pipetting with a clipped P1000, and the lysate was centrifuged at 600xg in 4C for 3 min. The free nuclei were then bound to 300 uL of activated concanavalin A beads at RT for 10mins. Nuclei were blocked for 5 min at RT then incubated in 1:100 dilution of primary antibody for 2 hr at 4C, washed, incubated in a 1:200 dilution of pA/G MNase for 1 hr at 4C, and washed again. The bound MNase was activated with 2 mM CaCl2 and allowed to digest for 30 mins, then stopped using 2x STOP buffer (200 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 ug/mL RNase A, 40 g/mL glycogen). Nuclei were incubated at 37C for 20 min followed by centrifuging for 5 min at 16,000xg, drawing off the DNA fragments with the supernatant. The extracted fragments were treated with SDS and proteinase K at 70C for 10 min followed by phenol chloroform extraction. Purified DNA was resuspended in 50 uL of water and verified by Qubit dsDNA high sensitivity and Fragment Analyzer.
Sequencing libraries were built using the NEB Next Ultra II library build kit (E7645S) and size selected on an agarose gel to 150-600 bp. Libraries were multiplexed and sequenced paired-end at the Health Sciences Sequencing Core at Children’s Hospital of Pittsburgh.

treatment_protocol: For transcription factor CUT&RUN, WT embryos were injected at Stage 1 with 400 pg of N-terminal V5 tagged pou5f3.3.L or sox3.S mRNA.

value: Whole embryos

value: WT

tag: developmental stage

value: Injected with 400 pg V5-sox3 mRNA

tag: antibody

value: Invitrogen #R960-25


title: Stage 8 Sox3 V5 rep 3

tag: strain


title: prostate cancer patient pre-treatment serum, DOD55

tag: patient id

value: prostate cancer

value: serum


title: Prom1_BcatGOF

city: New Haven

first: Vikas

last: Gupta

address: 1 Gilbert Street

institute: Yale School of Medicine

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Common Bile Duct

extract_protocol:
Whole bile ducts were isolated and micro dissected in petri dishes to remove all adjoining tissue. Ducts were placed in 1 ml of HBSS with 1.8 mM Ca, 0.8 mM Mg, 1 mg dispase (Roche), 2 mg protease from Bacillus licheniformis (Sigma) and cut into small pieces with a microdissecting scissors. These were incubated for 15 minutes at 37 C. This solution was removed and the remaining bile duct chunks were placed in a solution with 1x PBS, 5mM EDTA, and 0.5% BSA and incubated at 37 C for another 10 minutes. This was filtered through a 100 μm filter.
This single cell suspension was washed twice with a 1x PBS, 0.04% BSA solution prior to GEM and library generation according to manufacturer’s protocol (10X Genomics, Chromium Single Cell 3' Reagent Kits User Guide, v3 Chemistry)

value: Common Bile Duct

value: All


title: MERS, 2dpì, rep2 [E93_12_2]

description: Infected with SARS-CoV carrying PBM variant "MERS". Collected at 2dpi. Replicate 2

value: Lung

value: BALB/c

tag: time


title: HEK293T cells, shNT, Rep3


title: Stage 8 Pou5f3.3 V5 rep 3

tag: tissue

value: Injected with 400 pg V5-pou5f3.3 mRNA


title: prostate cancer patient pre-treatment serum, DOD54

tag: disease state

tag: sample type

value: microRNA


title: NL63, 4dpì, rep3 [E93_11_6]

description: Infected with SARS-CoV carrying PBM variant "NL63". Collected at 4dpi. Replicate 3


title: HEK293T cells, shSTAU2, Rep1

description:
shSTAU2_TPM.csv
shSTAU2_SE.MATS.JC.txt

value: Human Embryonic Kidney


title: HEK293T cells, shSCAF8, Rep3

description:
shSCAF8_TPM.csv
shSCAF8_SE.MATS.JC.txt

value: SCAF8 knockdown


title: prostate cancer patient pre-treatment serum, DOD53

tag: grade of prostate cancer at biopsy

value: low-grade (0)

tag: capra risk


title: prostate cancer patient pre-treatment serum, DOD52

tag: ap

value: high-grade (1)

value: LOW

tag: fraction


title: Stage 8 H3K27ac rep 4

value: Whole embryos

value: ActiveMotif #39135


title: Stage 8 H3K27ac rep 3

value: WT


title: prostate cancer patient pre-treatment serum, DOD51

value: INTERMEDIATE

tag: capra score


title: NL63, 4dpì, rep1 [E93_11_4]

description: Infected with SARS-CoV carrying PBM variant "NL63". Collected at 4dpi. Replicate 1


title: HEK293T cells, shSCAF8, Rep1

description:
shSCAF8_TPM.csv
shSCAF8_SE.MATS.JC.txt

tag: cell type


title: NL63, 4dpì, rep2 [E93_11_5]

description: Infected with SARS-CoV carrying PBM variant "NL63". Collected at 4dpi. Replicate 2


title: Stage 8 Pou5f3.3 V5 rep 2

value: Invitrogen #R960-25


title: NL63, 2dpì, rep3 [E93_11_3]

description: Infected with SARS-CoV carrying PBM variant "NL63". Collected at 2dpi. Replicate 3


title: Stage 9 H3K4me3 rep 3

value: Invitrogen #711958


title: MERS, 2dpì, rep1 [E93_12_1]

description: Infected with SARS-CoV carrying PBM variant "MERS". Collected at 2dpi. Replicate 1


title: prostate cancer patient pre-treatment serum, DOD49

value: prostate cancer

value: serum


title: prostate cancer patient pre-treatment serum, DOD50


title: NL63, 2dpì, rep2 [E93_11_2]

description: Infected with SARS-CoV carrying PBM variant "NL63". Collected at 2dpi. Replicate 2

value: Lung


title: HEK293T cells, shRTCA, Rep2

description:
shRTCA_TPM.csv
shRTCA_SE.MATS.JC.txt

tag: cell line

value: RTCA knockdown


title: HEK293T cells, shRTCA, Rep3

description:
shRTCA_TPM.csv
shRTCA_SE.MATS.JC.txt

tag: genotype


title: NL63, 2dpì, rep1 [E93_11_1]

description: Infected with SARS-CoV carrying PBM variant "NL63". Collected at 2dpi. Replicate 1

value: BALB/c

tag: treatment


title: HEK293T cells, shRTCA, Rep1

description:
shRTCA_TPM.csv
shRTCA_SE.MATS.JC.txt


title: Stage 9 animal cap ATAC rep 4 size selected open frags

description:
s9_pool_open_hq_v10.1.bw
s9_open_v10.1.narrowPeak

data_processing:
Reads were mapped to the X. laevis v10.1 genome using bowtie2 2.4.2 (--no-mixed --no-discordant -X2000), discarding reads on the mitochondrial chromosome. High quality (MAPQ>=30) sub-nucleosomal sized fragments (<=130 bp) were retained for analysis, allowing at most 1 fragment per unique coordinate
bigWigs were pooled across replicates and normalized to total number of retained fragments per million, using bedtools v2.30.0 genomecov and wigToBigWig. MACS 2.2.7.1 was used to call peaks on open fragments
Assembly: X. laevis v10.1
Supplementary files format and content: bigWig files of open chromatin coverage pooled across replicates, narrowPeak file of MACS peaks of open chromatin

