title: ctrl2_hisp

description: 200310_K00288_0194_BHH3T3BBXY_4_N2_HK_S62855_1


title: ctrl1_hisp

status: Public on Jul 18 2022

type: SRA

city: Vienna

first: Sylvia

last: Knapp

address: Währinger Gürtel 18-20

country: Austria

institute: Medical University of Vienna

description: 200310_K00288_0194_BHH3T3BBXY_4_N1_HK_S62856_1

library_source: transcriptomic

data_processing:
umi2index processto add  UMI sequence to identifier of each read and trim the UMI.: Lexogen, QuantSeq specific, technical parameters not provided
Trim adapter sequences and polyA tails: bbduk v35.92: bbduk.sh in=$fq out=${fq_clean} ref=$resource_dir/polyA.  fa.gz,$resource_dir/truseq-rna.fa.gz k=13 ktrim=r useshortkmers=t  mink=5 qtrim=r trimq=10 minlength=20
Read QC: FastQC v0.11.5: fastqc -o ${out_dir} -t 8 --nogroup $fq $fq_clean
Alignment: STAR v2.5.2a: STAR --runThreadN 8 --genomeDir $resource_dir/index  --readFilesIn ${fq_clean} --outFilterType BySJout  --outFilterMultimapNmax 20 --alignSJoverhangMin 8  --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999  --outFilterMismatchNoverLmax 0.6 --alignIntronMin 20  --alignIntronMax 1000000 --alignMatesGapMax 1000000  --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate  --outFileNamePrefix $out_prefix
UMI read collapsing tool: Lexogen, QuantSeq specific, technical parameters not provided
Read Indexing: samtools index v1.3: samtools index $bam
Gene Read Counting: HTSeq-count v0.6.0: htseq-count -m intersection-nonempty -s yes -f bam -r pos $bam  $resource_dir/annotation.gtf > $bam_dir/read_counts.txt
Mapping QC: RSeQC v2.6.4: read_distribution.py -i $bam -r $resource_dir/annotation.bed >  $bam_dir/read_distribution.txt
Genome_build: mm10
Supplementary_files_format_and_content: Raw_counts.txt:  raw counts per sample and gene, tabstop-delimited .txt file

molecule: total RNA

organism: Mus musculus

source_name: alveolar macrophages

extract_protocol:
After stimulation, cells were washed twice with cold PBS and lysed in RLT buffer (Qiagen) containing 1% 2-mercaptoethanol (Sigma). Total RNA was isolated using the RNeasy Micro kit (Qiagen) according to the manufacturer's instructions.
QuantSeq libraries were prepared using the QuantSeq 3’ mRNA-Seq Library Prep Kit (FWD) for Illumina in combination with the PCR Add-on Kit for Illumina and the UMI Second Strand Synthesis Module for QuantSeq FWD (all from Lexogen), following the manufacturers’ instructions. Libraries were prepared with 150 ng total RNA input and 15 amplification cycles. Sample quality was assessed on a Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: AMs were obtained by BAL, seeded at equal numbers (2 wells per biological replicate) and left to adhere in RPMI medium (10% FCS, 1%PS). After 2 h, non-adherent cells were washed off with PBS. Subsequently, each biological replicate was incubated with HISP (ATCC6303, MOI 100) in RPMI medium (3% FCS, 1% PS) or with medium only for 3 h.

tag: tissue

value: broncho-alveolar lavage (BAL) fluid

tag: treatment

value: Control

tag: restimulation

value: Heat-inactivated S. pneumoniae


title: lps4_medium

description: 200310_K00288_0194_BHH3T3BBXY_4_L4_med_S62797_1

value: LPS


title: saccule_EJ04_bulkATAC-seq

status: Public on Jul 19 2022

city: Bethesda

first: Erin

last: Jimenez

state: MD

address: 50 South Drive

department: NHGRI

country: USA

institute: NIH

library_source: genomic

data_processing:
Binary Base Call (BCL) files generated from an Illumina NextSeq 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 (10x Genomics).  Cell Ranger Version 3.0.2 (10x Genomics) was used to demultiplex, for barcode processing, for single cell gene counts, for single-cell accessibility counts, and aggregating files. For bulk ATAC-seq, libraries were sequenced on an Illumina HiSeq 2500 platform and run as indexed 50 base single end reads. Bulk ATAC-seq reads were aligned to reference zebrafish genome (danRer11) using bowtie2. Peaks were called by MACS2 from individual replicate.
Genome_build: danRer11
Supplementary_files_format_and_content: scRNA-seq and scATAC-seq outputs were generated using the 10x Cell Ranger pipeline. scRNA-seq H5 (filtered feature bc matrix) files contain the UMI counts for each cell. scATAC-seq processed data files include three file formats per sample: CSV, TBI, and H5. CSV (singlecell.csv) files contain per barcode QC information associated with the fragments per barcode, ATAC signal per barcode, and cell calling information. TBI (Fragments.tsv.gz.tbi) files are tabix index of the fragment intervals. H5 (filtered peak bc matrix.h5) files contain only detected cellular barcodes. For bulk ATAC-seq, narrowPeak files contain MACS2 called peaks in BED format.

molecule: genomic DNA

organism: Danio rerio

source_name: Untreated wild-type saccule

extract_protocol:
For single-cell experiments, non-regenerating (untreated) and regenerating inner ears (saccule and utricle) were dissected at consecutive time-points and dissociated into single-cells using trypsin and collagenase. For bulk ATAC-seq experiments, untreated inner ears (saccule and utricle) were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers.
For scRNA-seq, cDNA libraries were generatated with Chromium Controller and Chromium Single Cell 3' GEM, Library and Gel Bead Kit V3 (10x Genomics). For scATAC-seq, libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit (1000111, 10X Genomics). For bulk ATAC-seq, libraries were generated using Nextera DNA Library Preparation Kit (Catalog # FC-121-1030). Transposed DNA were amplified by PCR with indexed primers and libraries were purified.

tag: strain

tag: embryo age

value: 6-10 month old adult zebrafish


title: ctrl5_hisp

description: 200310_K00288_0194_BHH3T3BBXY_4_N5_HK_S62852_1


title: lps2_medium

description: 200310_K00288_0194_BHH3T3BBXY_4_L2_med_S62795_1


title: lps1_medium

description: 200310_K00288_0194_BHH3T3BBXY_4_L1_med_S62794_1


title: ctrl5_medium

description: 200310_K00288_0194_BHH3T3BBXY_4_N5_med_S62801_1


title: ctrl3_medium

description: 200310_K00288_0194_BHH3T3BBXY_4_N3_med_S62799_1


title: lps5_hisp

description: 200310_K00288_0194_BHH3T3BBXY_4_L5_HK_S62847_1


title: ctrl2_medium

description: 200310_K00288_0194_BHH3T3BBXY_4_N2_med_S62798_1


title: ctrl4_medium

description: 200310_K00288_0194_BHH3T3BBXY_4_N4_med_S62800_1


title: ctrl1_medium

description: 200310_K00288_0194_BHH3T3BBXY_4_N1_med_S62805_1


title: Dorsal polyA-enriched 3

city: Moscow

first: Alexander

last: Beletsky

address: Butlerova street, building 5a

country: Russia

institute: IHNA

data_processing:
Sequenced reads were mapped to the Rnor6.0 version of rat genome using STAR (v. 2.7.9a) with default parameters.
For each dataset, raw read counts were obtained using FeatureCounts (v 2.0.1) with GTF file for Rnor 6.0, taken from ENSEMBL ftp. Used parameters: -T 8 -p -a Rattus_norvegicus.Rnor_6.0.101.gtf -s 0 (for polyA dataset, unstranded) -s 2 (for ribosome-depleted dataset, reverse-stranded).
Counts from both datasets were combined in single matrix and normalized by “median-of-ratios” method from DESeq2 (v 1.29) R-package.
Assembly: Rnor6.0
Supplementary files format and content: tab-delimited text file, that includes normalized expression values for each sample (column).

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Dorsal Hippocampus

extract_protocol:
Poly-A enriched data: total RNA was extracted using Qiazol reagent according to manufacturer’s protocol. Ribosomal RNA depleted data: total RNA was extracted using ExtractRNA reagent (Evrogen, Russia) following manufacturer’s protocol. Depletion of ribosomal RNA was performed using MGIEasy rRNA Depletion kit.
1) mRNA isolation from total RNA with oligo(dT)-coated magnetic beads; 2) RNA fragmentation; 3) cDNA generation by reverse transcription using random primers followed by double-stranded cDNA synthesis; 4) reparation of ends, 3'-adenylation, ligation of adapters; 5) polymerase chain reaction using adapters. PCR products were purified with Ampure XP Beads and dissolved in EB solution; 6) the library has been validated with an Agilent Technologies 2100 bioanalyzer; 7) the double-stranded PCR product was denatured and cyclic molecules were synthesized from it using the splint oligo sequence. The result was a library of single-stranded cyclic molecules; 8) the library was amplified with phi29 DNA polymerase to form nanodroplets containing more than 300 copies of a single DNA molecule

treatment_protocol: Control handled rats not subjected to any treatments

tag: rna fraction

value: polyA-enriched

value: Dorsal Hippocampus

value: Wistar

tag: animal id

tag: Sex

value: male


title: lps3_atac

data_processing:
Raw bam to fastq bedtools v2.30.0: bedtools bamtofastq -i $bam -fq $fq
Read QC: FastQC v0.11.8: fastqc $fq -o $out_dir
Trim adapter trimmomatic v0.32: java -jar $EBROOTTRIMMOMATIC/trimmomatic-0.39.jar SE -threads 8 $fastq $fastq_trim ILLUMINACLIP:$fastq_adapter:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Alignment Bowtie v2.2.4 : bowtie2 -p 4 --very-sensitive --end-to-end -x $index_path -U $fastq_file | samtools view -@ 2 -u - | samtools sort -@ 2 -u - | samtools markdup - $bam
Index alignment bam file samtools v1.9: samtools index -@ 8 $bam
Filter alignment bam file samtools v1.9: samtools view -@ 8 -q 30 -b -o "$bam" $bam_filt chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chrX chrY
Peak calling: MACS v.2.1.0: macs2 callpeak -t $bam_file -n ${bam%.*}_peaks -g mm --nomodel --shift 100 --extsize 200 --keep-dup auto
Filter peaks by black list : subsetByOverlaps(peaks, black_list, invert=TRUE)
Count matrix Rsubread::featureCounts v2.4.3: featureCounts(files = bam_files, annot.ext = peaks, allowMultiOverlap = TRUE, minOverlap = 1, readShiftType = "upstream", readShiftSize = 0, ignoreDup = FALSE)
Filter count matrix edgeR::filterByExp v3.32.1: filterByExpr(y = DGEList, design = treatment, group = "group", min.count = 100, min.total.count = 100, large.n = 5, min.prop = 0.6)
genome_build: mm10
processed_data_files_format_and_content: read_counts.csv: read counts of unified and filtered peaks per sample
processed_data_files_format_and_content: log2cpm.csv: log2 CPM of unified and filtered peaks per sample

extract_protocol:
After collection by BAL, 50.000 AMs were pelleted by centrifugation at 4°C for 5 min at 500 g. Each pellet was lysed in 25 µL transposase reaction mix (9.75 µL RNase-free water, 12.5 µL 2 x TD buffer [Illumina], 0.5 µL 50x proteinase inhibitor cocktail [Roche], 2 µL TDE1 [Illumina], 0.25 µL 1% Digitonin [Promega]) and incubated at 37°C for 30 min. Subsequently, DNA was purified using the Qiagen MinElute kit and eluted in 12 µL.
The optimal number of amplification cycles was determined for each sample by qPCR [qPCR reaction mix per sample: 2.7 µL RNAse-free water, 0.2 µL ROX reference dye (Invitrogen), 0.5 µL index primer 1 noMX, 0.5 µL index primer 2.1, 0.1 µL 100x SYBR green (Sigma-Aldrich), 5 µL NEBnext High-Fidelity 2x PCR master mix (New England Biolabs) and 1 µL tagmented sample]. Subsequent library amplification was performed at the determined cycle numbers, using custom Nextera index primers (enrichment PCR reaction mix per sample: 10 µL RNAse-free water, 2.5 µL index primer 1 noMX, 2.5 µL barcoded index primer, 25 µL NEBnext High-Fidelity 2x PCR master mix, 10 µL tagmented sample). Enrichment was followed by SPRI (Beckman Coulter) size selection in order to exclude DNA fragments exceeding 1200 bp. DNA concentrations were determined using a Qubit fluorometer (Life Technologies), libraries were pooled at a final concentration of 4 nM before sequencing.


