title: ST2-U3C,interferon alpha,72h,IRF9,rep2

data_processing:
Quality assessment of raw reads was performed with FastQC
Alignment to the GRCh38.106 human genome assembly was done with Bowtie2 v2.4.1 and BAM files were sorted by SAMTools v1.6. PCR duplicates were removed using BamUtil v1.0.15
Peaks were called with MACS v2.2.6 with the significance cut-off q-value 0.01 and -nomodel -call-summits options. For peak annotation and motif enrichment (GAS and ISRE) HOMER v4.11 was used
In order to generate STAT1, STAT2, IRF9, pSTAT1 and pSTAT2 binding profiles upon IFN alpha treatment matrices were computed across 4 kb region centered on ChIP-Seq peak summits with deepTools v3.5.0 (reference-point TSS, upstream region 3000 bp, downstream region 1000 bp). Further steps were performed with profileplyr_1.10.0 R package
Data processing steps described above are valid for 2fTGH and ST2-U3C cell lines. Huh7.5 STAT1 K.O. has been processed in the same way as Huh7.5 wild-type cells submitted previously as part of GSE222668 SuperSeries
Assembly: hg38
Supplementary files format and content: narrowPeak for 2fTGH and ST2-U3C cell lines; regionPeak for Huh7.5 STAT1 K.O. (high-confidence peaks obtained after IDR evaluation between biological replicates - optimal output peak set; https://www.encodeproject.org/data-standards/terms/)

value: Human fibrosarcoma

tag: chip antibody

value: IRF9 (SantaCruz, #sc-10793)


title: Human female MIX tumor, rep2

status: Public on Nov 15 2023

type: SRA

city: Jerusalem

first: nofar

last: rosenberg

address: Hadassah University Hospital

country: Israel

institute: Hebrew university

library_source: transcriptomic

data_processing:
Assembly: GRCh38
The first 12 nucleotides of each read were trimmed with the FASTX package (v0.0.14), then adapter sequences were removed with Cutadapt (v1.12). Low quality reads were filtered out with the FASTX package, v0.0.14, using parameters -q 20 and -p 90.
Reads were aligned with Tophat (v2.1.1), using parameters -G genes.gtf (from Ensembl release 89), -N 2, --read-gap-length 5, --read-edit-dist 7, --segment-length 18, --read-realign-edit-dist 3, --no-coverage-search and --library-type fr-secondstrand.
Raw counts were obtained with htseq-count (v0.6.0), then normalization and differential expression were calculated with the R package DESeq2 (v1.12.4), using default parameters, except setting independentFiltering=F.
Supplementary files format and content: DESeq2_final_M.xlsx: columns A-J, general gene details; K-AB, raw counts; AC-AT, normalized counts; AU, baseMean (average expression); AV-AZ, result comparing HCC to DR samples; BA-BE, results comparing MIX to DR samples; BF-BJ, results comparing MIX to HCC samples.
Supplementary files format and content: DESeq2_final_H.xlsx: columns A-J, general gene details; K-AB, raw counts; AC-AT, normalized counts; AU, baseMean (average expression); AV-AZ, result comparing ICC to HCC samples; BA-BE, results comparing MIX to HCC samples; BF-BJ, results comparing MIX to ICC samples.

molecule: total RNA

organism: Homo sapiens

source_name: liver

extract_protocol:
Snap-frozen liver tissue samples were obtained, and 10 µm-thick sections were obtained by cryostat microtomy.  Tumor areas were localized by hematoxylin and eosin staining. Laser capture microdissection was performed using the Leica LMD6500 system. Total mRNA was extracted using RNeasy Plus Micro Kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions.
Libraries were prepared using the Lexogen QuantSeq 3′mRNA-Seq Library Prep Kit FWD (Lexogen, Vienna, Austria) which was followed by an amplification step according to the manufacturer’s instructions.

tag: tissue

value: liver

tag: cell type

value: HCC-CCA tumor

tag: gender

value: female


title: TG01b

first: Kirsi

middle: J.

last: Rautajoki

address: Arvo Ylpön katu 34

country: Finland

institute: Tampere University

description: patient TG01

data_processing:
Base-calling Illumina HiSeq 2000
Aligment STAR 2.7.0 against human genome assembly GRCh38 using GENCODE v.30 annotations
Gene counts using featureCounts Rsubread package v. 1.34.6
Differential expression and normalization using DESeq2
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including normalized gene expression values for each sample

source_name: brain

extract_protocol:
mirVana™ miRNA Isolation Kit (Life Technologies), large RNA (>200 nucleotides) molecules were divided into a separate fraction
Illumina, strand-specific 140-160 bp short insert library protocol

value: brain

tag: malignancy

value: IDHmut astrocytoma

tag: Sex

value: male

tag: age group_at_primary_diagnosis

tag: tumor stage

value: grade 4

tag: treatment

value: radiation and chemotherapy (PCV)


title: e12.5 mouse MGE, Nkx2.1-CreC/+;Ezh2;Ai9F/+_3

city: Bethesda

first: Timothy

last: Petros

state: Maryland

address: 35 Convent Drive, Bg 35 Room 3B-1002

country: USA

institute: NICHD

library_source: genomic

data_processing:
The Illumina NovaSeq's paired-end run produced two compressed fastq.gz files for each replicate.
Adaptor sequences were trimmed in individual fastq files using cutadapt.
The trimmed read files were then aligned to the reference genome using bowtie2, resulting in output .sam files. The .sam files were converted into .bam files using samtools view -Sb and samtools sort.
Multimappers were removed from each .bam file using samtools view with a parameter -q 20. Subsequently, Picard MarkDuplicates was used to remove PCR duplicates from the .bam files.
BigWig files from the deduplicated .bam files were created using bamCoverage. Peaks were called using epic2.
Assembly: GRCm38/mm10
Supplementary files format and content: bigwig for CUT&Tag reads
Supplementary files format and content: bed for CUT&Tag peaks
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Mus musculus

source_name: MGE

extract_protocol:
E12.5 and E15.5 embryos were removed and placed in ice-cold carbogenated ACSF. Tails were clipped for PCR genotyping. During genotyping, embryonic brains were harvested and MGEs were dissected from each embryo and stored in ice-cold carbogenated ACSF. For E12.5, the entire MGE was removed as previously described92. For E15.5, the MGE was dissected under a fluorescent dissecting microscope to ensure collection of only Tom+ MGE cells and minimize collection of postmitotic MGE-derived cells in the striatum anlage and other ventral forebrain structures. Upon obtaining genotyping results (~90 minutes), MGEs from embryos of the same genotype were combined (when applicable) to generate single nuclei dissociations. MGEs were transferred to a 1 mL Dounce homogenizer containing DNA Lysis Buffer (10 mM Tris-HCl (Ph.7.4), 10 mM NaCl, 3 mM CaCl2, 0.1% Tween-20, 1.5% BSA and 0.1% IGEPAL CA-630 in nuclease-free water, 1 mL per sample). Lyse cells by douncing with pestle A and pestle B, ~10-15 times each. Place a 40 μm filter onto a pre-chilled 50 mL conical tube on ice and wet with 1 mL of DNA Nuclei Wash Buffer (in mM: 10 Tris-HCl (Ph.7.4), 10 NaCl, 3 CaCl2, with 0.1% Tween-20 and 1.5% BSA in nuclease-free water, 5 mL per sample). Transfer lysed nuclei suspension through pre-wetted filter, then rinse dounce with 1 mL Nuclei Wash Buffer and transfer through filter. Divide nuclei suspension into 2 pre-chilled 2 mL tubes and spin at 500 g for 5 minutes at 4oC. After removing supernatant, wash nuclei pellet once with 1 mL Nuclei Wash Buffer and then once with 1 mL of 1X CUT&Tag Wash Buffer (from Active Motif CUT&Tag IT Assay kit). Remove CUT&Tag Wash Buffer, leaving ~30-50 μL in each, triturate and combine nuclei suspensions from both tubes. Nuclei concentration was determined on Countess II FL Automated Cell Counter. 100,000-125,000 nuclei were used for each CUT&Tag reaction. Proceed with CUT&Tag IT Assay Kit (Active Motif, #53610) per manufacturer’s instructions. Primary antibody was H3K27me3 (Cell Signaling, 9733T, 1:50) or H3K27ac (Cell Signaling, and secondary antibody was guinea pig anti-rabbit (Active Motif, 105465 from CUT&TagIT kit, 1:100).
DNA quantity was determined with a Thermo Qubit and library quality characterized with an Agilent Tapestation. Libraries were balanced for DNA content and pooled before performing a final SPRIselect bead 1x left size selection and paired-end sequenced (50 x 50 bp) on an Illumina NovaSeq.

value: MGE

tag: genotype

value: KO

tag: developmental stage

tag: biological replicate


title: e15_Het_2

data_processing:
Paired-end run Illumina NovaSeq produced 2 compressed fastq.gz files for each replicate. For each age (E12.5 and E15.5) and each genotype, a total of 3 different biological reps from 3 different experiments were combined. Duplicate reads from sequencing were removed and fastq_processing was executed to produce .bam and .bam.bai files for each replicate. For each genotype, ‘samtools merge -o’ was used to merge 3 sorted alignment biological replicates .bam files into one output file. The biological replicates were used to create bigwig files and for MACS peak calling. The biological bio.bam files also underwent bam_processing and had duplicates removed. The resulting biological nodup.bam files were merged using samtools to produce the final WT, Het, and KO replicates.
Assembly: GRCm38/mm10
Supplementary files format and content: bw for CUT&Tag signal
Library strategy: CUT&Tag

value: Het


title: 2fTGH,interferon alpha,24h,STAT1,rep1

city: Poznan

first: Hans

last: Bluyssen

address: Uniwersytetu Poznańskiego 6

department: Laboratory of Human Molecular Genetics

country: Poland

institute: Adam Mickiewicz University

source_name: Human fibrosarcoma

growth_protocol: DMEM; 10% fetal bovine serum (FBS); 2mM L-glutamine; 100 IU/ml penicillin,100 µg/ml streptomycin,250 ng/ml amphotericin B. Cells were cultured at 37C at 5% CO2

extract_protocol:
Cells were cross-linked with DSG for 30 min (or 45min for Huh STAT1KO) and then with formaldehyde for 10 min. After fixation chromatin was sonicated with a Diagenode Bioruptor Plus to generate 200–1000 bp fragments
ChIP-Seq libraries were performed using TruSeq ChIP Library Preparation Kit or NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina. 5-10ng of DNA was used as starting material. Libraries were amplified on the thermocycler. Post amplification libraries were size selected at 200-800bp using gel extraction (TruSeq) or 200bp using Agencourt AMPure XP beads (NEBNext). Libraries were then quantified using Qubit dsDNA HS assay kit and quality was assessed by the Agilent 2100 Bioanalyzer (High Sensitivity DNA Kit).

