title: iAM06, NRG1

description: Immortalized atrial cardiomyocytes - iAM06


title: MM_477, snATACseq

status: Public on Nov 13 2024

type: SRA

city: La Jolla

first: David

last: Brenner

state: CA

address: 10901 North Torrey Pines Road

country: USA

institute: Sanford Burnham Prebys

description: MASL

library_source: genomic

data_processing:
For each sequenced snATAC-Seq libraries, we obtained four FASTQ files paired-end DNA reads as well as the combinatorial indexes for i5 (768 different PCR indices) and T7 (96 different tagmentation indices; Supplementary Table 8). We selected all reads with <= 2 mistakes per individual index (Hamming distance between each pair of indices is 4) and subsequently integrated the full barcode at the beginning of the read name in the FASTQ files (https://gitlab.com/Grouumf/ATACdemultiplex/).
Next, we used trim galore (v.0.4.4) to remove adapter sequences from reads prior to read alignment.
We aligned reads to the reference genome using bwa mem (v.0.7.17) 10 and subsequently used samtools to remove unmapped, low map quality (MAPQ<30), secondary, and mitochondrial reads.
Downstream analysis of snATACseq peaks were conducted with the Signac tool.
Sequencing reads were demultiplexed (cellranger mkfastq) and processed (cellranger count) using the Cell Ranger software package v3.0.2 (10x Genomics). Reads were aligned to the human reference hg38 (Cell Ranger software package v3.0.2). Reads mapping to intronic and exon sequences were retained. Resulting UMI feature-barcode count matrices were loaded into Seurat for downstream processing
Assembly: hg38
Supplementary files format and content: snATAC-seq: bed files containing regions of open chromatin (peaks), per sample
Supplementary files format and content: snRNA-seq: hLIVER_processed_files.tar.gz. Contains sparse matrix file containing raw counts (one file for all samples), csv files containing gene names and cell ids, and csv file containing cell metadata (including cluster ID, sample ID, condition, QC metrics).

molecule: genomic DNA

organism: Homo sapiens

source_name: liver

extract_protocol:
Nuclei were isolated from frozen liver tissue using gentleMACS dissociation (Miltenyi). ~50-70 mg of frozen liver tissue was suspended in 1 ml of MACS dissociation buffer consisting of 5 mM CaCl2 (G-Biosciences, R040), 2 mM EDTA (Invitrogen, 15575-038), 1X protease inhibitor (Roche, 05-892-970-001), 3 mM MgAc (Grow Cells, MRGF-B40), 10 mM Tris-HCl pH 8 (Invitrogen, 15568-075), and 0.6 mM DTT (Sigma-Aldrich, D9779) in water (Corning, 46-000-CV) and placed on wet ice. Next, samples were homogenized using gentleMACS dissociator (Miltenyi) with gentleMACS M tubes (Miltenyi, 130-096-335) and the “protein_01” protocol. Suspension was filtered through a 30 µM CellTrics filter (Sysmex, 04-0042-2316). M tube and filters were washed with 1 ml of MACS dissociation buffer and combined with the suspension. Suspension was centrifuged in a swinging bucket centrifuge (Eppendorf, 5920R) at 500 rcf for 5 minutes (4°C, ramp speed 3/3). Supernatant was removed and pellet was resuspended in 1 mL Nuclear Permeabilization Buffer (1X PBS, 5% Bovine Serum Albumin, 0.2% IGEPAL CA-630 (Sigma), 1 mM DTT, 1X complete Protease inhibitor). Nuclei were rotated at 4 °C for 5 minutes before being pelleted again with a swinging bucket centrifuge (500 x g, 5 min, 4°C; 5920R, Eppendorf). After centrifugation, permeabilized nuclei were resuspended in 500 μL high salt tagmentation buffer (36.3 mM Tris-acetate (pH = 7.8), 72.6 mM potassium-acetate, 11 mM Mg-acetate, 17.6% DMF) and counted using a hemocytometer. For single nucleus RNA-seq, 75,000 nuclei were sorted using a SH800 sorter (Sony) into 50 ul of collection buffer consisting of 1 U/ul RNase inhibitor in 5% BSA; the FACS gating strategy sorted based on particle size and DRAQ7 fluorescence. Sorted nuclei were then centrifuged at 1000 rcf for 15 minutes (4°C, run speed 3/3) and supernatant was removed. For single nucleus ATAC-seq, unsorted nuclei were used as input for single nucleus ATAC-seq using combinatorial barcoding
For single nucleus ATAC-seq, unsorted nuclei were used as input for single nucleus ATAC-seq using combinatorial barcoding. Approximately 15,000 nuclei were loaded onto the Chromium controller (10x Genomics) for downstream single-nucleus RNA-seq processing with the Single Cell 3’ v3.1 GEM generation kit (10x Genomics).
single nucleus ATAC-seq, single nucleus RNA-seq

tag: tissue

value: liver


title: MM_473, snATACseq

description: NORMAL


title: YW83_sgRNA

city: Dallas

first: Yihan

last: Wang

state: Texas

address: 5323 Harry Hines Blvd.

institute: UT Southwestern

library_source: transcriptomic single cell

data_processing:
Basecalls performed 10x Cellranger v6 and fba v0.0.6
Mapping and combining the libraries with 10x Cellranger
Genome_build: hg38
processed_data_files_format_and_content: sgRNA library output csv

molecule: polyA RNA

source_name: MDAMB231 Cell line

growth_protocol: Cells were cultured in alpha modified MEM plus 10% FBS, 1mM sodium pyruvate, 10mM HEPES, 1X Glutamax supplement, 1X MEM non-essential amino acid, 1 mg/mL insulin, 1ng/mL hydrocortisone, 25 ug/mL EGF and pen/strep at 37C and 5% CO2.

extract_protocol:
Cells were collected, washed once with PBS and stained with Cell Hashing antibodies ot CellPlex followed by manuffacturer manual. Cells were resuspended in PBS containing 0.05% of BSA to the desired concentration and immediately load on the 10x Chromium controller for single-cell RNA-seq preparation.
For single-cell library preparation, we followed the standard protocol of 10x Genomics. After the cDNA amplification, 50 ng of samples were separated for the sgRNA enrichment library preparation.

