title: tRNA_MsLV_M_Expr3

description: tRNA

data_processing:
3′ adapter sequence were removed using Trimmomatic (with parameters ILLUMINACLIP, minlength, 10; seed mismatches, 2; palindrome clip threshold, 30; simple clip threshold, 5). Two nucleotides from the 5' end of each read were trimmed using FASTX-Toolkit Trimmer. Then, Trimmomatic was used for quality filtering (with parameters SLIDINGWINDOW:10:15; LEADING, 5; TRAILING, 5; MINLEN, 10).
Custom tRNA fasta and intron files prepared for tRNAseq pipeline by adding the sup-tRNATyr and oligo-standard sequences. tRNAscan-SE 2.0 (http://lowelab.ucsc.edu/tRNAscan-SE/) was used for getting intron-related information required by mim-tRNAseq.
Quality filtered reads were mapped and analyzed with mim-tRNAseq pipeline with parameters; --cluster --cluster-id 0.95  --threads 10 --min-cov 2000 --max-mismatches 0.1 --max-multi 1 --remap --remap-mismatches 0.075.
Data analysis was performed on the tRNA-Seq Pipeline of the DolphinNext, available at https://dolphinnext.umassmed.edu/index.php?np=1&id=744.
Genome_build: mm10
Supplementary_files_format_and_content: CSV and txt files cotaining anticodon raw  and normolized counts for differentially expressed analysis
Supplementary_files_format_and_content: CSV and txt files cotaining isodecoder raw  and normolized counts for differentially expressed analysis

extract_protocol:
Total RNA from approximately 30 mg of liver tissue powder was isolated using TRIzol and Phasemaker tubes according to the manufacturer’s instructions.
After RNA oxidation with 50 mM NaIO4 and β-elimination, two synthetic RNA standards were spiked-in followed by dephosphorylation. Mature tRNAs were purified by denaturing 10% TBE-Urea PAGE followed by ligation with the I4 3’ adapter using T4 RNA ligase 2, truncated KQ. TGIRT was used for primer-dependent reverse transcription at 42˚C for 16 hours. Ethanol purified cDNA was circularized with CircLigase ssDNA ligase followed by PCR amplification. Libraries were purified with 8% PAGE and  quantiﬁed with the high sensitivity fragment analysis assay, pooled in equimolar ratios and sequenced for 150 cycles on NextSeq 500.
mim-tRNA sequencing

treatment_protocol: 6-week old MPS1 KI male mice were injected with rAA9.2xsup-tRNATyr by IV. 10 weeks post injection,  mice were transcardially perfused with ice-cold PBS, and tissues were immediately dissected, snap-frozen in liquid nitrogen, and stored under -80 °C.


title: COVID-19 positive case [BQ_ST002_COVID_517_58_S56]

status: Public on Nov 30 2021

type: SRA

city: Abu Dhabi

first: Habiba

last: Alsafar

address: Al Saada St. Muroor Road

department: Center of Biotechnology

country: United Arab Emirates

institute: Khalifa University

library_source: genomic

data_processing:
BCL files from sequencing were demultiplexed using Illumina's bcl2fastq tool. We subsequently describe the analysis pipeline for microbial communities based on Qiime2, which underwent the paradigm shift from operational taxonomic units (OTUs) to Amplicon sequence variants (ASV), as the latter exhibit several advantages over the former. After demultiplexing using Qiime demux, sequence quality control and feature table construction have been performed with DADA2.
Visual summaries are generated with qiime commands feature-table summarize and feature-table tabulateseqs. Subsequently, we generate a phylogeny for diversity analysis using qiime phylogeny. The resulting phylogeny qiime artifact, particularly the rooted phylogenetic tree, enables a range of diversity analyses using qiime diversity commands.
Alpha diversity commonly applied qualitative measure of community richness.
Compregenive diversity analysis is conducted with Qiime's command core-diversity-phylogenetic (https://view.qiime2.org/)
Phylogenetic investigation of communities by reconstructing unobserved states (PICRUSt) functional analyses based on 16 S rRNA gene abundance profiles was conducted. PICRUSt un-normalized output was also analyzed using the standard DESeq2 workflow. PICRUSt not only estimates full metagenomes from 16S rRNA data, but it also estimates for each sample what operational taxonomic unit contributed to each predicted gene.

molecule: genomic DNA

organism: Homo sapiens

source_name: Nasal and Fecal samples from COVID-19 positive case

extract_protocol:
Faecal samples were subjected to DNA extraction using DNeasy PowerLyzer PowerSoil Kit
The primer sequence design included overhang adapter sequences optimized for the Illumina Sequencing, which in turn were further processed by employing the 16 S Metagenomic Sequencing Library Preparation Protocol
16 S Metagenomic Sequencing

tag: group

value: COVID-19 positive case

tag: gender

value: male

tag: age

tag: bmi


title: COVID-19 positive case [BQ_ST001_COVID_516_60_S58]


title: Ribo_MsLV_M_Ctrl1

city: Worcester

first: Yue

last: Zhang

state: Massachusetts

address: GeneTherapyCenter, 368 Plantation st

country: USA

institute: Umass medical school

description: ribosome proteced RNA fragments

library_source: transcriptomic

data_processing:
Illumina bcl2fastq was used to convert base call (BCL) files into FASTQ files.
3′ adapter sequences were removed using Trimmomatic (with parameters ILLUMINACLIP, minlength, 10; seed mismatches, 2; palindrome clip threshold, 30; simple clip threshold, 5). Then 1 nucleotide from the 3' end of each read was trimmed using FASTX-Toolkit Trimmer.
The trimed reads that mapped to noncoding RNA sequences (rRNA, from RefSeq; Mt_rRNA, Mt_tRNA, rRNA, miRNA, scRNA, scaRNA, snoRNA, snRNA, sRNA, vaultRNA from GENCODE v30 were discarded. STAR8 was used for this alignment step with following parameters: --limitBAMsortRAM 20000000000 --outFilterMismatchNmax 1 --outFilterMultimapNmax 100 --alignIntronMax 1 --outWigType wiggle read1_5p.
The remaining reads were mapped to the hg38 human or mm10 mouse genome using annotations from GENCODE (v30) and (v25), respectively. For this step, STAR was used with following parameters to keep only uniquely mapped reads: --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterType BySJout --outFilterMultimapNmax 200 --outSAMmultNmax 1 --outMultimapperOrder Random --outWigType wiggle read1_5p.
Following alignment, reads were assigned to a custom transcriptome annotation  where single transcripts are selected for each protein-coding gene. Further data analysis was performed on the Ribosome-Profiling pipeline of the DolphinNext, available at https://dolphinnext.umassmed.edu/index.php?np=1&id=695.
Genome_build: hg38 human or mm10 mouse
Supplementary_files_format_and_content: csv files containing raw counts and FPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: liver

growth_protocol: Patient and control fibroblasts were purchased from Coriell Institute and were maintained in EMEM supplemented with 15% (v/v) fetal bovine serum and antibiotics at 37 °C with 5% CO2.

extract_protocol:
PFB cells and ground  mouse livers powder were lysed on ice in the presence of cycloheximide.  Lysates were clarified by centrifugation. For ribosome profiling, monosomes were generated by RNaseI digest followed by ultracentrifugation and purified by miRNeasy mini kit.
Ribosome proteced RNA fragments ranging from 26-34 nt were gel purified. Upon dephosphorylation of sample RNA, linker was ligated and this product  was followed by reverse transcription and gel purification. Then the RT product was circularized by CircLigase ssDNA ligase followed by rRNA depletion with biotinylated subtraction oligo pool. Libraries were then PCR-amplified, and gel-purified libraries were pooled in equimolar ratios and submitted for sequencing.
Ribosome profiling

treatment_protocol: Patient fibroblasts were infected with lentiviral vectors in the presence of 8 µg/mL polybrene. G418 was added to culture media to a final concentration of 0.1 mg/mL or 0.5 mg/mL as indicated 24 hours prior to harvest. 6-week old MPS1 KI male mice were injected with rAA9.2xsup-tRNATyr by IV. 10 weeks post injection,  mice were transcardially perfused with ice-cold PBS, and tissues were immediately dissected, snap-frozen in liquid nitrogen, and stored under -80 °C.

tag: strain

tag: genotype

value: Idua-W401X KI/KI

tag: treat

value: untreat


title: COVID-19 positive case [BQ_ST023_COVID_539_84_S82]

value: female


title: COVID-19 positive case [BQ_ST014_COVID_523_43_S41]


title: tRNA_MsLV_M_Expr1

description: tRNA

tag: treatment


title: KPT-330-A [KA]

city: Houston

first: Yulin

last: Li

state: Texas

address: 6670 Bertner Avenue

institute: Houston Methodist Research Institute

data_processing:
library strategy: CRISPR screen
Computational analysis of the libraries was performed using MAGeCK (version 0.5.9.2)
First, cutadapt (version 2.6) was used to trim primer and other technical sequences from paired-end FASTQ files with the specified options: -j 0 --maximum-length 30 --pair-filter=both -e 0.3 -g GCTTTATATATCTTGTGGAAAGGACGAAACACC...GTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGT -G CCGACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTTAACTTGCTATTTCTAGCTCTAAAAC...GGTGTTTCGTCCTTTCCACAAGATATATAAAGC
Second, the command, mageck count, was run under default options with the trimmed paired-end FASTQ files supplied in the arguments --fastq and --fastq-2 to collect read counts
Genome_build: Brie mouse sgRNA library (Addgene #73633)
Supplementary_files_format_and_content: Tab-delimited text files containing raw counts for each sgRNA

source_name: pancreatic ductal adenocarcinoma cells

growth_protocol: The 4292 pancreatic ductal adenocarcinoma cell line, which has KRAS expressed controlled by the Tet-ON system, was cultured in RPMI 1640 supplemented with 10% FBS and 1% penicillin/streptomycin, containing 1μg/ml doxycycline.

extract_protocol:
Genomic DNA was isolated using the Zymo-Spin V column (Zymo Research).
HiSeq libraries were constructed by one-step PCR amplification following reported protocols (Joung J et al., Nat Protoc. 2017, 12(4):828-863. PMID: 28333914).

treatment_protocol: The 4292 pancreatic ductal adenocarcinoma cells with stable Cas9 expression were infected at low viral titers with the CRISPR lentiviral library so that approximately 10% of the cells were infected, and the infected cells were selected with puromycin (1µg/ml) for two days.

tag: cell line

tag: cell type

value: pancreatic ductal adenocarcinoma cells

value: 0.33μM selinexor (KPT-330)

tag: doxycycline induction


title: Gemcitabine-B [GB]

value: 20nM gemcitabine


title: KPT-330-B [KB]


