title: E_17_Seronegative

city: Bethesda

first: Hye Kyung

last: Lee

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

data_processing:
RNA-seq data were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) and subsequently aligned to the reference genome hg19 applying STAR RNA-seq aligner (Dobin et al., Bioinformatics, 2013). HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
Genome_build: hg19
Supplementary_files_format_and_content: HTSeq counts from RNA-seq samples

source_name: PBMCs

growth_protocol: Blood samples were collected from the healthy subjects, Seronegative subjects and COVID-19 patients.

extract_protocol:
The buffy coat was extracted by centrifuge after blood sample collection and RBC was removed using RBC lysis buffer in the buffy coat. Total RNA was isolated with TRIzol reagent.
Libraries for sequencing were prepared with TruSeq Stranded mRNA Kit following standard Illumina protocols.

tag: gender

tag: diseas state

value: highly exposed, Seronegative

tag: severity

value: Seronegative, highly exposed

tag: location

value: PBMC


title: MKO_GM_CTCF_ChIPseq_Rep1

status: Public on May 01 2021

type: SRA

city: Beijing

first: Yong

last: Zhang

address: 5 Dong Dan San Tiao

country: China

institute: School of Basic Medicine, Peking Union Medical College

description:
CTCF  ChIP-Seq of myod ko proliferating myoblasts
MKO_GM_CTCF.bw

library_source: genomic

data_processing:
RNA-seq reads were aligned to the mm9 genome with TopHat (v2.1.0) using default settings. Duplicates were removed, and aligned reads were calculated for each protein-coding gene using HTSeq, followed by FPKM transformation by normalizing gene exon length and sequencing depth.
ChIP-Seq reads were mapped to mm9  genome with Bowtie2. Aligned reads were filtered for a minimum MAPQ of 20, and duplicates were removed using SAMtools. Signal tracks and peaks were generated by using the –SPMR option in MACS2. Then, the UCSC Genome Browser utility bedGraphToBigWig was used with default parameters to transform the bedgraph files to bigwig files.
ChIA-PET2 was used to trim the bridge linkers of BL-Hi-C data and HiC-Pro to align reads, filter artifact fragments, and remove duplicates; Juicer was applied to the resulting uniquely mapped contacts to generate individual or merged Hi-C files that could be deposited as contact matrices with multiple resolutions.
Loops were called by HiCCUPS at 3kb, 5 kb and 10 kb resolutions with modified parameters for pooled Hi-C matrices of each  condition.
Genome_build: mm9
Supplementary_files_format_and_content: .hic files were genrated by Juicer which compress Hi-C matrix under mutiscale resolutions;.h5 files were generated by HiCExplorer which can be visualized by  pyGenomeTracks;.bedpe files were loops called by HiCCUPS;.bigwig files were generated using MACS2;.excel  file includes gene count for each sample

molecule: genomic DNA

organism: Mus musculus

source_name: Proliferating myoblasts

extract_protocol:
Primary myoblasts were isolated from the hindlimb skeletal muscle of WT and KO mice at 2~3 weeks, minced and digested in a mixture of type II collagenase and Dispase B (Roche Applied Science). Cells were filtered from debris, centrifuged and cultured in growth medium (F-10 Ham’s medium supplemented with 20% FBS, 10 ng/ml basic fibroblast growth factor, 1% penicillin– streptomycin and 1% glutamine) on collagen-coated cell culture plates at 37 °C in 5% CO2. At 60-70% confluence, cells can be switched to differentiation medium (DMEM with 2% horse serum).
Hi-C were performed on 0.5 million cells per sample according to the BL-Hi-C protocol (PMID: 29158486). Briefly, cells were cross-linked with formaldehyde and nucleuses were isolated by lysis buffers. The chromain was then randomly fragmented by 4-bp enzymes (HaeIII) and then two proximal fragments were connected by 20 bp biotinylated bridge linker in nucleus. A whole genome chromatin was extracted and sheared into 400 bp. Then the biotinylated junctions were captured by M-280 streptavidin magnetic beads. After amplification, the DNA were ready for library construction. RNA for NRA-seq was harvested using Trizol reagent. For ChIP-seq, lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with related antibody.
Hi-C libaries were performed on 0.5 million cells per sample according to the BL-Hi-C protocol (PMID: 29158486). RNA libraries were prepared for sequencing using standard Illumina protocols. ChIP libraries were constructed using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB E7645)

tag: passage

tag: chip antibody

tag: tissue

value: skeletal muscle

tag: genotype

value: myod KO


title: liverTissue_ATAC-seq_sample713

city: Chapel Hill

first: Karen

middle: L

last: Mohlke

state: NC

address: 120 Mason Farm Road

department: Genetics

country: USA

institute: University of North Carolina at Chapel Hill

description:
The first three digits of raw and processed filenames represent the sample IDs. For each tissue sample, nuclei was extracted and divided into three portions prior to library preparation. This resulted in triplicate libraries for each tissue sample. If a library did not receive high enough sequencing depth, the same library was resequenced. Consequently, some libraries have two sets of raw fastq files, designated by RG1 and RG2. The fastq files are named as follows: 3 digits sample ID followed by a ., number indicating one of the three triplicate libraries followed by _, and RG1 or RG2 indicating the first round of sequencing (all samples) or second round of sequencing (only samples that didn't reach sufficient read depth on first sequencing run).
consensusNarrowPeaksWithPeakIDs-1bpOverlap-min3samples_liver-firstPass-20samples.bed
DESeq2Datasets_GC-correct_consensusNarrowPeaks-1bpOverlap-min3samples_liver-secondPass-20samples.RData

data_processing:
We trimmed ATAC-seq reads to a uniform length of 126 bp using cutadapt and trimmed sequencing adapters using CTA (https://github.com/ParkerLab/cta)
We merged readgroups for the same library, aligned reads to the hg19 human genome using BWA-MEM, selected properly paired autosomal alignments with high mapping quality (mapq>30) with samtools, and removed duplicate alignments using Picard.
We merged the replicate bam files for each individual and used ataqv to generate ATAC-seq quality metrics and confirmed ATAC-seq libraries corresponded to the correct genotypes using verifyBamID.
To identify consensus peaks, we converted the merged .bam files for each individual to .bed files using BEDTools, called narrow peaks for each individual using MACS2 with parameters –nomodel –shift -100 –extsize 200 –keep-dup all, and removed peaks overlapping blacklisted regions (Duke-excluded and Dac-blacklist from ENCODE). We then merged peaks across individuals using BEDTools and defined consensus peaks as merged peaks that shared at least 1 base with a peak present in samples from at least 3 individuals.
Genome_build: hg19
Supplementary_files_format_and_content: .bam files contain ATAC-seq high-quality autosomal alignments (HQAA) to the hg19 genome in a compressed format
Supplementary_files_format_and_content: .narrowPeak files contain peaks called on individual ATAC-seq samples (after merging across replicates) using MACS2. The columns of the file are: peak_chromosome, peak_start, peak_stop, peak_name, score, strand, fold enrichment, -log10(p_value), -log10(q_value), and peak summit location relative to peak_start.
Supplementary_files_format_and_content: .bw files contain ATAC-seq signal values produced by MACS2 and can be loaded into the UCSC genome browser for visualization.
Supplementary_files_format_and_content: The .Rdata file 'DESeq2Datasets_GC-correct_consensusNarrowPeaks-1bpOverlap-min3samples_liver-secondPass-20samples.RData' contains R objects produced by DESeq2, known as DESeq datasets. The file contains two DESeq2 datasets: peaks.dds containing the raw peak counts across the 20 samples, and peaks.rlog containing the variance-stabilized peak counts. The raw peak counts can be extracted with the R command 'counts(peaks.dds,normalized=F)'. The normalization factors used are the combination of RASQUAL GC offsets per peak and DESeq2 size factors. Sample covariates can be obtained with 'colData(peaks.dds)'.
Supplementary_files_format_and_content: The .bed file 'consensusNarrowPeaksWithPeakIDs-1bpOverlap-min3samples_liver-firstPass-20samples.bed' contains the consensus peaks present in at least 3 samples. The file contains a header describing each column.

organism: Homo sapiens

source_name: liver tissue

extract_protocol:
Omni-ATAC-seq protocol. We pulverized 50-mg pieces of frozen human liver tissue in liquid nitrogen using a Cell Crusher (CellCrusher, Cork Island), homogenized the tissue powder in ice cold nuclei isolation buffer (NIB: 20 mM Tris-HCl, 50 mM EDTA, 5 mM spermidine, 0.15 mM spermine, 0.1% mercaptoethanol, 40% glycerol, pH 7.5) using a 1-mL dounce for 40 strokes, and rotated for 5 minutes at 4oC. We filtered the solution through a Miracloth (Calbiochem, San Diego, Ca USA), centrifuged at 1100g for 10 minutes at 4oC, washed the pellet with 250-uL NIB containing 0.5% Triton-X, centrifuged at 500g for 5 minutes at 4oC, and resuspended the pellet in 250-uL of resuspension buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, pH 7.4). After counting isolated nuclei, we pelleted 50,000 nuclei at 500g for 5 minutes at 4oC for each of three replicate ATAC-seq libraries per sample.
Libraries were prepared using Nextera kits (Illumina)

tag: Sex

value: Male

tag: age

value: liver


title: WT_DM_CTCF_ChIPseq_Rep2

description:
CTCF  ChIP-Seq of wildtype differentiating myocytes at 24h
WT_DM_CTCF.bw

source_name: Differentiating myocytes for 24h

value: wild type


title: WT_GM_H3K4me3_ChIPseq_Rep2

description:
H3K4me3  ChIP-Seq of wildtype proliferating myoblasts
WT_GM_K4me3.bw


title: WT_DM_CTCF_ChIPseq_Rep1


title: Total_mRNA_puf-8(ust221)_rep3

city: Hefei

first: Zheng

last: Xu

state: Anhui

address: Huangshan road

department: Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine

institute: University of Science and Technology of China

library_source: transcriptomic

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. 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.
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.
Genome_build: WS269
Supplementary_files_format_and_content: number of reads targeting each transcript

molecule: total RNA

organism: Caenorhabditis elegans

source_name: young adult stage

growth_protocol: C. elegans strains were cultured on NGM plates with E. coli OP50 as the food source in a temperature controlled incubator. Worms were maintained at 20°C prior to the experiment. Worms were synchronized by using the standard egg-prep protocol. L1s were released onto 10 cm NGM concentrated OP50 plate (approximately 3000 L1s per plate).

extract_protocol:
Total RNAs were isolated from young adult stage worms. Briefly, worms were harvested and dounced on ice with pestle B in TRIzol reagent (Invitrogen) followed by isopropanol precipitation. The precipitates were treated with calf intestinal alkaline phosphatase (CIAP, Invitrogen), re-extracted with TRIzol, and treated with T4 polynucleotide kinase (T4 PNK, New England Biolabs) in the presence of 1 mM ATP.
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: temperature

value: 20oC on OP50

tag: developmental stage

value: young adult


title: Total_mRNA_puf-8(ust221)_rep2


title: E_16_Seronegative

molecule: polyA RNA

value: Female

tag: cell type


title: E_13_Seronegative


title: WT_GM_CTCF_ChIPseq_Rep2

description:
CTCF  ChIP-Seq of wildtype proliferating myoblasts
WT_GM_CTCF.bw


title: Day10_HA_H3K27ac_rep2

city: Stanford

first: David

middle: G

last: Gennert

state: CA

address: 269 Campus Drive

institute: Stanford University School of Medicine

data_processing:
Library strategy: HiChIP
Sequencing reads were aligned and paired, filtered for long-range contacts, and removed of duplicates using the HiC-Pro pipeline (PMID: 26619908)
Filtered reads were converted to a .hic file for visualization with Juicebox (PMID: 25497547)
Genome_build: hg19
Supplementary_files_format_and_content: Juicebox .hic files were generated for each HiChIP sample

source_name: CAR T cells

growth_protocol: Primary human T cells were isolated from healthy donors using the RosetteSep Human T cell Enrichment kit (Stem Cell Technologies). Buffy coats were purchased from Stanford Blood Center and processed according to the manufacturer’s protocol using Lymphoprep density gradient medium and SepMate_50 tubes. Isolated T cells were cryopreserved at 2x10e7 T cells per vial in CryoStor CS10 cryopreservation medium (Stem Cell Technologies).  Cryopreserved T cells were thawed and either sorted (for Day 0 samples) or activated same day with Human T_Expander CD3/CD28 Dynabeads (Gibco) at 3:1 beads:cell ratio in T cell media (AIMV supplemented with 5% FBS, 10mM HEPES, 2mM GlutaMAX, 100 U/mL penicillin, and 100ug/mL streptomycin (Gibco)). Recombinant human IL_2 (Peprotech) was provided at 100 U/mL.  T cells were transduced with retroviral vector on days 2 and 3 post activation and maintained at 0.5_1 x10e6 cells per mL in T cell media with IL_2. Non_tissue culture treated 12_well plates were coated overnight at 4C with 1mL Retronectin (Takara) at 25ug/mL in PBS. Plates were washed with PBS and blocked with 2% BSA for 15min. Thawed retroviral supernatant was added at ~1mL per well and centrifuged for 2 hours at 32C at 3200 RPM before the addition of cells. CAR T cells were used for in vitro assays on Day 10 post-activation.