treatment_protocol: Cells were starved with medium containing 1% FBS and subsequently treated with 1000U/mL of IFN alpha up to 72h

tag: cell line

value: STAT1 (SantaCruz, #sc-346)


title: Human female MIX tumor, rep1


title: e12.5 mouse MGE, Nkx2.1-CreC/+;Ezh2;Ai9F/+_2


title: TG01a

description: patient TG01

value: grade 3

value: treatment naive


title: 2fTGH,interferon alpha,72h,IRF9,rep2


title: Human male HCC tumor, rep3

value: HCC tumor


title: e12.5 mouse MGE, Nkx2.1-CreC/+;Ezh2;Ai9F/+_1


title: Human male HCC tumor, rep2


title: PND1 WT Female Room Air

city: Philadelphia

first: Abiud

last: Cantu

state: Pennsylvania

address: 3615 Civic Center Blvd

department: Neonatology

institute: Children's Hospital of Philadelphia

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
To generate the metadata files. We first converted the cellranger output to a Seurat v4.1.1 object. Then we performed data filtering using SoupX v1.6.1,  doublet removal using DoubletFinder v 2.0.3. We used Seurat's PercentageFeatureSet to get percent of mitochondrial genes in each cell. Resulting cells were filtered using >= 500 molecular identifiers (nUMI >= 500), removing upper number of UMI outliers (nUMI <= outlier_threshold_nUMI), >250 detectable genes (nGene >= 250), removing upper number of gene outliers (nGene <= outlier_threshold_nGene), log10GenesPerUMI > 0.80, < 5% of transcripts coming from mitochondrial genes (mitoRatio < 0.05). Genes were filtered, only keeping those genes expressed in more than 10 cells. Genes 'Gm42418', 'S100a8', 'S100a9' were removed from Seurat object. We ran SCTransformV2 and Get clusters, resolution 0.6 was chosen. We integrated PND 1 and PND 21 respectively using Seurat's integration method. We got clusters again for the integrated object choosing a resolution of 0.6 and labeled each cluster based on markers given by Seurat's FindMarkers.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: Comma-separated metadata table.

source_name: Lung

growth_protocol: WT C57BL/6N mice were subjected to timed mating. Neonatal mouse pups from different litters were randomized to the treatment (hyperoxia) or control (room air) conditions. Mice were transitioned to room air on PND5.

extract_protocol:
The right ventricle was perfused with ice cold PBS and the lungs were harvested quickly and homogenized and dissociated using the Miltenyi MACS lung dissociation kit (Miltenyi Biotec, cat # 130-095-927), using the GentleMacs program m-Lung-1 on the AUTO MaCs. The lungs were incubated for 20min at 37 ◦C under continuous rotation and then run on the gentleMACS m-Lung-2 program on the gentleMACS (Miltenyi Biotec, Cat #130-095-937). This was followed by brief centrifugation and the passage of cells through the 70-uM filter, washed, centrifuged again and the pellet was treated with ACK lysis buffer, centrifuged, and resuspended in sorting buffer and passed through an 40uM filter. Live cells were sorted and subjected to single-cell RNA sequencing.
Single cell Gene Expression Library was prepared according to Chromium Single Cell Gene Expression 3v3.1 kit (10x Genomics). In Brief, single cells, reverse transcription (RT) reagents, Gel Beads containing barcoded oligonucleotides, and oil were loaded on a Chromium controller (10x Genomics) to generate single cell GEMS (Gel Beads-In-Emulsions) where full length cDNA was synthesized and barcoded for each single cell. Subsequently the GEMS are broken and cDNA from each single cell are pooled. Following cleanup using Dynabeads MyOne Silane Beads, cDNA is amplified by PCR. The amplified product is fragmented to optimal size before end-repair, A-tailing, and adaptor ligation. Final library was generated by amplification.

treatment_protocol: C57BL/6N neonatal mice were exposed to room air or hyperoxia from PND1-5 to 95% FiO2 or mainatined in room air. Mice were euthanized at PND21.

value: Lung

tag: age

value: PND 1

value: Mixed

value: WT

value: Room Air

value: Female


title: Human male MIX tumor, rep1

value: liver

value: HCC-CCA tumor


title: e12_Het_3


title: SET_Hypoxia small RNA #2

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

description: Hela cells with sgSETDB1 exposed to 1% oxygen for 6 hours

data_processing:
Illumina Casava1.7 software used for basecalling.
The reads were mapped to hg19 using bowtie1 (v.1.2.3).
Quantification of repetitive elements were calculated using a RepEnrich (v.1.2) standard protocol.
Heat map was constructed using Mev (v. 4.9.0). Statistical analyses were performed using R (v. 3.3.0) and PYTHON (v. 2.7.6).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include log2CPM (count per million) values for each sample

source_name: cervical cancer cells

growth_protocol: Hela cells with sgControl and sgSETDB1  were routinely generated by re-plating d 3 adherent cultures (typically 2–3× 106 cells into a 100mm dish) in DMEM medium (Gibco) supplemented with 10% FBS (Gibco) and 1X anti-anti (Gibco)

extract_protocol:
RNA-seq : Total RNA was isolated from cells using Trizol reagent and the quality of the RNA was confirmed by agarose gel electrophoresis.
RNA-seq : TruSeq Stranded mRNA Sample Preparation Guide, Part #15031047 Rev. The sequencing library was prepared using the IlluminaTruSeq Stranded mRNA LT Sample Prep Kit (Illumina).
RNA-seq : The mRNA derived from total RNA using poly-T oligo-attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.

treatment_protocol: Cells were exposed to Hyopxia (1% O2) for 6 hours or Normoxia ( ordinary incubator)

tag: strain

value: Human epithelial uterus adenocarcinoma

tag: molecular subtype

value: total RNA

tag: sgrna


title: SET_Hypoxia small RNA #1


title: SET_Normoxia small RNA #2

description: Hela cells with sgSETDB1


title: Stigma, P. syriaca, rep3 [SMWS]

first: Yuval

last: Nevo

address: Ein Kerem Campus

institute: The Hebrew University of Jerusalem

description:
processed data columns: A-E, microRNA annotations, including pre-miR name and genomic location; mature miR name, aliases (other mature miRs with the exact same sequence) and sequence; F-K, stigma exudates data, ExAA and ExAS for P. pyrifolia, ExEu for P. communis, ExWG, ExWM and ExWS for P. syriaca; L-Q, stigma tissue data, SMAA and SMAS for P. pyrifolia, SMEu for P. communis, SMWG, SMWM and SMWS for P. syriaca.
SMWS

data_processing:
Trimming raw reads with Cutadapt, v1.1, using a quality threshold of 32, removing adapter and poly-A sequences that were added by the CATS kit, and keeping reads 18 to 28 bases long.
Filtering low quality reads with fastq_quality_filter, FASTX package v0.0.14, using -q 20 and -p 85.
Alignment and counting of microRNAs expression with miRExpress, v2.0, using the ‘Raw_data_parse’, ‘alignmentSIMD’ and ‘analysis’ steps. Reference microRNAs were taken from miRBase, version 22, using all Rosaceae species in the database - Fragaria vesca, fve; Malus domestica, mdm; and Prunus persica, ppe. Alignment allowed up to 7% mismatches and mature microRNA assignment allowed for offset of up to 11 bases and required at least 50% overlap.
Mature microRNAs having the exact same sequence were collapsed to a unique representative, averaging the counts from all its appearances in the dataset.
Identified miRs were further analyzed to find potential targets in the plant A. thaliana, using the web server 'psRNATarget' with default parameters and expectation threshold <=2.5. Enrichment analysis using AgriGO2 was performed on the lists of potential targets in Arabidopsis.
Assembly: miRBase version 22
Supplementary files format and content: raw_counts_all.xlsx: an Excel file with a single header row, followed by a row for each unique mature microRNA in the dataset of Rosaceae miRs from miRBase v22. Columns A-E include miRs annotations; columns F-K include the data for stigma exudates samples; columns L-Q include the data for stigma tissue samples.
Supplementary files format and content: Supporting_dataset_1.docx: details of miRs identified in stigma exudates and tissue, as explained within the file.
Supplementary files format and content: Supporting_dataset_2.xlsx: potential target genes in A. thaliana, as given by 'psRNATarget'. Includes two sheets, one for exudate miRs and one for stigma specific ones.
Supplementary files format and content: Supporting_dataset_3.xlsx: enriched GO terms. Includes two sheets, one for predicted targets of exudate miRs and one for predicted targets of stigma specific miRs.
Supplementary files format and content: Supporting_dataset_4.xlsx: potential target genes of exudate miRs in A. thaliana pollen transcriptome.

organism: Pyrus syriaca

source_name: Stigma tissue

extract_protocol:
Stigma lobes were randomly excised from several flowers at 12 hours after anthesis (HAA). Stigma exudates were collected in a nondestructive manner as described earlier (Pusey et al., 2008). RNA was isolated with the cf-RNA isolation  kit, NORGEN BIOTEK, #29600.
Libraries were prepared using CATS Small RNA kit (C05010044), then size selected by 4% agarose gel.

treatment_protocol: Blooming branches were collected at the field during spring 2018 (March-April), immediately placed in water cans and transferred after removing all the open flowers, for overnight acclimation in growth room (day/night cycles of 16 h at 24 °C and 8 h at 18 °C, humidity of 40–60% and white light of 120–130 µmol/m2 sec).

value: Stigma tissue

tag: cultivar

value: Wild

tag: altitude

tag: sampling time

value: 12 HAA


title: Human male HCC tumor, rep1

tag: tissue

tag: cell type

tag: gender

value: male


title: e12_Het_2

value: MGE

value: Het


title: Stigma, P. syriaca, rep2 [SMWM]

description:
processed data columns: A-E, microRNA annotations, including pre-miR name and genomic location; mature miR name, aliases (other mature miRs with the exact same sequence) and sequence; F-K, stigma exudates data, ExAA and ExAS for P. pyrifolia, ExEu for P. communis, ExWG, ExWM and ExWS for P. syriaca; L-Q, stigma tissue data, SMAA and SMAS for P. pyrifolia, SMEu for P. communis, SMWG, SMWM and SMWS for P. syriaca.
SMWM


title: TG02a

description: patient TG02

value: brain

tag: malignancy

value: IDHmut oligoastrocytoma

tag: Sex

value: female

tag: age group_at_primary_diagnosis

value: grade 3

value: treatment naive


title: SET_Normoxia small RNA #1

description: Hela cells with sgSETDB1


title: e12_Het_1

tag: genotype


title: Stigma, P. syriaca, rep1 [SMWG]

description:
processed data columns: A-E, microRNA annotations, including pre-miR name and genomic location; mature miR name, aliases (other mature miRs with the exact same sequence) and sequence; F-K, stigma exudates data, ExAA and ExAS for P. pyrifolia, ExEu for P. communis, ExWG, ExWM and ExWS for P. syriaca; L-Q, stigma tissue data, SMAA and SMAS for P. pyrifolia, SMEu for P. communis, SMWG, SMWM and SMWS for P. syriaca.
SMWG


title: KO brain, mouse e15.5

description: 10x Genomics

library_source: genomic single cell

data_processing:
The Cell Ranger ARC (v2.0.0) pipeline was used to process sequenced libraries with default parameters unless otherwise noted. Demultiplexed FASTQ files were generated by cellranger-arc mkfastq from BCL files. Reads were aligned to custom-built mouse (GRCm38/mm10) reference genome modified to express tdTomato using cellranger-arc count. Reads with de-duplicated and valid cell barcodes were used to build peak-by-barcode matrices by cellranger-arc count per genotype.
Assembly: GRCm38/mm10
Supplementary files format and content: cellranger atac_fragments.tsv.gz
Supplementary files format and content: cellranger atac_peak_annotation.tsv