title: ctrl4_atac


title: lps5_medium

description: 200310_K00288_0194_BHH3T3BBXY_4_L5_med_S62857_1


title: lps1_atac


title: lps3_hisp

description: 200310_K00288_0194_BHH3T3BBXY_4_L3_HK_S62849_1


title: lps2_atac


title: ctrl3_atac


title: lps1_hisp

description: 200310_K00288_0194_BHH3T3BBXY_4_L1_HK_S62851_1


title: lps3_medium

description: 200310_K00288_0194_BHH3T3BBXY_4_L3_med_S62796_1


title: ctrl4_hisp

description: 200310_K00288_0194_BHH3T3BBXY_4_N4_HK_S62853_1


title: ctrl2_atac


title: ctrl1_atac


title: Spike protein transfected sample 1

city: Nyíregyháza

first: Judit

last: Dobránszki

state: Szabolcs-Szatmár-Bereg

address: Westsik Vilmos út 4-6.

department: Centre for Agricultural Genomics and Biotechnology

country: Hungary

institute: University of Debrecen

data_processing:
MGI DNBSEQ G400 sequencer built-in software was used for basecalling
Sequenced reads were trimmed for adaptor sequences, and filtered for low-complexity or low-quality sequence using Trimmomatic v0.36.
Trimmed reads were mapped to Ensembl GRCh38.104 whole genome using HISAT2 v.2.2.1 with default parameters.
Raw read counts were generated with featureCounts v1.6.2 with default settings using the Ensembl Build GRCh38.104 annotation gtf file. Read counts were normalized using the median-of-ratios method introduced with the DESeq2 v4.0.3 R package.
Assembly: GRCh38.104.primary assembly
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table including normalized gene counts for every sample and every gene, generated using the median-of-ratios method

organism: Homo sapiens

source_name: Human Monocyte

growth_protocol: THP-1 human monocyte cell line was obtained from ATCC (TIB-202, USA) and cells were maintained in T-75 flask in 15 ml RPMI-1640 culture medium (Sigma-Aldrich, USA) containing 10% heat-inactivated fetal bovine serum (FBS, Gibco, UK), 1% L-glutamine (Sigma-Aldrich, USA) and 1% penicillin-streptomycin (Sigma-Aldrich, USA) in a humidified incubator with 5% CO2 at 37°C. On the day of differentiation, THP-1 monocytes were plated onto 6-well plate (500.000 cells/well) in 2 ml RPMI-1640 culture medium supplemented with 10% FBS and 1% L-glutamine without antibiotics. After incubation for 3 hours, THP-1 monocytes were activated by 50 nM phorbol-12-myristate-13-acetate (PMA, Sigma-Aldrich, USA) for 1 hour, thereafter, PMA-containing medium was removed carefully, and the cells were incubated in fresh 2 ml antibiotic-free culture medium supplemented with 10% FBS, 1% L-glutamine for a further 24 hours.

extract_protocol:
5 hours after transfection, the media was removed carefully and cells were washed with 500 µl PBS and homogenized in 500 µl TRIzol Reagent (Molecular Research Center, USA), then the RNA isolation was carried out following the manufacturer’s protocol
Sequencing was performed on MGI DNBSEQ G400 sequencer (MGI Tech Co., Ltd., China) using MGI Easy RNA Library Prep Set

treatment_protocol: THP-1-derived macrophages were transfected with 2.5 µg of pcDNA3.1(+)-N-EGFP (mock control) or pcDNA3.1(+)-N-EGFP-S plasmids using Lipofectamine reagent (LTX) following the manufacturer’s protocol (Thermo Fisher Scientific, USA). Transfection control cells were only treated with LTX and native, non-transfected but in vitro-differentiated macrophages were prepared by replacing the medium with fresh one

tag: cell type

value: THP-1 monocyte cell line

value: treated with pcDNA3.1(+)-N-EGFP-S plasmid


title: lipofectamine treated control sample 2

value: treated with lipofectamine


title: mock transfected sample 2

value: treated with pcDNA3.1(+)-N-EGFP plasmid


title: untreated control sample 1

value: untreated


title: YU_3

city: Paris

first: Yann

last: Loe-Mie

address: 25 rue du Dr Roux

department: Computational Biology

country: France

institute: Institut Pasteur

data_processing:
we used the pipeline Bowtie-TopHat-Cufflinks
We mapped reads on mm10 genome and used the UCSC known genes as transcriptome index
We ran cuffmerge on all sample (YU, DYRK1A and their controls). We mapped the merged assembly on the Gencode (release M4) main annotation and removed all transcripts which are not described within (antisens genes, unknown transcript) in order to focus on protein coding genes. For the quantification (cuffquant) of the abundance we used the frag-bias-correct and the multi-read-correct options of the program on the merged assembly. The differential analysis was performed at 2 levels : gene level and transcript isoform level.
Assembly: mm10
Supplementary files format and content: The counts tables (isoforms and genes) are the normalized counts for each libraries according to the level of the analysis. cufflinks2UCSC.tab is the result of the cuffmerge and indicates the UCSC annotation according to the the cufflink annotation.

source_name: embryonic hippocampus

extract_protocol:
The hippocampi were dissected from genotyped E16-E18 embryos (n= 3 or 4 per genotype for 189N3 or Dp(16)1Yey transgenic mouse, respectively). Sample were homogenized in Trizol reagent (GIBCO), purified on nucleospin column (Macherey Nagel), treated with DNase I (Ambion) and processed according to the manufacturer’s instructions.
Total Stranded RNAseq sequencing was performed by the Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, Evry, FRANCE). After complete RNA quality control on each sample (quantification in duplicate on a NanoDrop™ 8000 spectrophotometer and RNA6000 Nano LabChip analysis on Bioanalyzer from Agilent), libraries have been prepared using the “TruSeq Stranded Total RNA” Kit from Illumina. An input of 1 µg total RNA was used for all samples, and libraries were prepared according to manufacturer’s instructions. After library quality control and quantification, sample libraries have been pooled before sequencing to reach the expected sequencing depth. Sequencing has been performed on a Illumina HiSeq200 as paired-end 100 bp reads, using Illumina sequencing reagents. Fastq files produced after RNA-seq sequencing have been be processed by in-house CNRGH tools in order to assess quality of raw and genomic-aligned nucleotides.

value: embryonic hippocampus

tag: genotype

value: extra copy of the mouse Chr16 syntenic region (Dp(16)1Yey)


title: YUWT_0

value: wt


title: lps5_atac

value: broncho-alveolar lavage (BAL) fluid


title: lipofectamine treated control sample 1


title: YUWT_3


title: Spike protein transfected sample 2


title: YU_1


title: DYRK1AWT_1


title: gd133_E+ replicate 2

city: Clemson

first: Susan

middle: K

last: Duckett

state: SC

address: 112 Biosystems Research Complex

department: Animal and Veterinary Sciences

institute: Clemson University

data_processing:
bcl2fastq v2.20 with defaults
FastQC
seqtk v1.3-t106 for downsampling
TrimGalore v0.38
GSNAP v2018-07-04
Subread's featureCounts v2.0.0
edgeR v3.22.5
Panther 16.0 for gene ontology enrichment
David v6.8
KEGG Mapper v4.3
Genome_build: Ovis aries (TEXEL) Ensembl release 96
Supplementary_files_format_and_content: All.samples.gene.counts.renamed.txt: Tab-delimited text file

organism: Ovis aries

source_name: cotyledon

extract_protocol:
Total cellular RNA was isolated from cotyledon samples using Trizol reagent and purified using a PureLink Mini RNA kit (Invitrogen, Thermo Fisher Scientific, Waltham, MA) according to manufacturer instructions.
Library preparation was conducted using the NEB Next Ultra II Library Prep Kit for Illumina according to manufacturer instructions.

tag: breed

value: Suffolk

tag: age

value: Ewe 133 +/- 1 gestation

value: Fed endophyte-infected tall fescue seed

tag: placentome type

value: Type B

value: cotyledon

tag: replicate

value: replicate 2


title: gd133_E+ replicate 3

value: replicate 3


title: YUWT_2


title: YUWT_1


title: YU_0


title: untreated control sample 2


title: DYRK1AWT_2


title: DYRK1AWT_0


title: DYRK1A_1

value: extra copy of the Dyrk1A gene


title: DYRK1A_2


title: mock transfected sample 1

value: THP-1 monocyte cell line


title: gd133_CON replicate 3

value: untreated (fed endophyte-free tall fescue seed)


title: DYRK1A_0


title: gd133_E+ replicate 1

value: replicate 1


title: 24 hour rep 1 [ATAC-Seq]

city: Gainesville

first: Daniel

last: Conde

state: FL

address: 2033 Mowry road

institute: University of Florida

data_processing:
RNA-seq
Between 8.7-17.9 million, 2×100 bp reads were obtained after sequencing the 24 RNA-seq libraries. Reads were aligned with Kallisto to the M. truncatula transcriptome (v5). The average of the alignment rates across time points was 87-95%. A total of 37,536 genes were detected with non-zero expression at any of the time points. The data were LOESS-normalized and processed with SLEUTH for further analysis. Finally, TPM expression values were quantile-normalized and log-transformed before being used as input for further analysis.
Genome_build: M. truncatula transcriptome v5; https://medicago.toulouse.inra.fr/MtrunA17r5.0-ANR/
Supplementary_files_format_and_content: txt table containing the TPM expression values quantile-normalized and log-transformed
Supplementary_files_format_and_content: transcript_expression_tpm_reordered.txt - TPM values for each of 24 samples
Supplementary_files_format_and_content: transcript_expression_tpm_qnorm.txt - values with quantile normalization and log transformation
Supplementary_files_format_and_content: normalizedExp.txt - values additionall median-collapsed across replicates per time point.
ATAC-seq
The data were aligned with Bowtie 2 to the M. truncatula v5 genome, with 46 to 75% alignment rates. Properly paired fragments were selected, and the duplicate fragments were removed. Peak calling was performed by applying MACS2 to ATAC-seq data from each time point. We mapped these peaks to genes if the center of a peak was within 10 kbp upstream and 1 kbp downstream of a gene transcription start site (TSS). Peaks called at each time point were merged across time points to generate a set of “universal peaks” using custom scripts
Genome_build: M. truncatula v5 genome
Supplementary_files_format_and_content: bed files containing the position of the ATAC-seq peaks in each time point, and the position of the universal peaks
Supplementary_files_format_and_content: mergeddata_merged_th_0.9_with_label.bed - merged data peaks

organism: Medicago truncatula

source_name: root

growth_protocol: Seeds of M. truncatula wild-type reference accession Jemalong A17 were sterilized and germinated in 1% agar plates, including 1µM GA3. Plates were stored at 4°C for three days in the dark and placed at room temperature overnight for germination. Seedlings were grown vertically for five days on a modified Fahraeus medium with no nitrogen, in a growth chamber (24°C, 16 h light/8h dark cycle, 70 µmol m-2 s-1 photosynthetic photon flux).

extract_protocol:
Before nuclei isolation, all materials were precooled to 4°C. Briefly, roots were chopped for 2 min in 1 ml of pre-chilled lysis buffer (15 mM Tris-HCl pH7.5, 2mM EDTA, 20 mM NaCl, 80 mM KCl, 0.5 mM spermine, 15 mM 2-ME, 0.15 % TritonX-100) in a cold room. This step was repeated four times with a 1 min interval. The homogenate was filtered through one layer of pre-wetted Miracloth, loaded on the surface of a 2 mL dense sucrose buffer (1.7 M sucrose, 10 mM Tris-HCl pH8.0, 2 mM MgCl2, 5 mM 2-ME, 1 mM EDTA, 0.15 % Triton X100), and centrifuged (2400 g, 20 min at 4°C). The supernatant was removed, the nuclei were resuspended in 500 µl of lysis buffer and then filtered in 70 µm and 40 µm filters consecutively. The nuclei were then collected by centrifuging the solution at 1000g for 5 min at 4°C. After washing with 950 µl 1×TAPS buffer (10 mM TAPS-NaOH, pH8.0, 5 mM MgCl2), the samples were centrifuged again at 1000 g for 5 min at 4°C. The supernatant was removed, leaving the nuclei suspended in approximately 10 µl of solution.
Next, 1.5 µl of Tn5 transposase (Illumina FC-121-1030), 15 µl of Tagmentation buffer, and 13.5 µl of ddH20 were added to the solution. The reaction was incubated at 37°C for 30 min. The product was purified using a QIAGEN MinElute PCR Purification kit and then amplified using Phusion DNA polymerase. 1 µl of the product was used in 10 µl qPCR cocktail with Sybr Green. Cycle number X was determined as the cycle were the ¼ of the maximum signal was reached. Then we amplified the rest of the product in a PHusion (NEB) PCR system with X-2 cycles (10 to 15 cycles, 50 µl of reaction). Amplified libraries were purified with AMPure beads (Beckman Coulter), and library concentrations were determined using a Qubit. Sequencing was carried out in an Illumina HiSeqX (2×150 cycles) at the HudsonAlpha Institute for Biotechnology (Huntsville, AL, USA).