extract_protocol:
500,000 cells per replicate were pelleted at 300 g for 5 minutes and resuspended in 500 µL 1% methanol-free formaldehyde (Thermo Fisher). After 10 minutes room temperature incubation with rotation, cross-linking was quenched with glycine to a final concentration of 125 mM.  Cross-linked cells were washed in PBS and pellets stored at -80 °C until subsequent next steps. Pellets were resuspended in 500 µL cold Hi-C lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2% NP-40, 1X protease inhibitor (Roche)) and rotated for 30 minutes at 4 °C. Samples were centrifuged at 2500 g for 5 minutes at 4 °C to pellet nuclei.
See Mumbach et al (2016, PMID: 27643841) for library construction protocol.  H3K27ac enrichment of 3C libraries.

value: CAR T cells

tag: time

tag: car target


title: Total_mRNA_puf-8(ust223)_rep1


title: Day10_CD19_H3K27ac_rep2


title: Day10_CD19_H3K27ac_rep1


title: Day10_HA_H3K27ac_rep1


title: Total_mRNA_puf-8(ust221)_rep1


title: Day0_H3K27ac_rep2

source_name: Primary T cells

value: Primary T cells


title: D_2100_Mild

value: mild COVID-19

value: Mild


title: Day0_H3K27ac_rep1


title: Total_mRNA_N2_rep3

value: wild type N2


title: WT_DM_MyoD_ChIPseq_Rep2

description:
MyoD  ChIP-Seq of wildtype differentiating myocytes at 24h
WT_DM_MyoD.bw


title: WT_GM_CTCF_ChIPseq_Rep1


title: WT_DM_MyoD_ChIPseq_Rep1


title: D_18_Mild


title: Total_mRNA_N2_rep2


title: Day14_CD8_N_HA_2

data_processing:
Adapter sequences were trimmed by a custom Python script.
Reads were aligned to the hg19 genome by Bowtie2.
Duplicate reads were filtered by Picard, mitochondrial reads were removed, and reads were filtered for MAPQ quality scores ≥10.
Peaks were called with MACS2 using an FDR cutoff of 0.01.
Sequencing tracks were generated with the Washington University Epigenome Browser using read_number normalized BigWig files.
Differential peak analysis was carried out using DESeq2.
Transcription factor motif deviation analysis was carried out using chromVAR.
TF motif enrichment was calculated using HOMER.
Genome_build: hg19
Supplementary_files_format_and_content: ENCODE narrowPeak files were generated for each ATAC_seq sample.

source_name: T cells

growth_protocol: Primary human T cells were isolated from healthy donors using the RosetteSep Human T cell Enrichment kit (Stem Cell Technologies). Buffy coats were purchased from Stanford Blood Center and processed according to the manufacturer’s protocol using Lymphoprep density gradient medium and SepMate_50 tubes. Isolated T cells were cryopreserved at 2x10e7 T cells per vial in CryoStor CS10 cryopreservation medium (Stem Cell Technologies).  Cryopreserved T cells were thawed and either sorted (for Day 0 samples) or activated same day with Human T_Expander CD3/CD28 Dynabeads (Gibco) at 3:1 beads:cell ratio in T cell media (AIMV supplemented with 5% FBS, 10mM HEPES, 2mM GlutaMAX, 100 U/mL penicillin, and 100ug/mL streptomycin (Gibco)). Recombinant human IL_2 (Peprotech) was provided at 100 U/mL.  T cells were transduced with retroviral vector on days 2 and 3 post activation and maintained at 0.5_1 x10e6 cells per mL in T cell media with IL_2. Non_tissue culture treated 12_well plates were coated overnight at 4C with 1mL Retronectin (Takara) at 25ug/mL in PBS. Plates were washed with PBS and blocked with 2% BSA for 15min. Thawed retroviral supernatant was added at ~1mL per well and centrifuged for 2 hours at 32C at 3200 RPM before the addition of cells. CAR T cells were used for in vitro assays on days 7 and 14 post-activation.

extract_protocol:
100,000 cells from each sample were sorted by FACS into culture media, centrifuged at 500g at 4°C, then resuspended in ATAC_seq Resuspension Buffer (RSB) (10 mM Tris_HCl, 10 mM NaCl, 3mM MgCl2) supplemented with 0.1% NP_40,0.1% Tween_20, and 0.01% Digitonin.  Samples were split into two replicates each prior to all subsequent steps.  Samples were incubated on ice for 3 minutes, then washed out with 1 mL RSB supplemented with 0.1% Tween_20.  Nuclei were pelleted at 500g for 10 minutes at 4°C.
The nuclei pellet was resuspended in 50 μL transposition mix (25 μl 2x TD buffer, 2.5 μl transposase (Illumina), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween_20, 5 μl H2O) and incubated at 37°C for 30 minutes in a thermomixer with 1000 RPM shaking.  The reaction was cleaned up using the Qiagen MinElute PCR Purification Kit. Libraries were PCR_amplified using the NEBNext Hi_Fidelity PCR Master Mix and custom primers (IDT) as described previously20. Libraries were sufficiently amplified following 5 cycles of PCR, as indicated by qPCR fluorescence curves20.  Libraries were purified with the Qiagen MinElute PCR Purification Kit and quantified with the KAPA Library Quantification Kit. Libraries were sequenced on the Illumina NextSeq at the Stanford Functional Genomics Facility with paired_end 75bp reads.

value: CAR T cell

value: 14 Days post-stimulation

tag: t cell type

tag: t cell memory

value: Naïve


title: D_15_Mild

tag: gender

value: PBMC


title: D_11_Mild

tag: diseas state


title: WT_GM_MyoD_ChIPseq_Rep1

description:
MyoD  ChIP-Seq of wildtype proliferating myoblasts
WT_GM_MyoD.bw

value: skeletal muscle


title: WT Petiole H96, rep3

city: Daegu

first: Kitae

last: Song

state: jung-gu

address: DGIST, 333, Techno jungang-daero,, Hyeonpung-myeon

country: South Korea

institute: Institute for Basic Science

data_processing:
Raw reads were checked quality and trimmed using FastQC (Andrews, 2010)
the trimmed reads were mapped to the Arabidopsis thaliana genome (TAIR10) using STAR (Dobin et al., 2013)
 After alignment, the gene-level raw count data files were generated using HTSeq (Anders et al., 2015)
Genome_build: Arabidopsis thaliana genome (TAIR10)
Supplementary_files_format_and_content: HTSeq count file (TXT)

organism: Arabidopsis thaliana

source_name: Excised leaf

extract_protocol:
Total mRNA was extracted from leaves using WelPrep.
Library construction and sequencing were performed using Illumina NovaSeq 6000 platform

value: WT

tag: time after excision

value: 96 hours

value: Excised leaf

value: 21-day-old plant

tag: treatment

value: excision


title: E_12_Seronegative

value: highly exposed, Seronegative

tag: severity

value: Seronegative, highly exposed

tag: location


title: Day14_CD8_N_CD19_2


title: RKO_shE2

city: shanghai

first: Yongfeng

last: Liu

address: 320 Yueyang Road, Shanghai, 200025 P.R. China

institute: The Institute of Health Sciences, SIBS, CAS / SJTUSM

description:
MGISEQ-2000
EZH2_deficiency_induced_gene_expression_change_in_CRCs.FPKM.xls

data_processing:
Filtering steps are as follows: 1) Remove reads with adaptors; 2) Remove reads in which unknown bases are more than 10%; 3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more than 5).
Use Bowtie2 to map clean reads to reference gene and use BWA to reference genome.
FPKM method is used in calculated expression level.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: EZH2_deficiency_induced_gene_expression_change_in_CRCs.FPKM.xls: Excel file includes read counts and FPKM values.

source_name: RKO without EZH2

extract_protocol:
RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

treatment_protocol: EZH2 in HCT116 and RKO is silenced by lenti-virus mediated shRNA.

tag: cell line

value: RKO

value: Colorectal cancer cell line

tag: shRNA

value: EZH2 knockdown


title: WT Petiole H96, rep2

tag: genotype

tag: tissue


title: C_413_Healthy

tag: age

value: Female


title: WT Petiole H96, rep1


title: C_407_Healthy

value: Male


title: Day14_CD8_N_CD19_1

value: CAR T cell


title: HCT116_shE2

source_name: HCT116 without EZH2


title: WT Petiole H72, rep3

value: 72 hours


title: C_401_Healthy


title: RKO_NC

source_name: CTRL of RKO

value: Control


title: Day14_CD8_CM_HA_2

value: 14 Days post-stimulation

value: Central Memory


title: WT Petiole H72, rep2

value: WT


title: C_397_Healthy

value: PBMC


title: C_379_Healthy


title: liverTissue_genotypes_sample_SJLB797

type: genomic

description: The 'SJLB' prefix stands for 'ST. Jude liver bank' and is prepended to sample IDs in the .idat and .vcf files. The 'SJLB' prefix is removed from sample IDs in the manuscript to save space.