extract_protocol:
E12.5 and E15.5 embryos were removed and placed in ice-cold carbogenated ACSF. Tails were clipped for PCR genotyping. During genotyping, embryonic brains were harvested and MGEs were dissected from each embryo and stored in ice-cold carbogenated ACSF. For E12.5, the entire MGE was removed as previously described92. For E15.5, the MGE was dissected under a fluorescent dissecting microscope to ensure collection of only Tom+ MGE cells and minimize collection of postmitotic MGE-derived cells in the striatum anlage and other ventral forebrain structures. Upon obtaining genotyping results (~90 minutes), MGEs from embryos of the same genotype were combined (when applicable) to generate single nuclei dissociations. MGEs were transferred to a 1 mL Dounce homogenizer containing Multiome Lysis Buffer (in mM: 10 Tris-HCl (Ph.7.4), 10 NaCl, 3 CaCl2, 1 DTT, with 0.1% Tween-20, 1.5% BSA and 0.1% IGEPAL CA-630 in nuclease-free water, 1 mL per sample). Lyse cells by douncing with pestle A and pestle B, ~10-15 times each. Place a 40 μm filter onto a pre-chilled 50 mL conical tube on ice and wet with 1 mL of Multiome Nuclei Wash Buffer (in mM: 10 Tris-HCl (Ph.7.4), 10 NaCl, 3 CaCl2, 1 DTT, with 0.1% Tween-20, 1.5% BSA and 1 U/μL in nuclease-free water, 5 mL per sample). Transfer lysed nuclei suspension through pre-wetted filter, then rinse dounce with 1 mL Multiome Wash Buffer and transfer through filter. Divide nuclei suspension into 2 pre-chilled 2 mL tubes and spin at 500 g for 5 minutes at 4oC. After removing supernatant, wash nuclei pellet twice with 1 mL Multiome Wash Buffer and spin as above. Remove Multiome Wash Buffer, leaving ~20-30 μL of solution in each tube. Triturate solution to dissociate pellets, then combine nuclei suspensions into 1 tube. Nuclei concentration was determined on Countess II FL Automated Cell Counter. Nuclei suspensions were diluted to ~3,000-4,000 nuclei/μL, with 5 μL being used for 10x Genomics Multiome kit per manufacturer’s instructions. E15.5 data: MGE from 4 WT, Het and KO embryos from 2 different E15.5 litters were combined to generate 1 biological rep. E12.5 data: MGE from 1 WT, Het and KO mouse from a single E12.5 litter were used to generate 1 biological rep. Total cell numbers that passed QC: E12.5 WT = 6,391; E12.5 Het = 6,608; E12.5 KO = 8,546; E15.5 WT = 11,477; E15.5 Het = 10,027; E15.5 KO = 8,607.
Joint libraries for scRNA-seq and scATAC-seq were created using 10X Genomics Single Cell Multiome ATAC + Gene Expression kit (1000285) by following manufacturer’s protocols.

value: KO


title: Exudates, P. syriaca, rep2 [ExWM]

description:
processed data columns: A-E, microRNA annotations, including pre-miR name and genomic location; mature miR name, aliases (other mature miRs with the exact same sequence) and sequence; F-K, stigma exudates data, ExAA and ExAS for P. pyrifolia, ExEu for P. communis, ExWG, ExWM and ExWS for P. syriaca; L-Q, stigma tissue data, SMAA and SMAS for P. pyrifolia, SMEu for P. communis, SMWG, SMWM and SMWS for P. syriaca.
ExWM

source_name: Stigma exudates

value: Stigma exudates


title: Human female HCC tumor, rep2

value: liver

value: HCC tumor


title: Human female HCC tumor, rep3


title: Con_Hypoxia small RNA #2

description: Hela cells with sgControl exposed to 1% oxygen for 6 hours

value: Human epithelial uterus adenocarcinoma

value: negative control


title: Con_Hypoxia small RNA #1

value: total RNA


title: Exudates, P. syriaca, rep1 [ExWG]

description:
processed data columns: A-E, microRNA annotations, including pre-miR name and genomic location; mature miR name, aliases (other mature miRs with the exact same sequence) and sequence; F-K, stigma exudates data, ExAA and ExAS for P. pyrifolia, ExEu for P. communis, ExWG, ExWM and ExWS for P. syriaca; L-Q, stigma tissue data, SMAA and SMAS for P. pyrifolia, SMEu for P. communis, SMWG, SMWM and SMWS for P. syriaca.
ExWG

value: Wild


title: Het brain, mouse e15.5

description: 10x Genomics


title: WT brain, mouse e15.5

description: 10x Genomics

value: WT


title: Con_Normoxia small RNA #2

description: Hela cells with sgControl


title: Fv-untreatment-3

city: yangzhou

first: yuchen

last: zhou

address: daxue southern road

country: China

institute: yangzhou university

data_processing:
The compound treatment was 0 and 2 g Luvangetin (2), which were represented by group A and group B, respectively. F.verticillioides was beaten into a 5 mm diameter block with a hole punch, a block was inoculated in liquid medium, and Luvangetin (2) was added after 3 days of culture in a constant temperature incubator at 28°C, and the hyphae were sampled after another 3 days of culture. The experiment is set up with three replicates.
Assembly: Fusarium verticillioides7600

organism: Fusarium verticillioides

source_name: mycelium

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: mycelium

value: fungus

value: fungus cell

tag: treatment

value: none luvangetin


title: Con_Normoxia small RNA #1

description: Hela cells with sgControl


title: Human male ICC tumor, rep1

value: ICC tumor

value: male


title: Human male ICC tumor, rep2


title: KO brain, mouse e15.5, lane 1 (R1, R2, I1, I2) & lane 2 (R3, R4, I3, I4)

description: 10x Genomics

data_processing:
The Cell Ranger ARC (v2.0.0) pipeline was used to process sequenced libraries with default parameters unless otherwise noted. Demultiplexed FASTQ files were generated by cellranger-arc mkfastq from BCL files. Reads were aligned to custom-built mouse (GRCm38/mm10) reference genome modified to express tdTomato using cellranger-arc count. Reads with de-duplicated and valid cell barcodes were used to build gene-by-barcode matrices by cellranger-arc count per genotype.
Assembly: GRCm38/mm10
Supplementary files format and content: cellranger filtered_feature_bc_matrix.h5

value: MGE


title: SET_Hypoxia #2

description: Hela cells with shSETDB1 exposed to 1% oxygen for 6 hours

data_processing:
Illumina Casava1.7 software used for basecalling.
The reads were mapped to hg19 using STAR v2.5.1.
Read counts were calculated using a STAR standard protocol.
Heat map was constructed using Mev (v. 4.9.0). Statistical analyses were performed using R (v. 3.3.0) and PYTHON (v. 2.7.6).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include log2CPM (count per million) values for each sample

extract_protocol:
RNA-seq : Total RNA was isolated from cells using Rneasy plus mini kit reagent and the quality of the RNA was confirmed by agarose gel electrophoresis.
RNA-seq : TruSeq Stranded mRNA Sample Preparation Guide, Part #15031047 Rev. The sequencing library was prepared using the IlluminaTruSeq Stranded mRNA LT Sample Prep Kit (Illumina).
RNA-seq : The mRNA derived from total RNA using poly-T oligo-attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.

treatment_protocol: Cells were exposed to Hyopxia (1% O2) for 12 hours or Normoxia ( ordinary incubator)

tag: shRNA


title: Human female ICC tumor, rep3

value: female


title: Fv-untreatment-1

tag: cell line


title: WT brain, mouse e15.5, lane 1 (R1, R2, I1, I2) & lane 2 (R3, R4, I3, I4)

description: 10x Genomics

tag: age


title: Fv-treatment-3

value: luvangetin


title: Exudates, P. syriaca, rep3 [ExWS]

description:
processed data columns: A-E, microRNA annotations, including pre-miR name and genomic location; mature miR name, aliases (other mature miRs with the exact same sequence) and sequence; F-K, stigma exudates data, ExAA and ExAS for P. pyrifolia, ExEu for P. communis, ExWG, ExWM and ExWS for P. syriaca; L-Q, stigma tissue data, SMAA and SMAS for P. pyrifolia, SMEu for P. communis, SMWG, SMWM and SMWS for P. syriaca.
ExWS

value: Stigma exudates

value: 12 HAA


title: Human female ICC tumor, rep2

value: liver


title: Human female HCC tumor, rep1

value: HCC tumor


title: SET_Normoxia #2

description: Hela cells with shSETDB1

tag: strain

value: Human epithelial uterus adenocarcinoma


title: Human male ICC tumor, rep3


title: Fv-treatment-1


title: Human female ICC tumor, rep1


title: Het brain, mouse e12.5, lane 1 (R1, R2, I1, I2) & lane 2 (R3, R4, I3, I4)

description: 10x Genomics

value: Het


title: sgIkzf1_Tex_5

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

data_processing:
Adapter sequences were removed using cutadapt v.1.9
and aligned them to the mouse genome mm10 (GRCm38_68 from Sanger;ftp://ftp-mouse.sanger.ac.uk/ref/GRCm38_68.fa) using the Burrows–Wheeler algorithm32(version 0.5.9-r26-dev, default parameter)
duplicated reads were then marked with Picard (version 1.65 (1160)) and only non-duplicated reads were kept, using samtools (parameter ‘-q 1 -F 1024’ version 0.1.18 (r982:295))
After adjustment using the Tn5 shift (by which reads were offset by +4bp for the sense strand and −5bp for the antisense strand), we separated reads into nucleosome-free, mononucleosome, dinucleosome and trinucleosome by fragment size
performed peak-calling for nucleosome-free reads using MACS2(version 2.1.0.20150603, default parameters with ‘–extsize 200 –nomodel’, merged by bedtoolsif within 100bp) for individual samples
Assembly: mm10
Supplementary files format and content: Consensus peaks and fragment counts for all samples

source_name: sgRNA-transduced OT-I cells from the dual-color transfer system at day 7 post adoptive transfer to B16-OVA tumor

growth_protocol: OT-I cells transduced with indicatd sgRNAs were sorted from B16-OVA tumor

extract_protocol:
Cells were lysed in 50μl ATAC-seq lysis buffer (10mM Tris-HCl, pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630 detergent) on ice for 10min. Resulting nuclei were pelleted at 500gfor 10min at 4 °C. Supernatant was carefully removed with a pipette and discarded. The pellet was resuspended in 50μl transposase reaction mix (25μl 2×TD buffer, 22.5μl nuclease-free water, 2.5μl transposase) and incubated for 30min at 37 °C. After the reaction, the DNA was cleaned up using the Qiagen MinElute kit
The barcoding reaction was run using the NEBNext HiFi kit on the basis of the manufacturer’s instructions and amplified for five cycles


title: WT brain, mouse e12.5, lane 1 (R1, R2, I1, I2) & lane 2 (R3, R4, I3, I4)

description: 10x Genomics


title: Con_Hypoxia #2

description: Hela cells with shControl exposed to 1% oxygen for 6 hours

tag: molecular subtype

value: total RNA

value: shControl


title: sgIkzf1_Tpex_5

value: sgRNA-transduced OT-I cells from the dual-color transfer system at day 7 post adoptive transfer to B16-OVA tumor


title: Con_Hypoxia #1


title: spike for sgIkzf1_Tex_5


title: Con_Normoxia #2

description: Hela cells with shControl


title: DF-1 cells, shNC, 48h,rep1

city: wuhan

first: qijun

last: wu

address: shizishan street

institute: huazhong agriculture university

data_processing:
Raw reads were aligned with Hisat2.
Alignment result were sorted with samtools.
Sorted alignment result was counted with stringTie to acquire the expression count matrix.
Differential analysis was conducted with DEseq2.
Assembly: galGal6
Supplementary files format and content: tab-delimited text files include counts for each Sample

organism: Gallus

growth_protocol: DF-1 cells were maintained in DMEM supplemented with 15% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1ug of total RNA was used for the construction of sequencing libraries.
Total RNA was used as input material for the RNA sample preparations. Sequencinglibraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA,Catalog #: E7530L) following manufacturer’s recommendations and index codes wereadded to attribute sequences to each sample.