treatment_protocol: LCOs were purified from Sinorhizobium meliloti strain 2011 as described previously. Next, seedling roots were immersed in a solution of purified LCOs (10-8 M) or 0.005% ethanol (control) for 1 h. Roots were cut and immediately used for nuclei extraction and generation of ATAC-seq libraries (see below), or snap-frozen in liquid nitrogen for posterior RNA isolation and sequencing. Roots were collected at 0 h (control), 15 min, 30 min, 1 h, 2 h, 4 h, 8 h after LCOs treatment. Roots from seven plants were pooled for each of three biological replicates used in RNA sequencing, while roots from 15 plants were pooled for one replicate used in ATAC-seq, in each time point of the experiment.

value: root

value: LCO

tag: time point

value: after 24 hour.

value: wild-type

tag: cultivar

value: Jemalong A17


title: gd133_CON replicate 1


title: gd110_E+ replicate 3

value: Ewe 110 +/- 1 gestation


title: gd110_E+ replicate 1

value: Suffolk


title: gd110_E+ replicate 2


title: YU_2

value: embryonic hippocampus

value: extra copy of the mouse Chr16 syntenic region (Dp(16)1Yey)


title: gd110_CON replicate 3

value: Type B


title: 1 hour rep 1 [ATAC-Seq]

value: after 1 hour.


title: 2 hour rep 1 [ATAC-Seq]

value: after 2 hour.


title: 4 hour rep 1 [ATAC-Seq]

value: after 4 hour.


title: gd110_CON replicate 2

value: cotyledon

value: replicate 2


title: 30 min rep 1 [ATAC-Seq]

value: after 30 min.


title: 15 min rep 1 [ATAC-Seq]

value: after 15 min.


title: Control rep 1 [ATAC-Seq]

value: root

value: time 0


title: gd133_CON replicate 2

value: Ewe 133 +/- 1 gestation

value: untreated (fed endophyte-free tall fescue seed)


title: gd110_CON replicate 1

value: replicate 1


title: gd85_CON replicate 3

value: Ewe 86 +/- 1 gestation

value: Type A

value: replicate 3


title: gd85_CON replicate 2

value: Suffolk


title: gd85_CON replicate 1

value: Type B


title: H3K9me3_Drosophila_embryo

city: Berkeley

first: Aaron

last: Streets

state: CA

address: Stanley Hall

department: Bioengineering

institute: University of California, Berkeley

data_processing:
Megalodon (v2.3.4), Guppy (v5.0.15), using a Rerio res_dna_r941_min_modbases-all-context_v001.cfg basecalling model
fast5s were aligned and modified bases were called using Megalodon (2.3.1 or 2.3.4) using  the rerio all-context basecalling model (res_dna_r941_min_modbases-all-context_v001.cfg) with parameters --outputs mod_mappings and --mod-min-prob 0
Assembly: CHM13v1.1 reference genome or dm6
Supplementary files format and content: bam files with alignment and modification basecalling info
Library strategy: DiMeLo-seq

organism: Drosophila melanogaster

source_name: Drosophila melanogaster embryos

growth_protocol:
OregonR flies were maintained on standard molasses medium before transfer to embryo collection cages with apple-juice plates with yeast paste.
Human cells grown in RPMI with 15% FBS, 1% penn/strep at 37C with 5% CO2

extract_protocol:
NEB HMW DNA extraction kit (T3050L)
Oxford Nanopore sequencing libraries were generated with SQK-LSK110

treatment_protocol: isolated nuceli were treated for DiMeLo-seq with conditions described above

tag: antibody

value: rabbit anti H3K9me3 (Active Motif 39062)


title: 3_kn_hs, rep1

city: Sinagpore

first: Daisuke

last: Urano

address: 1 Research Link

country: Singapore

institute: Temasek Life Science Laboratory

description:
3_raw_reads
HS1_1

data_processing:
STAR for genome mapping
Genome_build: M. polymorpha: v3.1 & v5.1 from Marchantia.info; K. nitens: GCA_000708835.1_ASM70883v1 from NCBI
Supplementary_files_format_and_content: raw counts

organism: Klebsormidium nitens

source_name: full grown alge

growth_protocol: M. polymorpha wildtype (accession BC3 (female), Tak-2 (female) and Tak-1 (male)), MpHSFA1 overexpression lines, and mphsfa1 and mphsfb1 knockout mutants were grown on ½ x Gamborg B5 media (pH 5.5) with 1% agar under continuous light (50-60 µmol m-2s-1) at 22°C; For K. nitens, droplets of algal suspension from a fully-grown plate were plated on C-medium plates and incubated for one month under continuous light at 22°C

extract_protocol:
Plant samples were frozen in liquid nitrogen, and followed by RNA extraction using Rneasy Plant Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Novoseq protocols

treatment_protocol: M. polymorpha, gemmalings were grown in ½ x B5 liquid media for 7 days at continuous light and heat shocked at 37°C for 0, 1 and 5 h; K. nitens, droplets of algal suspension from a fully-grown plate were plated on C-medium plates and incubated for one month. The algal plates were then immersed into a water bath at 37°C for 2 h.

tag: tissue

value: full grown alge

value: one-month

value: WT


title: 3_kn_hs, rep3

description:
3_raw_reads
HS3_1


title: 3_kn_cntr, rep3

description:
3_raw_reads
C3_1


title: 3_kn_hs, rep2

description:
3_raw_reads
HS2_1


title: XH001 + TM7x passage 6 time 6 rep 3

city: Seattle

first: Jeffrey

middle: S

last: McLean

state: WA

address: 1959 NE Pacific St, Box 357444

department: Periodontics

institute: University of Washington

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software
The paired end reads were trimmed of low-quality sequence at a quality cutoff of 30 using BBduk 38.37 in Geneious prime 2020.0.5
Trimmed sequences were mapped to a reference database containing XH001 and TM7x reference sequences using Geneious prime with the default settings.
For expression ratios and false discovery rates XH001 and TM7x data were analyzed separately via the Degust website using voom/limma with a significance cutoff of FDR 0.05
Genome_build: NZ_CP007496.1, LLVT00000000.1
Supplementary_files_format_and_content: Spread sheet with mapped reads for all samples as well as expression ratios and false discovery rates for the analyzed comparisons

organism:
Schaalia odontolytica
Candidatus Nanosynbacter lyticus

source_name: in vitro culture

growth_protocol: Naive XH001 (XH001n) monoculture and XH001/TM7x coculture were both grown in Bacto Brain Heart Infusion medium at 37 °C in microaerophilic chamber (2% O2, 5% CO2, balanced with N2). Samples were grown for 24 hours and then passaged by sub-culturing to 0.1 OD600 then grown for 24 hours. Cultures were passaged 6 times.

extract_protocol:
Cell pellets were resuspended in cold PBS buffer and beaten with glass beads 3 times for 30 seconds with 30 second breaks at 6 m/s speed. Total RNA was isolated using the High Pure RNA isolation kit. Isolated RNA was cleaned and concentrated with Zymo Research RNA clean & concentrator kit following kit protocol. DNA was removed using the Ambion TURBO DNA-free kit. rRNA was depleted with Ribo-Zero.
RNA sequencing library preparation used NEBNext Ultra RNA Library Prep Kit

tag: treatment

value: Saccharibacteria Nanosynbacter lyticus strain TM7x

tag: time

value: passage 6 time 6


title: 3_kn_cntr, rep1

description:
3_raw_reads
C1_1


title: 3_kn_cntr, rep2

description:
3_raw_reads
C2_1


title: XH001 + TM7x passage 4 time 15 rep 3

tag: strain

value: passage 4 time 15


title: 8 hour rep 1 [ATAC-Seq]

value: root

value: LCO

value: after 8 hour.

value: wild-type

value: Jemalong A17


title: XH001 + TM7x passage 4 time 15 rep 1


title: V_SC_2

city: Shenzhen

first: Songbin

last: Wu

state: Guangdong

address: 89 Taoyuan Rd., Nanshan District,

department: Department of Pain Medicine

country: China

institute: Huazhong University of Science and Technology Union Shenzhen Hospital

data_processing:
Sequencing using the DNBSEQ platform
SOAPnuke (v1.5.2) was used to filter the sequenced raw data. The clean reads were mapped to the GCF_000001635.26_GRCm38.p6 using HISAT2 (v2.0.4) with Q value ≤ 0.05.
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set, then the expression level of gene was calculated by RSEM (v1.2.12).
According to the quantitative results of gene expression, we screened differentially expressed genes among samples based on DEseq2 algorithm.
Assembly: GCF_000001635.26_GRCm38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: spinal cord, acute herpetic neuralgia mice, Day7

growth_protocol: All experimental animals were placed in individually ventilated colony cages and maintained in a normal 12 hour light / dark cycle with free access to food and water.

extract_protocol:
RNA was harvested using TRIzol reagent (Invitrogen, USA). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Mice were anesthetized with isoflurane (2%), and then the right mid-flank and right foot fur of the mice were shaved using a scraper. HSV-1 (1×106 PFU in 10 μL) was inoculated subcutaneously in the tibia of the right hind leg of mice with a microsyringe. The contralateral hindlimb was not inoculated with virus.
The control group was mock-infected as described for HSV-1 infection, but the viruses used were previously inactivated by heating at 60°C for 1 hour.

value: spinal cord

value: male

value: 9 weeks old

value: Inoculated with active HSV-1 virus solution

value: Day 7


title: XH001 + TM7x passage 4 time 15 rep 2


title: V_DRG_3

source_name: dorsal root ganglion, acute herpetic neuralgia mice, Day7

value: dorsal root ganglion


title: sevCCC58 [methylation]

type: genomic

city: Marseille

first: Pauline

last: Brochet

address: 13288 MARSEILLE cedex 09

hyb_protocol: Manufacturer protocol

scan_protocol: Manufacturer protocol

data_processing:
Analysis of DNA methylation data was performed with the R ChAMP package. Probe with a detection P value <= 0.01 and with a beadcount less than 3 have been discarded. The beta values were normalized with the BMIQ method, and the batch effect was corrected with the ComBat method.
normalized data: Average Beta

label: Cy5 and Cy3

source_name: Blood

label_protocol: Manufacturer protocol

extract_protocol: Tissue : DNAs, extracted from whole tissue, were bisulfite converted and amplified with elongation of primers with EZ DNA methylation kit (ZymoResearch, Saint Marcel, France). Amplified DNAs were fragmented and hybridized in beads (Infinium Human Methylation EPIC Bead Chip, Illumina, San Diego, California). Blood : Blood (5 to 15 ml of blood)  was  collected in EDTA tubes. Genomic DNA was isolated on a silica-membrane according to the manufacturer’s protocol (QIAamp DNA Blood Max Kit, Qiagen, Hilden, Germany). Amplified DNAs were fragmented and hybridized in beads (Infinium Human Methylation EPIC Bead Chip, Illumina, San Diego, California).

tag: group

value: chronic chagasic cardiomyopathy sample

value: Blood


title: sevCCC57 [methylation]

description: Blood (5 to 15 ml of blood)  was  collected in EDTA tubes. Genomic DNA was isolated on a silica-membrane according to the manufacturer’s protocol (QIAamp DNA Blood Max Kit, Qiagen, Hilden, Germany). Amplified DNAs were fragmented and hybridized in beads (Infinium Human Methylation EPIC Bead Chip, Illumina, San Diego, California).


title: V_SC_1


title: V_DRG_1


title: XH001 + TM7x passage 6 time 6 rep 2


title: V_SC_3


title: sevCCC56 [methylation]


title: XH001 + TM7x passage 4 time 6 rep 3

value: passage 4 time 6


title: XH001 + TM7x passage 4 time 10 rep 1

value: Saccharibacteria Nanosynbacter lyticus strain TM7x

value: passage 4 time 10


title: XH001 + TM7x passage 4 time 10 rep 2


title: XH001 + TM7x passage 4 time 6 rep 2


title: XH001 + TM7x passage 4 time 6 rep 1


title: C_SC_2

source_name: spinal cord, control mice, Day7

value: Inoculate HSV-1 virus solution inactivated at 60 C for 1 hour


title: sevCCC55 [methylation]


title: sevCCC54 [methylation]


title: XH001 + TM7x passage 0 time 6 rep 3

value: passage 0 time 6


title: XH001 + TM7x passage 0 time 6 rep 2


title: sevCCC53 [methylation]


title: C_SC_1


title: XH001 + TM7x passage 0 time 6 rep 1


title: C_DRG_3

source_name: dorsal root ganglion, control mice, Day7


title: saccule_EJ06_bulkATAC-seq

tag: embryo age

value: 6-10 month old adult zebrafish


title: C_SC_3


title: C_DRG_2


title: sevCCC51 [methylation]


title: sevCCC52 [methylation]


title: C_DRG_1


title: sevCCC50 [methylation]


title: XH001 + TM7x passage 6 time 6 rep 1

value: passage 6 time 6


title: lps4_atac

value: broncho-alveolar lavage (BAL) fluid


title: sevCCC49 [methylation]


title: TAA_1

city: Shanghai

first: Zhijie

last: Li

state: Other

address: Haike Road 230

institute: ShanghaiTech University

description:
RNA-seq method
PBS_TAA_counts.xlsx

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim_galore
Trimmed sequence reads were mapped to GrCM38/mm10 using hisat2
Read count extraction and normalization were performed using featurecount
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: liver

extract_protocol:
RNA was extracted using Trizol reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using ILLUMINA total RNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: For TAA-induced ALF model, all male mice (8-9 weeks old) were injected intraperitoneally with 200 mg/kg of TAA. For APAP-induced ALF model, all male mice (8-9 weeks old) were fasted overnight and injected intragastriclly with 500 mg/kg of APAP. Fasting was maintained for 6 h after APAP treatment. The same volume of sterilized PBS was injected into fed or fasted mice as a control group for TAA or APAP-induced ALF, respectively.