title: tRNA_MsLV_M_Expr2

description: tRNA


title: RNAPII-ChIA-PET_HD_Control

city: Farmington

first: Zhongyuan

last: Tian

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory for Genomic Medicine

description:
nuclear chromatin
HD Control

data_processing:
RChIA-PET raw reads were filtered by linker sequence composition and the PET reads with specific ligation linkers (R1D1 or R2D2 linkers) were kept for downstream mapping and analyses. BatMis (Tennakoon et al., 2012) was used to map the retained PET sequences to human genome build dm3. The mapping results were then filtered based on very stringent criteria: 1) both ends of the PET sequence had to be uniquely mapped (allowing a maximum of two mismatches on each end); 2) PET sequences with both ends mapped to precisely the same locations were merged and considered as one read, i.e., redundant reads were removed. With the mapped PETs, linker barcodes were used to distinguish the tag sequences that originated from the RNA molecules (RNA-tags) from the target chromatin DNA-tags.
ChIRP-Seq bioinformatics analysis was performed as previously described (Quinn, J.J. et al. 2014). Raw fastq data were mapped to dm3 reference genome by BWA mem with default parameters and minimum seed length (-k) set to 18. Duplicate reads were removed by using the Picard toolkit (http://broadinstitute.github.io/picard/). Only uniquely mapped reads (mapping score ≥ 20) were kept for further analysis. ChIRP-Seq peaks were identified by using MACS (version 2.0.10) with configuration of --nomodel and --keep-dup set to all.
ATAC-Seq raw reads in fastq format were first aligned to Drosophila dm3 genome assembly with BWA mem. PCR redundancy was removed by using the Picard toolkit (http://broadinstitute.github.io/picard/). Sequences with alignment score ≥ 20 were retained for further analysis. For each ATAC-Seq library, ATAC-Seq peaks were identified by using MACS (version 2.0.10) with default parameters.
Data processing of ChIA-PET reads was performed as previously described in Li et al., 2012 with slight modifications.
Pair-end read (PET) sequences were scanned for the bridge linker sequence and only PETs with the bridge linker were used for downstream processing.  After trimming the linkers, the sequences flanking the linker were mapped to the dm3 or hg19 using bwa-mem (Li and Durbin, 2010) and only uniquely aligned (MAPQ ≥ 30) PETs were retained.  PCR duplicates were removed using the MarkDuplicates tool of the Picard Tools library (http://broadinstitute.github.io/picard/).  Each PET was categorized as either a self-ligation PET (two ends of the same DNA fragment) or inter-ligation PET (two ends from two different DNA fragments in the same chromatin complex) by evaluating the genomic span between the two ends of a PET.
PETs with a genomic span less than 8 kb are classified as self-ligation PETs and are used as a proxy for ChIP fragments since they are derived in a manner analogous to ChIP-Seq mapping for protein binding sites. PETs with a genomic span greater than 8 kb are classified as inter-ligation PETs and represent the long-range interactions of interest. To accurately represent the frequency of interaction between two loci and to define the interacting regions, both ends of inter-ligation PETs were extended by 500 bp along the reference genome, and PETs overlapping at both ends (with extension) were clustered together as one PET cluster.
in situ ChIA-PET: Data were processed by ChIA-PIPE (Capurso, D., et al. bioRxiv (2018): 506683). Pair-end read (PET) sequences were scanned for the bridge linker sequence and only PETs with the bridge linker were used for downstream processing. After trimming the linkers, the sequences flanking the linker were mapped to the dm3 using bwa-mem and only uniquely aligned (MAPQ ≥ 30) PETs were retained. PCR duplicates were removed using Picard. Each PET was categorized as either a self-ligation PET (two ends of the same DNA fragment) or inter-ligation PET (two ends from two different DNA fragments in the same chromatin complex) by evaluating the genomic span between the two ends of a PET.
Genome_build: dm3
Supplementary_files_format_and_content: (I) “ *_coverage.bedgraph” files are of reads pileup coverage in bedgraph format.   (II) “ *_peak.bed” files are peaks called by MACS2 in bed format.  (III) “RChIA-PET_Combined_DNA-RNA_PET.txt” and “pRChIA-PET_Combined_DNA-RNA_PET.txt” are tab-delimited bedpe file documenting the genomic coordinates of DNA and RNA of each interaction PET with RNA strand information. “Combined” means this data are the combination of the two replicates of RChIA-PET and pRChIA-PET respectively.  (IV) “S2-RNAPII-ChIA-PET_Combined_PET_clusters.txt” is tab-delimited bedpe file documenting the genomic coordinates and frequency of each interaction PET clusters from the combination of two replicated ChIA-PET libraries. “S2-RNAPII-ChIA-PET_Combined_coverage.bedgraph” is the reads pileup coverage bedgraph file.

organism: Drosophila melanogaster

growth_protocol: S2 was cultured following manufacture’s instruction.

extract_protocol:
Chromatin was obtained and subjected to fragmentation with an average length of 500 bp by sonication. The anti-RNAPII monoclonal antibody 8WG16 (Biolegend, 920102) was used to enrich RNAPII-bound chromatin fragments, respectively.
The DNA fragments in the streptavidin beads-bound chromatin for RChIA-PET  or antibody beads-bound chromatin for RNAPII RChIA-PET were end-repaired using T4 polymerase (Promega) in mixture (70 µl 10× T4 polymerase buffer, 7 µl 10mM dNTP, 3.5 µl RI, 612.3 µl Nuclease-free water, with 7.2 µl of T4 polymerase), washed with RChIA-PET Wash Buffer (10 mM Tris.HCl pH 7.0, 10 mM Tris.HCl pH 8.0, 10 mM EDTA, 50 mM NaCl) three times. The RNA fragments were linked to RNA linker for first-strand cDNA synthesis using the Superscript III First Strand Synthesis System (Thermo Fisher Scientific). In more details, 1 µg of biotinylated and barcoded RNA linker R1 (tube 1) and R2 (tube 2) containing a flanking MmeI site were added to two tubes containing cDNA synthesis mixture (20 µl RNA liker, 20 µl dNTP, 80 µl 5× RT buffer, 20 µl 0.1 M DTT, 20 µl RI, 220 µl Nuclease-free water) and incubated at 65 °C for 5 min (Alternative, incubated at 42 °C for 5 min when performing RNAPII RChIA-PET), then placed on ice for at least 1 min, and added 20 µl superScriptIII RT, and incubated for 10 min at 25 °C on Intelli-Mixer (Program F1, 10rpm), followed by 30 min at 50 °C (Alternative, 1 hour at 37 °C when performing RNAPII RChIA-PET). The RNA linker ligated chromatin was washed with Wash Buffer three times, then incubated with 1 µg of DNA linker D1 (tube 1) and D2 (tube 2) respectively in the ligation mixture (15 µl DNA linker, 140 µl 5× T4 DNA ligase buffer with PEG, 3.5 µl RI, 536.5 µl Nuclease free water) by using 5 µl of T4 DNA ligase at 16 °C for overnight. The linker-added DNA fragments were washed with Wash Buffer three times and then phosphorylated with 14 µl of T4 polynucleotide kinase (NEB) in PNK master mix buffers (70 µl 10× T4 DNA ligase buffer, 3.5 µl RI in 612.5 µl Nuclease-free water). The samples from two tubes were washed with Wash Buffer three times and then were mixed and followed by proximity ligation with 34 µl of T4 DNA ligase in reaction buffer (1,000 µl 10× T4 DNA ligase buffer, 50 µl RI, 8,916 µl Nuclease-free water) overnight at 16 °C. After washing with Wash Buffer three times, the chromatin DNA fragments with linkers were subjected to second-strand cDNA synthesis with a Superscript Double-stranded cDNA Synthesis Kit (Thermo Fisher Scientific) and chromatin mixing with second-strand cDNA mixture (333 µl Nuclease-free water, 90 µl 5× second-strand reaction buffer, 9 µl 10 mM dNTP mix, 3 µl E.coli DNA ligase, 12 µl E.coli DNA Polymerase I, 3 µl E.coli RNase H) were incubated at 16 °C for 2 hours; then 6 µl of T4 DNA polymerase were added and continued to be incubated at 16 °C for 5 min. Crosslinks in the DNA/RNA/protein complexes were then reversed by incubation at 65 °C overnight with 0.5% SDS (Thermo Fisher Scientific) and proteinase K (Thermo Fisher Scientific), and the cDNA-DNA fragments were purified by phenol/chloroform isopropanol precipitation. The purified cDNA-DNA was then digested by 1 µl of MmeI (NEB) in buffer (5 µl 10× NE Buffer 4, 5 µl Half linker non-Biotinylated to quench excess MmeI, 5 µl 10× SAM) for 2 hours at 37 °C to release the [cDNA tag]-[RNA linker]-[DNA linker]-[DNA tag] Paired-End-Tag structure. The biotinylated PETs were then immobilized on streptavidin-conjugated magnetic Dynabeads (Thermo Fisher Scientific, 11206D-10ml) in 50 µl of 2× B&W buffer (10 mM Tris-HCl pH 7.5, 1mM EDTA, 1 M NaCl), and rotated at room temperature for 45 min. The ends of each PET structure were then ligated to a sequencing adaptor by 1 µl of T4 DNA ligase (Thermo Fisher Scientific, EL0013) in Adaptor ligation buffer (4 µl Adaptor A, 4 µl Adaptor B, 5 µl 10× T4 DNA ligase buffer, 36 µl Nuclease-free water) at 16 °C for overnight with rotation. Then the beads were washed three times with 1× B&W buffer (5 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 1 M NaCl). Nick translation was performed by adding 4 µl of E.coli DNA polymerase I solution mixture (38.5 µl Nuclease free water, 10× NEBuffer 2, 2.5 µl 10 mM dNTP) and incubated at room temperature for 2 hours with rotation on the Intelli-Mixer (F8, 30rpm, U = 50, u = 60). Then 10-16 rounds of PCR reactions were performed to amplify the PETs, and the resultant RChIA-PET libraries were subjected for sequencing by MiSeq with paired-end reads of 36 bp.
in situ ChIA-PET

treatment_protocol:
Drosophila S2 cells were permeabilized with DPBS containing 0.015% Triton X-100 for 5 min at room temperature, then treated with or without RNaseA at a series of concentration at 100 μg/ml, 200 μg/ml, 400 μg/ml and 800 μg/ml respectively for 10min, then washing with DPBS.
For phase separation experiment, the Drosophila S2 cells were incubated with 1,6-hexanediol (HD) at the concentration of 0% HD (control) and 10% HD for 30 min at room temperature. Then aliquot half of them for washout the HD with DPBS. All the cells of control, 10% HD treatment and HD washout(recovery) were subjected for crosslinked.

tag: method

value: in situ ChIA-PET

tag: factor

value: RNAPII


title: RNAPII-ChIA-PET_HD_Treatment

description:
nuclear chromatin
HD Treatment


title: RNAPII-ChIA-PET_HD_Recovery

description:
nuclear chromatin
HD Recovery


title: Gemcitabine-A [GA]


title: S2-RNAPII-ChIA-PET, Rep2

description:
Nuclear chromatin
Replicate 2
processed data file: S2-RNAPII-ChIA-PET_Combined_PET_clusters.txt.gz
processed data file: S2-RNAPII-ChIA-PET_Combined_coverage.bedgraph.gz

data_processing:
RChIA-PET raw reads were filtered by linker sequence composition and the PET reads with specific ligation linkers (R1D1 or R2D2 linkers) were kept for downstream mapping and analyses. BatMis (Tennakoon et al., 2012) was used to map the retained PET sequences to human genome build dm3. The mapping results were then filtered based on very stringent criteria: 1) both ends of the PET sequence had to be uniquely mapped (allowing a maximum of two mismatches on each end); 2) PET sequences with both ends mapped to precisely the same locations were merged and considered as one read, i.e., redundant reads were removed. With the mapped PETs, linker barcodes were used to distinguish the tag sequences that originated from the RNA molecules (RNA-tags) from the target chromatin DNA-tags.
ChIRP-Seq bioinformatics analysis was performed as previously described (Quinn, J.J. et al. 2014). Raw fastq data were mapped to dm3 reference genome by BWA mem with default parameters and minimum seed length (-k) set to 18. Duplicate reads were removed by using the Picard toolkit (http://broadinstitute.github.io/picard/). Only uniquely mapped reads (mapping score ≥ 20) were kept for further analysis. ChIRP-Seq peaks were identified by using MACS (version 2.0.10) with configuration of --nomodel and --keep-dup set to all.
ATAC-Seq raw reads in fastq format were first aligned to Drosophila dm3 genome assembly with BWA mem. PCR redundancy was removed by using the Picard toolkit (http://broadinstitute.github.io/picard/). Sequences with alignment score ≥ 20 were retained for further analysis. For each ATAC-Seq library, ATAC-Seq peaks were identified by using MACS (version 2.0.10) with default parameters.
Data processing of ChIA-PET reads was performed as previously described in Li et al., 2012 with slight modifications.
Pair-end read (PET) sequences were scanned for the bridge linker sequence and only PETs with the bridge linker were used for downstream processing. After trimming the linkers, the sequences flanking the linker were mapped to the dm3 or hg19 using bwa-mem (Li and Durbin, 2010) and only uniquely aligned (MAPQ ≥ 30) PETs were retained. PCR duplicates were removed using the MarkDuplicates tool of the Picard Tools library (http://broadinstitute.github.io/picard/). Each PET was categorized as either a self-ligation PET (two ends of the same DNA fragment) or inter-ligation PET (two ends from two different DNA fragments in the same chromatin complex) by evaluating the genomic span between the two ends of a PET.
PETs with a genomic span less than 8 kb are classified as self-ligation PETs and are used as a proxy for ChIP fragments since they are derived in a manner analogous to ChIP-Seq mapping for protein binding sites. PETs with a genomic span greater than 8 kb are classified as inter-ligation PETs and represent the long-range interactions of interest. To accurately represent the frequency of interaction between two loci and to define the interacting regions, both ends of inter-ligation PETs were extended by 500 bp along the reference genome, and PETs overlapping at both ends (with extension) were clustered together as one PET cluster.
Genome_build: dm3 and hg19
Supplementary_files_format_and_content: (I) *_coverage.bedgraph files are of reads pileup coverage in bedgraph format.
Supplementary_files_format_and_content: (II) *_peak.bed files are peaks called by MACS2 in bed format.
Supplementary_files_format_and_content: (III) RChIA-PET_Combined_DNA-RNA_PET.txt and pRChIA-PET_Combined_DNA-RNA_PET.txt are tab-delimited bedpe files documenting the genomic coordinates of DNA and RNA of each interaction PET with RNA strand information. "Combined" means these data are the combination of the two replicates of RChIA-PET and pRChIA-PET, respectively.
Supplementary_files_format_and_content: (IV) S2-RNAPII-ChIA-PET_Combined_PET_clusters.txt is a tab-delimited bedpe file documenting the genomic coordinates and frequency of each interaction PET clusters from the combination of two replicated ChIA-PET libraries.
Supplementary_files_format_and_content: (V) S2-RNAPII-ChIA-PET_Combined_coverage.bedgraph is the reads pileup coverage bedgraph file.

growth_protocol: S2 was cultured following manufacturer’s instruction.