treatment_protocol: DF-1 cells were treated with 100 μM CoCl2 for 4、24、48 h to induce hypoxia.

value: fibroblast

value: WT

value: hypoxia


title: Fv-treatment-2

value: mycelium

value: fungus

value: fungus cell


title: DF-1 cells, shNC, 24h,rep1


title: DF-1 cells, shNC, 24h,rep2


title: Insert4_male_cigarette-smoke_exposed

city: Baltimore

first: Baishakhi

last: Ghosh

state: MD

address: 615 N Wolfe St, E7209

department: Environmental Health and Engineering

institute: Johns Hopkins University - Bloomberg School of Public Health

description:
DESeq2_Male_Air_CS.csv
Normalized_Counts_Male_Air_Male_CS_Female_Air_Female_CS.csv
MCS4

data_processing:
Galaxy web platform - Usegalaxy.org
Quality control of raw data (raw reads) was verified using FastQC (version 0.11.9).
Low-quality bases, adapter contamination, and trimming reads to a specific length was performed by Trimmomatic (Galaxy Version 0.38.0).
The paired-end clean reads were aligned to the reference genome using HISTAT2.
HTseq-count was used to count aligned reads that overlapped with the reference mouse genome.
DESeq2 was used to determine differentially expressed features from count tables.
Assembly: Reference mouse genome GRCm38/mm10 (Accession ID: GCA_000001305.2, Assembly date: December 2011) - mm10.refGene.gtf.gz
Supplementary files format and content: tab-delimited text files

source_name: trachea

growth_protocol: Mice tracheal epithelial cells (mTECs) from male and female mice were expanded in submerged culture using PneumaCultTM-Ex Plus medium (Stemcell Technologies, Vancouver, Canada) in a humidified atmosphere with 5% CO2 at 37°C. The cells were differentiated into pseudostratified epithelium at an air-liquid interface using PneumaCultTM-ALI medium  (Stemcell Technologies, Vancouver, Canada) for 10 to 14 days in a humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA was harvested using NucleoSpin® TriPrep kit (Takara Bio USA, Inc., San Francisco, California, USA).
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: The differentiated pseudostratified epithelium from male and female mTECs was exposed to either cigarette smoke or humidified air for ten days. One cigarette smoke exposure consisted of 2 cigarettes that burned for ~8 minutes using the ISO puff regimen.

value: trachea

value: primary epithelial  cells

value: pseudostratified epithelium

value: Wild-type FVB/NJ

value: male

value: Cigarette-smoke exposure


title: Con_Normoxia #1

description: Hela cells with shControl

value: Human epithelial uterus adenocarcinoma


title: DF-1 cells, shNC, 48h,rep2


title: spike for sgIkzf1_Tpex_5


title: sgIkzf1_Tex_4


title: Insert3_male_cigarette-smoke_exposed

description:
DESeq2_Male_Air_CS.csv
Normalized_Counts_Male_Air_Male_CS_Female_Air_Female_CS.csv
MCS3


title: Insert2_male_cigarette-smoke_exposed

description:
DESeq2_Male_Air_CS.csv
Normalized_Counts_Male_Air_Male_CS_Female_Air_Female_CS.csv
MCS2


title: DF-1 cells, shNC, 4h,rep2


title: skeletal muscle KD [A56]

city: Würzburg

first: Jan

last: Dudek

address: Am Schwarzenberg 15

department: Department of Translational Research, Comprehensive Heart Failure Center

country: Germany

institute: University Clinic Würzburg

data_processing:
Raw fastq of 150bp paired-end reads were mapped to mouse reference genome (mm10 GRCm38) using RNA STAR  with default settings.
Read counts were derived using tool FeatureCounts v1.6.4.
Differential expression analysis was performed using Deseq2 version 2.11.40.6
Assembly: mm10 GRCm38
Supplementary files format and content: tab delimited text file stores the raw read counts for each sample

source_name: skeletal muscle

extract_protocol:
Total RNA was isolated using RNAeasy mini kit (Qiagen) from frozen mouse heart and femur muscle.
The library preparation and whole transcriptome sequencing were performed using Illumina platform by Novogene UK.
After the QC procedures, rRNA is removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs(dUTP, dATP, dGTP and dCTP), RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Then followed by purification by AMPure XP beads, terminal repair, polyadenylation, sequencing adapter ligation, size selection and degradation of second-strand U-contained cDNA by the USER enzyme. The strand-specific cDNA library was generated after the final PCR enrichment.

treatment_protocol: Doxycycline (625 mg/kg) was administered as part of the standard rodent chow to WT C57BL/6N mice and transgenic (ROSA26H1/tetO-shRNA:TAZ) animals to induce Taz knockdown. WT and transgenic animals recieived Doxycycline treatment  until the end of experiment at an age of 20 weeks.

value: skeletal muscle

value: Taz-KD

value: Doxicycline


title: sgIkzf1_Tpex_4

value: sgRNA-transduced OT-I cells from the dual-color transfer system at day 7 post adoptive transfer to B16-OVA tumor


title: DF-1 cells, shNC, 4h,rep1

value: fibroblast


title: Insert6_male_cigarette-smoke_exposed

description:
DESeq2_Male_Air_CS.csv
Normalized_Counts_Male_Air_Male_CS_Female_Air_Female_CS.csv
MCS6


title: spike for sgIkzf1_Tex_4


title: Insert5_male_cigarette-smoke_exposed

description:
DESeq2_Male_Air_CS.csv
Normalized_Counts_Male_Air_Male_CS_Female_Air_Female_CS.csv
MCS5


title: skeletal muscle KD [A52]


title: DF-1 cells, shNC, 0h,rep2

value: WT


title: spike for sgIkzf1_Tpex_4


title: Insert6_male_air_exposed

description:
DESeq2_Male_Air_Female_Air.csv
Normalized_Counts_Male_Air_Male_CS_Female_Air_Female_CS.csv
MA6

value: Air exposure


title: skeletal muscle KD [A39]


title: skeletal muscle KD [A58]


title: sgIkzf1_Tex_3


title: DF-1 cells, shNC, 0h,rep1

value: hypoxia


title: sgIkzf1_Tpex_3


title: skeletal muscle wild type [A57]


title: skeletal muscle KD [A34]


title: DF-1 cells, shHIF1A, 48h,rep2

value: HIF1A knockdow


title: DF-1 cells, shHIF1A, 48h,rep1


title: spike for sgIkzf1_Tex_3


title: Insert3_male_air_exposed

description:
DESeq2_Male_Air_Female_Air.csv
Normalized_Counts_Male_Air_Male_CS_Female_Air_Female_CS.csv
MA3


title: Fv-untreatment-2

value: mycelium

value: fungus

value: fungus cell

value: none luvangetin


title: skeletal muscle wild type [A55]


title: spike for sgIkzf1_Tpex_3


title: Insert5_male_air_exposed

description:
DESeq2_Male_Air_Female_Air.csv
Normalized_Counts_Male_Air_Male_CS_Female_Air_Female_CS.csv
MA5

value: trachea

value: primary epithelial  cells

value: pseudostratified epithelium

value: Wild-type FVB/NJ


title: skeletal muscle wild type [A51]

value: skeletal muscle


title: Insert1_male_cigarette-smoke_exposed

description:
DESeq2_Male_Air_CS.csv
Normalized_Counts_Male_Air_Male_CS_Female_Air_Female_CS.csv
MCS1

value: male

value: Cigarette-smoke exposure


title: sgIkzf1_Tex_2

value: sgRNA-transduced OT-I cells from the dual-color transfer system at day 7 post adoptive transfer to B16-OVA tumor


title: DF-1 cells, shHIF1A, 24h,rep1

value: fibroblast


title: Insert2_male_air_exposed

description:
DESeq2_Male_Air_Female_Air.csv
Normalized_Counts_Male_Air_Male_CS_Female_Air_Female_CS.csv
MA2


title: Insert1_male_air_exposed

description:
DESeq2_Male_Air_Female_Air.csv
Normalized_Counts_Male_Air_Male_CS_Female_Air_Female_CS.csv
MA1


title: skeletal muscle wild type [A40]

value: WT

value: Doxicycline


title: Insert4_male_air_exposed

description:
DESeq2_Male_Air_Female_Air.csv
Normalized_Counts_Male_Air_Male_CS_Female_Air_Female_CS.csv
MA4

value: Air exposure


title: DF-1 cells, shHIF1A, 4h,rep2

value: HIF1A knockdow

value: hypoxia


title: sgIkzf1_Tpex_2


title: Insert6_female_cigarette-smoke_exposed

description:
DESeq2_Female_exposed_Air_CS.csv
Normalized_Counts_Male_Air_Male_CS_Female_Air_Female_CS.csv
FCS6

value: female


title: spike for sgIkzf1_Tex_2


title: DF-1 cells, shHIF1A, 4h,rep1


title: skeletal muscle wild type [A33]


title: Insert5_female_cigarette-smoke_exposed

description:
DESeq2_Female_exposed_Air_CS.csv
Normalized_Counts_Male_Air_Male_CS_Female_Air_Female_CS.csv
FCS5


title: spike for sgIkzf1_Tpex_2


title: DF-1 cells, shHIF1A, 0h,rep2


title: DF-1 cells, shHIF1A, 24h,rep2


title: Insert4_female_cigarette-smoke_exposed

description:
DESeq2_Female_exposed_Air_CS.csv
Normalized_Counts_Male_Air_Male_CS_Female_Air_Female_CS.csv
FCS4


title: sgIkzf1_Tex_1


title: DF-1 cells, shHIF1A, 0h,rep1


title: cardiac tissue KD [R1796]

source_name: heart tissue

value: heart tissue

value: Taz-KD


title: Insert3_female_cigarette-smoke_exposed

description:
DESeq2_Female_exposed_Air_CS.csv
Normalized_Counts_Male_Air_Male_CS_Female_Air_Female_CS.csv
FCS3

value: trachea


title: sgIkzf1_Tpex_1


title: WBS sample 2

city: Zürich

first: Gerhard

last: Schratt

address: Winterthurerstrasse 190

department: D-HEST

country: Switzerland

institute: ETH Zürich

data_processing:
Reads were trimmed and filtered by Novogene using the adapter sequences 5'-GTTCAGAGTTCTACAGTCCGACGATC-3' (RA5) and 5'-AGATCGGAAGAGCACACGTCT-3' (RA3).
Mapping and quantification was performed using sports 1.1 and the GRCh38 annotations provided along with the software (ensembl release 89, miRbase 22, GtRNAdb hg19, and Rfam 12.3).
Assigned reads were aggregated across genome match/unmatch, and we focused on miRNAs.
Assembly: GRCh38
Supplementary files format and content: readcount_matrix.tab : miRNA read count matrix across samples.