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: We mapped the Illumina array probe sequences to the hg19 genome assembly using novoalign, excluding variants with ambiguous probe alignments and variants with 1000 Genomes (1000G) phase 3 minor allele frequency (MAF) >.01 within 7 bp of the 3’ end of probes. No individuals were related at a 3rd-degree relationship threshold using KING v1.4. Prior to genotype imputation, we combined the genotypes of the samples in this study with genotypes from 177 samples from a separate study genotyped on similar chips and removed variants that met the following criteria: allele frequency difference >20% with 1000G phase 3 Europeans, palindromic variants with MAF>.2, genotype missingness > 2.5%, and extreme deviation from Hardy-Weinberg Equilibrium (p<1x10-4). Using the Michigan Imputation Server, we phased 1,789,889 autosomal variants using Eagle v2.3 and imputed missing genotypes using minimac3 with the Haplotype Reference Consortium (hrc.r1.1.2016) panel. The VCF files contain all imputed variants with imputation r2>.3. However, we restricted to biallelic variants in the manuscript.

label: Cy5, Cy3

label_protocol: standard Illumina protocol

extract_protocol: standard Illumina protocol

tag: Sex

value: liver


title: Day14_CD8_CM_HA_1

tag: cell type


title: HCT116_NC

source_name: CTRL of HCT116


title: WT Petiole H72, rep1

value: Excised leaf

value: 21-day-old plant


title: Total_mRNA_N2_rep1

value: wild type N2

tag: temperature

value: 20oC on OP50

tag: developmental stage

value: young adult


title: WT_GM_MyoD_ChIPseq_Rep2

tag: passage

tag: chip antibody

value: skeletal muscle

value: wild type


title: WT Petiole H48, rep3

value: 48 hours

value: excision


title: Day14_CD8_N_HA_1

value: CAR T cell

tag: time

tag: t cell type

tag: t cell memory

value: Naïve

tag: car target


title: B_1573_Seronegative

tag: gender

value: Male

tag: diseas state

value: highly exposed, Seronegative

tag: severity

value: Seronegative, highly exposed


title: Day14_CD8_CM_CD19_2

value: 14 Days post-stimulation

value: Central Memory


title: liverTissue_genotypes_sample_SJLB795

value: liver


title: Day14_CD4_N_HA_2


title: Day14_CD8_CM_CD19_1


title: B_1562_Seronegative

tag: location

value: PBMC


title: WT Petiole H48, rep2

tag: genotype

value: WT

tag: time after excision

value: Excised leaf

value: 21-day-old plant

tag: treatment


title: liverTissue_genotypes_sample_SJLB794

tag: Sex

tag: age

tag: tissue


title: liverTissue_genotypes_sample_SJLB793

value: Female


title: WT Petiole H48, rep1


title: Day14_CD4_N_CD19_2

tag: cell type


title: WT Petiole H24, rep3

value: 24 hours


title: liverTissue_genotypes_sample_SJLB786


title: B_446_Seronegative


title: liverTissue_genotypes_sample_SJLB767


title: Day14_CD4_N_CD19_1


title: B_439_Seronegative


title: Day14_CD4_CM_HA_2


title: Day14_CD4_CM_HA_1


title: liverTissue_genotypes_sample_SJLB715


title: WT Petiole H00, rep3

value: 0 hour


title: Day14_CD4_CM_CD19_2


title: B_434_Seronegative


title: WT Petiole H00, rep2


title: Day14_CD4_CM_CD19_1


title: Day14_CD4_N_HA_1


title: B_1560_Seronegative


title: B_433_Seronegative


title: B_448_Seronegative


title: eur1-11 Petiole H96, rep3

value: 96 hours


title: liverTissue_genotypes_sample_SJLB684


title: Day7_CD8_N_HA_1

value: 7 Days post-stimulation


title: Day7_CD8_N_HA_2

value: CAR T cell


title: liverTissue_genotypes_sample_SJLB683


title: liverTissue_genotypes_sample_SJLB670


title: B_431_Seronegative


title: eur1-11 Petiole H96, rep2

value: excision


title: WT Petiole H24, rep2


title: liverTissue_genotypes_sample_SJLB753


title: WT Petiole H24, rep1


title: B_430_Seronegative


title: Day7_CD8_N_CD19_2

value: Naïve


title: eur1-11 Petiole H96, rep1


title: Day7_CD8_N_CD19_1


title: B_436_Seronegative

value: Male

value: highly exposed, Seronegative


title: liverTissue_genotypes_sample_SJLB713


title: B_429_Seronegative

value: Seronegative, highly exposed


title: WT Petiole H00, rep1


title: eur1-11 Petiole H72, rep3

value: 72 hours


title: Day7_CD8_CM_HA_2

value: Central Memory


title: liverTissue_genotypes_sample_SJLB651

value: liver


title: liverTissue_genotypes_sample_SJLB485


title: B_425_Seronegative

value: PBMC


title: B_427_Seronegative


title: eur1-11 Petiole H72, rep2

value: Excised leaf


title: Day7_CD8_CM_HA_1


title: Day7_CD8_CM_CD19_2


title: B_423_Seronegative


title: eur1-11 Petiole H48, rep2

value: 48 hours

value: 21-day-old plant


title: liverTissue_genotypes_sample_SJLB438

value: Female


title: B_422_Seronegative


title: Day7_CD8_CM_CD19_1


title: B_421_Seronegative


title: eur1-11 Petiole H72, rep1


title: liverTissue_genotypes_sample_SJLB459


title: Day7_CD4_N_HA_2


title: liverTissue_genotypes_sample_SJLB469


title: liverTissue_genotypes_sample_SJLB365


title: eur1-11 Petiole H24, rep3

value: 24 hours


title: liverTissue_genotypes_sample_SJLB348


title: eur1-11 Petiole H48, rep1


title: liverTissue_genotypes_sample_SJLB662


title: Day7_CD4_N_HA_1


title: B_419_Seronegative


title: Day7_CD4_N_CD19_2


title: eur1-11 Petiole H24, rep2


title: eur1-11 Petiole H24, rep1


title: eur1-11 Petiole H48, rep3


title: eur1-11 Petiole H00, rep3

value: 0 hour


title: Day7_CD4_CM_HA_2

value: 7 Days post-stimulation


title: B_417_Seronegative


title: B_410_Seronegative


title: eur1-11 Petiole H00, rep1


title: B_405_Seronegative


title: B_420_Seronegative


title: eur1-11 Petiole H00, rep2


title: Day7_CD4_CM_CD19_2

value: CAR T cell


title: B_403_Seronegative


title: Day7_CD4_CM_HA_1


title: B_398_Seronegative


title: Day7_CD4_CM_CD19_1


title: Colon Epithelium CD4 T Cells - IL23R Knockout rep2

city: Berkeley

last: DeTomaso

address: Stanley Hall

department: Computational Biology

institute: UC Berkeley

data_processing:
Samples were processed individually by alignment to the mm10 genome using CellRanger v2.0.2.  Genes expressed in less than 100 cells were filtered from downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: matrix.mtx: gene count matrix (genes x cells) in Matrix Market format.  barcodes.tsv: cell labels for the columns in matrix.mtx.  genes.tsv: gene labels (Ensembl ID and Symbol) for the rows of matrix.mtx.  cell_meta.txt: associated meta-data (tissue and genotype) for each cell in matrix.mtx

extract_protocol:
Spleens were extracted and then a single-cell suspension was prepared by homogenization with a syringe plunger and debris was filtered with a 70um filter. Red blood cells were lysed with ACK lysis buffer from Lonza. The intestinal T cells were isolated with the lamina propia dissociation kit (cat. # 130-097-410) from Miltenyi Biotec.
Cells were encapsulated into droplets and libraries were prepared using Chromium Single Cell 3' Reagent Kits v2 according to the manufacturer's instructions (10x Genomics).

tag: tissue origin

value: Colon Epithelium

value: IL23R Knockout

value: CD4 T Cells


title: Salmonella within Acanthamoeba replicate 2

city: Orenburg

first: Alexander

middle: S

last: Balkin

address: 11 Pionerskaya st.

country: Russia

institute: Institute for Cellular and Intracellular Symbiosis

data_processing:
Demultiplexed reads were trimmed against adapters with bbduk.
SortMeRNA was used to remove reads belonging to prokaryote and eukaryote rRNA sequences.
Clean reads were initially mapped against the full A. castellanii genome (GCF_000313135.1) with Bowtie2 [78] in local mode (L-16) and then mapped against the S. Typhimurium 14028s genome (GCA_000022165.1).
The reads per operon were evaluated with featureCounts in the Rsubread package of R.
Genome_build: GCA_000022165.1
Supplementary_files_format_and_content: Operon_count_matrix.csv  (Tabular file include operon coverage values for each sample .)
RNA-Seq_stat.xlsx  (base statistics)

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. ATCC 14028

source_name: Salmonella-Acanthamoeba coculture in PAS medium

growth_protocol: Salmonella was grown in Luria broth at 37°C without antibiotics. A. castellanii axenic culture was grown for 5 d in PYG medium to a density of 4-5 × 10^5 cells/mL.

extract_protocol:
Total RNA was extracted with ExtractRNA reagent (Evrogen, Moscow, Russia). The RNA samples were treated with a TURBO DNA-free™ kit (Thermo Fisher Scientific, Waltham, MA, USA) following the manufacturer’s instructions. The RNA content was determined in a Qubit fluorometer (Thermo Fisher Scientific, Waltham, MA, USA). RNA integrity, purity, and concentration were assessed with a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA).
The Cappable-Seq procedure was performed as previously described [Ettwiller et al., 2016].
Cappable-Seq

treatment_protocol: The Salmonella cells were added to the Acanthamoeba culture in sterile PAS at a 100:1 bacterium:amoeba ratio. The co-culture was incubated for 1 h until most of the bacteria had been ingested by the Acanthamoeba. The suspension was then washed thrice with PAS to remove extracellular bacteria. The co-cultures were then centrifuged at 800g for 5 min at 25 °C, the supernatants were transferred to sterile tubes, and the pellets were resuspended in 1 mL ExtractRNA reagent (Evrogen, Moscow, Russia).

tag: strain

tag: condition

value: infection

tag: sample type

value: Salmonella-Acanthamoeba coculture


title: Day7_CD4_N_CD19_1

tag: time

tag: t cell type

tag: t cell memory

value: Naïve


title: Day0_CD8_N_2

value: Primary T cell

value: 0 Days post-stimulation

tag: car target


title: Salmonella within Acanthamoeba replicate 3


title: Day0_CD8_N_1


title: Salmonella within Acanthamoeba replicate 1


title: Colon Epithelium CD4 T Cells - Control rep2

source_name: Colon Epithelium CD4 T Cells - Control

value: Control


title: Day0_CD8_CM_2

value: Central Memory


title: B_393_Seronegative

tag: gender

value: Male

tag: diseas state

value: highly exposed, Seronegative

tag: severity

value: Seronegative, highly exposed

value: PBMC


title: B_377_Seronegative

value: Female

tag: location


title: Small Intestine Lamina Propria CD4 T Cells - IL23R Knockout rep2

value: Small Intestine Lamina Propria

tag: genotype


title: Day0_CD8_CM_1


title: siH19 2

type: RNA

city: Heidelberg

first: Yiqiao

last: Luo

state: Deutschland

address: Im Neuenheimer Feld 365

country: Germany

institute: Section Surgical Research

description: Gene expression data

hyb_protocol: Microarray analyses was performed at the Microarray-Analytic Center of the Medical Faculty Mannheim, using Clariom™ D Assays (Thermo Fisher Scientific, Dreieich, Germany).

label: biotin

source_name: MIA-PaCa2 transfected with siH19

label_protocol: not provided

growth_protocol: Cells were cultured in DMEM/high glucose (Sigma, Deisenhoffen, Germany), which was supplemented with 10% FCS (Sigma) and 25mmol/L HEPES (Thermo Fisher, Dreieich, Germany)

extract_protocol: Total RNA was isolated with the RNeasy Mini Kit (QIAGEN, Hilden, Germany).

treatment_protocol: FlexiTube siRNAs siH19, and AllStars Negative Control siRNA (QIAGEN, Hilden, Germany), 20 µg each, were transfected with lipofectamine 2000 (Thermo Fisher Scientific, Dreieich, Germany) according to the instructions of the manufacturer.

tag: cell line

tag: cell  type

value: PDAC

tag: knockdown


title: siH19 1

description: Gene expression data

scan_protocol: Microarray analyses was performed at the Microarray-Analytic Center of the Medical Faculty Mannheim, using Clariom™ D Assays (Thermo Fisher Scientific, Dreieich, Germany).


title: NC 3

description: Gene expression data

data_processing: Microarray analyses was performed at the Microarray-Analytic Center of the Medical Faculty Mannheim, using Clariom™ D Assays (Thermo Fisher Scientific, Dreieich, Germany).