extract_protocol:
Chromatin was obtained and subjected to fragmentation with an average length of 500 bp by sonication. The anti-RNAPII monoclonal antibody 8WG16 (Biolegend, 920102) was used to enrich RNAPII-bound chromatin fragments, respectively.
The DNA fragments in the streptavidin beads-bound chromatin for RChIA-PET or antibody beads-bound chromatin for RNAPII RChIA-PET were end-repaired using T4 polymerase (Promega) in mixture (70 µl 10× T4 polymerase buffer, 7 µl 10mM dNTP, 3.5 µl RI, 612.3 µl Nuclease-free water, with 7.2 µl of T4 polymerase), washed with RChIA-PET Wash Buffer (10 mM Tris.HCl pH 7.0, 10 mM Tris.HCl pH 8.0, 10 mM EDTA, 50 mM NaCl) three times. The RNA fragments were linked to RNA linker for first-strand cDNA synthesis using the Superscript III First Strand Synthesis System (Thermo Fisher Scientific). In more details, 1 µg of biotinylated and barcoded RNA linker R1 (tube 1) and R2 (tube 2) containing a flanking MmeI site were added to two tubes containing cDNA synthesis mixture (20 µl RNA liker, 20 µl dNTP, 80 µl 5× RT buffer, 20 µl 0.1 M DTT, 20 µl RI, 220 µl Nuclease-free water) and incubated at 65 °C for 5 min (Alternative, incubated at 42 °C for 5 min when performing RNAPII RChIA-PET), then placed on ice for at least 1 min, and added 20 µl superScriptIII RT, and incubated for 10 min at 25 °C on Intelli-Mixer (Program F1, 10rpm), followed by 30 min at 50 °C (Alternative, 1 hour at 37 °C when performing RNAPII RChIA-PET). The RNA linker ligated chromatin was washed with Wash Buffer three times, then incubated with 1 µg of DNA linker D1 (tube 1) and D2 (tube 2) respectively in the ligation mixture (15 µl DNA linker, 140 µl 5× T4 DNA ligase buffer with PEG, 3.5 µl RI, 536.5 µl Nuclease free water) by using 5 µl of T4 DNA ligase at 16 °C for overnight. The linker-added DNA fragments were washed with Wash Buffer three times and then phosphorylated with 14 µl of T4 polynucleotide kinase (NEB) in PNK master mix buffers (70 µl 10× T4 DNA ligase buffer, 3.5 µl RI in 612.5 µl Nuclease-free water). The samples from two tubes were washed with Wash Buffer three times and then were mixed and followed by proximity ligation with 34 µl of T4 DNA ligase in reaction buffer (1,000 µl 10× T4 DNA ligase buffer, 50 µl RI, 8,916 µl Nuclease-free water) overnight at 16 °C. After washing with Wash Buffer three times, the chromatin DNA fragments with linkers were subjected to second-strand cDNA synthesis with a Superscript Double-stranded cDNA Synthesis Kit (Thermo Fisher Scientific) and chromatin mixing with second-strand cDNA mixture (333 µl Nuclease-free water, 90 µl 5× second-strand reaction buffer, 9 µl 10 mM dNTP mix, 3 µl E.coli DNA ligase, 12 µl E.coli DNA Polymerase I, 3 µl E.coli RNase H) were incubated at 16 °C for 2 hours; then 6 µl of T4 DNA polymerase were added and continued to be incubated at 16 °C for 5 min. Crosslinks in the DNA/RNA/protein complexes were then reversed by incubation at 65 °C overnight with 0.5% SDS (Thermo Fisher Scientific) and proteinase K (Thermo Fisher Scientific), and the cDNA-DNA fragments were purified by phenol/chloroform isopropanol precipitation. The purified cDNA-DNA was then digested by 1 µl of MmeI (NEB) in buffer (5 µl 10× NE Buffer 4, 5 µl Half linker non-Biotinylated to quench excess MmeI, 5 µl 10× SAM) for 2 hours at 37 °C to release the [cDNA tag]-[RNA linker]-[DNA linker]-[DNA tag] Paired-End-Tag structure. The biotinylated PETs were then immobilized on streptavidin-conjugated magnetic Dynabeads (Thermo Fisher Scientific, 11206D-10ml) in 50 µl of 2× B&W buffer (10 mM Tris-HCl pH 7.5, 1mM EDTA, 1 M NaCl), and rotated at room temperature for 45 min. The ends of each PET structure were then ligated to a sequencing adaptor by 1 µl of T4 DNA ligase (Thermo Fisher Scientific, EL0013) in Adaptor ligation buffer (4 µl Adaptor A, 4 µl Adaptor B, 5 µl 10× T4 DNA ligase buffer, 36 µl Nuclease-free water) at 16 °C for overnight with rotation. Then the beads were washed three times with 1× B&W buffer (5 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 1 M NaCl). Nick translation was performed by adding 4 µl of E.coli DNA polymerase I solution mixture (38.5 µl Nuclease free water, 10× NEBuffer 2, 2.5 µl 10 mM dNTP) and incubated at room temperature for 2 hours with rotation on the Intelli-Mixer (F8, 30rpm, U = 50, u = 60). Then 10-16 rounds of PCR reactions were performed to amplify the PETs, and the resultant RChIA-PET libraries were subjected for sequencing by MiSeq with paired-end reads of 36 bp.

treatment_protocol: Drosophila S2 cells were permeabilized with DPBS containing 0.015% Triton X-100 for 5 min at room temperature, then treated with or without RNaseA at a series of concentration at 100 μg/ml, 200 μg/ml, 400 μg/ml and 800 μg/ml respectively for 10min, then washing with DPBS.


title: COVID-19 positive case [BQ_ST004_COVID_528_26_S26]


title: tRNA_MsLV_M_Ctrl3

description: tRNA


title: ATAC-Seq (RNaseA + 800μg/ml), Rep2

description:
Open chromatin
Replicate 2


title: ATAC-Seq (RNaseA + 400μg/ml), Rep2

description:
Open chromatin
Replicate 2


title: tRNA_MsLV_M_Ctrl2

description: tRNA


title: S2-RNAPII-ChIA-PET, Rep1

description:
Nuclear chromatin
Replicate 1
processed data file: S2-RNAPII-ChIA-PET_Combined_PET_clusters.txt.gz
processed data file: S2-RNAPII-ChIA-PET_Combined_coverage.bedgraph.gz


title: ATAC-Seq (RNaseA + 800μg/ml), Rep1

description:
Open chromatin
Replicate 1


title: ATAC-Seq (RNaseA - control), Rep2

description:
Open chromatin
Replicate 2


title: ATAC-Seq (RNaseA + 200μg/ml), Rep2

description:
Open chromatin
Replicate 2


title: ATAC-Seq (RNaseA + 200μg/ml), Rep1

description:
Open chromatin
Replicate 1


title: ATAC-Seq (RNaseA + 400μg/ml), Rep1

description:
Open chromatin
Replicate 1


title: tRNA_MsLV_M_Ctrl1

description: tRNA


title: Input ChIRP-Seq

description: Nuclear chromatin

data_processing:
Library strategy: ChiRP-Seq
RChIA-PET raw reads were filtered by linker sequence composition and the PET reads with specific ligation linkers (R1D1 or R2D2 linkers) were kept for downstream mapping and analyses. BatMis (Tennakoon et al., 2012) was used to map the retained PET sequences to human genome build dm3. The mapping results were then filtered based on very stringent criteria: 1) both ends of the PET sequence had to be uniquely mapped (allowing a maximum of two mismatches on each end); 2) PET sequences with both ends mapped to precisely the same locations were merged and considered as one read, i.e., redundant reads were removed. With the mapped PETs, linker barcodes were used to distinguish the tag sequences that originated from the RNA molecules (RNA-tags) from the target chromatin DNA-tags.
ChIRP-Seq bioinformatics analysis was performed as previously described (Quinn, J.J. et al. 2014). Raw fastq data were mapped to dm3 reference genome by BWA mem with default parameters and minimum seed length (-k) set to 18. Duplicate reads were removed by using the Picard toolkit (http://broadinstitute.github.io/picard/). Only uniquely mapped reads (mapping score ≥ 20) were kept for further analysis. ChIRP-Seq peaks were identified by using MACS (version 2.0.10) with configuration of --nomodel and --keep-dup set to all.
ATAC-Seq raw reads in fastq format were first aligned to Drosophila dm3 genome assembly with BWA mem. PCR redundancy was removed by using the Picard toolkit (http://broadinstitute.github.io/picard/). Sequences with alignment score ≥ 20 were retained for further analysis. For each ATAC-Seq library, ATAC-Seq peaks were identified by using MACS (version 2.0.10) with default parameters.
Data processing of ChIA-PET reads was performed as previously described in Li et al., 2012 with slight modifications.
Pair-end read (PET) sequences were scanned for the bridge linker sequence and only PETs with the bridge linker were used for downstream processing. After trimming the linkers, the sequences flanking the linker were mapped to the dm3 or hg19 using bwa-mem (Li and Durbin, 2010) and only uniquely aligned (MAPQ ≥ 30) PETs were retained. PCR duplicates were removed using the MarkDuplicates tool of the Picard Tools library (http://broadinstitute.github.io/picard/). Each PET was categorized as either a self-ligation PET (two ends of the same DNA fragment) or inter-ligation PET (two ends from two different DNA fragments in the same chromatin complex) by evaluating the genomic span between the two ends of a PET.
PETs with a genomic span less than 8 kb are classified as self-ligation PETs and are used as a proxy for ChIP fragments since they are derived in a manner analogous to ChIP-Seq mapping for protein binding sites. PETs with a genomic span greater than 8 kb are classified as inter-ligation PETs and represent the long-range interactions of interest. To accurately represent the frequency of interaction between two loci and to define the interacting regions, both ends of inter-ligation PETs were extended by 500 bp along the reference genome, and PETs overlapping at both ends (with extension) were clustered together as one PET cluster.
Genome_build: dm3 and hg19
Supplementary_files_format_and_content: (I) *_coverage.bedgraph files are of reads pileup coverage in bedgraph format.
Supplementary_files_format_and_content: (II) *_peak.bed files are peaks called by MACS2 in bed format.
Supplementary_files_format_and_content: (III) RChIA-PET_Combined_DNA-RNA_PET.txt and pRChIA-PET_Combined_DNA-RNA_PET.txt are tab-delimited bedpe files documenting the genomic coordinates of DNA and RNA of each interaction PET with RNA strand information. "Combined" means these data are the combination of the two replicates of RChIA-PET and pRChIA-PET, respectively.
Supplementary_files_format_and_content: (IV) S2-RNAPII-ChIA-PET_Combined_PET_clusters.txt is a tab-delimited bedpe file documenting the genomic coordinates and frequency of each interaction PET clusters from the combination of two replicated ChIA-PET libraries.
Supplementary_files_format_and_content: (V) S2-RNAPII-ChIA-PET_Combined_coverage.bedgraph is the reads pileup coverage bedgraph file.


title: ATAC-Seq (RNaseA - control), Rep1

description:
Open chromatin
Replicate 1


title: RNA Ssrp1fl/+;CreERT2+/+ MCS treated with 4-OHT 1

city: Buffalo

first: Katerina

last: Gurova

state: NY

address: Elm and Carlton Str

institute: Roswell Park Cancer Institute

data_processing:
STAR --runMode genomeGenerate --runThreadN 16 --genomeDir ${output}mm10_STARgenome --genomeFastaFiles /mnt/lustre/users/kgurova/MyProjects/Genomes/mm10.fa --sjdbGTFfile /mnt/lustre/users/kgurova/MyProjects/Genomes/gencode.vM25.annotation.gtf
DESeq
Genome_build: mm10, gencode.vM25.annotation
Supplementary_files_format_and_content: tab delimited text file, DESeq results, dds

source_name: MSC

growth_protocol: DMEM 10% FBS

extract_protocol:
Trizol
The sequencing libraries were prepared from 500 ng total RNA using the mRNA HyperPrep kit (KAPA BIOSYSTEMS) following the manufacturer’s instructions. Briefly, PolyA RNA was purified using the mRNA Capture Beads. The purified RNA was fragmented and primed for cDNA synthesis. Fragmented RNA was reverse transcribed into first-strand cDNA using random primers. Second strand cDNA synthesis converted the cDNA:RNA hybrids to double-strand cDNA (dscDNA), with the 2nd strand marked by incorporating dUTP in place of dTTP. Pure Beads were used to separate the dscDNA from the second-strand reaction mix, resulting in blunt-ended cDNA. A single ‘A’ nucleotide was added to the 3’ ends of the blunt fragments. Multiple indexing adapters containing a single ‘T’ nucleotide on the 3’ end were ligated to the ends of the dscDNA to prepare them for hybridization onto a flow cell. The adapter-ligated libraries were amplified by PCR, purified using Pure Beads, and validated for the appropriate size using a 4200 TapeStation D1000 ScreenTape (Agilent Technologies, Inc.). The DNA libraries were quantitated using the KAPA Biosystems qPCR kit and pooled in an equimolar fashion. Each pool was denatured and diluted to 350 pM, with a 1% PhiX control library added. The resulting pools were loaded into NovaSeq Reagent cartridges for 100-cycle single-read analysis and sequenced with a NovaSeq6000 following the manufacturer’s recommended protocol (Illumina Inc.).