source_name: IPSC-derived, Ngn2-induced neurons (iNeurons)

extract_protocol:
Trizol-chloroform RNA extraction
The libraries were prepared by Novogene using the NEB Next® Multiplex Small RNA Library Prep Set for Illumina, selecting fragments between 18~40 bp for sequencing.

value: Isogenic WBS (7q11.23 deletion)


title: Insert2_female_cigarette-smoke_exposed

description:
DESeq2_Female_exposed_Air_CS.csv
Normalized_Counts_Male_Air_Male_CS_Female_Air_Female_CS.csv
FCS2

value: primary epithelial  cells

value: pseudostratified epithelium


title: CNS-tumor_pediatric-LGG_82251

type: genomic

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

institute: DKFZ

hyb_protocol: Illumina

scan_protocol: Illumina iScan System

data_processing: Raw signal intensities were obtained from IDAT-files using the minfi Bioconductor package. Signal intensities were normalized per sample by performing a background correction (shifting of mean negative control probe intensity to 0) and a dye-bias correction (scaling of mean normalization control probe intensity to 10,000). Standard beta-values were calculated.

label: biotin/DNP

source_name: CNS tumor

label_protocol: Illumina

extract_protocol: Extraction of high molecular weight DNA from fresh frozen or FFPE tumor samples was carried out using the Maxwell RSC Tissue DNA kit or the Maxwell RSC DNA FFPE kit, respectively.

value: Male

tag: location

value: infratentorial

tag: tumor subgroup

value: low grade glioma

value: CNS tumor


title: WBS sample 1

value: IPSC-derived, Ngn2-induced neurons (iNeurons)


title: cardiac tissue KD [R1793]


title: spike for sgIkzf1_Tex_1

value: sgRNA-transduced OT-I cells from the dual-color transfer system at day 7 post adoptive transfer to B16-OVA tumor


title: Insert1_female_cigarette-smoke_exposed

description:
DESeq2_Female_exposed_Air_CS.csv
Normalized_Counts_Male_Air_Male_CS_Female_Air_Female_CS.csv
FCS1

value: Wild-type FVB/NJ

value: Cigarette-smoke exposure


title: cardiac tissue KD [R2]

value: Doxicycline


title: spike for sgIkzf1_Tpex_1


title: CTRL sample 3

value: Isogenic control


title: Insert6_female_air_exposed

description:
DESeq2_Male_Air_Female_Air.csv
Normalized_Counts_Male_Air_Male_CS_Female_Air_Female_CS.csv
FA6

value: female

value: Air exposure


title: cardiac tissue KD [R1798]

value: heart tissue

value: Taz-KD


title: CTRL sample 2


title: cardiac tissue wild type [R1800]

value: WT


title: spike for sgEts1_Tex_4


title: Insert5_female_air_exposed

description:
DESeq2_Male_Air_Female_Air.csv
Normalized_Counts_Male_Air_Male_CS_Female_Air_Female_CS.csv
FA5

value: trachea

value: primary epithelial  cells


title: cardiac tissue KD [R1797]


title: CTRL sample 1


title: cardiac tissue wild type [R1795]


title: Insert4_female_air_exposed

description:
DESeq2_Male_Air_Female_Air.csv
Normalized_Counts_Male_Air_Male_CS_Female_Air_Female_CS.csv
FA4

value: pseudostratified epithelium


title: cardiac tissue wild type [R1792]


title: spike for sgEts1_Tpex_4


title: hCM, lopinavir, replicate 3, RNA-seq

city: Guangzhou

first: Ying

last: Zhang

state: Guangdong

address: No. 135, Xingang Xi Road

institute: Sun Yat-sen University

data_processing:
Paired-end reads were trimmed with Trimmomatic v.0.36 with options “ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:8:true LEADING:10 TRAILING:10 MINLEN:30,” and only those properly paired reads after trimming were retained.
Clean reads were then mapped against the human reference genome (GRCh38) using HISAT2 (v.2.1.0) software to generate read alignments for each sample.
The quantification of gene expression was performed using the featureCounts v.1.6.0 with parameters: -p -B -T 8 -t exon -g gene_name.
Differential expression analysis was performed with the R package DESeq2 v.1.30.0.
Gene ontology enrichment analysis was performed using the R package clusterProfiler v.3.18.0.
Assembly: hg38
Supplementary files format and content: csv file includes raw counts for each Sample

source_name: human pluripotent stem cell-derived cardiomyocytes

extract_protocol:
Total RNA was extracted using the TRIzol reagent (15596026, Invitrogen).
RNA libraries for RNA-seq were prepared using the KAPA Hyper Prep Kits (KK8504, Roche) following manufacture's protocols.

value: lopinavir


title: Insert3_female_air_exposed

description:
DESeq2_Male_Air_Female_Air.csv
Normalized_Counts_Male_Air_Male_CS_Female_Air_Female_CS.csv
FA3


title: Het brain, mouse e15.5, lane 1 (R1, R2, I1, I2) & lane 2 (R3, R4, I3, I4)

description: 10x Genomics

value: MGE

value: Het


title: cardiac tissue wild type [R1791]


title: hCM, lopinavir, replicate 2, RNA-seq

value: human pluripotent stem cell-derived cardiomyocytes


title: sgEts1_Tpex_4

value: sgRNA-transduced OT-I cells from the dual-color transfer system at day 7 post adoptive transfer to B16-OVA tumor


title: cardiac tissue wild type [R3]


title: hCM, lopinavir, replicate 1, RNA-seq


title: Insert2_female_air_exposed

description:
DESeq2_Male_Air_Female_Air.csv
Normalized_Counts_Male_Air_Male_CS_Female_Air_Female_CS.csv
FA2

value: Wild-type FVB/NJ


title: spike for sgEts1_Tex_3


title: hCM, ritonavir, replicate 3, RNA-seq

value: ritonavir


title: spike for sgEts1_Tpex_3


title: hCM, ritonavir, replicate 2, RNA-seq


title: sgEts1_Tex_3


title: Insert1_female_air_exposed

description:
DESeq2_Male_Air_Female_Air.csv
Normalized_Counts_Male_Air_Male_CS_Female_Air_Female_CS.csv
FA1


title: F376 E7, YAP/TAZ Osx-cKO, replicate 2, scRNAseq

first: Joseph

last: Collins

address: 36th and Hamilton Walk

department: Department of Bioengineering

institute: University of Pennsylvania

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: fetal forelimb

extract_protocol:
Embryonic forelimbs were isolated on ice and trimmed to removed excess and loose skin/soft tissue and the handpaw. Individual embryonic tails or yokesacs were placed aside for genotyping. A single cell susupension was generated in the presence of the transcriptional inhibitor Actinomyosin Actinomycin D (MP Biomedicals). Briefly, cells from individual samples were disassociated from the tissue with a digestion media including DMEM, fetal bovine serum (vendorSigma), Collagenase II (Gibco Thermo Fisher Scientific), Pronase (Sigma Aldrich), and Actinomyosin Actinomycin D (2 mg/ml) for 75 minutes at 37oC. Following, cells were washed with PBS/0.01% BSA and passed through 70 mm cell strainers. Then, red blood cells were lysed with a Red Blood Cell Lysis kit (Miltenyi Biotec, 130-094-183), per manufacturer instructions. Dead cells were then removed with a Dead Cell Removal kit (Miltenyi Biotec 130-090-101) and MACS MS columns (Miltenyi Biotec), and a MiniMACS Magnetic Cell Separator (Miltenyi Biotec). Following dead cell removal, each sample was confirmed to have >95% viability. To allow time for genotyping, cells were then processed according to 10x Genomics ‘Methanol Fixation of Cells for Single Cellingle-cell RNA Sequencing protocol, Rev D’. Cell suspensions were resuspended per 10x Genomics ‘Methanol Fixation of Cells for Single Cellingle-cell RNA Sequencing protocol, Rev D’ and processed for sequencing.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Samples OsxF289_E4, OsxF289_E5, OsxF289_E6, OsxF289_E8, and F350 E1 were processed by Chromium Next GEM Single Cell 3' Reagent Kits v3.1 with Single Index Kit T Set A. All others were processed with Chromium Next GEM Single Cell 3' Reagent Kits v3.1 with Dual Index Kit TT Set A

value: Mixed, fetal forelimb

value: fetal forelimb

value: YAPfl/fl; TAZfl/fl; Osx-cre, mixed background


title: F350 E1, YAP/TAZ Osx-cKO, replicate 3, scRNAseq

description: 10x Genomics


title: hCM, ritonavir, replicate 1, RNA-seq


title: sgEts1_Tpex_3


title: F376 E3, YAP/TAZ Osx-cKO, replicate 1, scRNAseq

description: 10x Genomics


title: hCM, remdesivir, replicate 3, RNA-seq

value: remdesivir


title: spike for sgEts1_Tex_2


title: P301L_4

city: Houston

first: Wei

last: Cao

state: Texas

address: 6431 Fannin Street

institute: The University of Texas Health Science Center at Houston

data_processing:
Quality control: Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: mm10
Supplementary files format and content: Text files include average count number for each group

source_name: Primary cultured neurons

extract_protocol:
RNA was harvested using Direct-zol RNA Microprep Kits
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

value: Primary cultured neurons


title: F376 E8, WT(fl/fl), replicate 4, scRNAseq

description: 10x Genomics

value: YAPfl/fl; TAZfl/fl, mixed background


title: sgEts1_Tex_4


title: CBir_undivided cells, ATAC-seq

city: Stockholm

first: Eduardo

last: Villablanca

address: CMM

department: Department of Medicine

country: Sweden

institute: Karolinksa Institute

data_processing:
Basecalls were performed using bcl2fastq v2.17 for sequencing output.
The adapter sequence from these ATAC-seq reads were trimmed with CutAdapt v1.12  from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
The trimmed reads of each sample were aligned to mouse reference genome (mm10) using bowtie2 v 2.3.2 with default setting
We use Picard’s MarkDuplicates program  to remove PCR duplicated reads. We also filtered out mitochondrial reads and only keeps mapping paired reads with quality score greater or equal to 30 for further downstream analysis.
We also remove non-uniquely aligned reads, using the -q parameter of samtools view. For peak calling peak calling, we use Model-based Analysis of ChIP-Seq (MACS2 v 2.1.0) program  to obtain the region of genomic enrichment. We only analyze properly paired alignments with MACS2 call peak program using -f BAMPE parameter.
By running MACS2, we obtained three files for each aligned sample. The files are in peak.xls, peak.narrrowPeak and summit.bed extension. The narrowPeak extension file is the most useful file, it is a plain-text BED file it contains a genomic coordinate of each peak called, along with fold change and p-values.
Assembly: mm10
Supplementary files format and content: peak.narrowPeak and summit.bed

source_name: T cells

extract_protocol:
Naïve CD4+ CBir1 T cells were enriched from the spleen of CBir1 transgenic mice, using Miltenyi kit 130-104-453, stained with CellTraceTM Violet and injected into four WT C57BL/6J recipient mice. Starting on the following day, recipient mice were treated with 2% dextran sulfate sodium (DSS) in drinking water for 7 days, followed by normal drinking water, to induce intestinal barrier disruption. Recipient mice received 1 mg/kg of body weight FTY720 on days 7, 10 and 13 after the beginning of DSS administration, to retain cells in the lymph nodes. On day 14 after the beginning of DSS treatment, we isolated cells from the colon-draining mesenteric lymph nodes (cMLNs) of recipient mice, and sorted them into 3 fractions: 1) undivided (CTVhi) CBir1 T cells, 2) divided (CTVdim) CBir1 T cells, and 3) total non-CBir1 endogenous CD4+ T cells (polyclonal Th cells).
Libraries were prepared using the method described in Buenrostro et al. (Nature Methods 2013)