source_name: MIA-PaCa2 transfected with NC

value: Negative Control siRNA


title: NC 2

description: Gene expression data


title: siH19 3

description: Gene expression data


title: B_376_Seronegative

source_name: PBMCs

tag: age

tag: cell type


title: NC 1

description: Gene expression data


title: Small Intestine Lamina Propria CD4 T Cells - Control rep2

tag: tissue origin


title: B_375_Seronegative


title: Salmonella control culture replicate 2

source_name: Free-living Salmonella culture in PAS medium

tag: strain

tag: condition

value: control

value: Free-living Salmonella culture


title: Day0_CD4_N_2

tag: time


title: Colon Lamina Propria CD4 T Cells - IL23R Knockout rep2

value: Colon Lamina Propria

value: IL23R Knockout

value: CD4 T Cells


title: Salmonella control culture replicate 1

tag: sample type


title: B_368_Seronegative


title: pre-adipocyte WT

city: Oxford

first: Michelle

last: Simon

address: Harwell Innovation Center

department: Bioinformatics

country: United Kingdom

institute: Medical Research Council

description: nuclei

data_processing:
Trimmed reads were aligned to the mm10 mouse reference genome using Bowtie 2 (73). Reads mapping to the mitochondrial genome and alternative contigs were excluded from further analysis. After removing reads with a mapping quality score < 30, peaks were filtered to exclude those with duplicates or that overlapped with a blacklisted region (21, 74) . We used
MACS2(75) with ‘--nomodel --shift -100 --extsize 200 -q 0.05’ for the detection of open chromatin. The resulting bed files were converted into coverage tracks (i.e. bigWig format) for visualisation
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: pre-adipocyte

extract_protocol:
Apologies for the delay in replying my amendments as requested are below:
Differentiating cells were lysed directly in the cell culture plate. Lysis buffer was added directly onto cells grown in a 12-well plate. Plates were incubated on ice for 10min until cells were permeabilized and nuclei released. Lysis buffer was gently pipetted up and down to wash nuclei off the well and transferred into a chilled 1.5ml tube to create crude nuclei. Nuclei were spun down at 600 x g for 10 min at 4°C, nuclei pellets were then re-suspended in 40ul TD Buffer, nuclei counted using trypan blue and volume of 50.000 nuclei was determined. Transposition reaction was performed following a previously published protocol (72). Tagmented DNA was PCR amplified for 11. Quality was assessed using a DNA1000 Chip (Applied Biosystems) and run on a Bioanalyzer (Applied Biosystems). The profiles showed that all libraries had a mean fragment size of ~190bp and characteristic nucleosome patterning, indicating good quality of the libraries.

value: pre-adipocyte

tag: Sex

value: male


title: Colon Lamina Propria CD4 T Cells - Control rep2

value: Control


title: Spleen CD4 T Cells - IL23R Knockout rep2

source_name: Spleen CD4 T Cells - IL23R Knockout

value: Spleen


title: Day0_CD4_CM_1

value: Primary T cell

value: 0 Days post-stimulation

tag: t cell type

tag: t cell memory

value: Central Memory

tag: car target


title: B_362_Seronegative

tag: gender

value: Male

tag: diseas state

value: highly exposed, Seronegative

tag: severity

value: Seronegative, highly exposed

value: PBMC


title: B_366_Seronegative

value: Female

tag: location


title: Spleen CD4 T Cells - Control rep2

source_name: Spleen CD4 T Cells - Control

tag: genotype


title: Salmonella control culture replicate 3

value: control


title: Day0_CD4_N_1

value: Naïve


title: Colon Lamina Propria CD4 T Cells - IL23R Knockout rep1

value: Colon Lamina Propria


title: Z226

city: East Lansing

first: Rance

last: Nault

state: United States

address: 1355 Bogue St. B403

department: Department of Pharmacology and Toxicology

institute: Michigan State University

description: Pregnant female mice doses every day for 10 days

data_processing:
Read quality was assessed using FastQC v0.11.5 and adapter trimming was performed using Trimmomatic v0.38.
Strain specific reference pseudogenomes (Build 37) and corresponding MOD files were downloaded from http://www.csbio.unc.edu/CCstatus/index.py?run=Pseudo and used for alignment using Bowtie2 v2.3.2.25 Alignment of reads for BXD strains (BXD30, BXD91, and BXD100) whose pseudogenomes were not available was performed using the pseudogenomes of parental strains C57BL/6J and DBA/2J. Coordinates of aligned reads were converted to a common mm9 reference genome coordinates using the Lapels package (https://github.com/shunping/lapels). Alignments made to two reference genomes (e.g. BXD mice) were merged using the Suspenders package (https://github.com/holtjma/suspenders)
Gene counts were determined using HTSeq-count v0.6.1.
Differential expression analysis was performed between treatment groups within strains using DESeq2 v3.8.
Genome_build: mm9 (build 37)
Supplementary_files_format_and_content: Tab-delimited text files represent the number of aligned reads to each gene

source_name: Liver

extract_protocol:
Frozen liver (~50 mg) was homogenized in 1 mL of TriZOL with chrome-steel beads using a Mixer Mill 300 (Life Sciences, Carlsbad, CA) for 4 minutes. Following, total RNA was extracted per the manufacturer’s instructions with an additional 5:1 phenol:chloroform extraction step (Sigma Aldrich, St. Louis, MO). RNA purity (260/280 ratio) and concentration (ng/µL) were assessed with a NanoDrop 1000 spectrophotometer. RNA quality was determined using an Agilent 2100 Bioanalyzer. All RNA samples had RNA integrity numbers (RINs) ≥7.
Library preparation was performed using a NEBNext Ultra RNA kit.

treatment_protocol: TCDD or vehicle control was administered to mice using peanut butter as the vehicle daily for 10 consecutive days .

value: week

value: pregnant

value: degree fahrenheit

value: percent

value: Innovive disposable cage

tag: bedding

value: PJ murphy course sani-chips

tag: water

value: in-house RO water

value: LabDiet 5058

value: LabDiet

tag: vendor

value: Accustandard

value: Peanut butter

value: day

value: oral dosage form

tag: dose

value: microgram per kilogram per day

value: NEBNext Ultra RNA kit


title: Z227

tag: strain

value: Female


title: Z224


title: Day0_CD4_CM_2

tag: cell type

value: Primary T cell

value: 0 Days post-stimulation

value: Central Memory


title: MSC_shRNA_TPM1_induced_d1

city: Jerusalem

first: Amnon

last: Buxboim

state: Jerusalem

address: The Edmond J. Safra Campus - Givat Ram, Jerusalem 9190401,Israel

department: The Department of Cell and Developmental Biology

country: Israel

institute: The Hebrew University of Jerusalem

description: scRNAseq_expression_matrix_TPM1_cell_lines.txt

data_processing:
For scRNA-seq, sequencing libraries were demultiplexed using indices and barcodes, permitting ≤ 1 nucleotide alignment substitution. After removing low-complexity poly-adenylated sequences, transcripts were aligned against an indexed reference genome (GRCh38.p12) using Bowtie 0.12.8, and gene intensities were evaluated based on UMI frequency. Cells with high representation of mitochondrial RNA (>25%) or low gene number (≤1,900 per 15,000 UMIs) were discarded. Mitochondrial and ribosomal genes were discarded as well as low-frequency genes that were detected in ≤ 5 cells.
For population-level RNA sequencing, human genome alignment (hg19/GRCh38) was performed using Bowtie2 and unique reads were counted using the HTSeq package. Count normalization was performed with DESeq2.
For scRNA-seq of TPM1 cell lines low-complexity poly-adenylated sequences were filtered out, the remaining sequences were de-multiplexed using the dropEst pipeline, and aligned to a human indexed reference genome (GRCh38.p12) using TopHat2 2.0.08.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: expression matrix table excel files include raw counts values for all samples
Supplementary_files_format_and_content: table with normalized gene counts for every gene and every sample
Supplementary_files_format_and_content: expression matrix table excel files include raw counts values for all samples

source_name: Bone marrow-derived cells

growth_protocol: MSC were seeded at D0 at 5,000 cells/cm2 density onto soft substrates with controlled elasticities (2 kPa and 25 kPa) composed of thin polyacrylamide hydrogel films and uniformly coated with rat-tail type-I collagen (Petrisoft; Matrigen). The hydrogels were coated with a 0.02 mg mL-1 rat tail type I collagen solution with a constant surface density. After  three days cells from each of the hydrogels, were  induced with a bipotential differentiation medium (D3). MSC TPM1 knockdown, overexpression and controls cells were cultured in polystyrene (PS) plates.

extract_protocol:
inDrop high-throughput single-cell labeling was performed as reported with minor adaptations. Briefly, cells were trypsin-detached, washed in phosphate-buffered saline (PBS, Sigma-Aldrich) and maintained dissociated in suspension supplemented with 15% OptiPrep (Sigma-Aldrich). Cells (~1000 cells/μl) were loaded into a chilled syringe pump and injected into a custom-designed microfluidics device. Flow settings were adjusted to allow individual cells to become encapsulated with single hydrogel beads presenting cell-specific barcoding oligonucleotide primers inside 3-5 nL encapsulation mixture droplets that contain 20 U μL-1 reverse transcriptase (SuperScript III, Thermo Fisher Scientific), First-Strand Buffer (Thermo Fisher Scientific), 0.6% (v/v) IGEPAL CA-630 (Sigma-Aldrich), 1 mM dNTPs (New England Biolabs), 6.67 mM DTT (Thermo Fisher Scientific), 2700 units mL-1 murine RNase inhibitor (New England Biolabs), and 0.1 M Tris-HCl (pH 8.0)). Primers consisted of a poly-T sequence to trap mRNA molecules, two 8-base cell-specific barcodes, 5-base unique molecular identifier (UMI) sequence, and a T7 promoter sequence. For population-level RNA sequencing DDR-TPM1.7 (overexpressed), shTPM1 (knockdown), and DDR Control MSCs were expanded on polystyrene plates in basal medium. Cell extracts were extracted by treating cells with Trizol reagent (Bio-Labs) and homogenizing with a 25-gauge needle. Cell lysates were mixed with Chloroform (Sigma-Aldrich) in a 5:1 ratio. The aqueous phase was separated via centrifugation and purified using RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol
Droplets were collected, the primers were photo-cleaved by exposing the emulsion to UV (365 nm 10 mW cm-2, BlackRay Xenon lamp) for 10 minutes at room temperature, and reverse transcription of trapped mRNA was performed at 50 ºC for 2 hours. Droplets were then demulsified by adding 1H,1H,2H,2H-perfluoro-1-octanol (Sigma Aldrich) dissolved in HFE-7500 (Novec) at 20% (v/v). Single-stranded DNA primers and primer dimers were digested using 1 unit μL-1 ExoI (New England Biolabs) and 1 U μL-1 HinFI (Thermo Fisher Scientific). mRNA:cDNA hybrids were purified using Agencout AMPure XP beads (Beckman Coulter Genomics) according to the manufacturer’s instructions. Second-strand cDNA synthesis was performed using NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module (New England Biolabs) and amplified by in vitro transcription (HiScribe, New England Biolabs). RNA products were fragmented using Ambion RNA Fragmentation Reagents (AM8740, Thermo Fischer Scientific), purified using Agencout AMPure XP beads, and reverse-transcribed using random hexamer primers (SuperScript III, Thermo Fisher Scientific). Single-stranded DNA fragments were linearly amplified via 14 PCR cycles (HiFi HotStart ReadyMix, Kapa Biosystems).  For population-level RNA sequencing biological triplicates of poly(A) RNA were extracted and genomic libraries were generated using the KAPA Stranded mRNA-Seq Kit (KAPA Biosystems).

treatment_protocol: Adipogenic induction was performed in low-glucose DMEM medium supplemented with 10 μg mL-1 insulin, 500 mM 3-isobutyl-1-methylxanthine (Sigma-Aldrich), 1 μM dextran (Sigma-Aldrich), and 100 μM indomethacin (Sigma-Aldrich). Osteogenic induction was performed in low-glucose DMEM medium supplemented with 50 μg mL-1 L-ascorbic acid 2-phosphate (Sigma-Aldrich), 10 mM glycerol 2-phosphate (Sigma-Aldrich), and 10 nM dexamethasone (Sigma-Aldrich). Bi-potential induction medium was prepared by mixing adipogenic and osteogenic induction media at equal volumes.