source_name: animal cap

extract_protocol:
ATAC procedure was based on Esmaeili et al Dev Biol 2020. Dejellied embryos were incubated in MR/3 (33 mM NaCl, 0.6 mM KCl, 0.67 mM CaCl2, 0.33 mM MgCl2, 1.67 mM HEPES, pH 7.8) at 23C until desired NF stage and then devitellinized with 1 mg/mL pronase. Ectodermal explants (animal caps) were dissected using watch-maker forceps in 0.7x MR. Two caps were used per transposition reaction. Caps were washed in ice cold PBS and centrifuged at 500xg in 4C for 5mins twice. Caps were washed again and lysed in 50 µl of RSB buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal CA-630) with a clipped P200 pipet. The lysate was pelleted at 500xg in 4C for 10 min and resuspended in in 47.5 µl TD buffer (10 mM Tris pH 7.6, 5 mM MgCl2, 10% dimethylformamide) and 2.5 µl of 3 µM Tn5 transposome (Addgene #112112). Nuclei were transposed with gentle shaking for 1 hr at 37C before adding 2.5 µl proteinase K and incubating overnight at 37C.
Transposed DNA was purified using EconoSpin Micro columns (Epoch) and amplified using 25 µM indexed Nextera primers with Thermo Phusion Flash master mix for 12 cycles. The amplified library was column cleaned and verified by Qubit dsDNA high sensitivity and Fragment Analyzer and sequenced multiplexed paired end at the Health Sciences Sequencing Core at Children’s Hospital of Pittsburgh. For reps 1 and 2, after initial sequencing, libraries were subsequently size selected on an agarose gel to enrich for 150-250 and 250-600 bp fragments and resequenced pooled. For reps 3 and 4, libraries were only size selected for 150-250 bp.

value: animal cap

tag: developmental stage


title: prostate cancer patient pre-treatment serum, DOD48

value: microRNA


title: prostate cancer patient pre-treatment serum, DOD47


title: Stage 9 animal cap ATAC rep 3 size selected open frags


title: HEK293T cells, shSCAF8, Rep2

description:
shSCAF8_TPM.csv
shSCAF8_SE.MATS.JC.txt

value: Human Embryonic Kidney

value: SCAF8 knockdown


title: HEK293T cells, shTRNAU1AP, Rep3

description:
shTRNAU1AP_TPM.csv
shTRNAU1AP_SE.MATS.JC.txt

value: TRNAU1AP knockdown


title: HKU1, 4dpì, rep2 [E93_10_5]

description: Infected with SARS-CoV carrying PBM variant "HKU1". Collected at 4dpi. Replicate 2


title: prostate cancer patient pre-treatment serum, DOD46

value: high-grade (1)

value: LOW


title: Stage 8 animal cap ATAC rep 3 size selected open frags


title: prostate cancer patient pre-treatment serum, DOD45


title: HKU1, 4dpì, rep1 [E93_10_4]

description: Infected with SARS-CoV carrying PBM variant "HKU1". Collected at 4dpi. Replicate 1


title: HEK293T cells, shTRNAU1AP, Rep2


title: Stage 9 CHX pou5f3.2, pou5f3.3, sox3 MO rep H2 - DISCARDED

description:
DISCARDED_s9_chx_pou.2_pou.3_sox_mo_H_2
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv

data_processing:
Reads were mapped to the X. laevis v9.2 genome using HISAT2 v2.2.1 (--no-discordant)
Mapped reads were assigned to gene exons (Xenbase v9.2 models) using featureCounts v2.0.1 in reversely-stranded paired-end mode with default parameters, or introns with --minOverlap 10 on a custom non-repeat non-exonic annotation based on Xenbase models
Assembly: X. laevis v9.2
Supplementary files format and content: CSV exon and intron raw and normalized read counts

extract_protocol:
Two embryos per sample were snap frozen and homogenized in 500ul of TRIzol Reagent (Invitrogen #15596026) followed by 100ul of chloroform. Tubes were spun at 18,000 x g at 4C for 15 minutes, the aqueous phase was transferred to a fresh tube with 340 ul of isopropanol and 1 ul of GlycoBlue (Invitrogen #AM9515), then precipitated at -20C overnight. Precipitated RNA was washed with cold 75% ethanol and resuspended in 50ul of nuclease-free water. Concentration was determined by NanoDrop.
rRNA depletion was performed as per Phelps et al NAR 2021: 1ul of antisense nuclear rRNA oligos and 1ul of antisense mitochondrial rRNA oligos (final concentration 0.1 uM per oligo) were combined with 1ug of total RNA in a 10ul buffered reaction volume (100mM Tris-HCl  pH 7.4, 200mM NaCl, 10mM DTT), heated at 95C for 2 minutes and cooled to 22C at a rate of 0.1C/s in a thermocycler. Next, 10U of thermostable RNaseH (NEB #M0523S) and 2uL of provided 10X RNaseH buffer were added and volume brought to 20uL with nuclease-free water. The reaction was incubated at 65C for 5 or 30 minutes, then 5U of TURBO DNase (Invitrogen #AM2238) and 5uL of provided 10x buffer was added, volume brought to 50uL with nuclease-free water and incubated at 37C for 30 minutes. The reaction was purified and size selected to >200 nts using Zymo RNA Clean and Concentrator-5 (Zymo #R1013) according to manufacturer’s protocol, eluting in 10uL of nuclease-free water. The WT Stage 5 sample was also depleted of mitochondrial COX2 and COX3 mRNA as part of Phelps et al NAR 2021. Strand-specific RNA-seq libraries were constructed using NEB Ultra II RNA-seq library kit (NEB #E7765) according to manufacturer’s protocol with fragmentation in first-strand buffer at 94C for 15 minutes. Following first and second strand synthesis, DNA was purified with 1.8X AmpureXP beads (Beckman #A63880), end repaired, then ligated to sequencing adaptors diluted 1:5. Ligated DNA was purified with 0.9X AmpureXP beads and PCR amplified for 8 cycles, then purified again with 0.9X AmpureXP beads. Libraries were verified by Qubit dsDNA high sensitivity (Invitrogen #Q32851) and Fragment Analyzer prior to multiplexed sequencing at the Health Sciences Sequencing Core at Children’s Hospital of Pittsburgh.

treatment_protocol: Dejellied embryos were incubated in MR/3 (33 mM NaCl, 0.6 mM KCl, 0.67 mM CaCl2, 0.33 mM MgCl2, 1.67 mM HEPES, pH 7.8) at 23C and collected at their respective NF stages based on morphology. All stage 9 embryos were collected halfway through the stage, at 8 hours post fertilization. Triptolide samples were bathed in 20 uM triptolide in DMSO at stage 1 and cycloheximide samples were bathed in 500 ug/mL cycloheximide in DMSO at stage 8; both were collected when batch-matched, untreated embryos reached stage 9. Equivalent volumes of DMSO were used to treat control samples. Morpholino treated embryos were injected at stage 1 with pou5f3.2, pou5f3.3, sox3, and/or GFP control morpholino.