value: T cells

tag: fraction

value: undivided CBir1 T cells


title: Polyclonal cells, ATAC-seq

value: non-CBir1 CD4+ T cells (endogenous TH)


title: hCM, remdesivir, replicate 2, RNA-seq

value: WT


title: P301L_2


title: spike for sgEts1_Tpex_2


title: P301L_3


title: hCM, remdesivir, replicate 1, RNA-seq


title: F376 E5, WT(fl/fl), replicate 3, scRNAseq

description: 10x Genomics


title: sgEts1_Tex_2


title: F376 E4, WT(fl/fl), replicate 2, scRNAseq

description: 10x Genomics


title: P301L_1


title: CBir_divided cells, ATAC-seq

value: divided CBir1 T cells


title: hCM, apilimod, replicate 3, RNA-seq

value: apilimod


title: F376 E2, WT(fl/fl), replicate 1, scRNAseq

description: 10x Genomics


title: spike for sgEts1_Tex_1


title: OsxF289 E8, WT(Osx-cre), replicate 4, scRNAseq

description: 10x Genomics

value: Osx-cre, mixed background


title: WT tau_5

value: AAV-WT tau


title: spike for sgEts1_Tpex_1

value: sgRNA-transduced OT-I cells from the dual-color transfer system at day 7 post adoptive transfer to B16-OVA tumor


title: WT tau_4


title: hCM, apilimod, replicate 1, RNA-seq

value: human pluripotent stem cell-derived cardiomyocytes


title: OsxF289 E6, WT(Osx-cre), replicate 3, scRNAseq

description: 10x Genomics


title: sgEts1_Tex_1


title: OsxF289 E5, WT(Osx-cre), replicate 2, scRNAseq

description: 10x Genomics


title: WT tau_3


title: sgEts1_Tpex_1


title: WT tau_2


title: hCM, DMSO, replicate 1, RNA-seq

value: DMSO


title: hCM, DMSO, replicate 2, RNA-seq


title: SET_Normoxia #1

description: Hela cells with shSETDB1

value: Human epithelial uterus adenocarcinoma

value: total RNA


title: F3_ testis_RNA_ treatment 3

city: Rennes

first: Fatima

last: SMAGULOVA

address: 9 av. Prof. Léon Bernard

country: France

institute: Irset - U1085

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.20.0.422.
Reads were mapped onto mm10 assembly of mouse genome using Hisat2 (v2.1.0).
For each biological replicate, a transcriptome was generated using featureCounts and Gene annotation file mm10.ncbiRefSeq.gtf
Differentially expressed genes were determined by DESeq2 (Version 2.11.40.7). All analyses were performed using Galaxy platform, Nucleic Acids Research, Volume 50, Issue W1, 5 July 2022, Pages W345–W351
Assembly: mm10
Supplementary files format and content: featureCounts

source_name: embryonic E15.5 testis

growth_protocol: Pregnant, outbred, Swiss (RjOrl), female mice were treated with thia (“0”, and "6" mg/kg/day). For each dose, a minimum of 10 unrelated pregnant female mice were treated, and for each assay. To generate each biological replicate, RNAs were extracted from a pool of 3 embryonic testis, three biological replicate of control or thia-derived RNA were used for a library construction.

extract_protocol:
Total RNA was extracted using the RNeasy plus mini kit (Qiagen) according to the manufacturer’s instructions. We added additional DNA extraction step using RNase-Free DNase Set (Qiagen, 79254).
The libraries were prepared using the NEBNEXT® Ultra II Directional RNA Library kit for Illumina® (NEB E7760S) using 1µg of total RNA according to the manufacturer’s instructions.

treatment_protocol: Mice were treated by administering the compound down the esophagus and into the stomach using a gavage needle (FST, 18060-20) from embryonic day E6.5 until E15.5, which corresponds to the somatic-to-germline transition window. The treated animals were dissected at embryonic day E15.5 to obtain F1 samples, and some other animals were kept alive to obtain F1 males and they were crossed with unrelated untreated females to get F2. F2 males were crossed with unrelated untreated females to get F3

value: testis

tag: developmental stage

value: embryonic day e15.5

value: male

tag: mouse strain

value: Swiss (RjOrl)

tag: sample type

value: treatment F3


title: FIR-5

city: guangzhou

first: shuang

last: zheng

address: 11 Fengxin Road, Science City, Huangpu District, Guangzhou City

institute: Guangdong Laboratory Animal Monitoring Institute

data_processing:
Illumina Casava1.8 software used for basecalling.
Original data were filtered to remove reads with joints, indeterminate base information and low quality, followed by sequencing error rate check and GC content distribution check to obtain clean reads used in subsequent analysis.
Clean  reads were than mapped to mm10 genome with HISAT2 compares software.
The featureCounts software was used to calculate FPKM.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

source_name: Hearts of fat-1 transgenic mice were isolated, balanced for 40 minutes, ischemia for 20 minutes, and reperfusion for 1 hour with langendorff

extract_protocol:
Total RNAs from the ventricular tissues of the control group and the ischemia-reperfusion groups were isolated using TRIzol® Reagent(Thermo Fisher Scientific, USA). Each group contains five independent samples.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: heart

value: Fat-1 transgenic


title: WT tau_1

tag: cell type

value: Primary cultured neurons

value: WT


title: WT tau_6


title: sgEts1_Tpex_2


title: FIR-4


title: F3_ testis_RNA_ treatment 2

tag: Sex


title: hCM, apilimod, replicate 2, RNA-seq

value: apilimod


title: FIR-3


title: Control_2

value: Control AAV


title: F3_ testis_RNA_ treatment 1


title: Resistant6

city: Hefei

first: Hanyuan

last: Liu

address: Huangshan Road

institute: University of Science and Technology of China

data_processing:
RNA-seq was performed on the Illumina platform using 150-bp paired-end reads. The reads were mapped to GRCh38 using hisat2 (v2.2.1) and converted the ENSG ID to Gene symbols.
Gene expression was analyzed, and p value < 0.05 in addition with absolute log2FC ≥1 was set as significant.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include reads for each RNA-seq Sample

source_name: Ovarian Cancer

extract_protocol:
Total RNA was extracted by TRIzol reagent (Invitrogen, 15596026) according to the manufacturer’s instructions.
Libraries were constructed by the TruSeq Ribo Profile Library Prep Kit (Illumina, RPHMR12126) according to the manufacturer’s instructions.

value: Ovarian Cancer


title: Resistant5


title: FIR-2


title: F3_ testis_RNA_ control 3

value: control F3


title: hCM, DMSO, replicate 3, RNA-seq

value: human pluripotent stem cell-derived cardiomyocytes


title: Resistant4


title: F3_ testis_RNA_ control 2


title: FIR-1


title: SET_Hypoxia #1

description: Hela cells with shSETDB1 exposed to 1% oxygen for 6 hours

source_name: cervical cancer cells


title: KO brain, mouse e12.5, lane 1 (R1, R2, I1, I2) & lane 2 (R3, R4, I3, I4)

city: Bethesda

first: Timothy

last: Petros

address: 35 Convent Drive, Bg 35 Room 3B-1002

institute: NICHD

description: 10x Genomics

source_name: MGE

value: MGE

value: KO


title: Resistant7


title: FS-5

source_name: Hearts of fat-1 transgenic mice were isolated and perfused for 120 min with langendorff


title: Resistant3


title: OsxF289 E4, WT(Osx-cre), replicate 1, scRNAseq

description: 10x Genomics

value: Mixed, fetal forelimb

value: fetal forelimb

value: Osx-cre, mixed background


title: Control_3


title: F3_ testis_RNA_ control 1

value: testis

value: embryonic day e15.5

value: male


title: Untreated_4

value: Untreated


title: F1_ testis_RNA_ control 3

value: Swiss (RjOrl)

value: control F1


title: Untreated_3

value: Primary cultured neurons

value: WT


title: Resistant1


title: F1_ testis_RNA_ treatment 3

value: treatment F1


title: FS-3

value: heart

value: Fat-1 transgenic


title: Untreated_1


title: Sensitive3

value: Ovarian Cancer


title: FS-4


title: Control_1

value: Control AAV


title: F1_ testis_RNA_ treatment 2


title: FS-2


title: F6.ProinsLo_readsnumber

city: Cleveland

first: Sisi

last: Lai

state: Ohio

address: 10900 Euclid Avenue, BRB 609A

department: Genetics and Genome Sciences

institute: Case Western Reserve University

data_processing:
All raw FASTQ files were analyzed with FASTX-Toolkit (Hannon’s lab).
The sgRNA sequence were aligned back to the mouse GeCKO library sequencing with Bowtie2
Supplementary files format and content: Tab-delimited text file with raw read couns over all sgRNAs.
Library strategy: PCR amplicon

growth_protocol: MIN6 cells were cultured in high glucose DMEM with 10% heat-inactivated Fetal Bovine Serum (Gibco), 2 mM GlutMAX (Gibco), 1 mM sodium pyruvate, 50 μM β-mercaptoethanol.

extract_protocol:
Dneasy Blood & Tissue kit (Qiagen)
illuminar Truseq library prep


title: Sensitive2


title: F1_ testis_RNA_control 2


title: FS-1


title: F5.ProinsHi_readsnumber


title: Sensitive1


title: KO brain, mouse e12.5

description: 10x Genomics

data_processing:
The Cell Ranger ARC (v2.0.0) pipeline was used to process sequenced libraries with default parameters unless otherwise noted. Demultiplexed FASTQ files were generated by cellranger-arc mkfastq from BCL files. Reads were aligned to custom-built mouse (GRCm38/mm10) reference genome modified to express tdTomato using cellranger-arc count. Reads with de-duplicated and valid cell barcodes were used to build peak-by-barcode matrices by cellranger-arc count per genotype.
Assembly: GRCm38/mm10
Supplementary files format and content: cellranger atac_fragments.tsv.gz
Supplementary files format and content: cellranger atac_peak_annotation.tsv