tag: matrix

value: polystyrene


title: B_346_Seronegative

tag: age

value: Male

value: highly exposed, Seronegative

value: Seronegative, highly exposed

value: PBMC


title: MSC_shRNA_TPM1_induced_d2


title: B_342_Seronegative


title: Colon Lamina Propria CD4 T Cells - Control rep1

tag: tissue origin

value: Colon Lamina Propria

value: Control

value: CD4 T Cells


title: Z181

tag: Sex

value: week

value: pregnant

value: degree fahrenheit

value: percent

value: Innovive disposable cage

value: PJ murphy course sani-chips

value: in-house RO water

value: LabDiet 5058

value: LabDiet

value: Accustandard

value: Peanut butter


title: Z220

value: Female

value: day

value: oral dosage form

value: microgram per kilogram per day

value: NEBNext Ultra RNA kit


title: MSC_DDR_TPM1.7_induced_d2

value: polystyrene


title: MSC_DDR_TPM1.7_induced_d1


title: Z177

value: week


title: B_151_Seronegative

value: highly exposed, Seronegative

value: Seronegative, highly exposed

value: PBMC


title: Spleen CD4 T Cells - Control rep1

value: Spleen

value: Control

value: CD4 T Cells


title: MSC_DDR_induced_d2


title: YM2

first: Justus

middle: M

last: Kebschull

address: 327 Campus Drive

institute: Stanford University

data_processing:
Libraries were sequenced on four differnet lanes of an Illumina HiseqX machine, and base called by Illumina
fastq files were processed through the 10X cellranger pipeline, aligning against the mm10 mouse genome, counting both exonic and intronic reads
genexcell count matrix was processed and analysed in Seurat V3
Genome_build: mm10
Supplementary_files_format_and_content: Seurat object containing good hcrt neurons from all 4 samples. RDATA file

source_name: Hcrt neurons

extract_protocol:
Hcrt neurons were labeled by reporter virus injection into yound and aged Hcrt:cre mice. Specifically, 0.3 μl AAV vectors carrying genes encoding Cre-dependent DsRed- hTRF2 (AAV-DJ-DIO-DsRed-hTRF2, 1.95 × 1012 genome copies per ml, customer virus packaged at Stanford Virus Core) were bilaterally injected to the LH (AP: −1.35 mm, ML: ±0.95 mm, DV: −5.15 mm) of young (3 months) and aged (18 months) Hcrt::Cre male and female mice with both genders to label telomere in the nuclei of Hcrt neurons. Lateral hypothalamus was dissected, nuclei liberated, and facs sorted for reporter signal. Sorted nuclei were then processed using 10X v3 3'end singel cell RNA seq pipeline
10x Genomics Chromium Single Cell 3’ Reagents v3
snRNAseq

value: male

value: 3 mo


title: YF2

value: female


title: B_144_Seronegative


title: OM2

value: 18 mo


title: B_143_Seronegative

value: Female


title: MSC_DDR_induced_d1


title: X151

value: pregnant

value: degree fahrenheit

value: percent

value: Innovive disposable cage

value: PJ murphy course sani-chips

value: in-house RO water

value: LabDiet 5058

value: LabDiet

value: Accustandard

value: Peanut butter

value: day


title: MSC_shRNA_TPM1_r2

description: RNAseq_deseq2_counts_TPM1_cell_lines.xlsx

value: basal

value: polystyrene


title: B_142_Seronegative

value: highly exposed, Seronegative

value: Seronegative, highly exposed

value: PBMC


title: MSC_shRNA_TPM1_r3


title: X147

value: Female

value: week

value: oral dosage form

value: microgram per kilogram per day

value: NEBNext Ultra RNA kit


title: OF2

value: female

value: 18 mo


title: MSC_shRNA_TPM1_r1


title: B_123_Seronegative

value: Male


title: X142

value: pregnant

value: degree fahrenheit

value: percent

value: Innovive disposable cage

value: PJ murphy course sani-chips

value: in-house RO water

value: LabDiet 5058

value: LabDiet


title: X135

value: Accustandard

value: Peanut butter

value: day


title: Spleen CD4 T Cells - IL23R Knockout rep1

value: Spleen

value: IL23R Knockout

value: CD4 T Cells


title: B_110_Seronegative

value: highly exposed, Seronegative

value: Seronegative, highly exposed

value: PBMC


title: MSC_shRNA_control_r3

value: basal

value: polystyrene


title: MKO_DM_RNAseq_Rep3

description:
RNA-Seq of myod ko differentiating myocytes at 24h
MyoD_project_count.xls

source_name: Differentiating myocytes for 24h

tag: passage

tag: tissue

value: skeletal muscle

value: myod KO


title: MKO_DM_RNAseq_Rep2


title: X122

value: Female

value: week

value: pregnant

value: degree fahrenheit

value: percent

value: Innovive disposable cage

value: PJ murphy course sani-chips

value: oral dosage form

value: microgram per kilogram per day

value: NEBNext Ultra RNA kit


title: MSC_shRNA_control_r2


title: B_103_Seronegative

tag: gender

value: highly exposed, Seronegative


title: X160

value: in-house RO water

value: LabDiet 5058

value: LabDiet

value: Accustandard

value: Peanut butter

value: day


title: SV141

value: Female


title: MSC_shRNA_control_r1

value: basal

value: polystyrene


title: B_88_Seronegative

tag: diseas state

value: Seronegative, highly exposed

value: PBMC


title: SV267

value: week

value: pregnant

value: degree fahrenheit

value: percent

value: Innovive disposable cage


title: MKO_GM_RNAseq_Rep3

description:
RNA-Seq of myod ko proliferating myoblasts
MyoD_project_count.xls

source_name: Proliferating myoblasts

value: skeletal muscle

value: myod KO


title: B_76_Seronegative

value: highly exposed, Seronegative

tag: severity


title: MKO_GM_RNAseq_Rep2


title: SV264

value: PJ murphy course sani-chips

value: in-house RO water

value: LabDiet 5058

value: LabDiet

value: oral dosage form

value: microgram per kilogram per day

value: NEBNext Ultra RNA kit


title: B_63_Seronegative

value: Male

value: Seronegative, highly exposed

tag: location


title: MSC_DDR_TPM1.7_r3

value: basal

value: polystyrene


title: MSC_DDR_TPM1.7_r2


title: B_59_Seronegative

value: PBMC


title: MSC_DDR_TPM1.7_r1


title: WT_DM_RNAseq_Rep3

description:
RNA-Seq of wildtype differentiating myocytes at 24h
MyoD_project_count.xls

tag: genotype

value: wild type


title: MKO_GM_RNAseq_Rep1


title: MSC_DDR_r3


title: SV157

value: Female

value: week

value: pregnant

value: degree fahrenheit

value: percent

value: Innovive disposable cage

tag: bedding

value: Accustandard

value: Peanut butter

value: day


title: SV253

value: PJ murphy course sani-chips

tag: water

value: in-house RO water

value: LabDiet 5058

value: LabDiet

value: oral dosage form

value: microgram per kilogram per day


title: B_53_Seronegative

value: highly exposed, Seronegative

value: Seronegative, highly exposed

value: PBMC


title: MKO_DM_RNAseq_Rep1

value: skeletal muscle

value: myod KO


title: MSC_DDR_r2

value: basal

value: polystyrene


title: B_29_Seronegative

value: Female


title: O144

value: week

value: pregnant

value: degree fahrenheit

value: percent

value: Innovive disposable cage

tag: vendor

value: Accustandard

value: NEBNext Ultra RNA kit


title: WT_DM_RNAseq_Rep2

value: wild type


title: MSC_DDR_r1


title: B_28_Seronegative


title: O149

value: PJ murphy course sani-chips

value: in-house RO water

value: LabDiet 5058

value: LabDiet

value: Peanut butter

value: day

value: oral dosage form

tag: dose

value: microgram per kilogram per day


title: MSC_D6_25kPa_r3

description: scRNAseq_expression_matrix_D0_D3_D6s.txt


title: B_21_Seronegative

value: Male

value: highly exposed, Seronegative

value: Seronegative, highly exposed

value: PBMC


title: O140

tag: strain

value: Female

value: week

value: pregnant

value: degree fahrenheit

value: percent


title: WT_GM_RNAseq_Rep3

description:
RNA-Seq of wildtype proliferating myoblasts
MyoD_project_count.xls

value: skeletal muscle

value: wild type


title: WT_GM_RNAseq_Rep2


title: MSC_D6_25kPa_r2


title: WT_GM_RNAseq_Rep1


title: CHIR99021 rep4

city: Shenzhen

first: Yifan

last: Li

state: Guangdong

address: No.89 Taoyuan Road, Nanshan District

department: Department of Laboratory Medicine

institute: Shenzhen Nanshan People's Hospital and the Affiliated Shenzhen Sixth Hospital of Guangdong Medical University

description: Sample 8 (EK8)

data_processing:
bcl2fastq2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Mus_musculus.GRCm38.90.chr whole genome using HISAT 2.0.5 with parameters --rna-strandness RF--dta –t –p 4
Fragments per Kilobase per Million Mapped Fragments (FPKM) were calculated using a protocol from Trapnell, C. et al., Nature Biotechnology, 2010.
Genome_build: Mus_musculus.GRCm38.90.chr
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and counts for each Sample

source_name: Embryonic kidney

growth_protocol: Embryonic kidney were removed, cultured in media as described in "Aresh, B., Peuckert, C. Dissection and Culture of Mouse Embryonic Kidney. J. Vis. Exp. (123), e55715, doi:10.3791/55715 (2017)". Briefly, the media components include the following:  DMEM/F12, 1% penicillin/streptomycin (v/v),1% glutamine (v/v),1% insulin-transferrin-selenium (v/v),50 μg/mL human holo-transferrin and 1.5 μg/mL amphotericin.

extract_protocol:
Embryonic kidney were removed, cultured in a droplet on a filter membrane that is floating on culture media, and RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina®（#E7530L, NEB) was used with 3 ug of total RNA for the construction of sequencing libraries.
Libraries were prepared according to instructions accompanying the NEBNext® Ultra™ RNA Library Prep Kit for Illumina®（#E7530L, NEB).

treatment_protocol: Embryonic kidney were treated with either 0.1% DMSO or 5 µM CHIR99021 for 72 hours.

value: embryonic kidney

tag: agent


title: O139

value: Innovive disposable cage

value: PJ murphy course sani-chips

value: in-house RO water

value: LabDiet 5058

value: LabDiet

value: Accustandard

value: NEBNext Ultra RNA kit


title: MSC_D6_25kPa_r1

tag: matrix


title: A_1526_Asymptom

data_processing:
RNA-seq data were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) and subsequently aligned to the reference genome hg19 applying STAR RNA-seq aligner (Dobin et al., Bioinformatics, 2013). HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
Genome_build: hg19
Supplementary_files_format_and_content: HTSeq counts from RNA-seq samples

extract_protocol:
The buffy coat was extracted by centrifuge after blood sample collection and RBC was removed using RBC lysis buffer in the buffy coat. Total RNA was isolated with TRIzol reagent.
Libraries for sequencing were prepared with TruSeq Stranded mRNA Kit following standard Illumina protocols.