treatment_protocol: Cells were treated with 4-OHT for five days and then split. Next days cells were used for total RNA isolation

tag: tissue

value: primary cells


title: RNA Ssrp1fl/+;CreERT2+/+ MCS control 1

value: control


title: RNA Ssrp1fl/+;CreERT2+/+ MCS control 2


title: RNA Ssrp1fl/fl;CreERT2+/+ MCS treated with 4-OHT 2


title: CPC_FLKO_5

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

data_processing:
Reads were aligned to the mouse genome (mm10) using the spliced read aligner STAR (version 2.5.2a_modified) with default parameters, except reporting only one hit in the final alignment for multimappers (outSAMmultNmax=1) and filtering reads without evidence in the spliced junction table (outFilterType=“BySJout”).
Sequencing and mapping quality was assessed by the qQCReport function of the R package QuasR (version 1.18) and with FastQC (version 0.11.3).
Gene expression was quantified by the qCount function of the R Bioconductor package QuasR (version 1.18) as the number of reads that started within any annotated exon of a gene from the Ensembl 88 annotation (irrespective of strand).
Genome_build: mm10
Supplementary_files_format_and_content: gzipped text file with tab-separated counts for each gene; each row contains the annotation and raw counts per gene; columns correspond to: 1. Ensembl Gene ID (release 88), 2.-7. read counts per gene and sample.

molecule: polyA RNA

source_name: Cardiac Side Population from flt3L-/- mouse

extract_protocol:
RNA was isolated from a total of three sorts of SP-CPCs using the NucleoSpin RNA XS kit (Macherey Nagel).
Each sort consisted of the cardiomyocyte- and erythrocyte-depleted cardiac cell suspension from 4 wt and 4 flt3L-/- mice.
RNA quality was controlled on an Agilent 2100 Bioanalyzer using RNA Pico CHIP (Agilent Technologies).
RNA-seq library preparation and sequencing were performed at the Quantitative Genomics Facility of the D-BSSE of the ETHZ (Basel, Switzerland).
RNA-seq library quality was assessed with a Fragment Analyzer (Advanced Analytical).
Unstranded RNA-seq libraries were produced using the low-input SMART-Seq v4 kit (Clontech/Takara).

tag: sorting date


title: PZ-BM-rep3-H3K9me3-H3K4me1

city: Utrecht

first: Jake

last: Yeung

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
fastq files were mapped using BWA-0.7.16a (r1181) to ENSEMBL Build 95
Count tables are 50 kb regions genome-wide across individual cells, counted from bam files
Single-cell data are clustered to create pseudobulk bam files
Genome_build: mm10
Supplementary_files_format_and_content: Cells annotated by UMAP from H3K4me1+H3K9me3 UMAP, each cell has a cluster label associated with H3K9me3 and with H3K4me1.

source_name: bone marrow

extract_protocol:
Cells were resuspended in 500ul wash buffer (47.5ml H2O RNAse free, 1ml 1M HEPES pH 7.5, 1.5ml 5M NaCl, 3.6ul pure spermidine solution). Aliquot in a 0.5ml protein low-binding tubes (1 per antibody to be used). Following steps are performed on ice.  Cells were pelleted at 600g for 3min and resuspended in 400 ul Wash Buffer 1 (wash buffer with extra 0.05% saponin (Sigma Aldrich), protease inhibitor cocktail (Sigma Aldrich), 4 ul/ml 0.5M EDTA) containing the primary antibody (1:100 dilution for H3K4me1, H3K9me3 and H3K27me3 and 1:200 dilution for H3K4me3, Saponin has to be prepared fresh every time as a 10% solution in PBS). Cells were incubated overnight at 4oC on a roller, before they were washed once with 500 ul Wash Buffer 2 (wash buffer with extra 0.05% saponin, protease inhibitor).  Afterwards cells were resuspended in 500 ul Wash Buffer 2 containing PaMN (3ng/ml) and incubated for 1h at 4C on a roller.  Finally, cells were washed an additional 2 times with 500 ul Wash Buffer 2 before passing it through a 70um cell strainer (Corning, 431751) and sorting them on a JAZZ FACS machine into 384 well plates containing 50nl Wash buffer 3 (Wash buffer containing 0,05% saponin) and 5ul sterile filtered mineral oil (Sigma Aldrich) per well. Small volumes were distributed using a Nanodrop II system (Innovadyme). 50nl of Wash Buffer 3, containing 4uM CaCl2, were added per cell to induce Protein A-MN mediated chromatin digestion that was performed for 30min on ice. Afterwards the reaction was stopped by adding 100nl of a stop solution containing 40mM EGTA (chelates Ca2+ and stops MN), 1.5% NP40 and 10ul 2mg/ml proteinase k (Ambion). Chromatin is subsequently released and PaMN permanently destroyed by proteinase k digestion at 65C for 6h followed by 80C for 20min to heat inactivate proteinase k. Afterwards plates can be stored at -20C until further processing.
DNA fragments are further blunt ended using Klenow large fragment (NEB) and T4 PNK (NEB) in the presence of dNTPs. Afterwards nonintegrated dNTPs are removed using schrimp alkaline phosphatase (NEB) to increase A-tail efficiency. Subsequently blunt fragments are A-Tailed using AmpliTaq™ 360 DNA Polymerase (Thermofisher) in the presence of fresh dATP and T4 PNK (NEB). Next fragments are ligated to T-tail adaptors containing 3 bp UMIs and an 8bp cell barcode (final concentration 9nM from IDT) for 16h at 16C using T4-ligase (NEB). Adaptors were added with a Mosquito HTS (ttp labtech). Ligation products were pooled by centrifugation and cleaned using Ampure XP beads at a bead to sample ratio of 0.8 (Beckman Coulter). The cleaned DNA is then linear amplified by invitro transcription with components of MessageAmp II (Invitrogen) for 16h at 37C. The produced RNA is purified 1-3 times depending on Adaptor dimer contamination using RNA Clean XP beads (Beckman Coulter) at 0.8 beads to sample ratio, followed by RNA fragmentation for 2.5 min at 94C. After another bead cleanup, 20% of the RNA is reverse transcribed with Superscript II (NEB) and PCR amplified to add the Illumina smallRNA barcodes and handles with NEBNext Ultra II Q5 Master Mix. PCR cycles depended on the abundance of the histone modification assayed and the number of RNA cleanup cycles after IVT needed (8-10 for H3K9me3 and H3K27me3 10-12 for H3K4me1 and 12-15 for H3K4me3).

value: bone marrow

value: FVB

tag: molecule subtype


title: CPC_Bl6N_3

source_name: Cardiac Side Population from wild-type mouse


title: RNA Ssrp1fl/fl;CreERT2+/+ MCS treated with 4-OHT 1


title: pRChIA-PET, Rep2

description:
Nuclear chromatin associated RNA
Replicate 2
pRChIA-PET
processed data file: pRChIA-PET_Combined_DNA-RNA_PET.txt.gz


title: pRChIA-PET, Rep1

description:
Nuclear chromatin associated RNA
Replicate 1
pRChIA-PET
processed data file: pRChIA-PET_Combined_DNA-RNA_PET.txt.gz


title: CPC_FLKO_4


title: roX2-ChIRP-Seq, Rep1

description:
Nuclear chromatin
Replicate 1

treatment_protocol: Drosophila S2 cells were permeabilized with DPBS containing 0.015% Triton X-100 for 5 min at room temperature, then treated with or without RNaseA at a series of concentration at 100 μg/ml, 200 μg/ml, 400 μg/ml and 800 μg/ml respectively for 10min, then washing with DPBS..


title: roX2-ChIRP-Seq, Rep2

description:
Nuclear chromatin
Replicate 2


title: RNA Ssrp1fl/fl;CreERT2+/+ MCS controlv2


title: RChIA-PET, Rep2

description:
Nuclear chromatin associated RNA
Replicate 2
RChIA-PET
processed data file: RChIA-PET_Combined_DNA-RNA_PET.txt.gz

value: All chromatin associated proteins


title: RChIA-PET, Rep1

description:
Nuclear chromatin associated RNA
Replicate 1
RChIA-PET
processed data file: RChIA-PET_Combined_DNA-RNA_PET.txt.gz


title: CPC_Bl6N_2


title: RNA Ssrp1fl/fl;CreERT2+/+ MCS control 1


title: CPC_Bl6N_1


title: RNA Ssrp1fl/+;CreERT2+/+ MCS treated with 4-OHT 2


title: DpnII Hi-C on mouse thyroid glad - R1

first: Job

last: Dekker

state: MA

address: 368 Plantation Street

department: Program in Systems Biology

institute: University of Massachusetts Medical School/HHMI

description:
Thyroid glands from 6 mice
GL-HiC-Thyroid__mm10.1000.multires.cool

data_processing:
Fastq files were mapped to the mm10 genome using the distiller pipeline (github.com/mirnylab/distiller-nf). Hi-C interaction data was stored in the cooler format (Abdennur, N., and Mirny, L. (2019).
All replicates for each tissue type were combined into one multires.cool file
Genome_build: mm10
Supplementary_files_format_and_content: Multiresolution cooler files (multires.cool) containing pairwise interactions

source_name: thyroid gland

growth_protocol: Following isolation and during sample preparation thyroid lobes are stored in medium containing TSH - DMEM/F-12; 20% FCS; Penicillin/Streptomycin; 2 mM L-Glut; 40 μg/ml vitamin C; 1 U/ml TSH, in a cell culture incubator at 37 ºC.

extract_protocol:
For each Hi-C library 3-15 million cells were crosslinked
Hi-C was performed as described in Belagzhal et al, 2017, Methods. Restriction enzyme: DpnII

tag: enzyme

value: DpnII

value: thyrocyte

value: thyroid gland


title: DpnII Hi-C on mouse myoblasts - R1

description:
Undifferentiated myoblasts, 15x10^6 cells
GL-HiC-Blasts__mm10.1000.multires.cool

source_name: Muscle cell culture

growth_protocol: Nutrient Mixture F-10 Ham supplemented with 20% fetal bovine serum (FBS) and 1% Penicillin/Streptomycin at 37°C and 5% CO2

value: myoblast

value: muscle

value: Pmi28 mouse myoblasts. Male.


title: CPC_FLKO_3


title: DpnII Hi-C on mouse myotubes - R1

description:
Differentiated myotubes, 10x10^6 cells
GL-HiC-Tubes__mm10.1000.multires.cool

growth_protocol: Myoblasts were seeded at a density of 8 x 10^4 cells/cm2 and incubated in differentiation medium- high glucose DMEM supplemented with 1% Penicillin/Streptomycin and 2% horse serum at 37°C and 5% CO2. Differentiation medium was replaced every 2 days.

value: myotube


title: DpnII Hi-C on mouse thyroid gland - R2


title: BM-H3K4me1-BM_Round1Round2Merged-CelltypesMerged.BM-H3K4me1-BM_Round1Round2Merged-CelltypesMerged

data_processing:
Fastq files were demultiplexed, trimmed, mapped (BWA-0.7.16a, ENSEMBL Build 95) using the single-cell multiomics pipeline: https://github.com/BuysDB/SingleCellMultiOmics
Count tables are 50 kb regions genome-wide across individual cells, counted from bam files
Single-cell data are clustered to create pseudobulk bam files
Bam files are tagged using the single-cell multiomics pipeline (https://github.com/BuysDB/SingleCellMultiOmics). Tagged bams include information such as UMI and cell barcode information. Bam tags are explained on the github: https://github.com/BuysDB/SingleCellMultiOmics/blob/master/TAGS.MD
Genome_build: mm10
Supplementary_files_format_and_content: Cells are annotated by total number of cuts in genome, spike-in cuts, cluster name, UMAP location. Bams come from clustering single cells and generating pseudobulk of each cell type. Count tables quantify cuts in 50 kb genome wide across cells.