extract_protocol:
E12.5 and E15.5 embryos were removed and placed in ice-cold carbogenated ACSF. Tails were clipped for PCR genotyping. During genotyping, embryonic brains were harvested and MGEs were dissected from each embryo and stored in ice-cold carbogenated ACSF. For E12.5, the entire MGE was removed as previously described92. For E15.5, the MGE was dissected under a fluorescent dissecting microscope to ensure collection of only Tom+ MGE cells and minimize collection of postmitotic MGE-derived cells in the striatum anlage and other ventral forebrain structures. Upon obtaining genotyping results (~90 minutes), MGEs from embryos of the same genotype were combined (when applicable) to generate single nuclei dissociations. MGEs were transferred to a 1 mL Dounce homogenizer containing Multiome Lysis Buffer (in mM: 10 Tris-HCl (Ph.7.4), 10 NaCl, 3 CaCl2, 1 DTT, with 0.1% Tween-20, 1.5% BSA and 0.1% IGEPAL CA-630 in nuclease-free water, 1 mL per sample). Lyse cells by douncing with pestle A and pestle B, ~10-15 times each. Place a 40 μm filter onto a pre-chilled 50 mL conical tube on ice and wet with 1 mL of Multiome Nuclei Wash Buffer (in mM: 10 Tris-HCl (Ph.7.4), 10 NaCl, 3 CaCl2, 1 DTT, with 0.1% Tween-20, 1.5% BSA and 1 U/μL in nuclease-free water, 5 mL per sample). Transfer lysed nuclei suspension through pre-wetted filter, then rinse dounce with 1 mL Multiome Wash Buffer and transfer through filter. Divide nuclei suspension into 2 pre-chilled 2 mL tubes and spin at 500 g for 5 minutes at 4oC. After removing supernatant, wash nuclei pellet twice with 1 mL Multiome Wash Buffer and spin as above. Remove Multiome Wash Buffer, leaving ~20-30 μL of solution in each tube. Triturate solution to dissociate pellets, then combine nuclei suspensions into 1 tube. Nuclei concentration was determined on Countess II FL Automated Cell Counter. Nuclei suspensions were diluted to ~3,000-4,000 nuclei/μL, with 5 μL being used for 10x Genomics Multiome kit per manufacturer’s instructions. E15.5 data: MGE from 4 WT, Het and KO embryos from 2 different E15.5 litters were combined to generate 1 biological rep. E12.5 data: MGE from 1 WT, Het and KO mouse from a single E12.5 litter were used to generate 1 biological rep. Total cell numbers that passed QC: E12.5 WT = 6,391; E12.5 Het = 6,608; E12.5 KO = 8,546; E15.5 WT = 11,477; E15.5 Het = 10,027; E15.5 KO = 8,607.
Joint libraries for scRNA-seq and scATAC-seq were created using 10X Genomics Single Cell Multiome ATAC + Gene Expression kit (1000285) by following manufacturer’s protocols.

value: MGE

value: KO


title: F1_ testis_RNA_control 1


title: Esophagus, EoE, positive response, ID 10

city: Utrecht

first: Mirelle

last: Kleuskens

address: Universiteitsweg 99

country: Netherlands

institute: Utrecht University

data_processing:
Reads containing adapter, reads containing ploy-N and low-quality reads were removed from the raw data.
In addition, Q20, Q30 and GC content of the clean data were calculated.
Paired-end clean reads were aligned against the GRCh38 human reference genome using Hisat2 v 2.0.5
FeatureCounts v 1.5.0-p3 was used to generate read counts mapped to each gene
FPKM of each gene was calculated based on the length of the gene and read counts mapped to this gene
Assembly: GRCh38
Supplementary files format and content: tab-delimited Excel file includes raw counts for each sample
Supplementary files format and content: tab-delimited Excel file includes FPKM for each sample

source_name: esophagus

extract_protocol:
Total RNA was extracted using the Allprep DNA/RNA/Protein Mini Kit from Qiagen per manufacturer's instructions
Libraries were constructed using the Novogene NGS RNA Library Prep Sep (PT042)

value: esophagus

value: F

tag: disease

value: eosinophilic esophagitis (EoE)

tag: pec (eos/hpf)

value: food injection


title: CIR-5

source_name: Hearts of wild mice were isolated, balanced for 40 minutes, ischemia for 20 minutes, and reperfusion for 1 hour  with langendorff

tag: genotype


title: F1_ testis_RNA_ treatment 1

value: testis

value: embryonic day e15.5

value: male


title: CIR-4


title: Het brain, mouse e12.5

description: 10x Genomics

value: Het


title: Esophagus, EoE, negative response, ID 10

tag: treatment


title: Input, DNA, MBD2-Fc, mouse spermatozoa

data_processing:
Libraries were sequenced on an Illumina Hiseq 4000 sequencer as single read mode of 50 base reads. Image analysis and base calling were performed using RTA version 2.7.7 and bcl2fastq version 2.20.0.422.
Adapter dimer reads were removed using DimerRemover. The reads were mapped to the reference genome mm10 using Bowtie2 v2.5.0. The numbers of mapped reads were normalized by a scale factor to adjust the total number of reads. From the aligned reads, DNA methylated peaks were identified using 20 biological replicates and the corresponding input by MACS2 (2.2.7.1) algorithm; the following parameters were applied: a shift-size window of 73 bp, no model, and q-value threshold <0.05.
To compare the control datasets of the thia-exposed and control samples, differential peaks were identified using counting reads at each peak using bedtools MultiCovBed (Version 2.30.0). Statistical significance was calculated using Limma v3.50.1 with filtering peaks with low counts.
Each normalized bam file was converted to BedGraph tracks by using the Genome Coverage 2.30.0. All analyses were performed using Galaxy platform, Nucleic Acids Research, Volume 50, Issue W1, 5 July 2022, Pages W345–W351.
Assembly: mm10
Supplementary files format and content: bedgraph

source_name: spermatozoa

growth_protocol: Pregnant, outbred, Swiss (RjOrl), female mice were treated with thia suspended in olive oil (“0”or “6” mg/kg/day). For each dose, a minimum of 10 unrelated pregnant female mice were treated, and for each experiment, a minimum of 3 males from different litters of control or thia-derived mice were used for Medip experiment.

extract_protocol:
Active fraction of sperm was received by placing mouse epididymis in DMEM media without serum, and a single excision in cauda was made so spermatozoa were released by incubation at 37C for 1 hour. Released spermatozoa were filtered and pelleted and kept in minus until until experiment. DNA extraction was performed using DNA easy blood and tissue kit (Qiagen, 69506). 180 μl Buffer ATL was added and sperm were disrupted by QIAGEN Tissue Lyser and metallic beads, DTT was added to a final concentration 10mM. 10 ul of proteinase K cells were added and cells were incubated at 56°C O/N with rotation. The buffer AL (Qiagen, 69506) and 96% ethanol were added, and tubes were mixed thoroughly by vortexing. Lysate was loaded onto Qiagen columns and columns were washed with RW1 and RW2 and eluted with AE buffer from Qiagen kit. The concentration of DNA was measured by fluorescent method using QuantiFluor® dsDNA System (Promega, E2670). For the DNA methylation analysis in spermatozoa, the EpiMark Methylated DNA Enrichment Kit (NEB, #E2600S) was used. A total of 6000 ng of DNA was sonicated using a Qsonica sonicator with the following parameters: efficiency, 60%; total sonication time, 8 min, 20 s “on” and 20 s “off”. The sonicated methylated DNA was precipitated using MBD2a-protein A-coated beads, the methylated DNA-MBD2a-protein A-coated bead complex was washed, and the DNA was eluted with miliQ water. The DNA concentration was determined according to the level of fluorescence produced by a dsDNA-binding dye QuantiFluor® dsDNA System (Promega, E2670). 6-10 ng of methylated DNA was recovered following precipitation, and the unprecipitated sonicated starting material was used as the input.
6 ng of methylated DNA or input were taken for library preparation. Sequencing libraries were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (E7645S; NEB). We performed 15 cycles for the library amplification.

treatment_protocol: Mice were treated by administering of the compound down the esophagus and into the stomach using a gavage needle (FST, 18060-20) from embryonic day E6.5 until E15.5, which corresponds to the somatic-to-germline transition window. Male progeny of the treated mice was crossed for three generations and spermatozoa of each generation males were collected

value: spermatozoa

value: adult 2-month-old

value: Swiss (RjOrl)

value: Input


title: F3 thia, DNA, MBD2-Fc, mouse spermatozoa 4

value: F3 thia


title: CIR-2

value: heart


title: WT brain, mouse e12.5

description: 10x Genomics

value: WT


title: Mouse MIX tumor, rep8

city: Jerusalem

first: nofar

last: rosenberg

address: Hadassah University Hospital

institute: Hebrew university

data_processing:
Assembly: GRCm38
The first 12 nucleotides of each read were trimmed with the FASTX package (v0.0.14), then adapter sequences were removed with Cutadapt (v1.12). Low quality reads were filtered out with the FASTX package, v0.0.14, using parameters -q 20 and -p 90.
Reads were aligned with Tophat (v2.1.1), using parameters -G genes.gtf (from Ensembl release 89), -N 2, --read-gap-length 5, --read-edit-dist 7, --segment-length 18, --read-realign-edit-dist 3, --no-coverage-search and --library-type fr-secondstrand.
Raw counts were obtained with htseq-count (v0.6.0), then normalization and differential expression were calculated with the R package DESeq2 (v1.12.4), using default parameters, except setting independentFiltering=F.
Supplementary files format and content: DESeq2_final_M.xlsx: columns A-J, general gene details; K-AB, raw counts; AC-AT, normalized counts; AU, baseMean (average expression); AV-AZ, result comparing HCC to DR samples; BA-BE, results comparing MIX to DR samples; BF-BJ, results comparing MIX to HCC samples.
Supplementary files format and content: DESeq2_final_H.xlsx: columns A-J, general gene details; K-AB, raw counts; AC-AT, normalized counts; AU, baseMean (average expression); AV-AZ, result comparing ICC to HCC samples; BA-BE, results comparing MIX to HCC samples; BF-BJ, results comparing MIX to ICC samples.

source_name: liver

extract_protocol:
Snap-frozen liver tissue samples were obtained, and 10 µm-thick sections were obtained by cryostat microtomy.  Tumor areas were localized by hematoxylin and eosin staining. Laser capture microdissection was performed using the Leica LMD6500 system. Total mRNA was extracted using RNeasy Plus Micro Kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions.
Libraries were prepared using the Lexogen QuantSeq 3′mRNA-Seq Library Prep Kit FWD (Lexogen, Vienna, Austria) which was followed by an amplification step according to the manufacturer’s instructions.

value: liver

value: HCC-CCA tumor

value: Mdr2 KO Foxl1-Cre; ROSA-YFP

tag: gender


title: CIR-1


title: Esophagus, EoE, negative response, ID 8

value: esophagus

value: M

tag: age


title: Esophagus, EoE, positive response, ID 8

value: eosinophilic esophagitis (EoE)

value: food injection


title: CS-5

source_name: Hearts of wild mice were isolated and perfused for 120 min with langendorff


title: F3 thia, DNA, MBD2-Fc, mouse spermatozoa 2


title: Mouse MIX tumor, rep7


title: F3 thia, DNA, MBD2-Fc, mouse spermatozoa 3


title: F3 thia, DNA, MBD2-Fc, mouse spermatozoa 1


title: CIR-3


title: Esophagus, EoE, positive response, ID 4


title: Esophagus, EoE, baseline, ID

value: baseline


title: Esophagus, EoE, baseline, ID 10

value: F


title: Esophagus, EoE, negative response, ID 4


title: CS-3


title: CS-2


title: Mouse MIX tumor, rep4

value: male


title: F3 control, DNA, MBD2-Fc, mouse spermatozoa 3

value: spermatozoa

value: F3 control


title: Mouse MIX tumor, rep6


title: Mouse MIX tumor, rep5


title: F3 control, DNA, MBD2-Fc, mouse spermatozoa 2

value: adult 2-month-old

value: Swiss (RjOrl)


title: Esophagus, EoE, baseline, ID 4


title: CS-4


title: Mouse MIX tumor, rep3


title: Untreated_2

value: Primary cultured neurons

value: Untreated


title: CS-1

value: heart


title: Mouse MIX tumor, rep2

value: liver


title: Esophagus, EoE, positive response, ID 3


title: F2 thia, DNA, MBD2-Fc, mouse spermatozoa 4

value: F2 thia


title: F3 control, DNA, MBD2-Fc, mouse spermatozoa 1


title: Hormone induced prostate tissue 3 [chu3-1]

city: GuiYang

first: XiaoHu

last: Tang

address: No. 83 Zhongshan East Road

institute: Guizhou Provincial People's Hospital

data_processing:
illumina novaseq 6000 used for basecalling
Sequenced reads were filtered for Seqtk, and get clean Reads that can be used for data analysis, using the bowtie2 (version: 2-2.0.5), the Genome mapping was performed on post-pretreatment reads, which was more suitable for the sequencing data of the prokaryotic transcriptome. The comparison result generated by Mapping is the BAM file
Fragments Per Kilobase of exon model per Million mapped reads.We first apply HTSeq in TopHat than after each gene Fragments could count to count, and then use TMM (trimmed mean of M values) normalization method, finally calculated using perl script FPKM value of each gene.
Assembly: not provided
Supplementary files format and content: FPKM and  count values for each Sample

source_name: prostate

growth_protocol: All the mice were kept in a standard laboratory environment (12/12 hours of light/dark cycle, 22±2 °C with 55±5% relative humidity), and allowed to consume standard laboratory pellets and water ad libitum.