treatment_protocol: Cells were infected with lenti-dCas9-KRAB-blast (Addgene:89567) to stablly express dCas9-KRAB. After stablly expressed dCAs9-KRAB, the cells were infected by a lentivirus sgRNA library targeting breast cancer associated enhancers and under antibiotics selection for two weeks.

tag: cell line

tag: experiment

value: Single-cell Expression


title: MM_471, snATACseq

description: MASH


title: Microbiota in mouse stool, sample MN32

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

description: 16s rRNA v3-v4 sequencing

data_processing:
from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
qiime cutadapt trim-paired --i-demultiplexed-sequences demux-paired-end.qza --p-front-f CCTACGGGNGGCWGCAG --p-front-r GACTACNVGGGTWTCTAATCC --p-cores 7 --o-trimmed-sequences trimmed-seqs.qza --p-discard-untrimmed --p-minimum-length 100 --verbose
qiime demux summarize --i-data trimmed-seqs.qza --o-visualization demux.qzv --p-n 500000
qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 274 --p-trunc-len-r 169 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 7
bowtie2 -x $BOWTIE2_DATABASE/INDEXED_mouse_GRCm39_BOWTIE2/GRCm39 -U dna-sequences.fasta --al eucar_contaminant_ASV_2.fasta -S eucar_contaminants_ASV/bowtie2_MICE_SAM_output.txt -f -p 4
qiime feature-classifier classify-consensus-vsearch --i-query clean_rep-seqs.qza --i-reference-reads ~/Scrivania/Tools/Database/silva-138-99-seqs.qza --i-reference-taxonomy ~/Scrivania/Tools/Database/silva-138-99-tax.qza --p-perc-identity 0.99 --p-threads 8 --o-classification taxonomy_vsearch.qza --o-search-results vsearch_hits.qza --verbose
R software (see the relative script publicly available at github.com/LeandroD94)
Assembly: NA
Supplementary files format and content: dna-sequences.fasta: text containing every processed ASV code and sequence
Supplementary files format and content: feature_table.tsv: tab delimited text file containing the abundances of ASVs in each sample and the related taxonomic assignments
Supplementary files format and content: taxonomy.tsv: tab delimited text file containing the complete taxonomic classification of the reference sequence

organism: feces metagenome

source_name: Stool

extract_protocol:
Genomic DNA was extracted using the DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany)
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)
paired-end (2x300) amplicon sequencing

tag: host

value: Mus musculus

value: Stool

tag: genotype

tag: strain mutation

tag: time

value: OS

tag: sequencing batch

tag: sample id


title: MM_472, snATACseq

description: MASH


title: Microbiota in mouse stool, sample MN33

description: 16s rRNA v3-v4 sequencing


title: iAM05, NRG1

city: Leuven

first: Llewelyn

last: Roderick

address: Herestraat 49

department: Department of Cardiovascular Sciences

country: Belgium

institute: KU Leuven

description: Immortalized atrial cardiomyocytes - iAM05

library_source: transcriptomic

data_processing:
Gene expression was quantified at the transcript level using Salmon, with the validatMappings and -gcBias parameters switched on, to the Rnor transcriptome. Transcript level counts were aggregated to gene level count using the import in the tximport package, setting countsFromAbundance to ‘lengthScaledTPM’ in the R.
DESeq2 was used for differential gene expression between different conditions. The batch variability of different sequencing runs was accounted for by defining “batch” as a covariate in the linear model to analyze differential gene expression.
Differential gene expression heat maps were generated by using the pheatmap, and volcano plots by EnhancedVolcano.
The overlapping genes between different conditions were obtained by VennDiagram.
Functional enrichment of the differentially expressed genes was determined using a hypergeometric test against the Gene Ontology database by using the ClueGO module of Cytoscape with Benjamini–Hochberg adjusted (FDR) P < 0.05.
Assembly: Rnor_6.0
Supplementary files format and content: tab-delimited text file includes raw count for each sample
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

organism: Rattus norvegicus

source_name: iAM

growth_protocol: Immortalized rat atrial cardiomyocytes (iAM) were cultured in Advanced DMEM F-12 supplemented with 2% heat-inactivated FBS, 1% penicillin/streptomycin, 1X GlutaMAX, and 100 ng/mL doxycycline for proliferation. To induce differentiation, iAM were transferred to medium without doxycycline.

extract_protocol:
Total RNA was isolated using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol.
RNA-seq library were prepared with TruSeq RNA Sample Preparation Kit following manufacturer's manual

treatment_protocol: iAM were seeded at a density of 6x106 cells/mL in a differentiation medium in T75-flasks and incubated for 9 days. Then, cells were treated with either compound EF-1 (32 µM), PBS, or NRG1 (0.1 µM), and cells were incubated for 16 h at 37 °C.

tag: genetic modification

value: Freshly isolated neonatal rat atrial cardiomyocytes (AMs) were transduced with a lentiviral vector conferring doxycycline (dox)-controlled expression of simian virus 40 large T antigen and stable cell lines generated through selection using puromycin

value: iAM

tag: cell type

value: atrial myocytes

value: WT

tag: treatment


title: MM_470, snATACseq

description: MASH


title: iAM04, Control

description: Immortalized atrial cardiomyocytes - iAM04

value: PBS


title: Microbiota in mouse stool, sample MN31

description: 16s rRNA v3-v4 sequencing


title: MM_469, snATACseq

description: MASH


title: iAM03, Control

description: Immortalized atrial cardiomyocytes - iAM03


title: MDAMB231_GWAS_Lane2

data_processing:
Basecalls performed 10x Cellranger v6 and fba v0.0.6
Mapping and combining the libraries with 10x Cellranger
Genome_build: hg38
processed_data_files_format_and_content: single cell process h5