source_name: BM

extract_protocol:
Femur and Tibia were extracted, the bones ends were cut away to access the bone marrow which was flushed out using a 22G syringe with HBSS (-ca, -mag, -phenol red, Gibco 14175053) supplemented with Pen-Strep and 1% FCS. The bone marrow was dissociated and debris was removed by passing it through a 70um cell strainer (Corning, 431751). Cells were washed with 25ml supplemented HBSS before depleting the sample of unnucleated cells using IOTest 3 Lysing solution (Beckman Coulter) following provider instructions. Cells were washed additional 2 times with PBS before processing them by the scChIC protocol for the 4 different histone modifications.
Cells were resuspended in 500ul wash buffer (47.5ml H2O RNAse free, 1ml 1M HEPES pH 7.5, 1.5ml 5M NaCl, 3.6ul pure spermidine solution). Aliquot in a 0.5ml protein low-binding tubes (1 per antibody to be used). Following steps are performed on ice.  Cells were pelleted at 600g for 3min and resuspended in 400 ul Wash Buffer 1 (wash buffer with extra 0.05% saponin (Sigma Aldrich), protease inhibitor cocktail (Sigma Aldrich), 4 ul/ml 0.5M EDTA) containing the primary antibody (1:100 dilution for H3K4me1, H3K9me3 and H3K27me3 and 1:200 dilution for H3K4me3, Saponin has to be prepared fresh every time as a 10% solution in PBS). Cells were incubated overnight at 4oC on a roller, before they were washed once with 500 ul Wash Buffer 2 (wash buffer with extra 0.05% saponin, protease inhibitor).  Afterwards cells were resuspended in 500 ul Wash Buffer 2 containing PaMN (3ng/ml) and incubated for 1h at 4C on a roller.  Finally, cells were washed an additional 2 times with 500 ul Wash Buffer 2 before passing it through a 70um cell strainer (Corning, 431751) and sorting them on a JAZZ FACS machine into 384 well plates containing 50nl Wash buffer 3 (Wash buffer containing 0,05% saponin) and 5ul sterile filtered mineral oil (Sigma Aldrich) per well. Small volumes were distributed using a Nanodrop II system (Innovadyme). 50nl of Wash Buffer 3, containing 4uM CaCl2, were added per cell to induce Protein A-MN mediated chromatin digestion that was performed for 30min on ice. Afterwards the reaction was stopped by adding 100nl of a stop solution containing 40mM EGTA (chelates Ca2+ and stops MN), 1.5% NP40 and 10ul 2mg/ml proteinase k (Ambion). Chromatin is subsequently released and PaMN permanently destroyed by proteinase k digestion at 65C for 6h followed by 80C for 20min to heat inactivate proteinase k. Afterwards plates can be stored at -20C until further processing.
DNA fragments are further blunt ended using Klenow large fragment (NEB) and T4 PNK (NEB) in the presence of dNTPs. Afterwards nonintegrated dNTPs are removed using schrimp alkaline phosphatase (NEB) to increase A-tail efficiency. Subsequently blunt fragments are A-Tailed using AmpliTaq™ 360 DNA Polymerase (Thermofisher) in the presence of fresh dATP and T4 PNK (NEB). Next fragments are ligated to T-tail adaptors containing 3 bp UMIs and an 8bp cell barcode (final concentration 9nM from IDT) for 16h at 16C using T4-ligase (NEB). Adaptors were added with a Mosquito HTS (ttp labtech). Ligation products were pooled by centrifugation and cleaned using Ampure XP beads at a bead to sample ratio of 0.8 (Beckman Coulter). The cleaned DNA is then linear amplified by invitro transcription with components of MessageAmp II (Invitrogen) for 16h at 37C. The produced RNA is purified 1-3 times depending on Adaptor dimer contamination using RNA Clean XP beads (Beckman Coulter) at 0.8 beads to sample ratio, followed by RNA fragmentation for 2.5 min at 94C. After another bead cleanup, 20% of the RNA is reverse transcribed with Superscript II (NEB) and PCR amplified to add the Illumina smallRNA barcodes and handles with NEBNext Ultra II Q5 Master Mix. PCR cycles depended on the abundance of the histone modification assayed and the number of RNA cleanup cycles after IVT needed (8-10 for H3K9me3 and H3K27me3 10-12 for H3K4me1 and 12-15 for H3K4me3).

value: BM


title: BM-H3K9me3-BM_Round1Round2Merged-CelltypesMerged.BM-H3K9me3-BM_Round1Round2Merged-CelltypesMerged


title: DpnII HiC on mouse myotubes - R2


title: DpnII Hi-C on mouse myoblasts - R2


title: DpnII Hi-C on mouse thyroid gland - R3


title: BM-H3K4me3-BM_Round1Round2Merged-CelltypesMerged.BM-H3K4me3-BM_Round1Round2Merged-CelltypesMerged


title: BM-H3K27me3-BM_Round2Only-CelltypesMerged.BM-H3K27me3-BM_Round2Only-CelltypesMerged


title: bone marrow nuclei H3K27me3

description:
BM-B6-freshNuclei-H3K27me3-20191008
Bone marow nuclei were incubated with H3K27me3 overnight and 1h with pa-Mnase.

data_processing:
library strategy: scChIC-seq
data was demultiplexed and trimmed with SCMO (https://github.com/BuysDB/SingleCellMultiOmics)
scChIC-seq reads were aligned to mus musculus ensemble build 98 using bwa 0.7.16a-r1181
binned count tables of valid scChIC-seq reads were generated with SCMO(https://github.com/BuysDB/SingleCellMultiOmics)
with ChIX we determined the splitting fraction in the double-incubated samples and splitted the BAM files accordingly
Genome_build: ensemble 98
Supplementary_files_format_and_content: BAM file of mapped reads
Supplementary_files_format_and_content: bigwig files of single, double incubated and split cells
Supplementary_files_format_and_content: text file or comma separated file of the probability fraction used to split the double-incubated samples
Supplementary_files_format_and_content: comma separated file containing the sorted celltypes with corresponding single cell barcode
Supplementary_files_format_and_content: comma separated files of binned counts

source_name: bone marrow nuclei

growth_protocol: Single cell from the mouse bone marrow were extracted.

extract_protocol:
Mouse leg bones ends were cut away to access the bone marrow which was flushed out using a 22G syringe with HBSS (-ca, -mag, -phenol red, Gibco 14175053) supplemented with Pen-Strep and 1% FCS. The bone marrow was dissociated and debris was removed by passing it through a 70um cell strainer (Corning, 431751). Cells were washed with 25ml supplemented HBSS before depleting the sample of unnucleated cells using IOTest 3 Lysing solution (Beckman Coulter) following provider instructions.
DNA fragments are further blunt ended using Klenow large fragment and T4 PNK in the presence of dNTPs. Subsequently blunt fragments are A-Tailed using AmpliTaq 360 DNA Polymerase. Next fragments are ligated to T-tail adaptors containing 3 bp UMIs and an 8bp cell barcode using T4-ligase. Ligation products were pooled by centrifugation and cleaned. The cleaned DNA is then linear amplified by invitro transcription. The produced RNA is purified, followed by DNAse1 digestion and aRNA fragmentation. aRNA is reverse transcribed. Single stranded DNA is purified through RNAseA incubation followed by PCR amplification to add the Illumina smallRNA barcodes and handles.

treatment_protocol: Cells were either fixed with 75% Ethanol or the nuclei was extracted from fresh cells. In case of the ethanol fixed cells three samples were incubated, two with a single antibody and one with a combination of both antibodies against H3K27me3 and H3K9me3 histone modifications. Before FACS-sorting ethanol fixed cells were incubated with surface marker antibodies for different mouse bone marrow cell types. In the case of extracted nuclei, the nuclei were incubated with antibodies against the histone modifications H3K4me1 or H3K27me3 and a combination of both. Single cells wereFACS-sorted without prior selection.

tag: cell/sample type

value: bone marrow nuclei

tag: antibody treatment


title: DpnII Hi-C on mouse myotubes - R3


title: bone marrow nuclei H3K4me1+H3K27me3

description:
BM-B6-freshNuclei-H3K4me1-H3K27me3-20191008
Bone marow nuclei were incubated with H3K4me1 and H3K27me3 overnight and 1h with pa-Mnase.


title: Chick_CB_MC_8

city: Saskatoon

first: Brian

last: Eames

state: Saskatchewan

address: 107 Wiggins Road

department: Anatomy and Cell Biology

country: Canada

institute: University of Saskatchewan

data_processing:
The paired-end Illumina reads were trimmed using Trimmomatic v0.36 (Bolger et al. 2014).
Mapped to the Gallus-gallus-5.0 chicken genome fom Ensembl using STAR v 2.5.3a (Dobin et al. 2013).
TMM normalization (Robinson and Oshlack 2010) was performed using edgeR. Cutoff of genes considered expressed was determined by calculationg the minimum value of the bimodal distribution of counts.
Genome_build: Gallus-gallus-5.0
Supplementary_files_format_and_content: tab-delimited text file includes raw counts for all samples

organism: Gallus gallus

source_name: mature cartilage

extract_protocol:
RNA was isolated using the ARCTURUS PicoPure RNA Isolation Kit (ThermoFisher Scientific; Cat# KIT0204) according to the manufacturer’s instructions and DNase treatment was done using RNase-Free DNase (Qiagen; Cat#79254). RNA was amplified one round using MessageAmp II aRNA Kit (ThermoFisher Scientific; Cat# AM1751). The RNA integrity was evaluated on the observation of a signature electropherogram pattern (Bioanalyzer). A minimum of 5-10 ng of amplified RNA was used per sample for the construction of each library.
RNA-seq libraries were prepared by the National Research Council (NRC, Saskatoon) using the Illumina TruSeq RNA Sample Prep Kit v2 with the following modification: the protocol was started at the Elute, Prime, Fragment step using 5 µl amplified mRNA (the minimum amount was 5-10 ng mRNA as determined using Quant-iT RiboGreen RNA Assay Kit (Invitrogen)).  The quality of each cDNA library was checked on a DNA 1000 chip using the 2100 Bioanalyzer (Agilent Technologies Inc.).

value: White leghorn

value: ceratobranchial

value: wild type


title: MC_11

value: humerus


title: Chick_CB_MC_6


title: MC3


title: Chick_CB_MC_13


title: MC1


title: Chick_CB_IC_14

source_name: immature cartilage


title: Chick_CB_IC_2


title: Chick_bone_17

source_name: bone


title: DpnII Hi-C on mouse myoblasts - R3


title: Chick_Bone_19


title: Chick_Hum_IC3


title: bone marrow nuclei H3K4me1

description:
BM-B6-freshNuclei-H3K4me1-20191008
Bone marrow nuclei were incubated with H3K4me1 overnight and 1h with pa-Mnase.


title: Chick_Hum_MC7


title: Chick_CB_IC_2_1


title: Chick_Hum_MC22


title: DpnII Hi-C on mouse bladder smooth muscle cells - R1

description:
Bladder from 1 mouse
GL-HiC-Bladder__mm10.1000.multires.cool

source_name: bladder

value: smooth muscle

value: bladder


title: IC27-1


title: DpnII Hi-C on mouse bladder smooth muscle cells - R2


title: bone marrow sorted fixed cells H3K27me3

description:
BM-B6-fixedCells-H3K27me3
Bone marrow cells were fixed with 70% ethanol and incubated with H3K27me3 overnight and 1h with pa-Mnase. Before sorting cells were incubated with different surface antibodies against B cells, NK cells, Granulocytes and T-cells.
processed data file: Cellbarcode_BI-tag_for_EtOH-fixed-sorted-celltypes.csv.gz

source_name: bone marrow cells

value: bone marrow cells


title: IC20


title: bone marrow sorted fixed cells H3K9me3+H3K27me3

description:
BM-B6-fixedCells-H3K27me3-H3K9me3
Bone marrow cells were fixed with 70% ethanol andl incubated with H3K27me3 and H3K9me3 overnight and 1h with pa-Mnase. Before sorting cells were incubated with different surface antibodies against B cells, NK cells, Granulocytes and T-cells.
processed data file: Cellbarcode_BI-tag_for_EtOH-fixed-sorted-celltypes.csv.gz


title: bone marrow sorted fixed cells H3K9me3

description:
BM-B6-fixedCells-H3K9me3
Bone marrow cells were fixed with 70% ethanol and incubated with H3K9me3 overnight and 1h with pa-Mnase. Before sorting cells were incubated with different surface antibodies against B cells, NK cells, Granulocytes and T-cells.
processed data file: Cellbarcode_BI-tag_for_EtOH-fixed-sorted-celltypes.csv.gz


title: B3


title: IC1


title: 2052d_48P_PolyIC_F_48

city: Charlottesville

first: David

middle: Michael

last: Johanson

state: VA

address: 200 Jeanette Lancaster Way

department: Department of Neuroscience

institute: UVa School of Medicine

data_processing:
Read Filtering and Trimming: Trimmomatic v0.39 in paired-end mode, phred33 scoring, a 4 bp sliding window, and minimum average, leading, and trailing quality scores of 15, 3, and 3 respectively. Minimum Fragment length was 36 bp.
Read QC Analysis: Performed before filtering and trimming and after filtering and trimming with FastQC v0.11.5
Transcript Quantification: Pseudo-alignment quantification was done with Salmon v0.8.2 with the GENCODE M13 reference genome.
Transcript Conversion: Conversion from ENSEMBL transcript to ENSEMBL gene abundances accomplished with Tximport v1.4.0
Genome_build: GENCODE M13
Supplementary_files_format_and_content: Processed data in quant.sf file format and contain ENSEMBL transcript abundances

growth_protocol: Adult female and adult male (8-12 weeks old) C57BL/6N mice from Taconic were mated overnight, then separated. Presence of a vaginal semen plug the following morning was used to indicate embryonic day 0.5.