tag: age

value: Male

value: Seropositive, asymptomatic COVID-19

value: Seropositive, asymptom

tag: cell type


title: O138

tag: Sex

value: Female

value: week

value: Peanut butter

value: day

value: oral dosage form

value: microgram per kilogram per day


title: SV164

value: pregnant

value: degree fahrenheit

value: percent


title: CHIR99021 rep3

description: Sample 7 (EK6)

value: embryonic kidney


title: O137

value: Innovive disposable cage

value: PJ murphy course sani-chips

value: in-house RO water

value: LabDiet 5058


title: MSC_D6_2kPa_r3


title: A_1574_Asymptom

value: PBMC


title: A_1195_Asymptom

value: Male

value: Seropositive, asymptomatic COVID-19


title: WT_DM_RNAseq_Rep1

data_processing:
RNA-seq reads were aligned to the mm9 genome with TopHat (v2.1.0) using default settings. Duplicates were removed, and aligned reads were calculated for each protein-coding gene using HTSeq, followed by FPKM transformation by normalizing gene exon length and sequencing depth.
ChIP-Seq reads were mapped to mm9  genome with Bowtie2. Aligned reads were filtered for a minimum MAPQ of 20, and duplicates were removed using SAMtools. Signal tracks and peaks were generated by using the –SPMR option in MACS2. Then, the UCSC Genome Browser utility bedGraphToBigWig was used with default parameters to transform the bedgraph files to bigwig files.
ChIA-PET2 was used to trim the bridge linkers of BL-Hi-C data and HiC-Pro to align reads, filter artifact fragments, and remove duplicates; Juicer was applied to the resulting uniquely mapped contacts to generate individual or merged Hi-C files that could be deposited as contact matrices with multiple resolutions.
Loops were called by HiCCUPS at 3kb, 5 kb and 10 kb resolutions with modified parameters for pooled Hi-C matrices of each  condition.
Genome_build: mm9
Supplementary_files_format_and_content: .hic files were genrated by Juicer which compress Hi-C matrix under mutiscale resolutions;.h5 files were generated by HiCExplorer which can be visualized by  pyGenomeTracks;.bedpe files were loops called by HiCCUPS;.bigwig files were generated using MACS2;.excel  file includes gene count for each sample

extract_protocol:
Primary myoblasts were isolated from the hindlimb skeletal muscle of WT and KO mice at 2~3 weeks, minced and digested in a mixture of type II collagenase and Dispase B (Roche Applied Science). Cells were filtered from debris, centrifuged and cultured in growth medium (F-10 Ham’s medium supplemented with 20% FBS, 10 ng/ml basic fibroblast growth factor, 1% penicillin– streptomycin and 1% glutamine) on collagen-coated cell culture plates at 37 °C in 5% CO2. At 60-70% confluence, cells can be switched to differentiation medium (DMEM with 2% horse serum).
Hi-C were performed on 0.5 million cells per sample according to the BL-Hi-C protocol (PMID: 29158486). Briefly, cells were cross-linked with formaldehyde and nucleuses were isolated by lysis buffers. The chromain was then randomly fragmented by 4-bp enzymes (HaeIII) and then two proximal fragments were connected by 20 bp biotinylated bridge linker in nucleus. A whole genome chromatin was extracted and sheared into 400 bp. Then the biotinylated junctions were captured by M-280 streptavidin magnetic beads. After amplification, the DNA were ready for library construction. RNA for NRA-seq was harvested using Trizol reagent. For ChIP-seq, lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with related antibody.
Hi-C libaries were performed on 0.5 million cells per sample according to the BL-Hi-C protocol (PMID: 29158486). RNA libraries were prepared for sequencing using standard Illumina protocols. ChIP libraries were constructed using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB E7645)

tag: passage

value: skeletal muscle

value: wild type


title: ND220

value: NOD/SHILTJ

value: Female

value: week

value: LabDiet

value: Accustandard

value: Peanut butter

value: NEBNext Ultra RNA kit


title: A_1093_Asymptom

value: Seropositive, asymptom


title: CHIR99021 rep2

description: Sample 6 (EK4)

tag: tissue

value: embryonic kidney


title: MSC_D6_2kPa_r1


title: MSC_D6_2kPa_r2


title: CHIR99021 rep1

description: Sample 5 (EK2)


title: A_1070_Asymptom

tag: gender


title: ND218

value: pregnant

value: degree fahrenheit

value: percent

value: Innovive disposable cage

value: PJ murphy course sani-chips

value: day

value: oral dosage form

value: microgram per kilogram per day


title: ND196

value: NOD/SHILTJ

value: in-house RO water

value: LabDiet 5058


title: MSC_D3_25kPa_r2


title: A_1069_Asymptom

value: Male

tag: diseas state

value: Seropositive, asymptomatic COVID-19

value: PBMC


title: ND194

value: Female

value: week

value: LabDiet

value: Accustandard

value: Peanut butter

value: NEBNext Ultra RNA kit


title: DMSO rep3

description: Sample 3 (EK5)

value: embryonic kidney

value: DMSO


title: MSC_D3_25kPa_r1


title: A_974_Asymptom

tag: severity

value: Seropositive, asymptom


title: A_1109_Asymptom

tag: location


title: ND168

value: pregnant

value: degree fahrenheit

value: percent

value: Innovive disposable cage

value: PJ murphy course sani-chips

value: day

value: oral dosage form


title: A_932_Asymptom

description: Mutationo on NEMO gene

value: Seropositive, asymptomatic COVID-19

value: PBMC


title: ND179

value: NOD/SHILTJ

value: Female

value: week

value: in-house RO water

value: LabDiet 5058

value: microgram per kilogram per day


title: DMSO rep1

description: Sample 1 (EK1)

value: embryonic kidney

value: DMSO


title: MSC_D3_2kPa_r3


title: DMSO rep2

description: Sample 2 (EK3)


title: A_923_Asymptom

value: Male

value: Seropositive, asymptom


title: N246

value: NZO/HILTJ

value: pregnant

value: degree fahrenheit

value: percent

value: LabDiet

value: Accustandard

value: Peanut butter

value: NEBNext Ultra RNA kit


title: MSC_D3_2kPa_r2


title: MSC_D3_2kPa_r1


title: A_907_Asymptom

value: Seropositive, asymptomatic COVID-19

value: PBMC


title: sRNA_carcass_2

city: Bloomington

first: Nick

last: Sokol

state: IN

address: 1001 E 3rd Street, Biology Building

institute: Indiana University

description: 18-29nt small RNA

data_processing:
Sequencing reads were trimmed using Cutadapt (release 1.9.1) to remove both 3’linker sequences and four random nucleotides at both ends
Aligned to the Drosophila genome using Bowtie2 (release 2.3.2)
MiRNA read counts were tallied using the featureCounts function of Subread (release 2.0.0)
Genome_build: Dmel_Release_6
Supplementary_files_format_and_content: Excel spreadsheet containing miRNA read counts with 5 columes corresponding to each library

organism: Drosophila melanogaster

source_name: Remaining carcass tissue

growth_protocol: Wildtype flies grown under standard conditions

extract_protocol:
Total RNA was prepared in triplicate with Trizol from both dissected intestines and remaining carcasses of 2- to 3-day old males reared on standard food.
This RNA was size fractionated by preparative PAGE and the 18- to 29-nt long contingent were extracted. 3’ and 5’ linkers were then sequentially ligated onto these small RNAs using T4 RNA ligase 2, truncated K227Q (NEB) and T4 RNA ligase (NEB), respectively, and properly sized fragments were PAGE purified after each ligation. The cloned small RNAs were reverse transcribed, PCR amplified, and sequenced on a NextSeq500 (Illumina) to a depth of 10-20 million reads per library

value: Remaining carcass tissue

tag: developmental stage

value: adult


title: N222

value: Female

value: week

value: Innovive disposable cage

tag: bedding

value: PJ murphy course sani-chips

value: in-house RO water

value: LabDiet 5058

value: day

value: oral dosage form

value: microgram per kilogram per day


title: A_883_Asymptom

value: Male

value: Seropositive, asymptom


title: N218

value: NZO/HILTJ

value: pregnant

value: degree fahrenheit

value: percent

tag: water

value: LabDiet

value: Accustandard

value: Peanut butter


title: MSC_D3_25kPa_r3


title: MSC_D0_r3

value: basal

value: polystyrene


title: DMSO rep4

description: Sample 4 (EK7)

value: embryonic kidney

value: DMSO


title: sRNA_intestine_3

description: 18-29nt small RNA

source_name: Dissected intestine tissue

value: Dissected intestine tissue

value: adult


title: MSC_D0_r2


title: sRNA_intestine_2

description: 18-29nt small RNA


title: N216

value: Female

value: week

value: Innovive disposable cage

value: PJ murphy course sani-chips

value: in-house RO water

value: LabDiet 5058

tag: vendor

value: day

value: oral dosage form

value: NEBNext Ultra RNA kit


title: A_881_Asymptom

value: Male

value: Seropositive, asymptomatic COVID-19

value: Seropositive, asymptom

value: PBMC


title: MSC_D0_r1

value: basal

value: polystyrene


title: N213

value: NZO/HILTJ

value: pregnant

value: degree fahrenheit

value: percent

value: LabDiet

value: Accustandard

value: Peanut butter

tag: dose

value: microgram per kilogram per day


title: A_875_Asymptom

value: Female


title: sRNA_intestine_1

description: 18-29nt small RNA

value: Dissected intestine tissue

tag: strain

value: adult


title: Healthy_control_3

city: Storrs

first: Rahul

middle: N

last: Kanadia

state: CT

address: 75 N. Eagleville Road

department: Physiology and Neurobiology

institute: University of Connecticut

data_processing:
Reads were aligned using Hisat2 against the hg38 genome (Ensembl v.95) after trimming 3bp
Gene expression was determined using IsoEM2
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files contain TPM values for each sample

extract_protocol:
PBMCs were isolated and collected in TRIzol, following total RNA extraction
Total RNA was depleted from rRNA, followed by construction of a stranded library using the standard Illumina protocols

tag: disease


title: A_862_Asymptom

last: Lee

address: 8 CENTER DR RM 107

institute: National Institutes of Health (NIH)


title: N157

value: week

value: Innovive disposable cage

value: PJ murphy course sani-chips

value: in-house RO water

value: LabDiet 5058

value: day

value: oral dosage form

value: NEBNext Ultra RNA kit


title: A_797_Asymptom

value: Male

value: Seropositive, asymptomatic COVID-19

value: Seropositive, asymptom

value: PBMC


title: Lowry-Wood_syndrome


title: sRNA_carcass_1

description: 18-29nt small RNA

value: Remaining carcass tissue


title: A_776_Asymptom


title: A_846_Asymptom


title: Roifman_carrier_2


title: L154

value: BALB/CJ

value: pregnant

value: degree fahrenheit

value: percent

value: LabDiet

value: Accustandard

value: Peanut butter

value: microgram per kilogram per day


title: Lowry-Wood_carrier


title: A_765_Asymptom

value: Female


title: L130

value: week

value: Innovive disposable cage

value: PJ murphy course sani-chips

value: in-house RO water

value: LabDiet 5058

value: day


title: Healthy_control_2


title: L124

value: oral dosage form

value: NEBNext Ultra RNA kit


title: Healthy_control_1


title: A_847_Asymptom

value: Male

value: Seropositive, asymptomatic COVID-19

value: Seropositive, asymptom

value: PBMC


title: A_779_Asymptom


title: wt-2h

city: beijing

first: Zhou

middle: wen

last: bin

address: 12 Zhongguancun South Street

institute: Chinese Academy of Agricultural Sciences

data_processing:
The clean reads were mapped to the Arabidopsis genome using HISAT (Kim et al., 2015) and Bowtie2 (Langmead et al., 2009) tools.
normalization was done and FPKM was calculated using RESM software (Li and Dewey, 2011)
Supplementary_files_format_and_content: FPKM values for each Sample

organism: Arabidopsis

growth_protocol: Seeds were then plated on half-strength MS medium containing 0.7% (w/v) agar. 22 °C.dark or 120 μmol·m-2·s-1 light

extract_protocol:
Total RNA was extracted using TRlzol Reagent (Invitrogen) according to the manufacturer's recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: wild type

tag: treatment

value: grown in dark for 4 days and exposed to light for 2h

value: leaf


title: wt-0.5h

value: grown in dark for 4 days and exposed to light for 0.5h


title: A_444_Asymptom

city: Bethesda

first: Hye Kyung

tag: age

tag: cell type


title: L193

value: BALB/CJ

tag: Sex

value: Female

value: pregnant

value: degree fahrenheit

value: percent

value: LabDiet

value: Accustandard

value: Peanut butter

value: microgram per kilogram per day


title: H163

value: week

value: Innovive disposable cage

value: PJ murphy course sani-chips

value: in-house RO water

value: LabDiet 5058

value: day

value: oral dosage form

value: NEBNext Ultra RNA kit


title: L122

value: BALB/CJ


title: RNAi-21-0h

source_name: PCD8 RNAi-21 mutant_leaf

value: PCD8 RNAi-21 mutant

value: grown in dark for 4 days

tag: tissue

value: leaf


title: L142

value: Female

value: pregnant

value: degree fahrenheit

value: percent


title: RNAi-21-0.5h

value: grown in dark for 4 days and exposed to light for 0.5h


title: Roifman_syndrome


title: Roifman_carrier_1


title: RNAi-21-2h

value: grown in dark for 4 days and exposed to light for 2h


title: wt-0h

value: wild type


title: U2 MO 3

data_processing:
Reads were aligned using Hisat2 against the hg38 genome (Ensembl v.95) with default settings
Gene expression was determined using IsoEM2
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files contain TPM values for each sample

extract_protocol:
Cells were harvested in TRIzol and nascent RNA was extracted using the Click-IT chemistry
5ng of total nascent RNA was depleted from rRNA, followed by construction of a stranded library using the standard Illumina protocols

treatment_protocol: HEK293 cells were electroporated with morpholinos, re-plated and pulsed with EU after 6 hours. After an additional two hours of culturing, cells were harvested.