title: Microbiota in mouse stool, sample MN30

description: 16s rRNA v3-v4 sequencing

value: Ntg


title: MM_468, snATACseq

description: MASL


title: Microbiota in mouse stool, sample MN3

description: 16s rRNA v3-v4 sequencing

value: PS


title: MDAMB231_GWAS_Lane1


title: YW151_HTO


title: iAM02, Control

description: Immortalized atrial cardiomyocytes - iAM02


title: Microbiota in mouse stool, sample MN29

description: 16s rRNA v3-v4 sequencing


title: YW82_HTO


title: iAM01, Control

description: Immortalized atrial cardiomyocytes - iAM01


title: MM_467, snATACseq

description: NORMAL


title: MM_456, snATACseq

description: MASH


title: YW150_HTO


title: optic tectum batch 12, scRNAseq, additional sequencing

city: Martinsried

first: Inbal

last: Shainer

address: Am Klopferspitz 18

country: Germany

institute: Max Planck Institute for Biological Intelligence

description:
10x Genomics
dr_7_dpf_tectum12_S1_b
dr_7_dpf_tectum12_S1_barcodes.tsv.gz
dr_7_dpf_tectum12_S1_features.tsv.gz
dr_7_dpf_tectum12_S1_matrix.mtx.gz

data_processing:
Demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0
Assembly: GRCz11 genome assembly (Ensembl release 98)
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Danio rerio

source_name: optic tectum

extract_protocol:
The optic tectum and torus longitudinalis of 6 and 7 dpf larvae were carefully dissected under a stereoscope. Cell dissociation was performed using the Papain Dissociation System (Worthington Biochemical Corporation).
libraries according to the manufacturer’s instructions (Chromium Single Cell 3′ Reagent Kit v3, 10x Genomics).
single-cell 3′ barcoded cDNA

value: optic tectum

tag: age

value: 7 day post fertilization

value: all cells

value: wild type

value: no treatment


title: Microbiota in mouse stool, sample MN28

description: 16s rRNA v3-v4 sequencing


title: YW149_HTO


title: Microbiota in mouse stool, sample MN27

description: 16s rRNA v3-v4 sequencing


title: YW148_HTO


title: MM_454, snATACseq

description: NORMAL

value: liver


title: Microbiota in mouse stool, sample MN26

description: 16s rRNA v3-v4 sequencing


title: YW151_sgRNA

value: Single-cell Expression


title: THP-1 PMD - 3

city: St. Louis

first: Tim

last: Kong

state: MO

address: CSRB 8838

institute: Washington University School of Medicine

data_processing:
Samples were demultiplexed, underwent adapter trimming, filtering, and alignment to the hg38 reference genome following the ENCODE ATAC-seq pipeline.
Processed samples were then imported into Partek Flow (Partek) following the ATAC-seq pipeline and peaks were generated with MACS.
Assembly: hg38
Supplementary files format and content: fastq
Supplementary files format and content: bigwig

extract_protocol:
ATAC-seq was performed using the ATAC-seq Kit (Active Motif) and following protocols.
Tagmented DNA was amplified with PCR and indexed with included i7 and i5 primers.
Samples were sequenced with standard paired-end reads (2x150) on a NovaSeq6000 with a target of 50M reads.

value: 5 uM PMD-026


title: YW82_sgRNA


title: optic tectum batch 12, scRNAseq

description:
10x Genomics
dr_7_dpf_tectum12_S1_a


title: MM_455, snATACseq

description: MASL


title: THP-1 PMD - 2


title: optic tectum batch 11, replica 1, scRNAseq

description:
10x Genomics
dr_7_dpf_tectum11_S1


title: YW150_sgRNA


title: Microbiota in mouse stool, sample MN25

description: 16s rRNA v3-v4 sequencing

value: Mus musculus

value: Stool


title: optic tectum batch 10, scRNAseq, additional sequencing

description:
10x Genomics
dr_6_dpf_tectum10_S1_b
dr_6_dpf_tectum10_S1_barcodes.tsv.gz
dr_6_dpf_tectum10_S1_features.tsv.gz
dr_6_dpf_tectum10_S1_matrix.mtx.gz

value: 6 day post fertilization


title: optic tectum batch 11, replica 2, scRNAseq

description:
10x Genomics
dr_7_dpf_tectum11_S2


title: Microbiota in mouse stool, sample MN24

description: 16s rRNA v3-v4 sequencing

value: OS


title: YW149_sgRNA


title: Microbiota in mouse stool, sample MN23

description: 16s rRNA v3-v4 sequencing


title: YW148_sgRNA


title: THP-1 PMD - 1


title: THP-1 DMSO - 3

value: DMSO


title: sample 23

city: Jacksonville

first: Yingxue

last: Ren

state: FL

address: 4500 San Pablo Rd S

institute: Mayo Clinic

data_processing:
A total of 23 samples were used for RNAseq using Illumina HiSeq 4000 at the Mayo Clinic. To generate raw gene counts, the MAP-RSeq (Mayo Clinic RNA-sequencing analytic pipeline) was used by mapping to the mouse genome mm10.
Conditional quantile normalization (CQN) was performed on the raw gene counts to correct for gene length differences, GC bias, and global technical variations and to obtain similar quantile-by-quantile distributions of gene expression levels across samples
Based on the bimodal distribution of CQN-normalized and log2-RPKM gene expression values, the detection threshold was defined by genes with an average log2 RPKM more than1 in at least one group.
Assembly: mm10
Supplementary files format and content: tab delimited text file with raw gene counts of all samples

organism: Mus musculus

source_name: AppNL-G-F mice

extract_protocol:
Total RNA was extracted from mouse cortex by using a RNeasy Mini Kit (74106, QIAGEN). The RNA quantity and quality were measured by an Agilent 2100 bioanalyzer.
The samples were processed according to the manufacturer’s protocol.

treatment_protocol: Both male and female homozygous AppNL-G-F knockin (AppNL-G-F) mice provided by Drs. Saito and Saido at RIKEN were utilized in the experiments. The liposomes containing GFP or APOE2 cDNA-chitosan complex (15.2 μM liposome and 1 mg plasmid/kg body weight) were injected into AppNL-G-F mice through tail vein at 12-month-old . Six males and seven females were injected with the APOE2 cDNA liposomes, and 10 mice (4 males and 6 females) were injected with the GFP cDNA liposomes as controls. The mice were subjected to behavioural tests one month after the injection, followed by sample collections for further biochemical experiments after being euthanized. The mice were housed in a 12-hour light-dark cycle at 25℃ according to the National Institutes of Health Guide for the Care and Use of Laboratory Animals.