value: Whole embryos

value: cycloheximide, 40ng pou5f3.2 + 40ng pou5f3.3 + 40ng sox3 morpholino


title: HEK293T cells, shTRNAU1AP, Rep1


title: Stage 9 CHX pou5f3.2, pou5f3.3, sox3 MO rep H1 - DISCARDED

description:
DISCARDED_s9_chx_pou.2_pou.3_sox_mo_H_1
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv

value: WT


title: HKU1, 2dpì, rep3 [E93_10_3]

description: Infected with SARS-CoV carrying PBM variant "HKU1". Collected at 2dpi. Replicate 3


title: prostate cancer patient pre-treatment serum, DOD44

value: INTERMEDIATE


title: HEK293T cells, FLAG_IP_2

description:
FLAG_IP2_enriched_windows.tsv.gz
FLAG_reproducible_enriched_windows.tsv.gz

data_processing:
Data was processed using Skipper, available at: http://github.com/yeolab/skipper
Reads were trimmed for adapter sequences and barcode sequences (eCLIP samples) using skewer.
Unique Molecular Identifiers (UMIs) were extracted from raw sequencing reads with fastp
Extracted reads were aligned using STAR: --alignEndsType EndToEnd --genomeDir {params.star_sjdb} --genomeLoad NoSharedMemory --outBAMcompression 10 --outFileNamePrefix {params.outprefix} --winAnchorMultimapNmax 100 --outFilterMultimapNmax 100 --outFilterMultimapScoreRange 1 --outSAMmultNmax 1 --outMultimapperOrder Random --outFilterScoreMin 10 --outFilterType BySJout --limitOutSJcollapsed 5000000 --outReadsUnmapped None --outSAMattrRGline ID:{wildcards.replicate_label} --outSAMattributes All --outSAMmode Full --outSAMtype BAM Unsorted --outSAMunmapped Within --readFilesCommand zcat --outStd Log --readFilesIn {input.fq} --runMode alignReads --runThreadN {threads}
Custom scripts called reproducible enriched windows and repetitive elements as part of Skipper
Assembly: GRCh38
Supplementary files format and content: single-replicate enriched window files contain p values, q values, enrichment, and annotations for significantly bound transcriptome tiled windows
Supplementary files format and content: reproducible enriched window files contain p values, q values, enrichment, and annotations for significantly bound transcriptome tiled windows

extract_protocol:
Cells were lysed and and sonicated in eCLIP lysis buffer, and RNA was fragmented using RNase I (Ambion) and UPF1:RNA complexes were immunoprecipitated with antibody
RNA was reverse transcripted with Superscript III, and adaptor was ligated with T4 RNA Ligase 1, then libraries were constructed with Q5 High-Fidelity 2x Master Mix (NEB)

treatment_protocol: For overexpression samples, cells at ~70% confluency were transfected in a 10cm plate with 14ug plasmid DNA encoding V5-tagged targets using Lipofectamine 3000 and collected at 48h

value: Overexpression of V5-tagged FLAG

tag: rip antibody

value: V5-specific antibody


title: prostate cancer patient pre-treatment serum, DOD43

data_processing:
The raw data (raw CT) values were input into GeneGlobe with a CT cutoff value of 33. In the GeneGlobe preprocessing, all CTs greater than 33 were changed to a value of 33 and the CTs were adjusted for the interplate calibrator (UniSp3) according to the miRCURY LNA miRNA PCR Panels & Assays Data Analysis Handbook.
Normalization values for each sample were calculated using the NormFinder method in GeneGlobe. The microRNAs used for normalization of serum samples included: miR-107, miR-24-3p, let-7i-5p, miR-19b-3p, miR-16-5p, miR-320a, miR-23a-3p, miR-21-5p, let-7b-5p, and miR-25-3p. The microRNAs included for normalization of serum EV samples included: included hsa-miR-107, hsa-miR-24-3p, hsa-miR-30c-5p, hsa-miR-93-5p, hsa-let-7i-5p, hsa-miR-222-3p, hsa-miR-27a-3p, hsa-miR-23a-3p, hsa-miR-21-5p, and hsa-miR-27b-3p.
These normalized values were then used to make comparisons between groups (adverse pathology versus not adverse pathology) to determine significantly different microRNAs using p < 0.05
The significant microRNAs were then used to generate random forest models to predict adverse pathology
The Fold Change Template shows the p-values for each microRNA. The microRNAs with p<0.05 were included in the random forest model to predict adverse pathology.

extract_protocol: Total RNA was extracted with the miRNeasy Serum/Plasma kit (Qiagen).

value: prostate cancer

value: serum

value: HIGH


title: Stage 9 CHX GFP MO rep H3 - DISCARDED

description:
DISCARDED_s9_chx_gfp_mo_H_3
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv

tag: strain

value: cycloheximide, 120ng GFP morpholino


title: Stage 8 H3K4me3 rep 2

tag: antibody

value: Invitrogen #711958


title: HKU1, 2dpì, rep2 [E93_10_2]

description: Infected with SARS-CoV carrying PBM variant "HKU1". Collected at 2dpi. Replicate 2

value: Lung

value: BALB/c

tag: time


title: Stage 9 CHX GFP MO rep H2 - DISCARDED

description:
DISCARDED_s9_chx_gfp_mo_H_2
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv

tag: tissue


title: HEK293T cells, FLAG_IP_1

description:
FLAG_IP1_enriched_windows.tsv.gz
FLAG_reproducible_enriched_windows.tsv.gz

value: Human Embryonic Kidney


title: HKU1, 4dpì, rep3 [E93_10_6]

description: Infected with SARS-CoV carrying PBM variant "HKU1". Collected at 4dpi. Replicate 3


title: HKU1, 2dpì, rep1 [E93_10_1]

description: Infected with SARS-CoV carrying PBM variant "HKU1". Collected at 2dpi. Replicate 1


title: prostate cancer patient pre-treatment serum, DOD42

tag: patient id

tag: disease state

value: microRNA


title: OC43, 4dpì, rep3 [E93_9_6]

description: Infected with SARS-CoV carrying PBM variant "OC43". Collected at 4dpi. Replicate 3


title: HEK293T cells, FLAG_IN_2


title: HEK293T cells, FLAG_IN_1


title: Stage 9 CHX GFP MO rep H1 - DISCARDED

description:
DISCARDED_s9_chx_gfp_mo_H_1
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv


title: prostate cancer patient pre-treatment serum, DOD41

tag: sample type

tag: grade of prostate cancer at biopsy

value: high-grade (1)


title: OC43, 4dpì, rep2 [E93_9_5]

description: Infected with SARS-CoV carrying PBM variant "OC43". Collected at 4dpi. Replicate 2


title: HEK293T cells, STAU2_IP_2

description:
STAU2_IP2_enriched_windows.tsv.gz
STAU2_reproducible_enriched_windows.tsv.gz

value: Overexpression of V5-tagged STAU2


title: Stage 9 GFP MO rep H2

description:
s9_gfp_mo_H_2
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv

value: Whole embryos

value: 120ng GFP morpholino


title: OC43, 4dpì, rep1 [E93_9_4]

description: Infected with SARS-CoV carrying PBM variant "OC43". Collected at 4dpi. Replicate 1


title: prostate cancer patient pre-treatment serum, DOD39

tag: ap

tag: capra risk


title: Stage 9 GFP MO rep H1

description:
s9_gfp_mo_H_1
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv

value: WT


title: prostate cancer patient pre-treatment serum, DOD38

tag: capra score

tag: fraction


title: OC43, 2dpì, rep3 [E93_9_3]

description: Infected with SARS-CoV carrying PBM variant "OC43". Collected at 2dpi. Replicate 3


title: HEK293T cells, STAU2_IN_2

tag: cell line

tag: cell type


title: Stage 9 CHX pou5f3.2, pou5f3.3, sox3 MO rep F2

description:
s9_chx_pou.2_pou.3_sox_mo_F_2
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv

tag: genotype

tag: treatment

value: cycloheximide, 40ng pou5f3.2 + 40ng pou5f3.3 + 40ng sox3 morpholino


title: prostate cancer patient pre-treatment serum, DOD37


title: Stage 9 CHX pou5f3.2, pou5f3.3, sox3 MO rep F3

description:
s9_chx_pou.2_pou.3_sox_mo_F_3
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv

tag: developmental stage


title: HEK293T cells, STAU2_IN_1

tag: rip antibody


title: OC43, 2dpì, rep2 [E93_9_2]

description: Infected with SARS-CoV carrying PBM variant "OC43". Collected at 2dpi. Replicate 2

tag: strain


title: OC43, 2dpì, rep1 [E93_9_1]

description: Infected with SARS-CoV carrying PBM variant "OC43". Collected at 2dpi. Replicate 1

tag: time


title: WT, 4dpì, rep3 [E93_4_6]

description: Infected with Wild-Type SARS-CoV. Collected at 4dpi. Replicate 3

tag: tissue

value: Infected with Wild-Type SARS-CoV


title: Stage 9 CHX pou5f3.2, pou5f3.3, sox3 MO rep F1

description:
s9_chx_pou.2_pou.3_sox_mo_F_1
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv


title: prostate cancer patient pre-treatment serum, DOD40

tag: patient id


title: Stage 9 pou5f3.2, pou5f3.3, sox3 MO rep F3

description:
s9_pou.2_pou.3_sox_mo_F_3
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv

value: 40ng pou5f3.2 + 40ng pou5f3.3 + 40ng sox3 morpholino


title: HEK293T cells, SCAF8_IP_2

description:
SCAF8_IP2_enriched_windows.tsv.gz
SCAF8_reproducible_enriched_windows.tsv.gz

value: Overexpression of V5-tagged SCAF8

value: V5-specific antibody


title: prostate cancer patient pre-treatment serum, DOD35

tag: disease state

value: prostate cancer

value: serum

value: low-grade (0)

value: INTERMEDIATE


title: HEK293T cells, SCAF8_IP_1

description:
SCAF8_IP1_enriched_windows.tsv.gz
SCAF8_reproducible_enriched_windows.tsv.gz


title: HEK293T cells, SCAF8_IN_2


title: Stage 9 pou5f3.2, pou5f3.3, sox3 MO rep F2

description:
s9_pou.2_pou.3_sox_mo_F_2
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv


title: WT, 4dpì, rep1 [E93_4_4]

description: Infected with Wild-Type SARS-CoV. Collected at 4dpi. Replicate 1

value: Lung

value: BALB/c


title: prostate cancer patient pre-treatment serum, DOD33

tag: sample type

value: HIGH

value: microRNA


title: Stage 9 pou5f3.2, pou5f3.3, sox3 MO rep F1

description:
s9_pou.2_pou.3_sox_mo_F_1
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv


title: prostate cancer patient pre-treatment serum, DOD32

tag: grade of prostate cancer at biopsy

value: high-grade (1)


title: HEK293T cells, STAU2_IP_1

description:
STAU2_IP1_enriched_windows.tsv.gz
STAU2_reproducible_enriched_windows.tsv.gz

value: Human Embryonic Kidney

value: Overexpression of V5-tagged STAU2


title: Stage 9 pou5f3.2, pou5f3.3 MO rep F3

description:
s9_pou.2_pou.3_mo_F_3
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv

value: Whole embryos

value: WT

value: 40ng pou5f3.2 + 40ng pou5f3.3 + 40ng GFP morpholino


title: HEK293T cells, RTCA_IP_2

description:
RTCA_IP2_enriched_windows.tsv.gz
RTCA_reproducible_enriched_windows.tsv.gz

value: Overexpression of V5-tagged RTCA


title: prostate cancer patient pre-treatment serum, DOD36

value: LOW


title: prostate cancer patient pre-treatment serum, DOD31


title: WT, 2dpì, rep1 [E93_4_1]

description: Infected with Wild-Type SARS-CoV. Collected at 2dpi. Replicate 1

value: Infected with Wild-Type SARS-CoV


title: prostate cancer patient pre-treatment serum, DOD30

value: prostate cancer

tag: ap


title: HEK293T cells, RTCA_IP_1

description:
RTCA_IP1_enriched_windows.tsv.gz
RTCA_reproducible_enriched_windows.tsv.gz

value: V5-specific antibody


title: WT, 2dpì, rep2 [E93_4_2]

description: Infected with Wild-Type SARS-CoV. Collected at 2dpi. Replicate 2


title: Stage 9 pou5f3.2, pou5f3.3 MO rep F1

description:
s9_pou.2_pou.3_mo_F_1
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv


title: HEK293T cells, RTCA_IN_2


title: prostate cancer patient pre-treatment serum, DOD34

value: serum

tag: capra risk


title: WT, 4dpì, rep2 [E93_4_5]

description: Infected with Wild-Type SARS-CoV. Collected at 4dpi. Replicate 2


title: Stage 9 pou5f3.2, pou5f3.3 MO rep F2

description:
s9_pou.2_pou.3_mo_F_2
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv


title: Mock, 4dpì, rep3 [E93_2_6]

description: Mock Infected. Collected at 4dpi. Replicate 3

value: Not Infected


title: Stage 9 GFP MO rep F3

description:
s9_gfp_mo_F_3
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv

value: 120ng GFP morpholino


title: HEK293T cells, RTCA_IN_1


title: Stage 9 GFP MO rep F2

description:
s9_gfp_mo_F_2
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv


title: Mock, 4dpì, rep2 [E93_2_5]

description: Mock Infected. Collected at 4dpi. Replicate 2

value: Lung

value: BALB/c


title: prostate cancer patient pre-treatment serum, DOD26

value: HIGH

tag: capra score

value: microRNA


title: prostate cancer patient pre-treatment serum, DOD29

value: high-grade (1)

value: INTERMEDIATE

tag: fraction


title: HEK293T cells, TRNAU1AP_IP_2

description:
TRNAU1AP_IP2_enriched_windows.tsv.gz
TRNAU1AP_reproducible_enriched_windows.tsv.gz

tag: cell line

value: Human Embryonic Kidney

value: No treatment

value: TRNAU1AP-specific antibody


title: Mock, 4dpì, rep1 [E93_2_4]

description: Mock Infected. Collected at 4dpi. Replicate 1


title: HEK293T cells, SCAF8_IN_1

tag: cell type

value: WT

value: Overexpression of V5-tagged SCAF8


title: prostate cancer patient pre-treatment serum, DOD27

value: low-grade (0)

value: LOW


title: Stage 9 GFP MO rep F1

description:
s9_gfp_mo_F_1
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv

value: Whole embryos

tag: genotype


title: WT, 2dpì, rep3 [E93_4_3]

description: Infected with Wild-Type SARS-CoV. Collected at 2dpi. Replicate 3

tag: treatment

value: Infected with Wild-Type SARS-CoV


title: HEK293T cells, TRNAU1AP_IP_1

description:
TRNAU1AP_IP1_enriched_windows.tsv.gz
TRNAU1AP_reproducible_enriched_windows.tsv.gz


title: prostate cancer patient pre-treatment serum, DOD25

value: prostate cancer

value: serum


title: Stage 9 pou5f3.3, sox3 MO rep G3

description:
s9_pou.3_sox_mo_G_3
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv

tag: developmental stage

value: 40ng pou5f3.3 + 40ng sox3 + 40ng GFP morpholino


title: HEK293T cells, TRNAU1AP_IN_2

tag: rip antibody


title: prostate cancer patient pre-treatment serum, DOD24


title: Mock, 2dpì, rep3 [E93_2_3]