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Paired-end libraries were synthesized by using the TruSeq® RNA Sample Preparation Kit (Illumina, USA) following TruSeq® RNA Sample Preparation Guide.
The cDNA fragments afterwards through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library.

treatment_protocol: Mice in the test group were subcutaneously implanted with 1 pellet containing testosterone and estradiol for 12 weeks and the control group only underwent skin incision and stapling.

value: prostate

tag: strain background

value: induction of testosterone and estradiol


title: Mouse MIX tumor, rep1

value: HCC-CCA tumor

value: Mdr2 KO Foxl1-Cre; ROSA-YFP


title: Hormone induced prostate tissue 2 [chu2-1]


title: F2 thia, DNA, MBD2-Fc, mouse spermatozoa 3


title: Mouse HCC tumor, rep5

value: HCC tumor


title: Esophagus, EoE, baseline, ID 3

value: esophagus

value: M

value: eosinophilic esophagitis (EoE)

value: baseline


title: Hormone induced prostate tissue 1 [chu1-1]


title: Mouse HCC tumor, rep3

value: male


title: Control prostate tissue 3 [zheng3]

value: no induction of testosterone and estradiol


title: Esophagus, EoE, negative response, ID 1

value: food injection


title: F2 thia, DNA, MBD2-Fc, mouse spermatozoa 1

value: spermatozoa

value: adult 2-month-old

value: Swiss (RjOrl)


title: Esophagus, EoE, baseline, ID 1


title: F2 control, DNA, MBD2-Fc, mouse spermatozoa 3

value: F2 control


title: Mouse HCC tumor, rep2

value: liver


title: Mouse HCC tumor, rep1


title: Esophagus, non-EoE, baseline, ID 6

value: control


title: Control prostate tissue 2 [zheng2]

value: prostate


title: F2 control, DNA, MBD2-Fc, mouse spermatozoa 2


title: Control prostate tissue 1 [zheng1]


title: Esophagus, EoE, negative response, ID 3


title: F2 control, DNA, MBD2-Fc, mouse spermatozoa 1


title: Esophagus, non-EoE, baseline, ID 5

value: F


title: HFD4

city: Shanghai

first: Junjie

last: Gao

address: 600 Yishan Road

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.

source_name: cortical bone

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

tag: strain

value: 12-month high fat diet


title: Mouse DR tumor, rep5

value: Ductlar reaction tumor

value: Mdr2 KO Foxl1-Cre; ROSA-YFP


title: HFD3


title: F1 thia, DNA, MBD2-Fc, mouse spermatozoa 3

value: F1 thia


title: Esophagus, non-EoE, baseline, ID 4

value: esophagus

value: M


title: Mouse DR tumor, rep6

value: male


title: F1 thia, DNA, MBD2-Fc, mouse spermatozoa 2


title: F2 thia, DNA, MBD2-Fc, mouse spermatozoa 2

value: F2 thia


title: Esophagus, EoE, positive response, ID 1

value: eosinophilic esophagitis (EoE)

value: food injection


title: Esophagus, non-EoE, baseline, ID 3

value: baseline


title: Mouse DR tumor, rep4


title: Mouse HCC tumor, rep4

value: HCC tumor


title: F1 thia, DNA, MBD2-Fc, mouse spermatozoa 1

value: spermatozoa

value: adult 2-month-old

value: Swiss (RjOrl)


title: CD4

value: 12-month chewing diet


title: CD2


title: Mouse DR tumor, rep1

value: liver


title: F1 control, DNA, MBD2-Fc, mouse spermatozoa 3

value: F1 control


title: Esophagus, non-EoE, baseline, ID 2

value: control


title: Mouse DR tumor, rep3

value: Ductlar reaction tumor

value: Mdr2 KO Foxl1-Cre; ROSA-YFP


title: EndoC-bH3_siPDIA6#1_10_batch3

data_processing:
RNA-seq reads were filtered for quality and trimmed for adaptor sequences.
Reads were alighed to reference genome assembly for mouse (mm10) and human (hg19) using HISAT2 with default parameters.
Read count tables were generated with FeatureCounts.
Normalized and differential expression analysis was performed with DESeq2.
Assembly: mm10 and hg19
Supplementary files format and content: Tab-delimited text file with normalized read couns over all genes.

molecule: polyA RNA

growth_protocol: MIN6 cells were cultured in high glucose DMEM with 10% heat-inactivated Fetal Bovine Serum (Gibco), 2 mM GlutMAX (Gibco), 1 mM sodium pyruvate, 50 μM β-mercaptoethanol. EndoC-βH3 were cultured in DMEM containing 5.6 mM glucose, 2% fatty acid free BSA fraction V, 10 mM nicotinamide, 5.5 mg/ml transferrin, 6.7 ng/ml sodium selenite, Penicillin (100 units/ml)/ Streptomycin (100 mg/ml). Cells were passaged and seeded onto matrigel- and fibronectin- coated cell culture dishes.

extract_protocol:
Trizol used to extract RNA from MIN6 cells. Quick-RNA™ Microprep Kit used for EndoC-bH3 RNA extraction.
Illumina TruSeq stranded mRNA kit for MIN6. mRNA-seq Lib Prep Kit (ABclonal) used for EndoC-bH3 cells.

tag: cell line


title: F1 control, DNA, MBD2-Fc, mouse spermatozoa 2


title: CD1


title: IM72h_RiboTag IP_3

city: Bonn

first: Reiner

last: Schneider

address: Venusberg-Campus 1

department: Surgery Department

institute: University Clinics Bonn

data_processing:
Library strategy: Ribo-seq
Pipeline: Data was analyzed with Partek Flow software and the publicly available Lexogen pipeline (Lexogen12112017)
Partek Flow Software - Trim adapters - CUTADAPT_1_12 - Version 10.0.21.1116 - Both ends trimmed -Adapter sequences:  AAAAAAAAAAAA,TTTTTTTTTTTT
Partek Flow Software - Pre-alignment QA/QC - Version 10.0.21.1116 - K-mer length 10
Partek Flow Software - Trim adapters - CUTADAPT_1_12 - Version 10.0.21.1116 - 3'-end trimmed -Min overlap length 5 - Min read length 25
Partek Flow Software - Pre-alignment QA/QC - Version 10.0.21.1116 - K-mer length 10
Partek Flow Software - Trim bases - Version 10.0.21.1116 - Trim on quality score Phred 10 - 3'-end timmed - Min read length 20
Partek Flow Software - Pre-alignment QA/QC - Version 10.0.21.1116
Partek Flow Software - Alignment STAR - 2.5.3a - Version 10.0.21.1116
Partek Flow Software - Post-alignment QA/QC - Version 10.0.21.1116
Partek Flow Software - Quantify to annotation model (Partek E/M) - Version 10.0.21.1116
Assembly: mm10 Ensembl Transcripts release 99
Supplementary files format and content: IM3h_RiboTag_Transcript_counts: raw transcript counts RiboTag Naive vs IM3h samples
IM3h_RiboTag_POI_Normalized GSA to Naive: normalized GSA of transcript counts RiboTag IM3h to naive controls
IM24h_RiboTag_Transcript_counts: raw transcript counts RiboTag Naive vs IM24h samples
IM24h_RiboTag_POI_Normalized GSA to Naive: normalized GSA of transcript counts RiboTag IM24h to naive controls
IM72h_RiboTag_Transcript_counts: raw transcript counts RiboTag Naive vs IM72h samples
IM72h_RiboTag_POI_Normalized GSA to Naive: normalized GSA of transcript counts RiboTag IM72h to naive controls
Total RNA_POI_Gene_counts: raw gene counts Total RNA input samples
Total RNA_POI_Transcript_counts: raw transcript counts Total RNA input samples
Total RNA_POI_Normalized GSA to Naive: normalized GSA of transcript counts Total RNA to naive controls

source_name: Small bowel muscularis externa

extract_protocol:
Muscularis externa was prepared from small bowel and subjected to an immunoprecipitation protocol for RiboTag (Leven et al 2021, Application of a RiboTag-based approach to generate and analyze mRNA from enteric neural cells,  https://doi.org/10.1111/nmo.14309). Input samples were generated from total lysate while IP samples underwent the entire precipitation process and were purified afterwards.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Animals underwent abdominal surgery (postoperative ileus model) and were sacrificed after indicated time points

value: Small bowel muscularis externa

value: B6 Tg(Sox10-icre/ERT2)388Wdr/J x B6N.129 Rpl22tm1.1Psam/J

value: RiboTag Pulldown mRNA (IP)


title: IM72h_RiboTag IP_4


title: EndoC-bH3_siNT_9_batch3

value: siNT


title: sgEts1_1_day 7 2

city: Memphis

first: Hongbo

last: Chi

address: 262 Danny Thomas Place

institute: St Jude Children's Research Hospital

data_processing:
The Cell Ranger 6.0 Single-Cell Software Suite (10x Genomics) was implemented to process the  raw sequencing data from the Illumina HiSeq run.
This pipeline performed de-multiplexing,  alignment (mm10), and barcode processing to generate gene-cell matrices used for downstream  analysis.
Assembly: mm10
Supplementary files format and content: cell ranger count matrix for single cells in each sample

source_name: sgRNA transduced OT-I cells

growth_protocol: OT-I cells transduced with indicatd sgRNAs were sorted from B16-OVA tumor after adoptive transfer

extract_protocol:
CD8+ OT-I T cells were sorted from the dual-color transfer system at day 7 post adoptive transfer from B16-OVA tumor and loaded onto  the Chromium Controller according to their respective cell counts to target 9000 single cell GEMs (gel beads in emulsion) per sample.
Libraries were prepared using the Chromium Single Cell 3’ v3 Library and Gel Bead Kit (10x Genomics)

value: sgRNA transduced OT-I cells

tag: transduced


title: F1 control, DNA, MBD2-Fc, mouse spermatozoa 1

value: male


title: IM72h_RiboTag IP_1

tag: fraction


title: EndoC-bH3_siNT_6_batch2


title: IM72h_RiboTag IP_2


title: HFD2

value: 12-month high fat diet