tag: treatment group

value: ApoE

tag: Sex

value: F


title: Microbiota in mouse stool, sample MN22

description: 16s rRNA v3-v4 sequencing


title: MDAMB231_SM_Lane8

data_processing:
Basecalls performed 10x Cellranger v6 and fba v0.0.6
Mapping and combining the libraries with 10x Cellranger
Genome_build: hg38


title: THP-1 DMSO - 2


title: sample 22


title: Microbiota in mouse stool, sample MN21

description: 16s rRNA v3-v4 sequencing


title: MDAMB231_SM_Lane7


title: THP-1 DMSO - 1


title: MDAMB231_SM_Lane6


title: Microbiota in mouse stool, sample MN20

description: 16s rRNA v3-v4 sequencing

value: Ntg


title: sample 20


title: sample 21


title: Microbiota in mouse stool, sample MN2

description: 16s rRNA v3-v4 sequencing

value: PS


title: THP-1 PMD IgG - 2

data_processing:
Post-sequencing, samples were demultiplexed,  and reads were aligned to the human genome hg38 following adapter trimming and filtering using the ENCODE ChIP-seq pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2, v2.1.6), with a custom alignment script to use Bowtie2 parameters.
The ENCODE ChIP-seq pipeline was then used to generate peaks with MACS2, and evaluate peaks consistency among replicates based on Irreproducible Discovery Rates.
Assembly: hg38
Supplementary files format and content: fastq files and bigwig files
Library strategy: CUT&RUN

extract_protocol:
CUT&Tag was performed using the Complete CUT&Tag Assay Kit (Active Motif) and following protocols.
Cells were then tagmented, after which extracted DNA underwent PCR amplification and indexed with included i7 and i5 primers.

tag: antibody

value: IgG


title: THP-1 PMD IgG - 1


title: sample 19


title: THP-1 PMD H3K27ac - 3


title: MDAMB231_SM_Lane5


title: YW127_HTO

data_processing:
Basecalls performed 10x Cellranger v6 and fba v0.0.6
Mapping and combining the libraries with 10x Cellranger
Genome_build: hg38
processed_data_files_format_and_content: single cell processs h5


title: sample 18


title: optic tectum batch 10, scRNAseq

description:
10x Genomics
dr_6_dpf_tectum10_S1_a

value: optic tectum


title: THP-1 PMD H3K27ac - 2


title: Microbiota in mouse stool, sample MN17

description: 16s rRNA v3-v4 sequencing


title: YW126_HTO


title: sample 17

value: GFP


title: THP-1 PMD H3K27ac - 1


title: Microbiota in mouse stool, sample MN16

description: 16s rRNA v3-v4 sequencing


title: YW125_HTO


title: Microbiota in mouse stool, sample MN18

description: 16s rRNA v3-v4 sequencing


title: THP-1 DMSO IgG - 2


title: THP-1 DMSO IgG - 1


title: Microbiota in mouse stool, sample MN15

description: 16s rRNA v3-v4 sequencing


title: sample 15


title: Microbiota in mouse stool, sample MN14

description: 16s rRNA v3-v4 sequencing


title: MDAMB231_SM_Lane4


title: Microbiota in mouse stool, sample MN19

description: 16s rRNA v3-v4 sequencing


title: MDAMB231_SM_Lane3


title: sample 13


title: sample 14


title: Microbiota in mouse stool, sample MN13

description: 16s rRNA v3-v4 sequencing


title: THP-1 DMSO H3K27ac - 2


title: Microbiota in mouse stool, sample MN12

description: 16s rRNA v3-v4 sequencing


title: sample 11

value: M


title: Microbiota in mouse stool, sample MN11

description: 16s rRNA v3-v4 sequencing


title: 551599 MF

description: 10x Genomics

data_processing:
Cellranger (10x Genomics, version 3.0.1) was used for transcript alignment, counting, and inter-library normalization of single cell samples. Seurat(version 4.0.0) was used for cluster analysis.
Assembly: GRCh38
Supplementary files format and content: Barcodes, features, and matrix files

source_name: PBMC

extract_protocol: Following the 10x genomics protocol, oligonucleotide labeled cells were subjected to droplet bead capture, followed by cell lysis, reverse transcription, and amplification following protocol.

value: PBMC

value: sorted non-lymphoid PBMCs


title: MDAMB231_SM_Lane2

value: Single-cell Expression


title: Microbiota in mouse stool, sample MN101

description: 16s rRNA v3-v4 sequencing


title: THP-1 DMSO H3K27ac - 1


title: MV4-11 Quiz 2

description:
mv4_11_quiz_2.CAGCGAATGC-TTAAGCTCGA.HT7LVDSX3_CAGCGAATGC-TTAAGCTCGA
MV411_all.gene_counts

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a.
TMM normalization size factors in EdgeR were calculated to adjust for samples for differences in library size.
Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.
Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
Assembly: GrCh38
Supplementary files format and content: Tab-separated values of raw counts.

extract_protocol:
Total RNA from cell lines was extracted with RNeasy Mini Kit (Qiagen, Hilden, Germany) with DNAse treatment following the manufacturer's protocol.
Samples were then indexed, pooled, and sequenced by Illumina NovaSeq 6000 following standard Illumina protocol.