tag: cell line

value: U2 MO


title: U2 MO 2


title: U6atac MO 3

value: U6atac MO


title: A_424_Asymptom

tag: gender

tag: diseas state

value: Seropositive, asymptomatic COVID-19

value: Seropositive, asymptom

value: PBMC


title: H158

value: week

value: Innovive disposable cage

value: PJ murphy course sani-chips

value: in-house RO water

value: LabDiet 5058

value: LabDiet

value: Accustandard

value: Peanut butter

value: day

value: oral dosage form

value: microgram per kilogram per day

value: NEBNext Ultra RNA kit


title: A_399_Asymptom

value: Male

tag: severity

tag: location


title: U2 MO 1

value: U2 MO


title: A_383_Asymptom

value: Female

value: Seropositive, asymptomatic COVID-19


title: U6atac MO 2

value: U6atac MO


title: U6atac MO 1


title: H129

value: week

value: pregnant

value: degree fahrenheit

value: percent

tag: bedding


title: H145

value: Innovive disposable cage

value: PJ murphy course sani-chips

tag: water

value: in-house RO water

value: LabDiet 5058


title: A_378_Asymptom

value: Seropositive, asymptom

value: PBMC


title: A_374_Asymptom


title: H128

value: LabDiet

tag: vendor

value: Accustandard

value: Peanut butter

value: day

value: oral dosage form

value: microgram per kilogram per day


title: F233

value: FVB/NJ

value: Female

tag: dose

value: NEBNext Ultra RNA kit


title: U4atac MO 3

value: U4atac MO


title: A_372_Asymptom

value: Seropositive, asymptomatic COVID-19


title: A_428_Asymptom

value: Male


title: F195

tag: strain

value: week

value: pregnant

value: degree fahrenheit

value: percent

value: Innovive disposable cage

value: PJ murphy course sani-chips


title: H143

value: in-house RO water

value: LabDiet 5058

value: LabDiet

value: Accustandard


title: U4atac MO 2


title: A_361_Asymptom

value: Seropositive, asymptom

value: PBMC


title: U4atac MO 1


title: A_358_Asymptom

value: Female


title: U12 MO 3

value: U12 MO


title: A_355_Asymptom


title: U12 MO 2


title: A_354_Asymptom


title: F141

value: FVB/NJ

value: Peanut butter

value: day

value: oral dosage form

value: microgram per kilogram per day

value: NEBNext Ultra RNA kit


title: F140

value: week

value: pregnant

value: degree fahrenheit

value: percent


title: Control MO 6

value: Control MO


title: F161

value: Innovive disposable cage

value: PJ murphy course sani-chips

value: in-house RO water

value: LabDiet 5058

value: LabDiet


title: F146

value: Female

value: Accustandard


title: A_128_Asymptom

value: Seropositive, asymptomatic COVID-19

value: Seropositive, asymptom

value: PBMC


title: A_343_Asymptom

value: Male


title: SRS, CID0131

city: Cambridge

first: Eguzkine

last: Ochoa

address: Addenbrookes Hospital

department: Medical Genetics

institute: University of Cambidge

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 BeadChips using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from peripheral blood using Gentra Puregene Blood Kit (Qiagen)

value: F

tag: disorder

value: CID

tag: disorder type

value: SRS

value: blood


title: U12 MO 1

tag: genotype/variation

value: U12 MO


title: Control MO 4

value: Control MO


title: A_100_Asymptom

tag: age


title: E180

value: week

value: pregnant

value: degree fahrenheit

value: percent

value: Innovive disposable cage

value: Peanut butter

value: day

value: oral dosage form

value: microgram per kilogram per day

value: NEBNext Ultra RNA kit


title: E167

value: Female

value: PJ murphy course sani-chips

value: in-house RO water

value: LabDiet 5058

value: LabDiet

value: Accustandard


title: Control MO 3

value: Control MO


title: A_85_Asymptom

value: Male

value: Seropositive, asymptomatic COVID-19

value: Seropositive, asymptom

tag: cell type

value: PBMC


title: E175

tag: Sex

value: week

value: pregnant

value: degree fahrenheit

value: percent

value: Innovive disposable cage


title: Control MO 2


title: SRS, CID0128

value: F

value: CID

value: SRS

tag: tissue

value: blood


title: SRS, CID0126

value: M


title: SRS, CID0125


title: A_74_Asymptom

value: Female


title: SRS, CID0124


title: SRS, CID0123


title: E143

value: PJ murphy course sani-chips

value: in-house RO water

value: LabDiet 5058

value: LabDiet

value: Accustandard

value: Peanut butter

value: day

value: oral dosage form

value: microgram per kilogram per day

value: NEBNext Ultra RNA kit


title: E150

value: week

value: pregnant

value: degree fahrenheit

value: percent

value: Innovive disposable cage


title: SRS, CID0129

value: F

value: CID

value: SRS

value: blood


title: E122

value: Female

value: PJ murphy course sani-chips

value: in-house RO water

value: LabDiet 5058


title: Control MO 5

tag: cell line

value: Control MO


title: Control MO 1


title: SRS, CID0121

tag: gender

value: M


title: D134

value: LabDiet

value: Accustandard

value: Peanut butter

value: day

value: oral dosage form

value: microgram per kilogram per day


title: Sample_NIGFAM-B6 BS panel sequencing

city: Milan

first: Jose

middle: Manuel

last: Garcia-Manteiga

address: Via Olgettina 58

department: Center for Translational Genomics and Bioinformatics

country: Italy

institute: OSR - San Raffaele Scientific Institute

description:
BS panel Sequencing from BS_Sample_NIGFAM-B6
NIGFAM_myDiff_results_CpGs_sex.age_as_covariates.xls
NIGFAM_myDiff_results_sex.age_as_covariates.xls

data_processing:
MeDIP: Basecalling using bcl2fastq v2.20.0.422
MeDIP: Quality Check with FASTQC 0.11.5
MeDIP: Trimming adapters and low quality with trimmomatic
MeDIP: Mapping to hg19 human reference with BWA-MEM v0.7.15
MeDIP: Deduplication with Picard Tools
MeDIP: Methylated Regions identified with MACS2
MeDIP: Merging regions with Bedtools
MeDIP: Differential Methyaltion Analysis with edgeR
Supplementary_files_format_and_content: MeDIP: peaks.bed.gz of Methylated regions identified with MACS2 and gzipped
BiSulfite: Basecalling using bcl2fastq v2.20.0.422
BiSulfite: Quality Check with FASTQC 0.11.5
BiSulfite: Trimming adapters and low quality with trimmomatic
BiSulfite: Alignment to hg19 human reference with Bsmap
BiSulfite: Deduplication with Picard Tools
BiSulfite: Filtering for properly paired reads and clipping overlapping regions in pairs
BiSulfite: Methylation analysis with methratio.py (supplied with Bsmap)
BiSulfite: Differential Methyaltion Analysis with methylKit
Genome_build: hg19
Supplementary_files_format_and_content: BiSulfite: Excel files with results coming from methylKit R package including interval region, pvalue, qvalue and methylation difference

source_name: whole blood

extract_protocol:
Whole blood was collected in EDTA tubes and genomic DNA (gDNA) extraction was performed with phenol–chloroform standard method or with the Maxwell 16 blood DNA purification kit (Promega) according to manufacturer’s protocol. Quantity and quality of gDNA were determined by Qubit BR dsDNA assay (ThermoFisher) and 1.5% agarose gel, respectively
MeDIP: One μg of each gDNA sample was mechanically fragmented on a focused ultrasonicator Covaris E220 (Covaris). Sequencing libraries were prepared with NextFlex Methylseq 1 kit (Bioo Scientific) according to the manufacturer’s protocol
MeDIP: The ligated libraries were pooled and immunoprecipitated in the same reaction using MagMeDIP kit (Diagenode), followed by purification with IPure v2 kit (Diagenode) and PCR amplification. Paired-end sequencing was performed on the Illumina HiSeq 2500 platform with read length of 100 bp.
BiSulfite: A SeqCap Epi custom panel (Roche) was designed by NimbleDesign software (Roche).   Sequencing libraries were prepared with KAPA Hyper Prep kit (Kapa Biosystems) according to the manufacturer’s protocol, starting from 1 μg of gDNA mechanically fragmented on a focused ultrasonicator Covaris E220 (Covaris). After ligation, bisulfite conversion was performed by EZ DNA Methylation-Lighting kit (Zymo Research), followed by enrichment of the regions of interest with custom probes using SeqCap Epi enrichment kit (Roche).

value: whole blood

tag: condition

value: MS

value: female

tag: family


title: SRS, CID0122

value: CID

value: SRS


title: A_57_Asymptom

value: Male

tag: diseas state

value: Seropositive, asymptomatic COVID-19

tag: severity

value: Seropositive, asymptom

tag: location

value: PBMC


title: D234

value: Female

value: week

value: pregnant

value: degree fahrenheit

value: percent

value: Innovive disposable cage

tag: bedding

value: PJ murphy course sani-chips

tag: water

value: in-house RO water

value: LabDiet 5058

tag: vendor

value: NEBNext Ultra RNA kit


title: A_72_Asymptom


title: A_20_Asymptom


title: SRS, CID0130

value: F

tag: disorder

value: blood


title: D231

tag: strain

value: LabDiet

value: Accustandard

value: Peanut butter

value: day

value: oral dosage form

tag: dose

value: microgram per kilogram per day


title: Sample_NIGFAM-B4 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NIGFAM-B4
NIGFAM_myDiff_results_CpGs_sex.age_as_covariates.xls
NIGFAM_myDiff_results_sex.age_as_covariates.xls

value: whole blood

value: MS

value: female

tag: age


title: Sample_NIGFAM-B5 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NIGFAM-B5
NIGFAM_myDiff_results_CpGs_sex.age_as_covariates.xls
NIGFAM_myDiff_results_sex.age_as_covariates.xls

value: healthy


title: D145

value: Female

value: week

value: pregnant

value: degree fahrenheit

value: percent

value: Innovive disposable cage


title: SRS, CID0119

value: M

value: CID

tag: disorder type

value: SRS

value: blood


title: A_1_Asymptom

value: Male

value: Seropositive, asymptomatic COVID-19

value: Seropositive, asymptom

tag: cell type

value: PBMC


title: SRS, CID0111

tag: tissue


title: SRS, CID0118

value: F


title: D132

tag: Sex

value: PJ murphy course sani-chips

value: in-house RO water

value: LabDiet 5058

value: LabDiet

value: Accustandard

value: Peanut butter

value: day

value: oral dosage form

value: microgram per kilogram per day

value: NEBNext Ultra RNA kit


title: SRS, CID0114

tag: gender

value: M

value: CID

value: SRS


title: SRS, CID0116

value: blood


title: SRS, CID0117


title: Sample_NIGFAM-B3 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NIGFAM-B3
NIGFAM_myDiff_results_CpGs_sex.age_as_covariates.xls
NIGFAM_myDiff_results_sex.age_as_covariates.xls