extract_protocol:
RNA was extracted from homogenized placental tissues using phenol/cholorform (Trizol reagent).
Libraries were prepared according to manufacturer instructions with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

treatment_protocol: Pregnant female mice received intraperitoneal injection of 20 mg/kg potassium polyI:C or saline at embryonic day 11.5 and 12.5.

value: placenta

tag: date of isolation

tag: perturbation

value: PolyIC

tag: fetal sex

value: F

tag: hours after injection

tag: fetal age at injection

tag: sequencing batch


title: B2

tag: strain

tag: genotype


title: DpnII Hi-C on mouse bladder smooth muscle cells - R3

value: DpnII

tag: cell type


title: B1


title: Msc.SCA1p..DC_1

city: Cambridge

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

description:
Mesenchymal SCA1+ ductal cells grown in a transwell with EpCAM+ ductal cells  for 15 days
RPKM_Experiment2a.csv
Co-cultured Msc SCA1+ d15_1

data_processing:
Reads were mapped to the GRCm38/mm10 UCSC reference genome using STAR aligner (version 2.5.0a).
Raw counts were generated using featureCounts (version 1.6.0) software
RPKMs were generated with raw counts and gene lengths reported by featureCounts package.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: RPKM (csv)

source_name: FACS sorted from liver and cultured

extract_protocol:
Arcturus PicoPure RNA Isolation Kit (Applied Biosystems)
SmartSeq2 followed by NexteraXT tagmentation (according to protocols published in PMID 24385147)

tag: developmental stage

value: Adult (8-12 weeks)

value: Mesenchymal SCA1+ ductal cells

tag: growth

value: liver


title: Msc.SCA1p_1

description:
Mesenchymal SCA1+ ductal cells grown for 15 days
RPKM_Experiment2a.csv
Msc SCA1+ d15_1

value: grown for 15 days

tag: tissue


title: Msc.SCA1p_2

description:
Mesenchymal SCA1+ ductal cells grown for 15 days
RPKM_Experiment2a.csv
Msc SCA1+ d15_2


title: 2052d_48M_Saline_M_48

value: Saline

value: M


title: SMAD4_KO_2

city: Nashville

last: Hanna

state: Tennessee

address: 1211 Medical Center Drive

institute: Vanderbilt University Medical Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Colon

extract_protocol:
three Smad4Lrig1 and three SMAD4+ control mice were dissected one month after administration of tamoxifen. Colons were stripped of crypts. Submucosa was gently scraped from underlying muscle and RNA was made using RNeasy kit (Qiagen, Germantown, MD).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Colon

tag: treatment

value: 1 month post-tamoxifen


title: SMAD4_WT_3


title: 2052d_12P_PolyIC_F_12


title: SMAD4_WT_2


title: Msc.SCA1p.t.0_2

description:
Mesenchymal SCA1+ ductal cells freshly sorted
RPKM_Experiment2a.csv
Msc SCA1+ t=0_2

source_name: FACS sorted from liver

value: wild type

value: freshly sorted


title: 2052d_48O_PolyIC_M_48


title: 2052d_12O_PolyIC_M_12


title: Msc.SCA1p..DC_2

description:
Mesenchymal SCA1+ ductal cells grown in a transwell with EpCAM+ ductal cells  for 15 days
RPKM_Experiment2a.csv
Co-cultured Msc SCA1+ d15_2


title: TH17_DKI_withCCL17_2

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

data_processing:
Subread package (PMC3664803) for mapping RNA-Seq reads to the mouse genome of mm10, featureCounts within the Rsubread R package (PMC6486549) for counting the number of reads mapped to genes, RPKM (PMID: 18516045) for gene expression level.
Genome_build: mm10
Supplementary_files_format_and_content: Txt file, columns from left to right represent "EntrzID", "Gene Symbol", and gene expression values (log2(RPKM+1)) for each sample from this study and three samples from GSE137801.

source_name: DKI Th17 cells with CCL17 during in vitro expansion_2

extract_protocol:
RNA from the purified monocytes and monocyte-derived cells was isolated using RNeasy Plus Mini Kit (Qiagen, Hilden, Germany).
RNA-Seq libraries were built using KAPA mRNA HyperPrep Kit (KAPA Biosystems, Wilmington MA, USA) with 300 ng of total RNA and 11 cycles of PCR according to manufacturer’s recommendation. The libraries were quantified using Qubit Fluorometer, and the quality of the libraries was determined by Bioanalyzer High Sensitivity DNA Analysis (Agilent, Santa Clara, CA, USA).

treatment_protocol: Experimental autoimmune encephalomyelitis (EAE) was induced in mice on a C57BL/6J background by subcutaneously injection of myelin oligodendrocyte glycoprotein peptide emulsified in complete Freund’s adjuvant. Pertussis toxin (250 ng) was injected intraperitoneally at 2- and 24-hours following the injection of emulsion.

value: Spleen and lymph nodes combined

value: CD4+ T cells isolated from the MOG35-55 primed mice, and expanded under Th17 condition in the presence of CCL17 in vitro


title: 2052d_48N_Saline_F_48


title: TH17_DKI_withCCL17_3

source_name: DKI Th17 cells with CCL17 during in vitro expansion_3


title: Msc.SCA1p.t.0_1

description:
Mesenchymal SCA1+ ductal cells freshly sorted
RPKM_Experiment2a.csv
Msc SCA1+ t=0_1


title: TH17_DKI_withCCL17_1

source_name: DKI Th17 cells with CCL17 during in vitro expansion_1


title: TH17_DKI_noCCL17_2

source_name: DKI Th17 cells expanded without the addition of CCL17_2

value: CD4+ T cells isolated from the MOG35-55 primed mice, and expanded under Th17 condition in vitro


title: 2052d_12N_Saline_F_12

value: placenta


title: SMAD4_KO_3


title: TH17_DKI_noCCL17_3

source_name: DKI Th17 cells expanded without the addition of CCL17_3


title: DC..Msc.SCA1p_2

description:
EpCAM+ ductal cells grown in a transwell with mesenchymal SCA1+ cells for 15 days
RPKM_Experiment2a.csv
Co-cultured organoid d15_2

value: EpCAM+ ductal cells


title: TH17_DKI_2

source_name: DKI Th17 cells_2


title: 2052d_12M_Saline_M_12


title: DC..Msc.SCA1p_1

description:
EpCAM+ ductal cells grown in a transwell with mesenchymal SCA1+ cells for 15 days
RPKM_Experiment2a.csv
Co-cultured organoid d15_1


title: SMAD4_WT_1


title: SMAD4_KO_1


title: TH17_DKI_noCCL17_1

source_name: DKI Th17 cells expanded without the addition of CCL17_1


title: TH17_DKI_1

source_name: DKI Th17 cells_1


title: 2052c_24P_PolyIC_F_24

value: PolyIC

value: F


title: TH17_WT_2

source_name: WT Th17 cells_2


title: DC.EM_2

description:
EpCAM+ ductal cells grown in growth-factor rich medium for 15 days
RPKM_Experiment2a.csv
Organoid d15_2

value: Adult (8-12 weeks)


title: TH17_WT_1

source_name: WT Th17 cells_1


title: 2052c_24O_PolyIC_M_24


title: SC-DKI-APCs

source_name: monocyte-derived APCs isolated from the spinal cord following EAE induction

value: Spine cord

value: Antigen presenting cells

value: EAE-induced by active immunzation with MOG35-55 in CFA and pertussis toxin


title: SC-DKI-monocytes

source_name: monocytes isolated from the spinal cord following EAE induction

value: Monocytes


title: 2052c_24N_Saline_F_24

value: Saline


title: DC.EM_1

description:
EpCAM+ ductal cells grown in growth-factor rich medium for 15 days
RPKM_Experiment2a.csv
Organoid d15_1

value: liver


title: 2052c_24M_Saline_M_24

value: M


title: DC.t.0_1

description:
EpCAM+ ductal cells freshly sorted
RPKM_Experiment2a.csv
Ductal cell t=0_1

value: wild type


title: 2052c_12L_PolyIC_F_12


title: 2052c_12K_PolyIC_M_12


title: 2052c_12J_Saline_F_12


title: Lung tissues-MMC treated 3

city: Hunan

first: Qing

last: Song

address: Renmin Road 139

country: China

institute: Central South University

data_processing:
MirDeep2 v 2.0.0.8 software was used to predict new miRNA
The software used for GO and KEGG enrichment analysis was clusterProfiler 3.4.4
network graph drawing software was igraph 1.1.2
Raw sequencing data were assessed for quality by FastQC v0.11.5, cutadapt 1.14 was used to remove connectors, Trimmomatic v 0.36 was used to remove low quality bases at both ends, and reads 3.4.1 were filtered
Genome_build: mm9
Supplementary_files_format_and_content: RPM
Supplementary_files_format_and_content: count

organism: Rattus norvegicus

source_name: Lung tissues

growth_protocol: the rats in the control group were injected intraperitoneally with phosphate buffer saline at the same doses and times.

extract_protocol:
We removed the bronchi, pulmonary arteriovenous and enclosed lung tissue near the right hilum, and tried to take the lung tissue near the periphery for detection under a dissecting microscope.  Finally, pulmonary veins and lung tissue were collected and placed in liquid nitrogen tanks for storage before RNA extraction and western blot
Libraries were prepared according to Illumina's instructions. The main steps for the preparation of miRNA libraries as follows. Firstly, pulmonary vein and lung tissues total RNA was isolated using Trizol reagent (CW0580S, CWBIO, China) and RNA quality was determined by using a Qubit RNA kit (Life Technologies Corporation, CA, USA). Secondly, the 3' end of RNA was spliced using T4 RNA ligase 2 (0511412, NEB, Herts, UK). Thirdly, RT primer was added to the 3' -end ligands for reverse transcription primer hybridization. Fourthly, the  5' end of RNA was spliced using T4 RNA ligase 1 (0011309, NEB, Herts, UK). Then, the cDNA strand of the linker was obtained by reverse transcription. Next, the reverse transcription was amplified by PCR. Finally, the cDNA purity was verified with 12% PAGE gelelectrophoresis, and PCR product bands of about 140-150 bp were recovered. We used a Qubit DNA kit to quantify DNA, and then used for library preparation and Illumina sequencing. Sequencing and analysis of the transcriptome of the samples were performed at Sangon biotech Co., Ltd (Shanghai, China).

treatment_protocol: The rats in the PVOD group were injected intraperitoneally with mitomycin-C (GC12353, GLPBIO, USA) on the first day (2 mg/kg) and eighth days (2 mg/kg),

value: SD

value: Lung

tag: treated

value: Treated with MMC

tag: Sex

value: male


title: Lung tissues-MMC treated 2


title: Lung tissues-MMC treated 1


title: 2052b_6P_PolyIC_F_6

value: placenta


title: Lung tissues 2

value: Untreated


title: 2052b_6O_PolyIC_M_6

value: PolyIC


title: Lung tissues 1


title: DC.t.0_2

description:
EpCAM+ ductal cells freshly sorted
RPKM_Experiment2a.csv
Ductal cell t=0_2

value: EpCAM+ ductal cells

value: freshly sorted


title: 2052b_6N_Saline_F_6

value: F


title: TCDD 2 [scRNA]

city: Kansas City

first: Khursheed

last: Iqbal

state: Kansas

address: 3901 Rainbow Blvd

department: Pathology

institute: University of Kansas Medical Center

data_processing:
The Cell Ranger Single-Cell Software Suite (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) was used to perform sample demultiplexing, barcode processing, and single-cell 3' gene counting. The reads were aligned to the rn6 reference genome. BAM files produced by the 10x Genomics/Cell Ranger pipeline
Genome_build: rn6
Supplementary_files_format_and_content:  Genes.tsv, Barcodes.tsv, Matrix.mtx

source_name: Uterine tissue

extract_protocol: Single cells were captured into droplets using 10x chromium device followed by preparation of single-cell cDNA libraries with the 10x protocol.

value: gestational day 13.5

tag: agent

value: TCDD


title: Huh7_1

type: RNA

city: Bellinzona

first: Giada

last: Sandrini

address: Via Chiesa 5

institute: IOR

hyb_protocol: Whole Genome Gene Expression Direct Hybridization

scan_protocol: Illumina HiScan

data_processing: The data were normalised using quantile method  Signal calculated by GenomeStudio Data Analysis Software’s Gene Expression Module (GSGX) Version 1.5.4 (Illumina, Inc.)

label: biotin

source_name: cell line

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification Kit for Illumina arrays

extract_protocol: RNA extraction was performed using a commercially available kit (RNeasy, Qiagen, Frederick,MD) according to the manufactures’ recommendations. RNA quality was confirmed based on a RNA integrity number >8 by use of an electrophoresis bioanalyzer (2100 Agilent Bioanalyser).