value: Quizartinib


title: MDAMB231_SM_Lane1


title: sample 12


title: Microbiota in mouse stool, sample MN100

description: 16s rRNA v3-v4 sequencing

value: Mus musculus


title: sample 16


title: YW107_HTO


title: MV4-11 Quiz 1

description:
mv4_11_quiz_1.TGAACCACAA-TTCAGAACAG.HT7LVDSX3_TGAACCACAA-TTCAGAACAG
MV411_all.gene_counts


title: YW124_HTO


title: 551599 early PV

description: 10x Genomics


title: sample 7


title: Microbiota in mouse stool, sample MN1

description: 16s rRNA v3-v4 sequencing

value: Stool


title: YW108_HTO


title: sample 9


title: Microbiota in mouse stool, sample MN10

description: 16s rRNA v3-v4 sequencing


title: sample 8


title: MV4-11 DMSO 2

description:
mv4_11_ut_2.CCACAAGCAC-TCACAGTGAA.HT7LVDSX3_CCACAAGCAC-TCACAGTGAA
MV411_all.gene_counts


title: YW105_HTO


title: YW106_HTO


title: sample 10


title: YW109_sgRNA


title: sample 5


title: set2-delta, rep1

city: Shanghai

first: Bing

last: Li

address: South Chongqing Road 280

department: Department of Biochemistry and Molecular Cell Biology

country: China

institute: Shanghai Jiao Tong University School of medicine

data_processing:
Clean reads were aligned to the Schizosaccharomyces pombe genome (ASM294v2) using STAR (version STAR_2.7.10a).
Low mapping quality reads and PCR duplicates were removed using SAMtools (version SAMtools _1.16.1) and Picard (version Pichard_3.1.0).
Counts per genes were generated using featureCounts tools (version subread_2.0.1).
The DESeq2 R package (version DESeq2_1.36.0) was used for principal component analysis (PCA)
For differential expression analysis, the edgeR package (version edgeR_3.38.4) was applied to evaluate changes. The threshold log2 fold change > 1 or < -1 and p-value < 0.05 was used to determine statistical significance.
Assembly: S. pombe ASM294v2
Supplementary files format and content: text file containing raw counts of each sample

organism: Schizosaccharomyces pombe

growth_protocol: S. pombe cells were cultured in 2xYES medium at 30°C until OD600 reached a range of 0.6-1.2.

extract_protocol:
Total RNAs were extracted with hot acidic phenol method and then cleaned up with the RNeasy Mini kit (Qiagen, cat. # 74004) for further procedures.
RNA-Seq libraries were prepared from total RNA using poly(A) enrichment of the mRNA to remove ribosomal RNA, and sequenced on an Illumina NovaSeq 6000 platform.

tag: strain

value: h- set2:null:KANMX

value: Set2 deletion


title: MV4-11 PMD 1

description:
mv4_11_pmd_1.GCGTTAAGTG-GAGTAAGCAG.HT7LVDSX3_GCGTTAAGTG-GAGTAAGCAG
MV411_all.gene_counts


title: sample 6


title: set2-delta, rep2


title: YW109_HTO


title: YW104_HTO


title: wt2, rep1

value: h-

value: parental strain of set2 deletion


title: MPN CD14+ Mono 3 DMSO

description:
439467_mono_ut.GTCATCAGTA-CTTCCTAGGC.HNYT7DSX3_GTCATCAGTA-CTTCCTAGGC
Mono_all.gene_counts

source_name: MPN monocyte

value: MPN monocyte

value: DMSO


title: MV4-11 DMSO 1

description:
mv4_11_ut_1.GTATCTGAGG-TCAAGAAGGA.HT7LVDSX3_GTATCTGAGG-TCAAGAAGGA
MV411_all.gene_counts


title: wt2, rep2


title: MPN CD14+ Mono 3 PMD

description:
439467_mono_pmd.CGCGTCTGTA-CTGAAGGCGT.HNYT7DSX3_CGCGTCTGTA-CTGAAGGCGT
Mono_all.gene_counts


title: YW108_sgRNA


title: sample 3


title: sample 2


title: MV4-11 PMD 2

description:
mv4_11_pmd_2.AATATCCAGG-ACCAAGGCGA.HT7LVDSX3_AATATCCAGG-ACCAAGGCGA
MV411_all.gene_counts


title: YW106_sgRNA


title: YW107_sgRNA


title: cph2-delta, rep1

value: dy1779 h- his3 d1 ura4-d18 leu1-32 ade6-m216  cph2-delta::KANMX

value: Cph2 deletion


title: YW105_sgRNA


title: MPN CD14+ Mono 2 DMSO

description:
178446_mono_ut.CGCGGAGATT-GCAACATTGG.HNYT7DSX3_CGCGGAGATT-GCAACATTGG
Mono_all.gene_counts


title: YW104_sgRNA


title: MPN CD14+ Mono 1 PMD

description:
120770_mono_pmd.TCTACAGCTA-TGTGAATTGG.HNYT7DSX3_TCTACAGCTA-TGTGAATTGG
Mono_all.gene_counts


title: MDAMB231_GWAS_Lane8


title: MPN CD14+ Mono 1 DMSO

description:
120770_mono_ut.CATAAGCGAC-CTTCTAACCG.HNYT7DSX3_CATAAGCGAC-CTTCTAACCG
Mono_all.gene_counts


title: cph1-delta, rep1

value: dy1779 h- his3 d1 ura4-d18 leu1-32 ade6-m216  cph1-delta::KANMX

value: Cph1 deletion


title: sample 4

value: ApoE

value: M


title: E9.5 posterior trunk, Prtg-/-, sample 3

city: Taipei

first: Yu-Hui

last: Wong

address: No. 155, Sec. 2, Linong St. Beitou Dist.

department: Department of Life Sciences and Institute of Genome Sciences, College of Life Sciences

country: Taiwan

institute: National Yang Ming Chiao Tung University

data_processing:
low-quality reads, contaminations and adapter sequences were removed using Cutadapt (version 1.9.1).
The 5' or 3' end bases that contains N’s or of quality values below 20 were removed.
Reads that are less than 75 bp long after trimming were removed.
Trimmed sequence reads were mapped to GRCm38.97/mm10 and using Hisat2 (v2.0.1).
Read counts for each transcribe were generated using HT-seq (V 0.6.1) and fragments per kilo bases per million reads (FPKM) was calculated by the formula “total exon fragments / (mapped reads [millions] x exon length [KB])”.
Assembly: GRCm38.97/mm10
Supplementary files format and content: Excel file includes raw counts and FPKM values for each sample