description: Mock Infected. Collected at 2dpi. Replicate 3

value: Lung

tag: strain

value: BALB/c

value: Not Infected


title: Mock, 2dpì, rep2 [E93_2_2]

description: Mock Infected. Collected at 2dpi. Replicate 2

tag: time


title: HEK293T cells, TRNAU1AP_IN_1


title: Stage 9 pou5f3.3, sox3 MO rep G2

description:
s9_pou.3_sox_mo_G_2
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv

tag: tissue


title: Stage 9 pou5f3.3, sox3 MO rep G1

description:
s9_pou.3_sox_mo_G_1
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv


title: Bjab cell line, stable transfection short version of TACI, replicate 3

first: Miguel

last: Fribourg

address: 1 Gustave Levy Pl

department: Medicine

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw RNaseq fastq reads were trimmed with bbtools and QC assesed with FASTQC
Reads were aligned to human genome (hg38) using STAR (v. 2.4.0h)
Gene-assignment and count of RNA reads were performed with HTseq.
Assembly: hg38
Supplementary files format and content: raw counts

source_name: Lymphocyte

extract_protocol:
RNA from the sorted cells was isolated using the RNeasy Plus Micro kit (QIAGEN).
Quality control was performed by bioanalyzer (Agilent), and RNA samples with an RNA integrity number (RIN) > 8 were processed for library preparation using Nextera XT DNA (Illumina) library preparation kits

value: Lymphocyte

value: cell line

value: lymphocyte

value: Burkitt lymphoma tumor

value: Untreated


title: prostate cancer patient pre-treatment serum, DOD23

tag: patient id

value: high-grade (1)

value: INTERMEDIATE

value: microRNA


title: Stage 9 GFP MO rep G3

description:
s9_gfp_mo_G_3
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv

value: WT

value: 120ng GFP morpholino


title: GGGG, 4dpì, rep3 [E87_11_6]

description: Infected with SARS-CoV carrying PBM variant "GGGG". Collected at 4dpi. Replicate 3


title: Bjab cell line, stable transfection short version of TACI, replicate 2


title: GGGG, 4dpì, rep2 [E87_11_5]

description: Infected with SARS-CoV carrying PBM variant "GGGG". Collected at 4dpi. Replicate 2


title: prostate cancer patient pre-treatment serum, DOD22

tag: disease state


title: Bjab cell line, stable transfection short version of TACI, replicate 1


title: prostate cancer patient pre-treatment serum, DOD21

tag: sample type


title: prostate cancer patient pre-treatment serum, DOD20

tag: grade of prostate cancer at biopsy

value: HIGH


title: GGGG, 4dpì, rep1 [E87_11_4]

description: Infected with SARS-CoV carrying PBM variant "GGGG". Collected at 4dpi. Replicate 1


title: Stage 10.5 rep 2

description:
s10.5_2
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv

value: Whole embryos


title: GGGG, 2dpì, rep3 [E87_11_3]

description: Infected with SARS-CoV carrying PBM variant "GGGG". Collected at 2dpi. Replicate 3


title: Bjab cell line, stable transfection long version of TACI, replicate 2


title: Bjab cell line, stable transfection long version of TACI, replicate 3


title: prostate cancer patient pre-treatment serum, DOD19

value: prostate cancer

value: serum

tag: ap

value: low-grade (0)


title: GGGG, 2dpì, rep2 [E87_11_2]

description: Infected with SARS-CoV carrying PBM variant "GGGG". Collected at 2dpi. Replicate 2

value: Lung

value: BALB/c


title: Stage 10.5 rep 1

description:
s10.5_1
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv


title: prostate cancer patient pre-treatment serum, DOD17

tag: capra risk


title: prostate cancer patient pre-treatment serum, DOD18

tag: capra score


title: GGGG, 2dpì, rep1 [E87_11_1]

description: Infected with SARS-CoV carrying PBM variant "GGGG". Collected at 2dpi. Replicate 1


title: Bjab cell line, stable transfection long version of TACI, replicate 1

value: Lymphocyte


title: prostate cancer patient pre-treatment serum, DOD16

tag: fraction


title: Mock, 2dpì, rep1 [E93_2_1]

description: Mock Infected. Collected at 2dpi. Replicate 1

value: Not Infected


title: Stage 8 rep 2

description:
s8_2
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv


title: 3a, 4dpì, rep3 [E82_4_6]

description: Infected with SARS-CoV carrying PBM variant "3a". Collected at 4dpi. Replicate 3


title: Bjab cell line replicate 3

tag: cell line

value: cell line

value: lymphocyte


title: Stage 9 GFP MO rep G2

description:
s9_gfp_mo_G_2
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv


title: DG, MeOH-fixed, rep1

country: Germany

description:
SORTseq
JEN-AU-s002

data_processing:
Raw sequencing data were mapped to the GRCm38 mouse reference genome and preliminary count matrices were generated for each sample using STAR (Spliced Transcripts Alignment to a Reference; dimension of the matrices: number of barcodes x number of transcripts). Briefly, read 1 was used for assigning reads to correct cells and libraries, read 2 was mapped to gene models and reads that mapped equally well to multiple genomic locations were discarded. Read counts were then corrected for amplification bias by using the UMI barcodes. Reads that had identical combinations of library, cellular, and molecular barcodes and were mapped to the same gene were considered duplicates and were removed. Transcript counts were then adjusted to the expected number of molecules based on counts, 4096 possible UMI’s and Poisson distribution. Bioinformatic analysis was conducted using R programming language (R v4.2.0). Raw count matrices were pre-processed using the Seurat package v4.1.0. Firstly, ERCC RNA spike-in counts were removed from the count matrices and added into the metadata from the Seurat object. Barcodes with total transcript counts between 800 and 35000, more than 500 total genes, a transcript to gene ratio greater than 1.2 and more than 500 ERCC counts were considered to contain successfully sequenced cells and were positively selected in the filtering step. This resulted in 64 fresh cells and 132 MeOH-fixed cells in the filtered dataset. After removing low quality barcodes, samples were normalized by regularized negative binomial regression (SCTransform) and integrated using the top 2000 variable genes. Based on the elbow plot after principal component analysis, the top 12 principal components (PCs) were selected for dimensionality reduction and graph-based clustering, and the first 15 PCs were applied for Uniform Manifold Approximation and Projection visualization. The marker genes of each cluster were identified with a Wilcoxon rank sum test implemented in the 'FindAllMarkers' Seurat function with the following criteria: adjusted p-value < 0.05 (FDR correction), log-fold change ≥ 0.5 and ratio of the detection fraction between the cluster and the rest (pct.1/pct.2) > 2.5.
Assembly: GRCm38 mouse reference genome
Supplementary files format and content: Raw_count_matrix.csv (comma-separated files including expression values for Freshly-isolated and MeOH-fixed barcodes)
Supplementary files format and content: Metadata_barcodes.csv (comma-separated files including metadata for Freshly-isolated and MeOH-fixed barcodes)
Supplementary files format and content: Filtered_raw_count_matrix.csv (comma-separated files including expression values for Freshly-isolated and MeOH-fixed filtered cells)
Supplementary files format and content: Metadata_filtered.csv (comma-separated files including metadata for Freshly-isolated and MeOH-fixed filtered cells)