value: whole blood

tag: condition

value: MS

value: female


title: Sample_NIGFAM-B2 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NIGFAM-B2
NIGFAM_myDiff_results_CpGs_sex.age_as_covariates.xls
NIGFAM_myDiff_results_sex.age_as_covariates.xls

value: healthy

tag: family


title: SRS, CID0110

value: F


title: SRS, CID0115


title: C213

value: CBA/J

value: Female

value: week

value: pregnant

value: degree fahrenheit

value: percent

value: Innovive disposable cage

value: PJ murphy course sani-chips

value: in-house RO water

value: LabDiet 5058


title: C220

value: LabDiet

value: Accustandard

value: Peanut butter

value: day

value: oral dosage form

value: microgram per kilogram per day

value: NEBNext Ultra RNA kit


title: D125


title: Sample_NEUFAM82-05 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM82-05
NEUFAM82_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM82_myDiff_results_sex.age_as_covariates.xls

value: whole blood

value: MS

value: male


title: A_118_Asymptom

description: Cystic fibrosis

value: Female

tag: diseas state

value: Seropositive, asymptomatic COVID-19

value: Seropositive, asymptom

value: PBMC


title: Sample_NIGFAM-B1 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NIGFAM-B1
NIGFAM_myDiff_results_CpGs_sex.age_as_covariates.xls
NIGFAM_myDiff_results_sex.age_as_covariates.xls

value: female


title: Sample_NEUFAM82-04 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM82-04
NEUFAM82_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM82_myDiff_results_sex.age_as_covariates.xls


title: SRS, CID0109

value: F

value: CID

value: SRS

value: blood


title: Sample_NEUFAM82-03 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM82-03
NEUFAM82_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM82_myDiff_results_sex.age_as_covariates.xls

value: healthy


title: C176

description: Pregnant female mice doses every day for 10 days

value: CBA/J

value: week

value: pregnant

value: degree fahrenheit

value: percent

value: Innovive disposable cage

value: PJ murphy course sani-chips

value: in-house RO water

value: LabDiet 5058

value: LabDiet

value: Accustandard

value: Peanut butter

value: day


title: C195

value: Female

value: oral dosage form

value: microgram per kilogram per day

value: NEBNext Ultra RNA kit


title: SRS, CID0108

value: M

value: CID

value: SRS

value: blood


title: C141

value: CBA/J

value: week

value: pregnant

value: degree fahrenheit

value: percent


title: Sample_NEUFAM82-01 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM82-01
NEUFAM82_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM82_myDiff_results_sex.age_as_covariates.xls

value: whole blood

value: MS

value: male


title: Sample_NEUFAM78-06 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM78-06
NEUFAM78_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM78_myDiff_results_sex.age_as_covariates.xls

value: healthy


title: Sample_NEUFAM78-05 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM78-05
NEUFAM78_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM78_myDiff_results_sex.age_as_covariates.xls


title: Sample_NEUFAM82-02 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM82-02
NEUFAM82_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM82_myDiff_results_sex.age_as_covariates.xls

value: female


title: B262

value: Female

value: Innovive disposable cage

value: PJ murphy course sani-chips

value: in-house RO water

value: LabDiet 5058

value: LabDiet

value: Accustandard

value: Peanut butter

value: day

value: oral dosage form


title: SRS, CID0105

value: M

value: CID

value: SRS

value: blood


title: SRS, CID0106

value: F


title: Sample_NEUFAM78-04 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM78-04
NEUFAM78_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM78_myDiff_results_sex.age_as_covariates.xls

value: whole blood

value: healthy


title: B297

value: Female

value: week

value: pregnant

value: degree fahrenheit

value: percent

value: microgram per kilogram per day

value: NEBNext Ultra RNA kit


title: B300

value: Innovive disposable cage

value: PJ murphy course sani-chips

value: in-house RO water

value: LabDiet 5058

value: LabDiet

value: Accustandard

value: Peanut butter


title: C128

value: CBA/J

value: day

value: oral dosage form


title: Sample_NEUFAM78-03 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM78-03
NEUFAM78_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM78_myDiff_results_sex.age_as_covariates.xls

value: whole blood

value: MS

value: female


title: Sample_NEUFAM78-02 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM78-02
NEUFAM78_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM78_myDiff_results_sex.age_as_covariates.xls


title: B195

value: Female

value: week

value: pregnant

value: degree fahrenheit


title: B200

value: percent

value: Innovive disposable cage

value: microgram per kilogram per day

value: NEBNext Ultra RNA kit


title: BWS, CID0059

value: M

value: CID

value: BWS

value: blood


title: B171

value: PJ murphy course sani-chips

value: in-house RO water

value: LabDiet 5058

value: LabDiet

value: Accustandard

value: Peanut butter

value: day


title: Sample_NEUFAM78-01 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM78-01
NEUFAM78_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM78_myDiff_results_sex.age_as_covariates.xls

value: whole blood

value: MS

value: male


title: Sample_NEUFAM76-06 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM76-06
NEUFAM76_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM76_myDiff_results_sex.age_as_covariates.xls

value: healthy


title: Sample_NEUFAM76-05 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM76-05
NEUFAM76_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM76_myDiff_results_sex.age_as_covariates.xls


title: A307

value: A/J

value: Female

value: week

value: pregnant

value: degree fahrenheit

value: percent

value: Innovive disposable cage

value: oral dosage form

value: microgram per kilogram per day


title: Sample_NEUFAM76-04 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM76-04
NEUFAM76_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM76_myDiff_results_sex.age_as_covariates.xls

value: female


title: A302

value: PJ murphy course sani-chips

value: in-house RO water

value: LabDiet 5058

value: LabDiet

value: Accustandard

value: NEBNext Ultra RNA kit


title: Sample_NEUFAM76-03 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM76-03
NEUFAM76_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM76_myDiff_results_sex.age_as_covariates.xls

value: whole blood

value: healthy


title: A257

value: A/J

value: Female

value: Peanut butter

value: day


title: Sample_NEUFAM76-02 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM76-02
NEUFAM76_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM76_myDiff_results_sex.age_as_covariates.xls

value: MS

value: male


title: A305

value: week

value: pregnant

value: degree fahrenheit

value: percent

value: Innovive disposable cage

value: oral dosage form


title: A246

value: PJ murphy course sani-chips

value: in-house RO water

value: LabDiet 5058

value: LabDiet

value: microgram per kilogram per day


title: BWS, CID0056

value: F

value: CID

value: BWS

value: blood


title: BWS, CID0057


title: Sample_NEUFAM76-01 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM76-01
NEUFAM76_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM76_myDiff_results_sex.age_as_covariates.xls

value: whole blood

value: MS

value: female


title: A239

value: A/J

value: Female

value: week

value: pregnant

value: Accustandard

value: Peanut butter

value: day

value: NEBNext Ultra RNA kit


title: Sample_NEUFAM41-11 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM41-11
NEUFAM41_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM41_myDiff_results_sex.age_as_covariates.xls

value: male


title: Sample_NEUFAM41-10 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM41-10
NEUFAM41_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM41_myDiff_results_sex.age_as_covariates.xls

value: healthy


title: BWS, CID0043

value: M


title: BWS, CID0051

value: CID


title: BWS, CID0052

value: BWS


title: BWS, CID0041

value: F

value: blood


title: Sample_NEUFAM41-09 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM41-09
NEUFAM41_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM41_myDiff_results_sex.age_as_covariates.xls

value: whole blood

value: MS


title: atac_iWATpos

city: NEW ORLEANS

first: Zhi

address: 2734 CALHOUN

institute: Tulane

data_processing:
[scRNA-seq]  Sequencing data were processed on CellRanger v.3.1.0 pipeline with default parameters, including demultiplexing, conversion to FASTQs using bcl2fastq2 v.2.27.1 software, alignment to the mm10 mouse reference genome, filtering, and unique molecular identified (UMI) counting.
[scATAC-seq]  Peak matrixes and metadata were generated by Cell Ranger ATAC v.1.1.0 pipeline with default parameters and aligned to the mm10 mouse reference genome.
Genome_build: mm10
Supplementary_files_format_and_content: [scRNA-seq]  Matrix table with raw gene counts for every gene and every cell
[scATAC-seq]  Matrix table with raw chromatin accessibility counts for every barcode and every cell

source_name: Inguinal white adipose tissues

growth_protocol: Isolated adipose SVF cells were seeded into plates at the density of 4 x 10e3 cells/cm2 in MesenCultTM Expansion medium (STEMCELL, 05513), and treated with MesenCultTM Adipogenic Differentiation cocktail (STEMCELL, 05507) with 90% cell confluence. Cells were cultured for 7 days after pro-adipogenic induction prior to being harvested for following sequencing experiments.

extract_protocol:
For isolation of adipose SVF cells, fat tissues were dissected into ice-cold PBS and minced with scissors in a sterile 5 ml tube containing 4 ml of either iBAT digestion buffer (1X HBSS, 3.5% BSA, and 2 mg/ml collagenase type II) and incubated at 37°C for 1 hr under agitation or WAT digestion buffer (1X DPBS, 1% BSA, 2.5 mg/ml dispase and 4 mg/ml collagenase D) for 40 min. The digestion mixture was passed through a 100 μm cell strainer into a 50 ml tube. Digestion was stopped by adding 15 ml PBS containing 2% fetal bovine serum (FBS; Gibco, 10270106) and centrifuged at 500 g for 5 min at room temperature. The supernatant was aspirated, and red blood cells were lysed by incubating the SVF pellet with 2 ml RBC lysis buffer (Invitrogen, 00433357). The number and viability of cells in the suspension were determined using Trypan Blue stain according to the manufacturer’s recommendations.
Following separation by FACS,cells were loaded using Chromium Single Cell 3’ v2 Reagent Kit, and libraries were run on the Illumina NextSeq 550 Sequencing System as 150-bp paired-end reads. To isolate nuclei for scATAC-seq assay, cells were lysed for 4 min on ice according to 10x genomics protocol (CG000169 Rev D). ScATAC-seq libraries were prepared using the 10x Genomics platform with the Chromium Single Cell ATAC Library & Gel Bead Kit as recommended by the manufacturer and sequenced on the Illumina NextSeq 550 Sequencing System as 150-bp paired-end reads.

value: Inguinal white adipose tissue

value: Cultured Wnt+ adipocytes

value: C57/B6 or B6/CD1 mixed background

value: 7-9 weeks old

tag: number and sex

value: 7 males and 2 females


title: atac_iBATpos

source_name: Interscapular brown adipose tissues

value: Interscapular brown adipose tissue

value: 11 males


title: BWS, CID0044


title: BWS, CID0036


title: BWS, CID0045


title: atac_iBATneg

value: Cultured Wnt- adipocytes


title: BWS, CID0037


title: BWS, CID0034


title: rna_iWATpos

value: 7-8 weeks old

value: 10 males and 10 females


title: rna_iBATpos

value: 3 males and 4 females


title: Sample_NEUFAM41-06 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM41-06
NEUFAM41_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM41_myDiff_results_sex.age_as_covariates.xls

value: healthy

value: female


title: BWS, CID0033

value: F

value: CID

value: BWS


title: BWS, CID0032

value: blood


title: Sample_NEUFAM41-07 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM41-07
NEUFAM41_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM41_myDiff_results_sex.age_as_covariates.xls

value: whole blood

value: male


title: BWS, CID0029

value: M


title: atac_iWATneg

value: Inguinal white adipose tissue

value: C57/B6 or B6/CD1 mixed background

value: 7-9 weeks old


title: BWS, CID0028


title: rna_iBATneg

value: Interscapular brown adipose tissue


title: BWS, CID0035