source_name: Embryo posterior trunk

extract_protocol:
RNA was extracted using Tissue Total RNA Mini Kit (Geneaid). 1 μg total RNA was used for following library preparation.
Next generation sequencing library preparation was constructed according to the manufacturer’s protocol (NEBNext® Ultra™ RNA Library Prep Kit for Illumina®). The poly(A) mRNA isolation was performed using a NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB). The mRNA fragmentation and priming was performed using NEBNext RNA First Strand Synthesis Reaction Buffer and NEBNext Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA obtained by AxyPrep Mag PCR Clean-up (Axygen) was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tail; this was done in a single reaction, and was followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using AxyPrep Mag PCR Clean-up (Axygen), and fragments of ~420 bp (with the approximate insert size being 300 bp) were recovered. Each sample was then amplified by PCR for 13 cycles using the P5 and P7 primers, with both primers carrying sequences that are able to anneal with the flow cell in order to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean-up (Axygen), validated using a Qsep100 (Bioptic), and quantified by Qubit 3.0 Fluorometer (Invitrogen).

tag: tissue

value: Embryo posterior trunk

value: Embryo

value: Prtg-/-


title: MDAMB231_GWAS_Lane7

tag: cell line

value: Single-cell Expression


title: HEL PMD 2

description:
hel_pmd_2.CCTAGCCAGA-ATCTAGAGCG.HT7VNDSX3_CCTAGCCAGA-ATCTAGAGCG
HEL_all.gene_counts

source_name: HEL

value: HEL


title: MDAMB231_GWAS_Lane6

tag: experiment


title: E9.5 posterior trunk, Prtg+/-, sample 3

value: Prtg+/-


title: wt, rep1

value: parental strain of cph1/2 deletion


title: cph2-delta, rep2


title: MDAMB231_GWAS_Lane5


title: E9.5 posterior trunk, Prtg+/-, sample 2


title: wild-type, input,rep2

data_processing:
ChIP-seq reads were trimmed from 3'end until the final base had a quality score > 20 by using Trim_galore (version 0.6.7 ), discarding reads shorter than 25 bp
Clean reads were mapped to S. cerevisiae S288C R64-2-1 and S. pombe ASM294v2 using Bowtie2 (version bowtie2_2.2.5), respectively.
Multiple-mapped reads were filtered using SAMtools (version SAMtools _1.16.1), and PCR-duplicated reads were removed using Picard (version Pichard_3.1.0). Index of the bam files was generated using SAMtools.
BigWig files were generated for visualizing in Integrative Genomics Viewer (IGV) using BamCoverage of deepTools (version deeptools_3.5.1)
BamCompare was applied to calculate the log2 fold change of mutant versus wild-type. ComputeMatrix, plotProfile and plotHeatmap functions from deepTools was also used to plot the gene body and flanking region heatmap graphs using the normalized signal intensity.
Assembly: S. cerevisiae S288C R64-2-1 and S. pombe ASM294v2
Supplementary files format and content: bigWig generated by BamCoverage
Supplementary files format and content: bigWig generated by BamCompare

growth_protocol: S.cerevisiae strains were cultured in YPD medium at 30°C. S.pombe were cultured on YES medium at 30°C.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15min. After quenching and cell lysis, chromatin was sonicated using Sonicator with duty cycle 90% (0.9 sec ON; 0.1 sec OFF) 12 pulses for 5 times.
The ChIP-seq library was constructed using VAHTS® Universal DNA Library Prep Kit for Illumina V3 (Vazyme, ND607). 2 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 14 cycles on the thermocycler. Post amplification libraries were size selected at 250-500 bp in length using Qiagen gel purification kit.

treatment_protocol: No additional treatment.


title: HEL DMSO 2

description:
hel_ut_2.TGAGATCAAG-TACCGGAGCA.HT7VNDSX3_TGAGATCAAG-TACCGGAGCA
HEL_all.gene_counts


title: MPN CD14+ Mono 2 PMD

description:
178446_mono_pmd.GTAATCACGC-TATACCAGGA.HNYT7DSX3_GTAATCACGC-TATACCAGGA
Mono_all.gene_counts


title: sample 1

value: GFP


title: E9.5 posterior trunk, Prtg+/-, sample 1


title: wt, rep2


title: HEL PMD 1

description:
hel_pmd_1.CGGTCTTACG-GATCCTCTCG.HT7VNDSX3_CGGTCTTACG-GATCCTCTCG
HEL_all.gene_counts


title: wild-type, input,rep1


title: HEL DMSO 1

description:
hel_ut_1.CGTACTATAC-GATCAACAAG.HT7VNDSX3_CGTACTATAC-GATCAACAAG
HEL_all.gene_counts


title: E9.5 posterior trunk, Prtg-/-, sample 2


title: MDAMB231_GWAS_Lane4


title: cph1-delta, rep2


title: E9.5 posterior trunk, WT, sample 2

value: WT


title: cph2-delta,H4Ac, ChIP,rep2

tag: chip antibody

value: H4 acetylation


title: E9.5 posterior trunk, Prtg-/-, sample 1

tag: genotype


title: MDAMB231_SM_Lane8_NovaSeq


title: DAA278_CellPlex

source_name: MDAMB361 Cell line


title: E9.5 posterior trunk, WT, sample 1


title: cph2-delta,H4Ac, ChIP,rep1


title: DAA277_CellPlex


title: cph1-delta,H4Ac, ChIP,rep2


title: DAA276_CellPlex


title: MDAMB231_SM_Lane7_NovaSeq


title: YW127_sgRNA_NovaSeq


title: HFD-Atractylodin 1

city: Chuncheon-si

first: Yoon Mee

last: Yang

state: Gangwon-do

address: 1 Kangwondaehak-gil

department: Pharmacy

country: South Korea

institute: Kangwon National University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Liver