value: liver

value: WT

value: TAA


title: TAA_2

description:
RNA-seq method
PBS_TAA_counts.xlsx


title: XH001 + TM7x passage 4 time 10 rep 3


title: PBS_2

description:
RNA-seq method
PBS_TAA_counts.xlsx

value: PBS


title: sevCCC47 [methylation]


title: Peripheral Blood-MDD patients-YJ-04

type: RNA

city: Beijing

first: Zijing

last: Liu

state: Beijing

address: No. 9, Dongdan

institute: Chinese Academy of Medical Sciences

hyb_protocol: Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (MN) and resuspended in elution buffer. Labeled controls and test samples labeled with Cy3-dCTP were dissolved in 80uL hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide. DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 4 x 180K array slides

data_processing: The array data were analyzed for data summarization, normalization and quality control by using the GeneSpring software V13 (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: human blood of MDD patients

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction, followed by Nucleospin® Extract II( Cat. No.740609.250) kit purification. Dye incorporation and cRNA yield were checked with the NanoDrop2000 Spectrophotometer.

extract_protocol: Total RNA was extracted from peripheral blood leukocytes using the PAXgene Blood RNA kit (Qiagen, USA) according to the manufacturer’s protocol. The purity and concentration of RNA were measured spectrophotometrically by using a NanoDrop2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: whole blood

tag: subject status

value: MDD patients

tag: gender

value: male


title: PBS_1

description:
RNA-seq method
PBS_TAA_counts.xlsx


title: Peripheral Blood-MDD patients-YJ-26

value: female


title: Peripheral Blood-MDD patients-YJ-20


title: Peripheral Blood-MDD patients-YJ-09


title: Peripheral Blood-MDD patients-YJ-52


title: sevCCC46 [methylation]

value: chronic chagasic cardiomyopathy sample

value: Blood


title: Peripheral Blood-MDD patients-YJ-14


title: Control 2

city: Hobart

first: Kate

last: Brettingham-Moore

state: Tasmania

address: 17 Liverpool Street

department: School of Medicine

country: Australia

institute: University of Tasmania

hyb_protocol: Standard illumina protocol

scan_protocol: Illumina iScan

data_processing: Performed at Australian Genome Research Facility

label: Cy3 Cy5

source_name: genomic DNA extracted from untreated 22Rv1 Prostate cancer cells replicate 2

label_protocol: 500ng of DNA was bisulfite converted, processed and hybridised to Illumina Infinium MethylationEPIC BeadChip using the standard illumina protocol

growth_protocol: 22Rv1 cells were cultured in RPMI medium supplemented with 10% FBS and 100 units/ml penicillin and 100 micrograms/ml streptomycin. Cells were maintained at a density of 30 to 90% confluency.

extract_protocol: DNA was extracted using the Qiagen Dneasy blood and tissue mini kit.

treatment_protocol: 1 microgram per ml phleomycin added to 22Rv1 cell culture daily (week days only) for a period of 6 weeks; cells were also left untreated and DNA harvested at day 0 or the end of week 6 (age matched)

tag: cell line

tag: cell type

value: Prostate cancer cell line


title: Peripheral Blood-MDD patients-YJ-18


title: day7_PBS_5

city: Syracuse

first: Adam

middle: Tully

last: Waickman

state: New York

address: 766 Irving Avenue

institute: SUNY Upstate Medical University

data_processing:
Raw sequencing data (BCL files) were demultiplexed and coverted to fastq files using the CellRanger v2.1.1 mkfastq pipline (10xGenomics) and bcl2fastq2 v 2.20.0 (Illumina)
Data qualty control, data filtering, cell barcode processing, UMI compression, 5' transcript alignment, and single-cell gene counting was performed using the CellRanger v2.1.1 count pipeline (10x Genomics)
Genome_build: Mmul_10
Supplementary_files_format_and_content: tsv, mtx files generated by CellRanger v2.1.1

organism: Macaca mulatta

source_name: bronchoalveolar lavage

extract_protocol:
Single-cell RNAseq libraries were generated using the Next GEM Single Cell 5′ Library and Gel Bead Kit v1.1 (10x Genomics) and the Chromium Analyzer (10x Genomics) according to the manufacture's protocol (User guide RevF)
Indexed sequencing libraries were generated using the Chromium Single Cell 5’ Library Construction Kit (User gude RevF). In short, sequencing libraries were generated by 1) transcript fragmentation and end-repair, 2) post-fragmentation size-selection using SPRIselect beads, 3) Adaptor ligation and 4) sample index PCR and SPRIselect cleanup

treatment_protocol: Cells from fresh bronchoalveoloar lavage samples were washed 1X in PBS, counted, and resuspended at a concentration of 1e6 cells/ml in Ca++Mg++ free PBS supplemented with 2% fetal calf serum prior to analysis

tag: days post challenge

tag: treatment before challenge


title: Peripheral Blood-MDD patients-YJ-05

tag: age


title: Peripheral Blood-MDD patients-YJ-39


title: Age match 2

source_name: genomic DNA extracted from 22Rv1 Prostate cancer cells grown in culture for 6 weeks replicate 2


title: 6 Week Phleo 1

source_name: genomic DNA extracted from 22Rv1 Prostate cancer cells exposed to daily DNA damage for 6 weeks replicate 1


title: Age match 1

source_name: genomic DNA extracted from 22Rv1 Prostate cancer cells grown in culture for 6 weeks replicate 1


title: Peripheral Blood-MDD patients-YJ-19


title: sevCCC45 [methylation]


title: day7_PBS_4


title: sevCCC44 [methylation]


title: Peripheral Blood-MDD patients-YJ-64


title: Peripheral Blood-MDD patients-YJ-06


title: V_DRG_2

value: dorsal root ganglion

tag: Sex

value: 9 weeks old

value: Inoculated with active HSV-1 virus solution

value: Day 7


title: Peripheral Blood-MDD patients-YJ-59


title: Peripheral Blood-MDD patients-YJ-11


title: sevCCC43 [methylation]


title: sevCCC42 [methylation]


title: day7_PBS_2


title: day7_PBS_1


title: Peripheral Blood-MDD patients-YJ-30


title: Peripheral Blood-MDD patients-YJ-23


title: sevCCC41 [methylation]


title: day7_PBS_3


title: sevCCC48 [methylation]


title: day7_1ugVac_6

value: 1ug vaccine


title: sevCCC39 [methylation]


title: Peripheral Blood-MDD patients-YJ-57


title: day7_1ugVac_5


title: sevCCC38 [methylation]


title: Peripheral Blood-MDD patients-YJ-10


title: day7_1ugVac_3


title: Peripheral Blood-healthy controls-13c-202

source_name: human blood of heathy controls

value: heathy controls


title: Peripheral Blood-MDD patients-YJ-27


title: Peripheral Blood-healthy controls-13c-255


title: day7_1ugVac_4


title: sevCCC36 [methylation]


title: sevCCC37 [methylation]


title: Peripheral Blood-MDD patients-YJ-33


title: Peripheral Blood-healthy controls-13c-088


title: day7_1ugVac_2


title: Peripheral Blood-healthy controls-13c-184


title: 6 Week Phleo 2

source_name: genomic DNA extracted from 22Rv1 Prostate cancer cells exposed to daily DNA damage for 6 weeks replicate 2


title: Peripheral Blood-healthy controls-13c-201


title: Peripheral Blood-healthy controls-13c-210


title: day7_1ugVac_1


title: Peripheral Blood-healthy controls-13c-251


title: Peripheral Blood-healthy controls-13c-087


title: sevCCC35 [methylation]


title: Peripheral Blood-healthy controls-13c-278


title: day7_30ugVac_4

value: 30ug vaccine


title: Peripheral Blood-healthy controls-13c-277


title: Peripheral Blood-healthy controls-13c-241


title: day7_30ugVac_3


title: sevCCC33 [methylation]


title: Peripheral Blood-healthy controls-13c-287


title: sevCCC34 [methylation]


title: Peripheral Blood-healthy controls-13c-262


title: day7_30ugVac_2


title: 24 hour rep 3 [RNA-Seq]

source_name: root

extract_protocol:
For each RNA extraction, roots from 7 plants were pooled and ground while keeping the sample frozen. RNA extraction was performed as described previously (DOI: 10.1007/BF02670468)
Libraries were prepared using 1 μg of RNA in the NEBNext® Ultra™ Directional RNA Library Prep Kit following the supplier’s instructions (New England Biolabs, Ipswich, MA, USA). Sequencing was carried out with an Illumina HiSeq3000 (2×100 cycles) at the Interdisciplinary Center for Biotechnology Research at the University of Florida (Gainesville, FL, USA).

value: root

value: LCO

tag: time point

value: after 24 hour.

tag: genotype

value: wild-type

value: Jemalong A17


title: 8 hour rep 3 [RNA-Seq]

value: after 8 hour.

tag: cultivar


title: 24 hour rep 1 [RNA-Seq]

tag: tissue


title: Peripheral Blood-healthy controls-13c-231

value: whole blood

value: male


title: sevCCC32 [methylation]

value: chronic chagasic cardiomyopathy sample

value: Blood


title: 8 hour rep 2 [RNA-Seq]

tag: treatment


title: Peripheral Blood-healthy controls-13c-181


title: Peripheral Blood-healthy controls-13c-143


title: day7_30ugVac_1


title: 24 hour rep 2 [RNA-Seq]


title: 8 hour rep 1 [RNA-Seq]


title: day2_PBS_6

value: PBS


title: sevCCC31 [methylation]


title: Peripheral Blood-healthy controls-13c-006


title: Peripheral Blood-healthy controls-13c-035


title: Peripheral Blood-healthy controls-13c-004


title: 4 hour rep 3 [RNA-Seq]

value: after 4 hour.


title: day2_PBS_4


title: 2 hour rep 3  [RNA-Seq]

value: after 2 hour.


title: sevCCC28 [methylation]


title: 4 hour rep 2 [RNA-Seq]


title: day2_PBS_5


title: 4 hour rep 1 [RNA-Seq]


title: 2 hour rep 1 [RNA-Seq]


title: sevCCC30 [methylation]


title: 2 hour rep 2 [RNA-Seq]


title: 1 hour rep 2 [RNA-Seq]

value: after 1 hour.


title: sevCCC27 [methylation]


title: sevCCC26 [methylation]


title: day2_PBS_3


title: sevCCC29 [methylation]


title: 30 min rep 3 [RNA-Seq]

value: after 30 min.


title: 1 hour rep 3 [RNA-Seq]


title: 30 min rep 2 [RNA-Seq]


title: 1 hour rep 1 [RNA-Seq]


title: sevCCC25 [methylation]


title: day2_PBS_2


title: Control 1

source_name: genomic DNA extracted from untreated 22Rv1 Prostate cancer cells replicate 1

value: Prostate cancer cell line


title: day2_1ugVac_6

value: 1ug vaccine


title: 30 min rep 1 [RNA-Seq]

value: root


title: sevCCC24 [methylation]


title: 15 min rep 3 [RNA-Seq]

value: LCO

value: after 15 min.