extract_protocol:
DGs were dissected in PBS with 10mM glucose and individually subjected to an enzymatic and mechanical dissociation according to manufacturer's protocols (Neural Tissue Dissociation Kit P, Miltenyi Biotec). Single cells were obtained in DPBS wo Ca2+/Mg2+ containing 0.1 M D-(+)-Trehalose dihydrate at 4°C. The cell suspensions were pooled at equal ratios, and either MeOH-fixed or immediately processed for FAC-sorting. MeOH fixation was adapted from a protocol provided by 10X Genomics (CG000136). After dissociation, cells were transferred to 1.5 mL LoBind DNA Eppendorf tubes and pelleted at 300 rcf at 4°C for 5 min. The supernatant was removed carefully and the cell pellet resuspended in one volume of ice-cold DPBS wo Ca2+/Mg2+ containing 0.5 M D-(+)-Trehalose dihydrate, and four volumes of 100% MeOH pre-chilled to -20°C were added dropwise while gently mixing the cell suspension (final concentration:  106 cells/ml in 20:80 PBS/MeOH 0,1M Trehalose). The MeOH-fixed cells were kept at -20°C for 30 min and then stored at -80°C for 3 weeks. For rehydration, suspensions were moved from -80°C to 4°C on ice and kept for 5 min to equilibrate the temperature. Cells were pelleted at 1000 rcf at 4°C for 5 min, and resuspended in 3X SSC Buffer with 0.04% BSA, 0.2 U/µl of RNase inhibitor and 1 mM DL-Dithiothreitol. Subsequently, MeOH-fixed cells were processed either for FAC-sorting. After rehydration of the pooled MeOH-fixed cells (n = 4 mice), the cell suspension was centrifuged at 300 rcf at 4°C for 5 min and cells were resuspended in ice-cold DPBS wo Ca2+/Mg2+ containing 5% HEPES PUFFERAN® ≥99,5 %, p.a.. Next, single cells were FAC-sorted into 384-well microplates containing well-specific barcoded primers, ERCC spike-ins and reverse transcription reagents using a FACSAria™ Fusion cell sorter (BD Biosciences). Wells O21-O24 and P21-P24 were left empty as a no-template control. Different forward and side-scatter parameters were used for gating to discriminate single cells from debris and doublets or aggregates. To have the lowest bias between samples, control cell suspensions from age-matched mice (n = 3 mice) were freshly prepared, pooled and FAC-sorted the same day into another 384-well cell capture microplate. In this case, Sytox AADvanced™ Dead Cell Stain was added (5 min, at 4°C, in the dark) prior to FAC-sorting for excluding dead cells. The filled microplates were sealed and centrifuged at 2000 rcf for 2 min at 4°C, snap-frozen on dry ice and stored at -80°C.
Libraries of microplates containing FAC-sorted cells from freshly-isolated and MeOH-fixed samples were prepared according to the CEL-Seq2 protocol. After cell lysis at 65°C, the RNA was reverse transcribed into cDNA followed by second-strand cDNA synthesis. The barcoded cDNA of all wells from one plate was pooled and amplified by In Vitro Transcription. The amplified RNA was fragmented, reverse transcribed into cDNA and again amplified using TruSeq small RNA primers (Illumina) to generate the final sequencing libraries. The quality and yield of the amplified RNA and the final cDNA libraries were checked on an Agilent Bioanalyzer. Thereafter, the libraries were paired-end sequenced on an Illumina Nextseq™ 500, high output, with a 1×75 bp Illumina kit (R1: 26 cycles, index read: 6 cycles, R2: 60 cycles) aiming at 75000 reads/cell.
Cel-Seq2

value: Brain

tag: cell type

value: DG cells

tag: age

value: 4-5 weeks old

value: MeOH-fixed


title: Bjab cell line replicate 2

tag: genotype

value: Burkitt lymphoma tumor

tag: treatment

value: Untreated


title: prostate cancer patient pre-treatment serum, DOD15

value: HIGH

value: microRNA


title: DG, Freshly-isolated, rep1

description:
SORTseq
JEN-AU-s004

value: freshly-isolated


title: Stage 9 GFP MO rep G1

description:
s9_gfp_mo_G_1
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv

value: Whole embryos

value: WT

tag: developmental stage

value: 120ng GFP morpholino


title: 3a, 4dpì, rep2 [E82_4_5]

description: Infected with SARS-CoV carrying PBM variant "3a". Collected at 4dpi. Replicate 2

value: Lung

tag: strain

value: BALB/c


title: Bjab cell line replicate 1

value: Lymphocyte


title: prostate cancer patient pre-treatment serum, DOD14

value: prostate cancer

value: serum

value: high-grade (1)

value: INTERMEDIATE


title: 3a, 4dpì, rep1 [E82_4_4]

description: Infected with SARS-CoV carrying PBM variant "3a". Collected at 4dpi. Replicate 1

tag: time


title: HLADR-CD38-CD8Tcells_S8

city: New Delhi

first: Anmol

last: Chandele

state: Delhi

address: Aruna Asaf Ali Marg

country: India

institute: International Center for Genetic Engineering and Biotechnology

data_processing:
The raw reads were processed using FastQC for quality assessment and pre-processing which includes removing the adapter sequences and low-quality bases (<q30) using TrimGalore.
The high-quality reads were considered for alignment with reference genome using a splice aligner.
Aligned to reference (Homo sapiensGRCh38.p13 build genome downloaded from Ensembl database) using Hisat2 with the default settings. Hisat2 was used to calculate raw read counts for each gene after alignment.
Differential expression analysis done by DESeq2 package followed by removal of low count genes with average raw counts < 100 in all sumples.
filter criteria: adjusted p value < 0.05; p value < 0.01; log2 fold change >= 1 (up); log2 fold change =< -1 (down)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
For each condition approximately 200-500 cells were sorted and collected in 10x lysis buffer of SMART-Seq v4 ultra low input RNA seq kit. From this 8μl was taken as input for SMARTer Stranded Total RNA-Seq Kit v2.
RNA sequencing libraries from the bulk sorted cell subsets were prepared with Illumina compatible SMARTer Stranded Total RNA-Seq Kitv2 - Pico Input Mammalian (TakaraBio, Inc.  CA, USA) at Genotypic Technology Pvt. Ltd., Bangalore, India.

tag: source

value: PBMC

tag: disease

value: Dengue


title: 3a, 2dpì, rep3 [E82_4_3]

description: Infected with SARS-CoV carrying PBM variant "3a". Collected at 2dpi. Replicate 3

tag: tissue


title: WT_d6_3

city: Würzburg

first: hao

last: wu

address: Versbacher stress 7-9

institute: institute for systemsimmunology, wurzburg university

description: DESeq2_comparison_mPiC_d6_vs_WT_d6_table

data_processing:
Demultiplexed FASTQ files were generated with bcl2fastq2 v2.20.0.422 (Illumina). To assure high sequence quality, Illumina reads were quality- and adapter-trimmed via Cutadapt [1] version 2.5 using a cutoff Phred score of 20 in NextSeq mode, and reads without any remaining bases were discarded (command line parameters: --nextseq-trim=20 -m 1 -a CTGTCTCTTATACACATCT). Processed reads were subsequently mapped to the mouse genome (GRCm38.p6 primary assembly and mitochondrion) using STAR v2.7.2b with default parameters based on RefSeq annotation version 108.20200622 for GRCm38.p6
Read counts on exon level summarized for each gene were generated using featureCounts v1.6.4 from the Subread package. Multi-mapping and multi-overlapping reads were counted non-strand-specific with a fractional count for each alignment and overlapping feature (command line parameters: -s 0 -t exon -M -O --fraction). The count output was utilized to identify differentially expressed genes using DESeq2 version 1.24.0. Read counts were normalized by DESeq2 and fold-change shrinkage was applied by setting the parameter “betaPrior=TRUE”. Differences in gene expression were considered significant if padj < 0.05.
Assembly: GRCm38.p6 primary assembly and mitochondrion
Supplementary files format and content: DESeq2_comparison