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: Liver

value: High fat diet, Atractylodin (10 mg/kg)


title: MDAMB231_SM_Lane5_NovaSeq


title: DAA273_CellPlex


title: HFD-Atractylodin 2


title: DAA275_CellPlex


title: wild-type, H4Ac, ChIP,rep2


title: HFD-Vehicle 3

value: High fat diet, vehicle


title: YW126_sgRNA_NovaSeq


title: MDAMB231_GWAS_Lane3


title: YW125_sgRNA_NovaSeq


title: DAA274_CellPlex


title: cerulein-AP3

city: Wenzhou

first: Chaohao

last: Huang

state: Zhejiang

address: Nanbaixiang Town, Ouhai District, Wenzhou City, Zhejiang Province, China 325000, China,

department: Department of Surgery

institute: First affiliated hospital of Wenzhou Medical University

data_processing:
Library sequencing was performed on the HiSeq X10 platform with a paired-end 2*150 bp, dual-index format.
Trimmomatic software was employed to remove Illumina sequencing adapters and trim low-quality bases from both ends of the raw reads (using parameters LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15) and to discard reads shorter than 36 bp.
The cleaned reads were then aligned to the mouse mm10 reference genome with the STAR aligner, and the resulting alignment bam files were input into htseq-count, a command from the HTSeq Python package, to obtain gene read counts.
Assembly: mm10
Supplementary files format and content: gene read counts for each sample

source_name: pancreas

extract_protocol:
pancreatic tissue  was stored in RNAlater and using TRIzol (ThermoFisher Scientific) to extract RNA according to the manufacturer's instructions.
RNA libraries were  prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina), following the manufacturer’s instructions.

value: pancreas

value: cerulein intraperitoneal injection


title: wild-type, H4Ac, ChIP,rep1


title: HFD-Vehicle 2


title: YW124_sgRNA_NovaSeq

data_processing:
Basecalls performed 10x Cellranger v6 and fba v0.0.6
Mapping and combining the libraries with 10x Cellranger
Genome_build: hg38
processed_data_files_format_and_content: sgRNA library output scv


title: cerulein-AP2


title: MDAMB231_SM_Lane6_NovaSeq


title: cph1-delta,H4Ac, ChIP,rep1

value: dy1779 h- his3 d1 ura4-d18 leu1-32 ade6-m216  cph1-delta::KANMX

value: Cph1 deletion


title: HFD-Vehicle 1


title: DAA272_CellPlex


title: cerulein-AP1


title: DAA271_sgRNA


title: saline-ctlr3

value: saline intraperitoneal injection


title: MDAMB231_SM_Lane3_NovaSeq


title: DAA271_CellPlex


title: Rco1-13KR-to-A_CO, H4Ac, ChIP, rep2

organism: Saccharomyces cerevisiae

value: MATa his3-delta-1 leu2-delta-0 met15-delta-0 ura3-delta-0 2xFlag-Rco1 13KR-to-A_CO


title: Rco1-13KR-to-A_CO, input


title: saline-ctlr2


title: MDAMB361_GWAS_SM_Lane1


title: MDAMB231_SM_Lane2_NovaSeq


title: Rco1-13KR-to-A_CO, H4Ac, ChIP, rep1


title: saline-ctlr1


title: MDAMB231_SM_Lane4_NovaSeq


title: HCC1954-dCas9-KRAB_Rep2__

data_processing:
custom pipeline
Mapped with bwa mem
Assembly: hg38

extract_protocol:
Cells were collected, washed once with PBS and followed by ATAC-seq library construction.
50,000 cells were collected for ATAC-seq library construction. 100 nM of Tn5 were used during the transposition reaction followed by the column cleanup. We used KAPA HiFi polymerase (Roche) for PCR amplification with 7 cycles and a 1.4X SPRI beads cleanup.

treatment_protocol: Cells were infected with lenti-dCas9-KRAB-blast (Addgene:89567) to stablly express dCas9-KRAB with two weeks of blasticidin selection.


title: MDAMB231_SM_Lane1_NovaSeq


title: Rco1-13KR-to-A, H4Ac, ChIP, rep2

value: MATa his3-delta-1 leu2-delta-0 met15-delta-0 ura3-delta-0 2xFlag-Rco1 13KR-to-A


title: HCC1954-dCas9-KRAB_Rep1__


title: YW109_sgRNA_NovaSeq

data_processing:
Basecalls performed 10x Cellranger v6 and fba v0.0.6
Mapping and combining the libraries with 10x Cellranger
Genome_build: hg38
processed_data_files_format_and_content: sgRNA library output csv

value: Single-cell Expression


title: BALB-c-hash, scRNA-seq

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

description: BALB/C  hasing antibody-derived tags library

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using Cell Ranger software.
The generated FASTQ files were further demultiplexed using TotalSeq™hashtags via the Cell Ranger multi pipeline by BioLegend to clarify which mouse-derived data
The single-cell RNA-seq dataset was initially processed, explored, and visualized using the Cellenics ® community instance (https://scp.biomage.net/) hosted by Biomage (https://biomage.net/).
Downstream analyses were performed using Cellenics and Seurat (v5.1.1)
Assembly: Mus musculus GRCm38
Supplementary files format and content: c57090e6_processed_matrix.rds (seurat object)
Supplementary files format and content: cell_id-and-cluster.csv (cell-cluster mapping info)

source_name: Spleen

growth_protocol: C57BL/6 and Balb/c mice were housed in pathogen-free conditions at 22 °C with a 12-hour light-dark cycle and had free access to a chow diet and water.

extract_protocol:
Monocytes were isolated from the freshly collected spleens of sham-operated and CLP-surviving mice using EasySep™ Mouse Monocyte Isolation Kit (STEMCELL Technologies) according to the manufacturer’s protocol. Isolated monocytes were blocked with rat anti-mouse CD16/32 antibody (BioLegend), followed by staining with PE-Cy7-anti-CD11b and FITC-anti- Ly6C antibodies and FVD efluor506 with Total Seq™-B 0302 anti-mouse Hashtag 2 Antibody or TotalSeq™-B0303 anti-mouse Hashtag 3 Antibody or TotalSeq™-B0304 anti-mouse Hashtag 4 Antibody or TotalSeq™-B03050 anti-mouse Hashtag 5 Antibody, or TotalSeq™-B0306 anti-mouse Hashtag 6 Antibody (BioLegend). Five different Total Seq™-B antibodies were used for BALB/c and C57BL/6, respectively, to distinguish them in the later analysis. After combining cells from 2 sham-operated or 3 CLP-surviving mice, CD11b+ Ly6C high populations were sorted using BD FACSAria IIu (BD Biosciences).
Cells were put onto the 10X Chromium Controller (10X Genomics). Gel Bead-in Emulsions were generated using Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10X Genomics), following the manufacturer’s recommendations.