title: 15 min rep 2 [RNA-Seq]

value: wild-type


title: day2_1ugVac_5


title: day2_1ugVac_4


title: day2_PBS_1


title: 15 min rep 1 [RNA-Seq]

value: Jemalong A17


title: sevCCC23 [methylation]


title: Control rep 3 [RNA-Seq]

value: time 0


title: sevCCC40 [methylation]


title: Control rep 2 [RNA-Seq]


title: day2_1ugVac_2


title: Control rep 1 [RNA-Seq]


title: day2_1ugVac_3


title: sevCCC20 [methylation]


title: day2_1ugVac_1


title: shLUC_rep6

first: Stepan

last: Nersisyan

address: Vavilova str 7

department: Faculty of Biology and Biotechnology

institute: HSE University

data_processing:
Quality of RNA-seq FASTQ files was assessed with FastQC v0.11.9 (Babraham Bioinformatics, Cambridge, UK).
Adapter sequences were removed with the use of cutadapt v2.10.
Adapter-free RNA-seq reads were mapped to the reference human genome (GENCODE GRCh38.p13) with STAR v2.7.5b. GENCODE genome annotation (release 34) was used to generate the gene-level read counts matrices.
DESeq2 v1.28.1 was used to carry out the differential expression analysis for RNA-seq data.
Assembly: GENCODE GRCh38.p13
Supplementary files format and content: counts.tsv – tab-delimited read counts table
Supplementary files format and content: diff_expr.tsv – tab-delimited results of differential expression analysis

growth_protocol: The human colon adenocarcinoma cell line HT-29 was purchased from the European Cell Culture Collection (Porton Down, Wiltshire, UK). Cells were grown in RPMI 1640 + L-Glutamine (Gibco, Thermo Fisher Scientific, MA, USA) supplemented with 10% fetal calf serum (Gibco), 1% penicillin and streptomycin (Gibco) and cultured under standard cell culture conditions (37°C, saturated humidity, 5% CO2). The HT-29 cells were additionally tested for mycoplasma contamination. CD44 knockdown in HT-29 cells was achieved by a shRNA-mediated approach. All animals used were pathogen-free Balb/c severe combined immunodeficient (SCID) mice aged 9-14 weeks with a weight of 25-30 g at the beginning of the experiment. Each animal was inoculated subcutaneously (s. c.) above the right scapula with 1 x 106 shLUC or shCD44 HT-29 cells in medium without supplements. The mice were euthanized when the tumors ulcerated or reached a size of ~1.5 cm³.

extract_protocol:
Approximately 50 mg of fresh-frozen primary tumor tissue was crushed in liquid nitrogen in presence of QIAzol Lysis Reagent (Qiagen, Hilden, Germany). The total RNA was isolated using miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. All RNA samples were treated by DNase I during the isolation procedure. The RNA yield was determined by UV absorbance using a NanoDrop 1000 spectrophotometer (Peqlab, Erlangen, Germany). The RNA quality was assessed by analyzing the ribosomal RNA integrity number (RIN) on an Agilent 2100 Bioanalyzer using the RNA 6000 Nano kit (Agilent Technologies, Palo Alto, CA, USA). The RIN values of the isolated RNA samples ranged from 6.7 to 9.6.
Libraries for mRNA sequencing were prepared from total RNA samples using the Illumina Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

tag: origin

value: Xenograft

value: SCID

value: shLUC


title: sevCCC21 [methylation]

value: chronic chagasic cardiomyopathy sample

value: Blood


title: sevCCC19 [methylation]


title: shLUC_rep5

tag: strain


title: shLUC_rep4


title: day2_30ugVac_4

value: 30ug vaccine


title: shLUC_rep7


title: sevCCC18 [methylation]

tag: group


title: shLUC_rep2


title: shLUC_rep3


title: shCD44_rep6


title: shLUC_rep1


title: shCD44_rep7


title: sevCCC22 [methylation]


title: shCD44_rep2


title: sevCCC16 [methylation]


title: sevCCC17 [methylation]


title: shCD44_rep5


title: shCD44_rep1


title: shCD44_rep4


title: shCD44_rep3


title: day2_30ugVac_1


title: day2_30ugVac_2


title: A6V055_D2_RSA_trimmed

tag: vaccine dose

value: PBS


title: sevCCC14 [methylation]


title: sevCCC12 [methylation]


title: sevCCC13 [methylation]


title: Peripheral Blood-healthy controls-13c-071

value: whole blood

tag: subject status

value: heathy controls

value: female


title: day2_30ugVac_3


title: A12V163_D2_RSA_trimmed


title: Patient7

city: Paterna

first: María José

last: Garzón Garzón

address: Carrer del Catedràtic Agustín Escardino Benlloch, 9

country: Spain

institute: EpiDisease SL

data_processing:
The quality of the Illumina raw sequences, pre-processing, quality control and normalization was assessed using FastQC software (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Sequence reads were trimmed to remove sequencing adapters and low-quality bases using the software Cutadapt (http://cutadapt.readthedocs.org/en/stable/) subread, multiqc, edgeR, limma, limma-voom and deseq2.11-14 Once quality was assessed, data were mapped to the human GRCh38 build reference sequence (iRbase release 225). Next, the aligned reads were obtained with miRbase v22. Alignments and quantification were performed using Subread and Rsubread Packages.14,15  A multi-dimensional scaling (MDS) plot was used to analyse sample distribution according to miRs expression values. miRs with very low counts across all libraries provide little evidence for differential expression. Consequently, these miRs were filtered out prior to further analysis. Subsequently, trimmed mean of M-values (TMM) normalization method was used to eliminate composition biases between libraries.16 Specific dispersions per gene with a negative binomial distribution were also estimated.17,18
Four packages (edgeR, voom, limma-voom and deseq2) were used to analyse differential expression of miRs between patient and control samples. Functional analysis of target genes for statistically different miRs was performed by two different methodologies: ORA (over-representation analysis, FDR <0.05) and GSEA (Gene set enrichment analysis) implemented in clusterProfiler of R.19 Data analysed by GSEA was arranged by miRs Fold Change log values. The enrichment analysis was performed to obtain the significant KEGG pathways or GO terms in both methodologies.

source_name: plasma

extract_protocol:
Blood samples were collected from LGMD, DMD and FSHD patients and healthy participants in EDTA tubes. Each sample was centrifuged to separate plasma; then, a second centrifugation was performed at 16000g and 4 ºC for 10 minutes. Finally, plasma samples were stored at −80 ºC until RNA extraction. Cell-free total RNA (including miRs) was isolated from 400 µL of plasma using the miRNeasy Serum/Plasma kit (Qiagen, Hilden, Germany), following the manufacturer’s protocol. RNA was eluted with 25 µL of RNase-free water. The concentration of total cell-free RNA (including miRs) was quantified using NanoDrop™ One Microvolume UV-Vis Spectrophotometer (Thermo Scientific Inc, Waltham, MA, USA).
Small RNA libraries were generated and indexed using the Lexogen’s Small RNA-Seq Library Prep Kit for Illumina sequencing (Lexogen GmbH Campus Vienna Biocenter 5, 1030 Vienna, Austria). Briefly, for library generation 3‘-adapter was ligated to RNA and their excess removed by column purification. Next, 5’-adapter was ligated and the RNA, flanked by 5‘and 3’ adapters, was converted into cDNA. Library amplification was performed to add the complete adapter sequences necessary for the generation of clusters and to assure enough material for quality control and sequencing. External i7 indexes were added during this step to enable multiplexing of libraries for sequencing. The library product was then purified to remove interfering PCR components. Single-end sequencing was performed on Illumina NextSeq550 platform (Illumina, San Diego, CA, USA) on High Output 1x50pb RUN (NextSeq 500/550 High Output v2 75 cycles kit, FC-404-2005).

value: plasma

tag: disease state

value: LGMD


title: Patient10


title: Patient16


title: Patient1


title: DFZi_D2_RSA_trimmed


title: Patient8


title: sevCCC11 [methylation]


title: DGEI_D2_RSA_trimmed


title: Control10

value: healthy


title: Control12


title: Control5


title: modCCC48 [methylation]


title: sevCCC15 [methylation]


title: Control6


title: 36845_D2_vac_trimmed


title: Control7


title: modCCC47 [methylation]


title: MB13_D2_vac_trimmed


title: DH49_D2_vac_trimmed


title: DH26_D2_vac_trimmed


title: Control3


title: CMM12 cells, podoplanin KO#2

city: Tokyo

first: Masahiro

last: Shinada

address: Bunkyo-ku yayoi 1-1-1

country: Japan

institute: The University of Tokyo

data_processing:
Sequencing libraries were prepared with the NEBNext Ultra RNA LP Kit (Illumina). RNA-Seq was conducted using NovaSeq 6000 (Illumina)  and a minimum of 33 million read-pairs was generated for each sample.
Quality controls and adaptor trimmings of fastq files for each sample were performed by Novogene.
Trimmed fastq data were mapped to canine genomes (CanFam3.1) by STAR V.2.7.3a, and transcript abundance was estimated using RSEM V.1.3.3 with gene transfer file for Ensembl (CanFam3.1.98).
Gene expression was normalized by TPM.
Assembly: CanFam3.1
Supplementary files format and content: tab-delimited text files include raw count and TPM normalized values for each Sample

organism: Canis lupus familiaris

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
NEBNext Ultra RNA LP Kit

tag: cell line

value: canine melanoma

value: podoplanin KO


title: Patient6


title: modCCC45 [methylation]


title: modCCC46 [methylation]


title: modCCC44 [methylation]


title: CMM2 cells, podoplanin KO#1

tag: cell type


title: CMM2 cells, podoplanin KO#2


title: CMM12 cells, control

value: WT


title: CMM2 cells, control


title: Blood-healthy-rep39

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing:
GenomeStudio V2011.1
Processed data file matrix_norm.txt represents normalized Average Beta.  The R minfi package (version 1.40.0) was used for the normalization.

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from the whole blood samples using the QuickGene-610L with QuickGene DNA Whole Blood Kit according to standard instructions

tag: gender

value: Female

value: Healthy


title: Blood-healthy-rep38


title: modCCC43 [methylation]


title: modCCC42 [methylation]


title: D30

city: Livermore

first: Stephen

middle: Patrick

last: Wilson

address: 7000 East Ave

department: BBTD

institute: LLNL

library_source: transcriptomic single cell

data_processing:
Cellranger mkfastq to generate FASTQ.
Cellranger count to generate count matrix.
Assembly: mm10 (GRCm38)
Supplementary files format and content: Cell Ranger files: Gene list (features.tsv), cell barcodes (barcodes.tsv), and gene/barcode matrices (matrix.mtx) are provided for each experimental group.

source_name: Immune cells from the knee joints

extract_protocol:
Mice were euthanized and femur and tibia of injured and uninjured hindlimbs were dissected, and superficial tissue were thoroughly removed, taking care to maintain the integrity of the knee joint. Joint residing cells were liberated by first dissociating the two bones into 7.5 mL of 3% Collagenase 1 solution (Worthington Biochemical, Lakewood, NJ; CLS-1) and 100 µg/mL DNase I (Roche, Basel, Switzerland; 11284932001) in DMEM/F12 shaking at 37 °C for two 1-hour digests followed by PBS wash steps between digests. Cells released from the joint were filtered through a 70 μm nylon cell strainer prior to red blood cell (RBC) lysis using ammonium-chloride-potassium (ACK) lysis buffer (Thermo Fisher Scientific, Waltham, MA, USA; A1049201). Separation of immune cells was performed using CD45 conjugated magnetic microbeads followed by Miltenyi Biotech MACS separation with LC columns for CD45+ cell enrichment.
Both immune (CD45+) and non-immune (CD45-) cell populations were independently sequenced using a Chromium Single Cell 3' Reagent Kit and Chromium instrument (10X Genomics, Pleasanton, CA). Library preparation was performed according to manufacturer’s protocol.

treatment_protocol: 10-week-old C57Bl/6J (BL6) mice (purchased from Jackson Laboratory Bar Harbor, ME, USA; Stock No: 000664) were subjected to anterior cruciate ligament injury using a non-invasive single dynamic tibial compressive overload model.

tag: condition

value: Injured joints

value: Day 30

value: Knee joints

value: CD45+ cells


title: Non-immune

source_name: Non-immune cells from the knee joint

value: Uninjured joints

value: Day 0

value: CD45- cells


title: D15

value: Day 15


title: modCCC41 [methylation]

source_name: Blood

value: chronic chagasic cardiomyopathy sample

value: Blood


title: Blood-healthy-rep36

tag: age


title: CMM12 cells, podoplanin KO#1


title: Blood-healthy-rep40


title: D3

value: Day 3


title: D7

value: Day 7


title: D1

value: Day 1


title: KO_Uninjured 3

data_processing:
Sequence reads were aligned against Mus musculus reference genome (mm10) using STAR. After read alignment, the number of read counts per gene locus was summarized with ‘featureCounts’ from Rsubread package using mm10 gene annotation. Read counts were subsequently normalized using TMM normalization from edgeR.
Assembly: mm10 (GRCm38)
Supplementary files format and content: normCounts.txt: Tab-delimited text file includes TMM normalized CPM values for each Sample.