tag: cell line

tag: replicate


title: Soraf-R4_1


title: Lung tissues 3


title: 2052c_12I_Saline_M_12

tag: date of isolation

tag: perturbation


title: Soraf-R4_3


title: NaïveCD4_TCR_2h_HC3

city: London

first: Paul

last: Lavender

address: 5th Floor, Tower Wing, Great Maze Pond

department: School of Immunology and Microbial Sciences

institute: King's College London

description:
HC3
200673740059_H

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina Genome Studio

label_protocol: Biotinylated cRNA were prepared with the Ovation PicoSL WTA System V2 from NuGen for Illumina arrays

growth_protocol: Isolated PBMCs from GPA and HC blood were cryopreserved until naive CD4 T cell isolation by usting magnetic beads isolation kit from eBioscience. Isolated naive CD4 T cells were rested overnight in RPMI media including 10% FBS and penicillin streptomycin

extract_protocol: RNA was extrated by using the Allprep DNA/RNA micro kit from Qiagen according to manufacturer’s protocol.

treatment_protocol: Rested naive CD4 T cells were incubated with or without plate bounded anti-CD3 and anti-CD28 antibodies for 2hours prior RNA isolation.

tag: subject status

value: healthy control (HC)

tag: antibody

value: Not available

value: human peripheral naive CD4 T cells


title: NaïveCD4_rested_HC5

description:
HC5
200673740059_K

value: rested


title: TCDD 1 [scRNA]


title: NaïveCD4_rested_HC2

description:
HC2
200673740059_E


title: NaïveCD4_rested_HC3

description:
HC3
200673740059_G


title: Soraf-R4_2


title: 2052b_6M_Saline_M_6

value: Saline

tag: fetal sex

value: M

tag: hours after injection

tag: fetal age at injection

tag: sequencing batch


title: Huh7_3


title: NaïveCD4_rested_GPA6

description:
GPA6
200673740047_J

value: Granulomatosis with Polyangiitis (GPA) patient

value: C ANCA

tag: cell type


title: NaïveCD4_TCR_2h_HC5

description:
HC5
200673740059_L


title: 2052b_12H_PolyIC_F_12

tag: strain


title: NaïveCD4_TCR_2h_HC2

description:
HC2
200673740059_F


title: Huh7_2


title: NaïveCD4_TCR_2h_HC4

description:
HC4
200673740059_J


title: NaïveCD4_rested_HC4

description:
HC4
200673740059_I


title: NaïveCD4_TCR_2h_GPA6

description:
GPA6
200673740047_L


title: 2052b_12G_PolyIC_M_12

tag: tissue


title: NaïveCD4_rested_GPA5

description:
GPA5
200673740047_I

tag: treatment


title: 2052b_12F_Saline_F_12


title: NaïveCD4_rested_GPA4

description:
GPA4
200673740047_G


title: NaïveCD4_TCR_2h_GPA4

description:
GPA4
200673740047_H


title: TCDD 3

data_processing:
Following generation of sequencing images, the pixel-level raw darta collection, image analysis, and base-calling were performed by Real Time Analysis software (Illumina)
Base call files were converted to qseq files by BCL converter (Illumina), and qseq files were converted to fastq files for downstream analysis.
Reads from fastq files were mapped to the rat reference genome (Rnor_5.0.7) using CLC Bio Genomics Workbench 7.0 (CLC Bio, Aarhus, Denmark)
Genome_build: Rnor6
Supplementary_files_format_and_content: excel file containing reads per kilobase per million reads (RPKM).

source_name: uterine placental interface

extract_protocol:
RNA was extracted from uterine tissue  using TriReagent according to the manufacturer's recommendations.
Libraries were prepared from poly-A containing RNAs according to protocols provided by the TruSeq RNA sample preparation kits (Illumina).

value: uterine placental interface

tag: developmental stage


title: TCDD 4


title: TCDD 2


title: NaïveCD4_TCR_2h_GPA5

description:
GPA5
200673740047_K


title: 2052a_3O_PolyIC_M_3

value: placenta


title: TCDD 1


title: OIL 1 [scRNA]

value: OIL


title: OIL Control 4

value: control


title: 2052a_3N_Saline_F_3


title: 2052a_3P_PolyIC_F_3

value: PolyIC


title: NaïveCD4_TCR_2h_GPA3

description:
GPA3
200673740047_F

value: P ANCA


title: H246 PDGF-BB 10 ng/mL 24 h (CS373)

city: Auckland

first: Leon

last: Smyth

address: 85 Park Road

country: New Zealand

institute: University of Auckland

data_processing:
Illumina sequenceers (Novaseq 6000) were used to generate pair-ended reads
Raw data returned as FASTQ files was filtered for adapters, low quality reads and polyA sequences with Trimmomatics (v0.38)
Filtered paired-end reads from each sample was then aligned to reference genome, Homo Sapiens GRCh38, using HISAT2 (v2.1.0)
The aligned reads were then assembled and quantified by StringTie (v1.3.4).
Transcript abundance tables were then generated using Ballgown (R version 3.5.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw counts and FPKM values for every gene in every sample

source_name: Pericyte

growth_protocol: Pericytes were derived from the middle temporal gyrus from autopsy specimens

extract_protocol:
mRNA was extracted using RNeasy® mini kit (Qiagen, Netherlands) as per manufacturer’s instructions from duplicate wells. Samples quality was verified with Nanodrop, Agarose Gel Electrophoresis and Agilent 2100. Any samples with a RIN < 8, low quantity or purity was discarded.
Standard illumina protocols were used to generate RNA libraries

treatment_protocol: Pericyte cultures were treated with PDGF-BB 10ng/ml at 1h and 24h

value: Primary human pericyte culture

value: 10 ng/ml PDGF-BB 24 hr

tag: disease state

value: Neurologically normal


title: H246 PDGF-BB 10 ng/mL 1 h (CS372)

value: 10 ng/ml PDGF-BB 1 hr


title: E8 72 hrs

city: Macau

first: Ren

last: Zhili

address: Avenida da Universidade

institute: University of Macau

hyb_protocol: cRNA was hybridized onto HumanHT-12 v4 Expression BeadChip (Illumina) using standerd protocol.

scan_protocol: BeadChips were scanned with the iScanner (Illumina).

data_processing: Data was normalized by quantile normalization.

source_name: Human embryonic stem cell H1

label_protocol: RNA was converted to cRNA using the TargetAmp™-Nano Labeling Kit for Illumina Expression BeadChip (Epibio).

growth_protocol: Human ESCs (H1) were maintained in E8 medium on matrigel-coated plates with daily medium change. When the confluence of ESC is about 80%, the cells were passaged with Y27632 3 μM by 1:12 dilution.

extract_protocol: Toatal RNA was isolated by RNAiso Plus.

treatment_protocol: Human embryonic stem cell (hESC) H1 was cultured in E8 medium for 3 days (E8 72 hrs), and nicotinamide 10 mM was added into E8 medium for 3 days treatment (Nam 72 hrs) with daily medium change.

value: ESCs (H1)

tag: agent

value: E8 medium


title: H246 Veh (CS371)

value: untreated


title: OIL Control 3


title: 2052b_12E_Saline_M_12

value: Saline


title: NaïveCD4_rested_GPA3

description:
GPA3
200673740047_E

value: human peripheral naive CD4 T cells

value: rested


title: NaïveCD4_TCR_2h_GPA2

description:
GPA2
200673740047_D

value: Granulomatosis with Polyangiitis (GPA) patient


title: H209 PDGF-BB 10 ng/mL 24 h (CS370)


title: 2052a_3M_Saline_M_3

value: M


title: NaïveCD4_rested_GPA2

description:
GPA2
200673740047_C


title: 2052a_12D_PolyIC_F_12

value: placenta

value: F


title: H209 PDGF-BB 10 ng/mL 1 h (CS369)


title: OIL Control 2

value: control

value: uterine placental interface


title: H209 Veh (CS368)


title: 2052a_12C_PolyIC_M_12

value: PolyIC


title: P38i

source_name: hESC-induced Cardiomyocytes at day 10 of differentiation

growth_protocol: Human ESCs (H1) were maintained in E8 medium on matrigel-coated plates with daily medium change. For cardiac differentiation, CHIR99021 5 μM was used for 1 day to induce mesoderm differentiation in E5 basal medium, and then IWP-2 3 μM was applied from day 2 to day 5 as differentiation control. Nicotinamide or SB202190 was added from day 1 to day 5 to induce cardiomyocytes. After that, the differentiated cells were maintained in E5 basal medium for another 2 days, and then insulin 10 μg/mL was added to E5 medium for long time culture.

treatment_protocol: For cardiac differentiation, CHIR99021 5 μM was used for 1 day (day 0) to induce mesoderm differentiation in E5 basal medium, and then nicotinamide 10 mM or SB202190 10 μM was added after CHIR99021 withdrawal, and treated for 4 days (day 1 to day 5) with daily change of medium. IWP-2 3 μM was applied from day 2 to day 5 as differentiation control. After that, the differentiated cells were continued to maintain in E5 basal medium for another 2 days, and then insulin 10 μg/mL was added to E5 medium for long time culture. At day 10 of differentiation, the cells were harvested for microarray analysis.


title: H189 PDGF-BB 10 ng/mL 24 h (CS367)

value: Primary human pericyte culture


title: NaïveCD4_rested_GPA1

description:
GPA1
200673740047_A

value: P ANCA


title: OIL Control 1


title: H189 PDGF-BB 10 ng/mL 1 h (CS366)

value: Neurologically normal


title: Nam

value: Nam


title: Control

value: Control

value: ESCs (H1)


title: IWP-2


title: NaïveCD4_TCR_2h_GPA1

description:
GPA1
200673740047_B


title: 1911c_48L_PolyIC_F_48


title: 2052a_12A_Saline_M_12


title: OIL 2 [scRNA]

value: gestational day 13.5

value: OIL


title: 1911c_48I_Saline_M_48

value: Saline


title: C9: mRNA_hFibroblast_lenti_suptRNA_rep3

city: Worcester

first: Yue

last: Zhang

address: GeneTherapyCenter, 368 Plantation st

institute: Umass medical school

data_processing:
3′ adapter sequence were removed using Trimmomatic (with parameters ILLUMINACLIP, minlength, 10; seed mismatches, 2; palindrome clip threshold, 30; simple clip threshold, 5)
Then, reads were mapped to mm10 mouse genome or hg38 human genome using STAR。
To estimate expression levels, RSEM was used to align reads to a predefined set of transcripts from GENCODE. Finally, the RSEM quantification matrix, i.e., estimated counts for each gene and/or for each annotated isoform, was used for differential gene expression analysis. Count matrix was loaded into DEBrowser software for interactive analysis.
Genome_build: mm10 or hg38
Supplementary_files_format_and_content: Matrix table with raw transcript counts for each sample
Supplementary_files_format_and_content: tab-delimited text files include differential expression analysis for each Sample

source_name: human fibroblast

extract_protocol:
RNA from mouse liver samples was extracted RNA by RNeasy plus mini kit (Qiagen). Paramagnetic beads coupled with oligo d(T)25 are combined with total RNA to isolate poly(A)+ transcripts based on NEBNext® Poly(A) mRNA Magnetic Isolation Module manual (New England BioLabs Inc.,).
Prior to first strand synthesis, samples are randomly primed (5´ d(N6) 3´ [N=A,C,G,T]) and fragmented based on manufacturer’s recommendations. The first strand is synthesized with the Protoscript II Reverse Transcriptase with a longer extension period, approximately 30 minutes at 42⁰C. All remaining steps for library construction were used according to the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (New England BioLabs Inc.,). Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® NovaSeq S4 (Illumina, California, USA) with a read length configuration of 150 PE for 40 M PE reads per sample (20M in each direction).

treatment_protocol: 6-week old C57BL/6 wild type male mice were injected with  rAAV9_mCherry and rAA9.2xsup-tRNATyr by IV. 4 weeks post injection,  mice were transcardially perfused with ice-cold PBS, and tissues were immediately dissected, snap-frozen in liquid nitrogen, and stored under -80 °C. For human fibroblast, Idua +/- (GM00799, Coriell Institute) were treated with lenti-EGFP or lenti-EGFP_sup-tRNATyr.

value: fibroblast

tag: genotype

value: Idua+/-

value: human fibroblast


title: C7: mRNA_hFibroblast_lenti_suptRNA_rep1


title: 1911c_24L_PolyIC_F_24

value: placenta


title: 2052a_12B_Saline_F_12

value: F


title: H189 Veh (CS365)

value: untreated


title: DCC40 (RNA-seq)

city: Houston

first: James

middle: Cushing

last: Bayley

address: One Baylor Plaza

department: Neurosurgery

institute: Baylor College of Medicine

data_processing:
Raw reads from the RNA-seq data were processed using an in-house pipeline that uses STAR for read alignment; FastQC and RSeQC (for read and alignment quality assessment) and in-house pipeline for expression count.
The reads were aligned to GRCh38 Human reference genome and mapping to the human transcriptome according to UCSC gene annotations.
Genome_build: hg38
Supplementary_files_format_and_content: CSV file of the raw counts data for the entire cohort of 110 primary meningiomas.

source_name: meningioma

extract_protocol: FFPE fixed tumor samples were sent, along with whole blood, to Tempus (Tempus Labs | 600 West Chicago Ave, Suite 510 | Chicago, IL 60654) for whole exome RNA-sequencing according to their protocol.