extract_protocol:
1x10^6 T cells were harvested in RNAprotect Cell Reagent and stored at -80°C o/n before total RNA was extracted using the RNeasy Plus Micro Kit (both Quiagen)
RNA quality and quantity were checked using a 2100 Bioanalyzer with the RNA 6000 Nano kit (Agilent Technologies) and RNA Pico kit depending on the sample concentration. The RIN for all samples was >7. cDNA libraries suitable for sequencing were prepared from 5 ng of total RNA with SMART-Seq v4 Ultra Low Input RNA Kit (Takara) according to manufacturer’s instructions (1/4 volume). Libraries were quantified by QubitTM 3.0 Fluometer (ThermoFisher) and quality was checked using 2100 Bioanalyzer with High Sensitivity DNA kit (Agilent). 0.5 ng of each library was subjected to a tagmentation-based protocol (Nextera XT, Illumina) using a quarter of the recommended reagent volumes. Libraries were quantified again by QubitTM 3.0 Fluometer (Thermo Fisher) and quality was checked using 2100 Bioanalyzer with High Sensitivity DNA kit (Agilent) before pooling. Sequencing of pooled libraries, spiked with 1% PhiX control library, was performed at 19-36 million reads/sample in single-end mode with 75 nt read length on the NextSeq 500 platform (Illumina) with 1 High Output Kit v2.5.
Sequencing of pooled libraries, spiked with 1% PhiX control library, was performed at ~20 million reads/sample in single-end mode with 75 nt read length on the NextSeq 500 platform (Illumina) with 1 High Output Kit v2.5. Demultiplexed FASTQ files were generated with bcl2fastq2 v2.20.0.422 (Illumina).

treatment_protocol: Day0 samples were directly purified from spleen and lymph node. Day2 samples were purified from naïve mice and stimulated with anti-CD3/CD28. Day6 samples  were acitivated as day2 samples followed with a 4 days treatment of IL-2.

value: CD8 T cells

value: wild type

value: Day 6


title: prostate cancer patient pre-treatment serum, DOD12

first: Morgan

last: Zenner

address: 909 South Wolcott Ave

institute: University of Illinois at Chicago College of Medicine

tag: patient id

tag: disease state

tag: sample type

value: microRNA


title: WT_d6_2


title: HLADR-CD38-CD8Tcells_S7


title: prostate cancer patient pre-treatment serum, DOD11

tag: ap

tag: grade of prostate cancer at biopsy

tag: capra risk


title: 3a, 2dpì, rep2 [E82_4_2]

description: Infected with SARS-CoV carrying PBM variant "3a". Collected at 2dpi. Replicate 2


title: HLADR-CD38-CD8Tcells_S6


title: prostate cancer patient pre-treatment serum, DOD10

tag: capra score

tag: fraction


title: 3a, 2dpì, rep1 [E82_4_1]

description: Infected with SARS-CoV carrying PBM variant "3a". Collected at 2dpi. Replicate 1


title: WT_d6_1

tag: cell line

tag: cell type


title: WT_d2_3

tag: genotype

value: Day 2


title: HLADR-CD38-CD8Tcells_S4


title: prostate cancer patient pre-treatment serum, DOD9

value: HIGH


title: WT_d2_2


title: KO3

city: Hangzhou

first: Jiaqi

last: Xu

address: 866 Yuhangtang Road, Hangzhou, Zhejiang, China

institute: Sir Run Run Shaw hospital, Zhejiang University School of Medicine

data_processing:
Clustering and sequencing (Novogene Experimental Department) The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Quality control Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: hg18
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: colon tissue

extract_protocol:
RNA were extracted from PBS-flushed colons
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Eight- to ten-week-old IEC-conditional Gab1 knockout mice and their littermates were treated with 3% DSS (MP Biomedicals) in drinking water (w/v) for 7 days and sacrificed for further study

value: colon

value: Gab1IEC KO

tag: treatment

value: 7-day DSS


title: KO2


title: WT_d2_1


title: UnstimulatedHLADR+CD38+CD8Tcells_S6


title: KO1


title: prostate cancer patient pre-treatment serum, DOD7


title: UnstimulatedHLADR+CD38+CD8Tcells_S5


title: WT_d0_3

description: DESeq2_comparison_mPiC_d2_vs_WT_d2_table

value: Day 0


title: prostate cancer patient pre-treatment serum, DOD6


title: WT3

value: WT


title: WT_d0_2


title: prostate cancer patient pre-treatment serum, DOD5

value: prostate cancer

value: LOW


title: UnstimulatedHLADR+CD38+CD8Tcells_S4


title: WT2


title: WT_d0_1


title: HLADR+CD38+CD69-IFNg-CD8Tcells_S3


title: WT1


title: mPiC_d6_3

value: Slc25a3-fl/fl Cd4-cre


title: prostate cancer patient pre-treatment serum, DOD4

value: serum

value: high-grade (1)


title: HLADR+CD38+CD69-IFNg-CD8Tcells_S2

value: PBMC

value: Dengue


title: prostate cancer patient pre-treatment serum, DOD3


title: prostate cancer patient pre-treatment serum, DOD1

value: INTERMEDIATE


title: prostate cancer patient pre-treatment serum, DOD8


title: HLADR+CD38+CD69-IFNg-CD8Tcells_S1


title: mPiC_d6_2

value: CD8 T cells

value: Day 6


title: UnstimulatedHLADR+CD38+CD8Tcells_S7


title: iKPC3_on

city: Houston

first: Jincheng

last: Han

address: 1901 East Rd

department: Cancer Biology

institute: UT Health MD Anderson Cancer Center

data_processing:
Performed by BGI via manufacturer protocols
Assembly: mm10
Supplementary files format and content: Text file including TPM values for each sample

source_name: PDAC Cancer Cells

growth_protocol: 50000 iKPC cells were resuspended in 500 µL Matrigel and plated in 6-well plates in the presence of complete culture medium and dox.

extract_protocol:
RNA extraction from cell samples was performed using the RNA Extraction Kit (Qiagen #) 74034). RNA concentration was determined by the Nanodrop 2000 (Thermo Fisher Scientific)
RNA samples were sent to BGI for sequencing (DNBseq PE 150), with libraries constructed based on manufacturer protocols

treatment_protocol: Seventy-two hours later, the wells were washed with and soaked in PBS until the phenol red in the Matrigel completely disappeared and to remove any remaining dox. Then the PBS was removed and complete culture medium with or without dox was added for another 48 hours. To collect the cells, the Matrigel was disrupted by pipette in cold PBS and digested with 100 µg/mL Dispase II (Roche #04942078001) at 37°C for 10 minutes to obtain cell pellets.