source_name: Cells from knee joints

extract_protocol:
Control and T1DM mice were euthanized at 16 weeks old. Knee joints were collected, dissected and cut at the edges of the joint region with small traces of soft tissue to preserve the articular integrity. Joints were then homogenized in Qiazol (79306, Qiagen, Valencia, CA, USA) using a PRO tissue homogenizer (Bio-Gen PRO 200, PRO Scientific Inc.). Total RNA was purified using RNeasy Mini Kit (QIAGEN Inc., Germantown, MD, USA) according to the manufacturer’s protocol and the RNA integrity was assessed using a bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Poly(A)+-enriched cDNA libraries were generated using the Illumina TruSeq RNA Library Prep kit v2 (Illumina Inc., Hayward, CA, USA).

treatment_protocol: 10-week-old C57BL/6 mice and Trem2 KO mice (purchased from Jackson Laboratory, Bar Harbor, ME, USA) were subjected to anterior cruciate ligament injury using a non-invasive single dynamic tibial compressive overload model.

value: Trem2 KO

value: 16 weeks

value: Uninjured


title: Blood-healthy-rep35

value: Male

value: Healthy


title: KO_Uninjured 4


title: Blood-healthy-rep34

value: Female


title: modCCC39 [methylation]


title: modCCC38 [methylation]


title: Blood-healthy-rep37


title: KO_Uninjured 2

value: Knee joints


title: modCCC37 [methylation]


title: KO_Injured 3

value: Injured


title: KO_Uninjured 1


title: KO_Injured 4


title: modCCC36 [methylation]


title: KO_Injured 2


title: WT_Uninjured 4

value: Wildtype


title: modCCC35 [methylation]


title: D0

value: Uninjured joints

value: Day 0

value: CD45+ cells


title: WT_Uninjured 3


title: Blood-healthy-rep31


title: Blood-healthy-rep30


title: WT_Uninjured 2


title: modCCC40 [methylation]

value: chronic chagasic cardiomyopathy sample


title: modCCC34 [methylation]

value: Blood


title: modCCC33 [methylation]


title: WT_Uninjured 1


title: Blood-healthy-rep29


title: Blood-healthy-rep33


title: WT_Injured_4


title: WT_Injured_3


title: WT_Injured_2


title: Blood-healthy-rep27


title: modCCC32 [methylation]


title: Blood-healthy-rep28


title: Fmr1-KO-N4

city: Philadelphia

first: Erica

last: Korb

state: PENNSYLVANIA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

data_processing:
Fastq files were aligned by Salmon
DESeq2 was used for differential gene expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2 output

source_name: Cortical tissue

extract_protocol:
Qiagen RNA extraction kits were used to isolate RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

value: C57B6 strain

tag: infection

value: Fmr1 KO

tag: sample type

value: Tissue harvested at 5-7 weeks


title: Blood-healthy-rep32


title: Blood-healthy-rep26


title: WT_Injured_1

tag: genotype


title: KO_Injured 1

value: Trem2 KO


title: Fmr1-KO-N2


title: Fmr1-KO-N3


title: modCCC31 [methylation]


title: modCCC30 [methylation]


title: modCCC29 [methylation]


title: Blood-healthy-rep25


title: Fmr1-WT-N4

value: WT


title: Fmr1-WT-N2


title: Fmr1-WT-N3


title: modCCC28 [methylation]


title: modCCC27 [methylation]


title: Fmr1-WT-N1


title: Blood-healthy-rep23


title: modCCC26 [methylation]


title: Male_Pollen_S5_R2

city: Urbana

first: Dessiree

middle: Patricia

last: Zerpa Catanho

state: Illinois

address: 1201 W. Gregory Dr, 279 ERML

institute: University of Illinois at Urbana-Champaign

data_processing:
Raw read quality was analyzed using FastQC (Version 0.11.5).
Adapters and low-quality reads were removed using Trimmomatic (Version 0.36).
Clean paired reads were aligned to a reference containing both the MSY and the X pseudomolecules using Hisat2 (Version 2.0.5).
SAM files were converted to BAM files using samtools (Version 1.3.1).
BAM files were used to count reads aligned to the X and Y alleles using featureCounts (Version 1.5.2). Reads aligned to exons were counted and summarized per gene ID.
Assembly: Fasta file containing the "X_pseudomolecule-5.4M-091211.fasta" and "MaleY_reassembly_pseudomolecule_6-29-12.fasta" sequences for Carica papaya.
Supplementary files format and content: .txt' files containing read counts for each gene.

organism: Carica papaya

source_name: Pollen of mature male flower bud (size 15-20 mm)

extract_protocol:
Total RNA extraction
Illumina

tag: Sex


title: Male_Pollen_S5_R3

tag: tissue

value: Pollen of mature male flower bud (size 15-20 mm)


title: No_infection_N3

source_name: Primary cultured cortical neurons

value: Neurons harvested at e16.5

value: Infected at 5 DIV

value: RNA isolated at 10 DIV


title: Fmr1-KO-N1


title: No_infection_N2


title: Male_Pollen_S5_R1

value: Male


title: Blood-healthy-rep21

value: Healthy


title: modCCC24 [methylation]


title: Blood-healthy-rep20

value: Female


title: Blood-healthy-rep22


title: Blood-healthy-rep19


title: modCCC25 [methylation]


title: Blood-healthy-rep24


title: No_infection_N1


title: Male_Stamen_S5_R2

source_name: Stamens of mature male flower bud (size 15-20 mm)


title: Blood-healthy-rep18


title: Luciferase_N3


title: Luciferase_N2


title: modCCC23 [methylation]


title: Male_Stamen_S5_R1

value: Stamens of mature male flower bud (size 15-20 mm)


title: Luciferase_N1


title: Male_Stamen_S4_R3

source_name: Stamens of post-meiotic male flower bud (size 7-12 mm)


title: Blood-healthy-rep17


title: modCCC21 [methylation]


title: Blood-healthy-rep16


title: Male_Stamen_S5_R3


title: Nsd1_sh5_N3


title: Nsd1_sh5_N2


title: modCCC20 [methylation]


title: Blood-healthy-rep15


title: Male_Stamen_S3_R3

source_name: Stamens of pre-meiotic male flower bud (size 4.5-6.5 mm)


title: Male_Stamen_S4_R1

value: Stamens of post-meiotic male flower bud (size 7-12 mm)


title: modCCC19 [methylation]


title: Male_Stamen_S3_R2

value: Stamens of pre-meiotic male flower bud (size 4.5-6.5 mm)


title: modCCC17 [methylation]

value: chronic chagasic cardiomyopathy sample


title: Ehmt1_sh2_N3


title: Nsd1_sh5_N1


title: Male_Stamen_S3_R1


title: modCCC18 [methylation]

value: Blood


title: Blood-healthy-rep14


title: modCCC16 [methylation]


title: modCCC22 [methylation]


title: Ehmt1_sh2_N2


title: Blood-healthy-rep12


title: Blood-healthy-rep13


title: Blood-healthy-rep11


title: modCCC15 [methylation]


title: Male_Stamen_S2_R2

source_name: Stamens of pre-meiotic male flower bud (size 2-4.5 mm)


title: Male_Stamen_S4_R2


title: Ehmt1_sh2_N1


title: Crebbp_sh5_N3


title: modCCC14 [methylation]


title: Male_Stamen_S2_R1

value: Stamens of pre-meiotic male flower bud (size 2-4.5 mm)


title: Blood-healthy-rep9


title: Crebbp_sh5_N2


title: Blood-healthy-rep8


title: Male_Stamen_S1_R3

source_name: Stamens of pre-meiotic male flower bud (size 1-1.5 mm)


title: Crebbp_sh5_N1


title: Male_Stamen_S1_R2

value: Stamens of pre-meiotic male flower bud (size 1-1.5 mm)


title: Blood-healthy-rep7


title: modCCC11 [methylation]


title: Chd8_sh5_N2


title: Male_Pistillode_S5_R3

source_name: Pistillode of mature male flower bud (size 15-20 mm)


title: Blood-healthy-rep10


title: Chd8_sh5_N3


title: Blood-healthy-rep5


title: modCCC12 [methylation]


title: Male_Stamen_S1_R1


title: modCCC13 [methylation]


title: modCCC9 [methylation]


title: Blood-healthy-rep6


title: modCCC8 [methylation]


title: Male_Pistillode_S5_R2

value: Pistillode of mature male flower bud (size 15-20 mm)


title: Ash1l_sh5_N3


title: Blood-healthy-rep3


title: Blood-healthy-rep4


title: Male_Pistillode_S5_R1


title: modCCC7 [methylation]


title: Male_Pistillode_S4_R3

source_name: Pistillode of post-meiotic male flower bud (size 7-12 mm)


title: Blood-healthy-rep2


title: modCCC10 [methylation]


title: modCCC6 [methylation]


title: Ash1l_sh5_N1


title: Chd8_sh5_N1


title: Male_Pistillode_S4_R2

value: Pistillode of post-meiotic male flower bud (size 7-12 mm)


title: Blood-healthy-rep1


title: Male_Stamen_S2_R3


title: Male_Pistillode_S4_R1


title: Male_Pistillode_S3_R2

source_name: Pistillode of pre-meiotic male flower bud (size 4.5-6.5 mm)


title: Blood-major depressive disorder-rep39

value: Major depressive disorder


title: Blood-major depressive disorder-rep38


title: Male_Pistillode_S2_R2

source_name: Pistillode of pre-meiotic male flower bud (size 2-4.5 mm)


title: modCCC4 [methylation]


title: modCCC5 [methylation]


title: Ash1l_sh5_N2


title: modCCC2 [methylation]


title: modCCC3 [methylation]


title: MLE12 cell line, Troy_24h

first: De'Broski

last: Herbert

state: PA

address: 3900 Spruce Street

department: Pathobiology

data_processing:
Fastq files were trimmed with trimmomatic version 0.39, to remove Truseq universal and indexed adapter sequences, and low quality reads
trimmed fastq files were aligned to version 81 of mouse reference genome GRCm38 using the STAR aligner
Sorted BAM files resulting from the alignments were quantified to genes using htseq-count, using the union mode for read overlap resolution
Count data was filtered to remove genes with less than 5 counts, normalized using the trimmed mean of m-values calculation in the EdgeR package in R, and then RPKM values were calculated from normalized data using the EdgeR package in R.
Genome_build: version 81 of mouse reference genome GRCm38
Supplementary_files_format_and_content: the tab-delimited text file includes un-normalized counts for each sample, and csv file contains Reads Per Kilobase of transcript per Million  (RPKM) values for each sample, and Log2FoldChange values.

source_name: MLE12 cell line

growth_protocol: Mouse immortalized cell line MLE12 cells were grown to a monolayer

extract_protocol:
Cell pellets were lysed and RNA was extracted using the Qiagen RNAeasy plus kit
Libraries were prepared using the Illumina Truseq mRNA prep kit

treatment_protocol: Cells grown to a monolayer were scratched with a pipet tip, or un scratched, and collected 24 hours later

value: TROY KO

tag: treatment

value: 24 hours post scratch


title: Male_Pistillode_S2_R1

value: Pistillode of pre-meiotic male flower bud (size 2-4.5 mm)


title: Blood-major depressive disorder-rep37


title: Male_Pistillode_S3_R1

value: Pistillode of pre-meiotic male flower bud (size 4.5-6.5 mm)


title: MLE12 cell line, Lingo2_24h

value: Lingo2 KO


title: MLE12 cell line, Lingo1_24h

value: Lingo1 KO


title: CTRL55 [methylation]

value: non-chagasic control


title: MLE12 cell line, WT_24h

value: wild-type


title: MLE12 cell line, WT_NS

value: un-scratched


title: Blood-major depressive disorder-rep36

value: Male


title: Colon epithelial cell fraction, Lingo2_rep3

data_processing:
Fastq files were trimmed with trimmomatic version 0.39, to remove Truseq universal and indexed adapter sequences, and low quality reads
trimmed fastq files were aligned to version 81 of mouse reference genome GRCm38 using the STAR aligner
Sorted BAM files resulting from the alignments were quantified to genes using htseq-count, using the union mode for read overlap resolution
Genes with group average counts of less than 5 were removed from the dataset in R, and expression count data was normalized using DESeq2 in R
Genome_build: GRCm38 version 81
Supplementary_files_format_and_content: tab delimited text files include read counts from htseq-count, and normalized expression values, and statistical output from DESeq2

source_name: Colon epithelial cell fraction

growth_protocol: Colon tissue was harvested, and epithelial cells were washed off in a EDTA DTT wash, and RNA was isolated within 1 hour of tissue harvesting

extract_protocol:
total RNA was isolated with the Qiagen RNAeasy plus kit, RNA yield was determined by Qubit fluorometer, and RNA quality was determined with TapeStation
libraries were prepared using the TruSeq Stranded Total RNA LT Kit with Ribo-Zero Gold, according to the manufacturer’s instructions.