value: meningioma tumor


title: C4: mRNA_hFibroblast_lenti-EGFP_rep1

value: lenti-EGFP


title: C5: mRNA_hFibroblast_lenti-EGFP_rep2


title: DCC53 (RNA-seq)


title: DCC43 (RNA-seq)


title: DCC38 (RNA-seq)


title: DCC51 (RNA-seq)


title: 1911c_48K_PolyIC_M_48

value: PolyIC

value: M


title: C6: mRNA_hFibroblast_lenti-EGFP_rep3


title: 1911c_24K_PolyIC_M_24


title: Nam 72 hrs

value: E8 medium with nicotinamide 10 mM


title: 1911c_48J_Saline_F_48


title: DCC36 (RNA-seq)


title: PBMC_RA4_IL-1B_ST2825

city: Atlanta

first: Sergio

last: Ramirez-Perez

state: Georgia

address: 615 Michael St NE

department: Orthopaedics

institute: Emory University

data_processing:
NovaSeq 6000 Paired-end sequencing was used, PE150, Q30≥85%.
Sequenced reads were mapped to the hg19 human genome assembly using Strand NGS v4.0, normalization was performed using DESeq with a threshold at 1 for all aligned reads. We obtained 57736 genes.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table - delimited text files include normalized expression levels for each sample

source_name: PBMC

extract_protocol:
PBMC from RA patients and healthy controls were cultured and RNA was harvested using Trizol reagent.
Human mRNA Sequencing (WOBI) was used to perform RNA sample QC. Poly A enrichment was implemented for mRNA library preparation. NovaSeq PE150 was used to generate 6 G raw data per sample.

value: PBMC

tag: diagnosis

value: Rheumatoid arthritis


title: PBMC_RA4_LPS_ST2825

value: LPS + ST2825


title: PBMC_RA3_LPS_ST2825


title: DCC37 (RNA-seq)


title: 1911c_24J_Saline_F_24

tag: date of isolation


title: PBMC_RA3_IL-1B_ST2825


title: PBMC_RA2_IL-1B_ST2825


title: C8: mRNA_hFibroblast_lenti_suptRNA_rep2


title: DCC42 (RNA-seq)


title: DCC35 (RNA-seq)


title: PBMC_RA2_LPS_ST2825


title: 1911b_6K_PolyIC_M_6

tag: perturbation


title: PBMC_RA4_ST2825


title: 1911b_6J_Saline_F_6


title: 1911c_24I_Saline_M_24


title: PBMC_RA4_IL-1B


title: PBMC_RA3_ST2825


title: 1911b_6I_Saline_M_6


title: DCC34 (RNA-seq)


title: PBMC_RA2_ST2825


title: DCC32 (RNA-seq)


title: DCC33 (RNA-seq)


title: PBMC_RA4_LPS

value: LPS


title: PBMC_RA3_IL-1B


title: 1911b_6L_PolyIC_F_6


title: DCC31 (RNA-seq)


title: PBMC_RA3_LPS


title: 1911b_24H_PolyIC_F_24


title: PBMC_RA2_LPS


title: 1911b_24F_Saline_F_24


title: DCC30 (RNA-seq)


title: DCC29 (RNA-seq)


title: 1911b_24G_PolyIC_M_24


title: PBMC_RA4_UTx

value: Untreated


title: PBMC_RA3_UTx


title: 1911b_24E_Saline_M_24

value: Saline


title: PBMC_RA2_IL-1B


title: PBMC_CS1_UTx

value: Healthy


title: PBMC_CS4_UTx


title: DCC28 (RNA-seq)


title: DCC27 (RNA-seq)


title: 1911a_24C_PolyIC_M_24


title: DCC25 (RNA-seq)


title: 1911a_24B_Saline_F_24


title: 1911a_24A_Saline_M_24


title: DCC23 (RNA-seq)


title: DCC22 (RNA-seq)


title: 1911a_144P_PolyIC_F_144


title: DCC21 (RNA-seq)


title: DCC19 (RNA-seq)


title: 1911a_144O_PolyIC_M_144


title: DCC13 (RNA-seq)


title: 1911a_144M_Saline_M_144


title: 1911a_144N_Saline_F_144


title: DCC18 (RNA-seq)


title: 1855b_48G_PolyIC_M_48


title: 1855b_48H_PolyIC_F_48


title: 1911a_24D_PolyIC_F_24


title: DCC09 (RNA-seq)


title: DCC12 (RNA-seq)


title: 1855b_48E_Saline_M_48


title: RNA-seq_VC_UV Round 2_re-analyzed

city: Saint Louis

first: Ryan

last: McCulla

state: Missouri

address: 3501 Laclede Ave

department: Chemistry

institute: Saint Louis University

description:
Control - cells treated with 1% DMSO in VC and UV-A irradiated for 30 minutes in a photoreactor with 8 LZC-UVA bulbs
Union_for_cluster-round2
fpkm_genename-round2
fpkm_group-round2
fpkm_sample-round2
readcount_genename-round2
readcount-round2
1-S_UVvsVC_UV_DEG
VC_UVvsVC_NoUV_DEG-2
Re-analysis of GSM4680435

data_processing:
Data analysis: Downstream analysis was performed using a combination of programs including STAR, HTseq, Cufflink and our wrapped scripts. Alignments were parsed using Tophat program and differential expressions were determined through DESeq2/edgeR. GO and KEGG enrichment were implemented by the ClusterProfiler. Gene fusion and difference of alternative splicing event were detected by Star-fusion and rMATS software
Reads mapping to reference genome: Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result for junction reads.
Quantification of gene expression level: HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Mortazavi et al., 2008).
Differential expression analysis: Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.16.5). The P values were adjusted using the Benjamini & Hochberg method.
Clustering: To identify the correlation between difference, we clustered different samples using expression level FPKM to see the correlation using hierarchical clustering distance method with the function of pheatmap package in R
Genome_build: Homo_sapiens_hg19 (1-SO_NoUV and 1-SO_UV)  and Homo_sapiens_hg38 ( (Sample  1-S_UV and 1-S_NoUV)
Supplementary_files_format_and_content: xls files include FPKM count of each sample and DEG list for each comparison.

source_name: breast cancer cells

growth_protocol: MDA-MB-231 cell line was purchased from ATCC (Manassas,VA). The cells were incubated at 37°C in 95% relative humidity with 5% CO2. The cells were cultured in DMEM medium containing 10% FBS, and 1% L-glutamine. The cells were grown to 90% confluency and passaged by removing media, washing the cells with PBS buffer, and splitting the cells.

extract_protocol:
Following treatment protocol, cell media was aspirated and each well was washed with PBS. 350 µL of lysis buffer (included in Gen Elute™ Total RNA Purification Kit) was added. Wells were coated in lysis buffer for 5 minutes and transfered to seperate microcetrifuge tubes. 200 µL absolute ethanol was added and tubes were vortexed for 10 seconds. Columns were assembled with elution tubes and the lysates were applied directly onto seperately assembled columns. Tubes were centrifuged at 3,500 g for 1 minute. If lysate hasn't passed through the column. Centrifuge an additional minute at 14,000 g. Flowthrough was discarded. 400 µL of wash solution A was applied to each column and centrifuged for 1 minute at 3,500 g (or increased to 14,000 g as necessary). Flowthrough was discarded and the column was washed twice more with a 2 minute centrifuge time for the last wash. The columns were placed into fresh elution tubes and 50 µL of elution solution was added to each. The columns were centrifuged at 200 g for 2 minutes, followed by 14,000 g for 1 minute. The elution procedure was repeated to maximize yield. Samples were stored at -80 C until shipping at -20 C.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. The mRNA was fragmented by addition of fragmentation buffer. NEB library and strand specific libraries were then chosen. (Novogene Corporation - protocol associated with NEB library and strand specific library) Libraries were constructed using standard Illumina protocol.

treatment_protocol: MDA-MB-231 cells (600,000 cells/1.8mL/well) were plated on a six-well plates. The plates were incubated with compounds (10uM-final concentration) for 24 hours (VC - 1% DMSO). For UV experiment, one plate was placed in a Luzchem photoreactor equipped with 8 LZC-UVA bulbs  (fwhm, 325-375 nm) for 30 minutes and for the No_UV experiment, the plate was covered with an aluminum foil for 30 minutes

tag: cell line

tag: passage

value: 1 percent DMSO in VC  and UV-A irradiated for 30 minutes in a photoreactor with 8 LZC-UVA bulbs


title: RNA-seq_1-S_UV

description:
Sample - cells treated with 10uM of 1-S and UV-A irradiated for 30 minutes in a photoreactor with 8 LZC-UVA bulbs
Union_for_cluster-round2
fpkm_genename-round2
fpkm_group-round2
fpkm_sample-round2
readcount_genename-round2
readcount-round2
1-S_UVvs1-S_NoUV_DEG
1-S_UVvsVC_NoUV_DEG
1-S_UVvsVC_UV_DEG


title: RNA-seq_VC_UV Round 1_re-analyzed

description:
Control - cells treated with 1% DMSO in VC and UV-A irradiated for 30 minutes in a photoreactor with 8 LZC-UVA bulbs
Union_for_cluster-round1
fpkm_genename-round1
fpkm_group-round1
fpkm_sample-round1
readcount_genename-round1
readcount-round1
1-SO_UVvsVC_UV_DEG
VC_UVvsVC_NoUV_DEG-round1
Re-analysis of GSM4680433


title: DCC10 (RNA-seq)


title: RNA-seq_VC_No UV Round 2_re-analyzed

description:
Control - cells treated with 1%DMSO in VC
Union_for_cluster-round2
fpkm_genename-round2
fpkm_group-round2
fpkm_sample-round2
readcount_genename-round2
readcount-round2
1-S_NoUVvsVC_NoUV_DEG
1-S_UVvsVC_NoUV_DEG
VC_UVvsVC_NoUV_DEG-2
Re-analysis of GSM4680434

value: 1 percent DMSO in VC


title: H929_WT_IP

city: Nan jing

first: Feng

middle: Jie

last: Jiang

state: Jiangsu

address: Xianlin Avenue 138

department: School of Medicine&Holistic Integrative Medicine

institute: Nanjing University of Chinese Medicine

data_processing:
library strategy: m6A-seq
150 bp paired-end reads were mapped to the reference human genome build GRCh38/hg38 by using Bowtie2.
Only unique mapping paired reads were sorted using SAMtools and kept for subsequent analysis.
Peaks of each samples and differential methylation peak were called  using the exomePeak R-package.
Genome_build: GRCh38/hg38

source_name: wildtype(WT) cells cells for m6a-seq

extract_protocol:
RNA fragments were incubated with anti-N6-methyladenosine (m6A) antibodies (Sigma-Aldrich, Burlington, USA) inimmunoprecipitation (IP) buffer for 2 h at 4℃. The samples were then washed with low-salt precipitation buffer and high-salt buffer thrice continuously. RNA was extracted using a phenol-chloroform lysate to obtain a purified product.
The purified RNA was collected for the generation of an RNA-seq library with NEBNext R Ultra™ RNA Library Prep Kit (New England Biolabs, MA, USA). The quality of the library was done using Bioptic Qsep100 analyzer and sequencing was done using NovaSeq's high-throughput sequencing platform

value: Multiple Myeloma cells

value: wildtype


title: 1855b_144L_PolyIC_F_144

value: placenta

tag: fetal sex

value: F


title: DCC06 (RNA-seq)

value: meningioma tumor


title: RNA-seq_1-S_No UV

description:
Sample - cells treated with 10uM of 1-S
Union_for_cluster-round2
fpkm_genename-round2
fpkm_group-round2
fpkm_sample-round2
readcount_genename-round2
readcount-round2
1-S_NoUVvsVC_NoUV_DEG
1-S_UVvs1-S_NoUV_DEG

value: 10uM of 1-S


title: 1855b_144K_PolyIC_M_144

value: PolyIC

value: M

tag: hours after injection


title: RNA-seq_1-SO_UV

description:
Sample - cells treated with 10uM of 1-SO and UV-A irradiated for 30 minutes in a photoreactor with 8 LZC-UVA bulbs
Union_for_cluster-round1
fpkm_genename-round1
fpkm_group-round1
fpkm_sample-round1
readcount_genename-round1
readcount-round1
1-SO_UVvsVC_NoUV_DEG
1-SO_UVvsVC_UV_DEG


title: 1855b_144I_Saline_M_144

tag: fetal age at injection


title: 1855b_48F_Saline_F_48

tag: sequencing batch


title: ARP1_WT_IP

tag: cell type


title: H929_shHNRNPA2B1_IP

source_name: HNRNPA2B1 kockdown(KD) cells for m6a-seq

value: knockdown


title: ARP1_shHNRNPA2B1_IP


title: ARP1_WT_input

source_name: wildtype(WT) cells cells for input RNA


title: 1855b_144J_Saline_F_144

tag: strain


title: H929_WT_input