value: PDAC Cancer Cells

value: iKPC 3

value: Pancreatic Epithelial Cells

value: on dox


title: HLADR+CD38+CD69+IFNg-CD8Tcells_S3


title: iKPC3_off

value: off dox 48h


title: mPiC_d2_3

description: DESeq2_comparison_mPiC_d0_vs_WT_d0_table

value: Day 2


title: iKPC2_on

value: iKPC 2


title: mPiC_d2_2


title: HLADR+CD38+CD69+IFNg-CD8Tcells_S2


title: HLADR+CD38+CD69+IFNg-CD8Tcells_S1


title: iKPC1_on

value: iKPC 1


title: mPiC_d2_1


title: mPiC_d0_3

value: Day 0


title: iKPC1_off


title: HLADR+CD38+CD69+IFNg+CD8Tcells_S3


title: mPiC_d0_2

value: Slc25a3-fl/fl Cd4-cre


title: day51

city: Tokyo

first: Shugo

last: Tohyama

address: 35 Shinanomachi, Shinjuku

country: Japan

institute: Keio University

description: miRNAs expression in supernatant on day 51 during cardiac differentiation and maturaion from hiPSCs

hyb_protocol: Labeled RNA was hybridized to the Human miRNA microarray, Release 21.0 (Agilent Technologies) with the miRNA Complete Labeling Reagent and Hybridization kit (Agilent Technologies) according to the manufacturer’s instructions.

scan_protocol: Microarray slides were scanned at 3 μm resolution using an Agilent SureScan (G4900DA).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.1.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Supernatant on day 51 during cardiac differentiation and maturaion from hiPSCs

label_protocol: Each RNA sample was labeled with the miRNA Complete Labeling Reagent and Hybridization kit (Agilent Technologies) according to the manufacturer’s instructions.

growth_protocol: hiPSC-derived cardiomyocytes (hiPSC-CMs) were generated as previously described(Cell Stem Cell. 2013 Jan 3;12(1):127-37.). hiPSC-CMs were cultured in low-glucose medium (MEMα) plus 5% fetal bovine serum (FBS) over the long term  and supernatant samples were collected on day -1, day 3, day 5, day 7, day 9, day 21, day 35, and day 51 after the initiation of differentiation induction.

extract_protocol: Total RNA were isolated from cell culture supernatant using by miRNeasy Serum/Plasma Kit (QIAGEN N.V.).

value: supernatant

value: hiPSC-derived cardiomyocytes


title: day21

description: miRNAs expression in supernatant on day 21 during cardiac differentiation and maturaion from hiPSCs

source_name: Supernatant on day 21 during cardiac differentiation and maturaion from hiPSCs


title: mPiC_d6_1


title: day35

description: miRNAs expression in supernatant on day 35 during cardiac differentiation and maturaion from hiPSCs

source_name: Supernatant on day 35 during cardiac differentiation and maturaion from hiPSCs


title: CAF1_off

value: CAF 1

value: Fibroblast


title: day9

description: miRNAs expression in supernatant on day 9 during cardiac differentiation and maturaion from hiPSCs

source_name: Supernatant on day 9 during cardiac differentiation and maturaion from hiPSCs


title: mPiC_d0_1


title: obob_beta, biological replicate 6 (RNA-seq)

status: Public on Sep 21 2023

city: Davis

first: Mark

middle: O.

last: Huising

address: One Shields Avenue

department: Neurobiology, Physiology and Behavior

institute: University of California, Davis

description: bulk RNA expression

data_processing:
FastQC
Trimmomatic
STAR Aligner
edgeR
Assembly: mm10
Supplementary files format and content: Raw Expression Counts

source_name: FACS-sorted beta cells

growth_protocol: Pancreatic islets were isolated by injection of collagenase up the common bile duct after clamping of the Ampulla of Vater. Isolates were purified by density gradient centrifugation and dissociated by gentle trituration in 0.25% Trypsin -EDTA. mIns1-H2b-mCherry positive beta cells were collected and processed immediately for ATAC-Seq library preparation.

extract_protocol:
Cells were collected in Trizol post FACS purification and isolated by a chloroform extraction, assisted by phase lock tubes. RNA was precipitated by isopropanol and cleaned up over an RNEasy microcolumn per the Qiagen's taking great care to avoid carry over of ethanol following the column washes. Elution volume was 30 microliter.
Indexed sequencing libraries were constructed using the TruSeq RNA sample prep Kit v2 per Illumina instructions.

value: beta

tag: Sex

value: female

tag: status

value: obob


title: HLADR+CD38+CD69+IFNg+CD8Tcells_S1

tag: source

value: PBMC

value: Dengue


title: day3

description: miRNAs expression in supernatant on day 3 during cardiac differentiation and maturaion from hiPSCs

source_name: Supernatant on day 3 during cardiac differentiation and maturaion from hiPSCs


title: day5

description: miRNAs expression in supernatant on day 5 during cardiac differentiation and maturaion from hiPSCs

source_name: Supernatant on day 5 during cardiac differentiation and maturaion from hiPSCs


title: obob_alpha, biological replicate 6 (RNA-seq)

description: bulk RNA expression

source_name: FACS-sorted alpha cells

value: alpha


title: day-1

description: miRNAs expression in supernatant on day -1 during cardiac differentiation and maturaion from hiPSCs

source_name: Supernatant on day -1 during cardiac differentiation and maturaion from hiPSCs


title: obob_alpha, biological replicate 5 (RNA-seq)

description: bulk RNA expression

value: male


title: lean_beta, biological replicate 10 (RNA-seq)

description: bulk RNA expression

value: lean


title: obob_beta, biological replicate 5 (RNA-seq)

description: bulk RNA expression


title: lean_alpha, biological replicate 10 (RNA-seq)

description: bulk RNA expression


title: iKPC2_off

value: PDAC Cancer Cells

value: Pancreatic Epithelial Cells

value: off dox 48h


title: HLADR+CD38+CD69+IFNg+CD8Tcells_S2

tag: disease


title: lean_alpha, biological replicate 9 (RNA-seq)

description: bulk RNA expression


title: lean_beta, biological replicate 8 (RNA-seq)

description: bulk RNA expression


title: day7

description: miRNAs expression in supernatant on day 7 during cardiac differentiation and maturaion from hiPSCs

source_name: Supernatant on day 7 during cardiac differentiation and maturaion from hiPSCs


title: lean_alpha, biological replicate 8 (RNA-seq)

description: bulk RNA expression


title: lean_beta, biological replicate 7 (RNA-seq)

description: bulk RNA expression


title: obob_beta, biological replicate 3 (RNA-seq)

description: bulk RNA expression


title: lean_alpha, biological replicate 6 (RNA-seq)

description: bulk RNA expression


title: lean_beta, biological replicate 5 (RNA-seq)

description: bulk RNA expression


title: lean_alpha, biological replicate 5 (RNA-seq)

description: bulk RNA expression


title: lean_beta, biological replicate 6 (RNA-seq)

description: bulk RNA expression


title: lean_beta, biological replicate 4 (RNA-seq)

description: bulk RNA expression


title: lean_alpha, biological replicate 4 (RNA-seq)

description: bulk RNA expression


title: obob_beta, biological replicate 2 (RNA-seq)

description: bulk RNA expression


title: lean_beta, biological replicate 3 (RNA-seq)

description: bulk RNA expression


title: obob_beta, biological replicate 1 (RNA-seq)

description: bulk RNA expression


title: obob_alpha, biological replicate 1 (RNA-seq)

description: bulk RNA expression


title: lean_alpha, biological replicate 2 (RNA-seq)

description: bulk RNA expression


title: obob_alpha, biological replicate 2 (RNA-seq)

description: bulk RNA expression


title: lean_beta, biological replicate 9 (RNA-seq)

description: bulk RNA expression


title: lean_alpha, biological replicate 1 (RNA-seq)

description: bulk RNA expression


title: lean_beta, biological replicate 1 (RNA-seq)

description: bulk RNA expression