treatment_protocol: Mice were grown under niave conditions

value: Colon

value: Epithelial cells obtained by EDTA wash

value: 2 months


title: Blood-major depressive disorder-rep35

value: Female

value: Blood


title: Male_Pistillode_S1_R3

source_name: Pistillode of pre-meiotic male flower bud (size 1-1.5 mm)


title: CTRL54 [methylation]

source_name: Blood


title: Blood-major depressive disorder-rep40


title: Male_Pistillode_S1_R2

value: Pistillode of pre-meiotic male flower bud (size 1-1.5 mm)


title: MLE12 cell line, Lingo3_24h

value: Lingo3 KO


title: Colon epithelial cell fraction, Lingo2_rep2


title: CTRL53 [methylation]


title: modCCC1 [methylation]

value: chronic chagasic cardiomyopathy sample


title: Blood-major depressive disorder-rep33

value: Major depressive disorder


title: Blood-major depressive disorder-rep32


title: Blood-major depressive disorder-rep31


title: Male_Bud_S0_R3

source_name: Male flower bud (size < 1 mm)

value: Male flower bud (size < 1 mm)


title: Colon epithelial cell fraction, WT_rep2

value: wild type


title: Colon epithelial cell fraction, Lingo2_rep1


title: Colon epithelial cell fraction, WT_rep3


title: CTRL51 [methylation]


title: CTRL50 [methylation]


title: Blood-major depressive disorder-rep30


title: Male_Bud_S0_R1


title: Male_Bud_S0_R2


title: Female_Ovule_S5_R3

source_name: Ovules of mature female flower bud (size 15-20 mm)


title: Colon epithelial cell fraction, WT_rep1


title: Blood-major depressive disorder-rep29


title: CTRL49 [methylation]


title: Combination_rep3

city: COLUMBIA

first: HAO

last: JI

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

data_processing:
Indexed sequences were checked by FastQC | version: 0.11.5
Trimed adapter by TrimGalore-0.4.5
Reads were mapped to the hg38 reference genome using STAR | version 2.4 with default parameters (generation of sam files)
Convert .sam files to .bam files using samtools | version: 1.2 with parameters -bh -F 3840 -q 255
Read counts over annotated genes were obtained using featureCount (subreads | version: 1.4.6) with parameters -p -T 10
Genome_build: GRCh38.77
Supplementary_files_format_and_content: tab-delimited text files include gene counts for each sample

source_name: HCC1954 cell line

growth_protocol: HCC1954 cells were cultured in RPMI1640 + 10% FBS + 1% pen/strep/Glutamine

extract_protocol:
Qiagen Rneasy mini kit
Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit(NEB#E7490/NEB#E7760)

treatment_protocol: DMSO, 1 µM of SNXB, 1 µM of Lapatinib, and Combination for 24 hours, with three biological repeats


title: Blood-major depressive disorder-rep34


title: Blood-major depressive disorder-rep28


title: CTRL48 [methylation]

extract_protocol: Tissue : DNAs, extracted from whole tissue, were bisulfite converted and amplified with elongation of primers with EZ DNA methylation kit (ZymoResearch, Saint Marcel, France). Amplified DNAs were fragmented and hybridized in beads (Infinium Human Methylation EPIC Bead Chip, Illumina, San Diego, California). Blood : Blood (5 to 15 ml of blood)  was  collected in EDTA tubes. Genomic DNA was isolated on a silica-membrane according to the manufacturer’s protocol (QIAamp DNA Blood Max Kit, Qiagen, Hilden, Germany). Amplified DNAs were fragmented and hybridized in beads (Infinium Human Methylation EPIC Bead Chip, Illumina, San Diego, California).


title: Lapatinib_rep3


title: CTRL47 [methylation]


title: Male_Pistillode_S1_R1


title: SNXB_rep3


title: CTRL46 [methylation]


title: Female_Pistil_S5_R3

source_name: Pistil of mature female flower bud (size 15-20 mm)


title: Blood-major depressive disorder-rep27


title: CTRL52 [methylation]


title: CTRL45 [methylation]


title: DMSO_rep3


title: Blood-major depressive disorder-rep25


title: Blood-major depressive disorder-rep26


title: Female_Pistil_S5_R2

value: Pistil of mature female flower bud (size 15-20 mm)


title: CTRL43 [methylation]


title: Blood-major depressive disorder-rep23


title: Female_Ovule_S5_R2

value: Ovules of mature female flower bud (size 15-20 mm)


title: Blood-major depressive disorder-rep24


title: Female_Pistil_S5_R1


title: Combination_rep2


title: CTRL42 [methylation]

value: non-chagasic control


title: CTRL44 [methylation]


title: Female_Pistil_S4_R3

source_name: Pistil of post-meiotic female flower bud (size 7-12 mm)


title: SNXB_rep2


title: Female_Pistil_S4_R2

value: Pistil of post-meiotic female flower bud (size 7-12 mm)


title: CTRL41 [methylation]


title: Lapatinib_rep2


title: Combination_rep1


title: Female_Pistil_S4_R1


title: DMSO_rep2


title: Blood-major depressive disorder-rep20


title: Blood-major depressive disorder-rep22


title: Female_Ovule_S5_R1


title: Blood-major depressive disorder-rep21


title: Female_Pistil_S3_R3

source_name: Pistil of pre-meiotic female flower bud (size 4.5-6.5 mm)


title: CTRL40 [methylation]


title: Lapatinib_rep1


title: Blood-major depressive disorder-rep19


title: CTRL39 [methylation]


title: SNXB_rep1


title: Female_Pistil_S3_R2

value: Pistil of pre-meiotic female flower bud (size 4.5-6.5 mm)


title: CTRL38 [methylation]


title: Female_Pistil_S3_R1


title: Blood-major depressive disorder-rep18


title: CTRL37 [methylation]


title: DMSO_rep1


title: HA_EC_3 (RNASeq)

city: Singapore

first: Benjamin

last: Ng

address: 8 College Road

institute: Duke-National University of Singapore Medical School

data_processing:
Sequenced libraries were demultiplexed using bcl2fastq v2.19.0.316 with the --no-lane-splitting option
Adapter sequences were then trimmed using trimmomatic6 v0.36 in paired end mode with the options MAXINFO:35:0.5 MINLEN:35. For reference, the adapter sequences are:  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA (read 1) and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT (read 2)
Trimmed reads were aligned using STAR v. 2.2.1 with the options --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 in paired end, single pass mode. to human genome hg38 using the combined transcript models from Ensembl and FANTOM5.
Only unique alignments were retained for counting. Counts were calculated at the gene level using the FeatureCounts module from subread v. 1.5.1, with the options -t CDS -g gene_id -O -s 2 -J -T 8 -R -G Homo_sapiens.GRCh38.dna.primary_assembly.fa -a ensemble_hg38_fCAT_V3.gtf.
Genome_build: Homo sapiens hg38 Ensembl release 92
Supplementary_files_format_and_content: Gene-level counts calculated by FeatureCounts (.txt)

source_name: untreated human coronary artery endothelial cells

growth_protocol: Fibroblasts, hepatocytes, hESCs and endothelial cells were grown to 90% confluence in a 10cm culture dish, while vascular smooth muscle cells (VSMC) were pooled from 5 wells of a 6-well culture plate at baseline conditions in basal M231 medium (M-231-500) for 24h, and pelleted before snap-freezing in liquid nitrogen and stored at -80°C prior to lysis for Ribo-Seq.

extract_protocol:
Total RNA was extracted from either HSCs or HLFs using Trizol (Invitrogen) followed by Purelink RNA mini kit (Invitrogen) purification.
Illumina Truseq Stranded mRNA (Poly A selection) kit

treatment_protocol: Cells were either untreated, treated with TGF-beta with or without anti-IL11 or anti-IgG antibody or IL-11 alone as described above

value: untreated

tag: fraction

value: polyA mRNA


title: CTRL36 [methylation]

data_processing:
Analysis of DNA methylation data was performed with the R ChAMP package. Probe with a detection P value <= 0.01 and with a beadcount less than 3 have been discarded. The beta values were normalized with the BMIQ method, and the batch effect was corrected with the ComBat method.
normalized data: Average Beta


title: Female_Pistil_S2_R3

source_name: Pistil of pre-meiotic female flower bud (size 2-4.5 mm)


title: CTRL35 [methylation]


title: CTRL34 [methylation]


title: Blood-major depressive disorder-rep15

value: Male


title: Blood-major depressive disorder-rep17


title: Blood-major depressive disorder-rep13


title: Blood-major depressive disorder-rep16


title: Female_Pistil_S2_R1

value: Pistil of pre-meiotic female flower bud (size 2-4.5 mm)


title: Female_Pistil_S2_R2

value: Female


title: HA_EC_5 (RNASeq)

value: untreated human coronary artery endothelial cells


title: Female_Pistil_S1_R3

source_name: Pistil of pre-meiotic female flower bud (size 1-1.5 mm)


title: HA_EC_4 (RNASeq)


title: Blood-major depressive disorder-rep14

value: Blood


title: CTRL32 [methylation]


title: Female_Pistil_S1_R2

value: Pistil of pre-meiotic female flower bud (size 1-1.5 mm)


title: HA_EC_2 (RNASeq)


title: Female_Bud_S0_R3

source_name: Female flower bud (size < 1 mm)

value: Female flower bud (size < 1 mm)


title: Female_Pistil_S1_R1


title: Blood-major depressive disorder-rep12

value: Major depressive disorder


title: CTRL31 [methylation]


title: HA_EC_1 (RNASeq)


title: HA_EC_6 (RNASeq)


title: Blood-major depressive disorder-rep11


title: 2-D08+SARS-CoV-2 24 h rep3

city: guangzhou

first: shi

middle: jun

last: jie

institute: sysu

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the human genome (hg38) using Hisat2
The gene expression level was calculated by using  featureCounts.
Fold-change (FC) and p-values were calculated with DEseq2
Genome_build: hg38
Supplementary_files_format_and_content: Csv file containing reads count.

growth_protocol: Calu-3 cells were cultured in MEM (Gibco) with 1% NEAA (Gibco), 1% sodium pyruvate (Gibco) and 10% (vol/vol) fetal bovine serum (Gibco). Cells were either mock-infected or infected with SARS-CoV-2 (Accession number: MT123290),virus was allowed to adsorb at 37 °C for 1 hr with gentle rocking every 15 min before incubation at 37 °C for indicated time points. Cells were infected at different MOI and time points as indicated.

extract_protocol:
Total RNA was harvested using Trizol reagent.
Total RNA was isolated from cells using TRIzol reagent (Invitrogen), and sequencing was performed by Sangon Biotech. Sample quality was assessed using a Bioanalyzer (Agilent 2100 Bioanalyzer). RNA-seq libraries of polyadenylated RNA were prepared using mRNA-seq V2 Library Prep Kit and sequenced on MGISEQ-2000 platform.

treatment_protocol: Calu-3 cells were infected with SARS-CoV-2 (MOI = 0.5) together with or without 2-D08 (100 μM) treatment for 24 h.

value: SARS-CoV-2 24h


title: CTRL30 [methylation]


title: CTRL29 [methylation]


title: Female_Bud_S0_R2


title: Female_Bud_S0_R1


title: 2-D08+SARS-CoV-2 24 h rep2


title: Blood-major depressive disorder-rep9


title: CTRL33 [methylation]


title: 2-D08+SARS-CoV-2 24 h rep1


title: 2-D08 rep3

value: Mock


title: H3K4me3_GM12878

city: Berkeley

first: Aaron

last: Streets

address: Stanley Hall

institute: University of California, Berkeley

data_processing:
Megalodon (v2.3.1), Guppy (v4.5.4), using a Rerio res_dna_r941_min_modbases-all-context_v001.cfg basecalling model
fast5s were aligned and modified bases were called using Megalodon (2.3.1 or 2.3.4) using  the rerio all-context basecalling model (res_dna_r941_min_modbases-all-context_v001.cfg) with parameters --outputs mod_mappings and --mod-min-prob 0
Assembly: CHM13v1.1 reference genome or dm6
Supplementary files format and content: bam files with alignment and modification basecalling info
Library strategy: DiMeLo-seq

growth_protocol:
Cells grown in RPMI-1640 with 15% FBS, 1% penn/strep at 37C with 5% CO2
Human cells grown in RPMI with 15% FBS, 1% penn/strep at 37C with 5% CO2

extract_protocol:
NEB Monarch genomic DNA extraction kit (T3010S)
Oxford Nanopore sequencing libraries were generated with SQK-LSK110

tag: antibody

value: rabbit anti H3K4me3 (Active Motif 39916)


title: CTRL27 [methylation]

tag: group


title: CTRL26 [methylation]


title: Blood-major depressive disorder-rep7


title: 2-D08 rep2


title: Blood-major depressive disorder-rep10


title: H3K27ac_GM12878

value: rabbit anti H3K27ac (Active Motif 39133)


title: Blood-major depressive disorder-rep5


title: S2_WC_RNAseq_n2_(210820_NK_dm_869)

first: Jorja

last: Henikoff

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: RNA-seq in S2 cells, whole cell, replicate 2

data_processing: 1. We used trim-galore 0.6.4_dev with parameters "-q 20 --length 20" to trim adapters from 50bp single-end reads. 2. We used hisat2 2.1.0 with parameters "--max-intronlen 5000" to map the trimmed reads to the reference sequence for Drosophilia melanogaster, dm6 from UCSC. 3. We used deepTools 3.3.1 bedCoverage to with parameters "--normalizeUsing CPM" to make bigwig files (Supplementary file .bw).

source_name: RNA-seq

value: none cell type:S2 cell line


title: 2-D08 rep1


title: CTRL24 [methylation]

first: Pauline

last: Brochet

value: non-chagasic control


title: S2_RTnTag_noHS_m6A_n2_(211004_NK_dm_1054)

description: RT&Tag for m6A in S2 cell, no heat shock, replicate 2

source_name: RT&Tag

value: m6A Megabase cat# AP60500

value: S2 cell line

value: no heat shock


title: Blood-major depressive disorder-rep3


title: CTRL23 [methylation]


title: Blood-major depressive disorder-rep8

value: Male


title: Mock+SARS-CoV-2 24 h rep2


title: Blood-major depressive disorder-rep4


title: S2_RTnTag_noHS_m6A_n1_(211004_NK_dm_991)

description: RT&Tag for m6A in S2 cell, no heat shock, replicate 1


title: S2_RTnTag_noHS_IgG_n2_(211004_NK_dm_1053)

description: RT&Tag for IgG in S2 cell, no heat shock, replicate 2

value: IgG Abcam cat# ab172730


title: CTRL25 [methylation]


title: Blood-major depressive disorder-rep2


title: CTRL22 [methylation]


title: CTRL28 [methylation]


title: S2_RTnTag_noHS_IgG_n1_(211004_NK_dm_990)

description: RT&Tag for IgG in S2 cell, no heat shock, replicate 1


title: Mock rep3


title: CTRL20 [methylation]


title: CTRL19 [methylation]


title: S2_RTnTag_MSL2_n4_(211004_NK_dm_1048)

description: RT&Tag for MSL2 in S2 cells, replicate 4

value: MSL2 gift from Mitzi Kuroda


title: Mock rep2


title: CTRL21 [methylation]


title: Mock rep1


title: S2_RTnTag_MSL2_n3_(211004_NK_dm_1025)

description: RT&Tag for MSL2 in S2 cells, replicate 3


title: S2_RTnTag_MSL2_n2_(210820_NK_dm_908)

description: RT&Tag for MSL2 in S2 cells, replicate 2


title: CTRL17 [methylation]


title: Mock+SARS-CoV-2 24 h rep1


title: S2_RTnTag_MSL2_n1_(210820_NK_dm_888)

description: RT&Tag for MSL2 in S2 cells, replicate 1


title: HPDLC-3S

city: Fukuoka

first: Risa

last: Sugiura

address: 3-1-1, Maidashi, Higashi-ku

institute: Kyushu University

description:
23-year-old male
S2

data_processing:
Sequenced reads were mapped to hg19 using BWA. Unmapped reads are then mapped to hg19 whole genome using HiSAT2 with the parameters set as default, to map the reads that covers at least a part of exon2 as well as exon1.
TSS clustering and tags per million reads (TPM) were calculated using CAGEr (Nucleic Acids Res. 2015 Apr 30;43(8)).
Assembly: hg19
Supplementary files format and content: tab-delimited text files include CPM values for each sample.

source_name: periodontal ligament

extract_protocol:
RNA was isolated from each cells using TRIzol Reagent (Invitrogen, Carlsbad, CA).
Cap analysis of gene expression (CAGE) allows genome-wide analysis of gene transcription start sites and quantitative study of RNA transcribed from them by DNAFORM (Yokohama, Kanagawa, Japan). In brief, RNA quality was assessed with a Bioanalyzer (Agilent, Santa Clara, CA) to ensure that the RNA integrity number was over 7.0, and A260/280 and 260/230 ratios were over 1.7. First-strand cDNAs were transcribed to the 5ʹ end of capped RNAs and attached to CAGE “barcode” tags, which upon sequencing were mapped to the mouse mm9 genomes using BWA software (v0.5.9) after discarding ribosomal or non-A/C/G/T base-containing RNAs. For tag clustering, CAGE-tag 5ʹ coordinates were input for CAGEr clustering using 20 bases as a maximal allowed distance between two neighboring tags and a minimum counts per million (CPM) value of 2 (Haberle et al., Nucleic Acids Research 2015 43:e51).

value: periodontal ligament

value: periodontal ligament cell

value: male


title: HPDLC-3U

description:
25-year-old female
S3

value: female


title: Blood-major depressive disorder-rep1

first: Zijing

last: Liu

value: Major depressive disorder

value: Blood


title: HDF

description:
26-year-old female
S1

source_name: dermal

value: dermal

value: dermal fibroblasts


title: S2_RTnTag_METTL3RNAi_m6A_n1_(211004_NK_dm_1069)

city: Seattle

description: RT&Tag for m6A in S2 cells treated with METTL3 RNAi, replicate 1

value: METTL3 RNAi


title: CTRL15 [methylation]

address: 13288 MARSEILLE cedex 09


title: S2_RTnTag_METTL3RNAi_IgG_n1_(211004_NK_dm_1068)

description: RT&Tag for IgG control in S2 cells treated with METTL3 RNAi, replicate 1


title: VSMC_6 (RNASeq)

source_name: untreated normal human vascular smooth muscle cells

value: vascular smooth muscle cells

value: untreated

value: polyA mRNA


title: CTRL14 [methylation]

value: non-chagasic control


title: VSMC_3 (RNASeq)


title: CTRL13 [methylation]


title: S2_RTnTag_m6A_n2_(210820_NK_dm_889)

description: RT&Tag for m6A in S2 cells, replicate 2

value: m6A Megabase cat# AP60500

value: S2 cell line


title: CTRL12 [methylation]


title: VSMC_2 (RNASeq)


title: CTRL16 [methylation]


title: Mock+SARS-CoV-2 24 h rep3

value: Mock

value: SARS-CoV-2 24h


title: CTRL11 [methylation]


title: Blood-major depressive disorder-rep6

value: Female


title: VSMC_1 (RNASeq)


title: S2_RTnTag_m6A_IgGcontrol_n1_(211227_NK_dm_1177)

description: RT&Tag for IgG control in S2 cells, replicate 1

value: IgG Abcam cat# ab172730


title: CTRL18 [methylation]


title: VSMC_5 (RNASeq)


title: CTRL10 [methylation]


title: HUVEC_3 (RNASeq)

source_name: untreated normal human umbilical vein endothelial cells

value: umbilical vein endothelial cells


title: S2_RTnTag_m6A_n3_(210820_NK_dm_909)

description: RT&Tag for m6A in S2 cells, replicate 3


title: S2_RTnTag_Ime4RNAi_m6A_n2_(211227_NK_dm_1164)

description: RT&Tag for m6A in S2 cells treated with METTL3 RNAi, replicate 2


title: H3K27me3_GM12878

value: rabbit anti H3K27me3 (Active Motif 39055)


title: HUVEC_2 (RNASeq)


title: S2_RTnTag_Ime4RNAi_IgG_n2_(211227_NK_dm_1163)

description: RT&Tag for IgG control in S2 cells treated with METTL3 RNAi, replicate 2


title: Post-intervention monocyte genomic DNA methylation for participant 30-15

city: Honolulu

first: Christian

middle: Ka'ikekuponoaloha

last: Dye

state: HI

address: 641 Ilalo St. BSB 222K

department: Native Hawaiian Health

institute: University of Hawaii at Manoa

description: Diabetic participant total monocytes

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450 BeadChip using standard Illumina procedures.

scan_protocol: Imaging was performed using Illumina iScan using recommended settings

data_processing: Raw IDAT files were processed using RnBeads version 0.99.18 in R studio (3.1.2)

extract_protocol: Peripheral blood mononuclear cells were subjected to magnetic bead enrichment via negative selection for CD14+ (without CD16 depletion) to enrich for monocytes. Monocytes were isolated for genomic DNA using Qiagen AllPrep DNA/RNA Universal Kit following stanard protocols

tag: participant

value: Male

tag: ethnicity

value: Native Hawaiian

tag: disease status

value: Diabetic

value: Monocyte


title: HUVEC_1 (RNASeq)


title: CTRL9 [methylation]

city: Marseille

source_name: Blood

value: Blood


title: CTRL8 [methylation]


title: S2_RTnTag_IgG_n5_(211004_NK_dm_1014)

description: RT&Tag for IgG control in S2 cells, replicate 5


title: Hepatocytes_1 (RNASeq)

source_name: untreated normal human hepatocytes

value: hepatocytes


title: sevCCC8 [methylation]

description: DNAs, extracted from whole tissue, were bisulfite converted and amplified with elongation of primers with EZ DNA methylation kit (ZymoResearch, Saint Marcel, France). Amplified DNAs were fragmented and hybridized in beads (Infinium Human Methylation EPIC Bead Chip, Illumina, San Diego, California).

source_name: Heart

value: chronic chagasic cardiomyopathy

value: Left ventricular wall


title: Post-intervention monocyte genomic DNA methylation for participant 30-14

description: Diabetic participant total monocytes


title: S2_RTnTag_IgG_n4_(211004_NK_dm_1045)

description: RT&Tag for IgG control in S2 cells, replicate 4


title: Hepatocytes_3 (RNASeq)

value: untreated

value: polyA mRNA


title: sevCCC7 [methylation]


title: Post-intervention monocyte genomic DNA methylation for participant 30-05

description: Diabetic participant total monocytes


title: Post-intervention monocyte genomic DNA methylation for participant 30-12

description: Diabetic participant total monocytes


title: sevCCC6 [methylation]


title: S2_RTnTag_IgG_n2_(210820_NK_dm_907)

description: RT&Tag for IgG control in S2 cells, replicate 2

value: S2 cell line


title: Monocyte genomic DNA methylation from lab donor 1

description: Non-diabetic lab donor total monocytes

value: Unknown

value: Non-diabetic


title: S2_RTnTag_IgG_n3_(211004_NK_dm_1022)

description: RT&Tag for IgG control in S2 cells, replicate 3


title: sevCCC5 [methylation]


title: Post-intervention monocyte genomic DNA methylation for participant 30-03

description: Diabetic participant total monocytes


title: S2_RTnTag_IgG_n1_(210820_NK_dm_887)


title: sevCCC4 [methylation]


title: HCAEC_1 (RNASeq)

value: untreated human coronary artery endothelial cells


title: S2_RTnTag_m6A_n1_(211227_NK_dm_1178)

description: RT&Tag for m6A in S2 cells, replicate 1

value: m6A Megabase cat# AP60500


title: S2_RTnTag_HS_m6A_n2_(211004_NK_dm_1057)

description: RT&Tag for m6A in S2 cell, heat shock, replicate 2

value: heat shock


title: Monocyte genomic DNA methylation from lab donor 2

description: Non-diabetic lab donor total monocytes


title: HCAEC_2 (RNASeq)


title: S2_RTnTag_HS_m6A_n1_(211004_NK_dm_994)

description: RT&Tag for m6A in S2 cell, heat shock, replicate 1


title: S2_RTnTag_HS_IgG_n2_(211004_NK_dm_1056)

description: RT&Tag for IgG in S2 cell, heat shock, replicate 2

value: IgG Abcam cat# ab172730


title: Fibroblast_52 (RNASeq)

source_name: IL11 treated normal human fibroblast

value: fibroblast

value: IL11 stimulated


title: Fibroblast_23 (RNASeq)

source_name: TGF-beta + anti-Ig-G antibody treated normal human fibroblast

value: TGF-B stimulated and anti-IgG antibody treatment


title: sevCCC2 [methylation]


title: Post-intervention monocyte genomic DNA methylation for participant 30-04

description: Diabetic participant total monocytes

value: Female

value: Native Hawaiian

value: Diabetic

value: Monocyte


title: sevCCC3 [methylation]

value: chronic chagasic cardiomyopathy

value: Left ventricular wall


title: Fibroblast_40 (RNASeq)

source_name: TGF-beta + anti-IL-11 antibody treated normal human fibroblast

value: TGF-B stimulated and anti-IL11 antibody treatment

value: polyA mRNA


title: Pre-intervention monocyte genomic DNA methylation for participant 30-14

description: Diabetic participant total monocytes


title: sevCCC1 [methylation]