treatment_protocol: CLP or sham surgery

value: Spleen

value: CD11b+Ly6C high monocytes

value: BALB/c

value: Male

value: CLP or sham surgery


title: BALB-c-Gexp, scRNA-seq

description: BALB/C Sham and CLP


title: SKBR3-dCas9-KRAB_Rep2__


title: YW108_sgRNA_NovaSeq


title: Rco1-13KR-to-A, H4Ac, ChIP, rep1

value: H4 acetylation


title: B6-hash, scRNA-seq

description: C57BL/6 l hasing antibody-derived tags library


title: wild-type, input

value: MATa his3-delta-1 leu2-delta-0 met15-delta-0 ura3-delta-0 2xFlag-Rco1 WT

value: 2xFlag-Rco1 wt


title: SKBR3-dCas9-KRAB_Rep1__


title: YW107_sgRNA_NovaSeq


title: B6-Gexp, scRNA-seq

description: C57BL/6 Sham and CLP


title: YW106_sgRNA_NovaSeq


title: MDAMB231-dCas9-KRAB_Rep2__


title: wild-type, H4Ac, ChIP, rep2

value: MATa his3-delta-1 leu2-delta-0 met15-delta-0 ura3-delta-0 2xFlag-Rco1 wt


title: Input-16h

city: shanghai

first: kun

last: chen

address: No.800 Xiangyin Road, Yangpu District

institute: Zhejiang University

data_processing:
cDNA library construction and sequencing were performed by Beijing Novogene using Illumina Hiseq platform.
High-quality reads were aligned to the mouse reference genome (GRCm38) using Bowtie2
peaks were called using MACS2 software (Chilin pipline).
Genome_build: mm10

source_name: bone marrow-derived macrophages

growth_protocol: Bone marrow-derived monocyte are cultured in DMEM medium plus M-CSF for 5 days to generate BMDMs.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K36me3 antibody.
cDNA library construction and sequencing were performed by Beijing Novogene using Illumina Hiseq platform.

treatment_protocol: BMDMs  are treated with LPS (100ng/ml) for 4h and 16h.

tag: stain

tag: time point


title: MDAMB231-dCas9-KRAB_Rep1__


title: YW105_sgRNA_NovaSeq

extract_protocol:
Cells were collected, washed once with PBS and stained with Cell Hashing antibodies ot CellPlex followed by manuffacturer manual. Cells were resuspended in PBS containing 0.05% of BSA to the desired concentration and immediately load on the 10x Chromium controller for single-cell RNA-seq preparation.
For single-cell library preparation, we followed the standard protocol of 10x Genomics. After the cDNA amplification, 50 ng of samples were separated for the sgRNA enrichment library preparation.


title: MDAMB436-dCas9-KRAB_Rep2__


title: MDAMB436-dCas9-KRAB_Rep1__


title: wild-type, H4Ac, ChIP, rep1


title: Input-4h


title: YW104_sgRNA_NovaSeq


title: Input-0h


title: MDAMB231_GWAS_Lane8_NovaSeq

data_processing:
Basecalls performed 10x Cellranger v6 and fba v0.0.6
Mapping and combining the libraries with 10x Cellranger
Genome_build: hg38
processed_data_files_format_and_content: single cell process h5


title: s_ovotestis_WT_S7_Av007Ovo_r1.SE

city: Prague

first: Filip

last: Horvat

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR

data_processing:
Small RNA-seq reads were trimmed in two rounds using bbduk.sh version 38.87 (https://jgi.doe.gov/data-and-tools/bbtools/). First, NEXTflex adapter were trimmed from right end: bbduk.sh -Xmx20G threads=6 in=$ {FILE}.fastq.gz out=$ {FILE}.atrim.fastq.gz literal= TGGAATTCTCGGGTGCCAAGG stats=$ {FILE}.atrim.stats overwrite=t ktrim=r k=19 rcomp=t mink=10 hdist=1 minoverlap=8 Next, 4 random bases from both sides of reads were trimmed: bbduk.sh -Xmx20G threads=6 in=$ {FILE}.atrim.fastq.gz out=$ {FILE}.trimmed.fastq.gz stats=$ {FILE}.ftrim.stats overwrite=t forcetrimright2=4 forcetrimleft=4 minlength=15
Trimmed reads were mapped to the Arion vulgaris genome (GCA_020796225.1) with following parameters: STAR --readFilesIn $ {FILE}.fastq.gz --genomeDir $ {GENOME_INDEX} --runThreadN 12 --genomeLoad LoadAndRemove --limitBAMsortRAM 20000000000 --readFilesCommand unpigz –c --outFileNamePrefix $ {FILENAME} --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --outFilterMismatchNmax 1 --outFilterMismatchNoverLmax 1 --outFilterMismatchNoverReadLmax 1 --outFilterMatchNmin 19 --outFilterMatchNminOverLread 0 --outFilterScoreMinOverLread 0 --outFilterMultimapNmax 99999 --outFilterMultimapScoreRange 0 --alignIntronMax 1 --alignSJDBoverhangMin 999999999999
Genome browser coverage tracks in bigWig format were produced using bedtools v2.26.0 and wigToBigWig v 4 from UCSC: genomeCoverageBed -ibam ${FILE}.bam -bg -split -g chrNameLength.txt > ${FILE}.bedGraph wigToBigWig ${FILE}.bedGraph chrNameLength.txt ${FILE}.bw
coverage genome browser tracks files:
- bigWig format
- generated in a non-stranded mode
- not normalized for library size
Assembly: GCA_020796225.1
Supplementary files format and content: bigWig

organism: Arion vulgaris

source_name: ovotestis

extract_protocol:
Total RNA was extracted from samples through phenol-chlorofom isolation, by using QIAzol Lysis Reagent according to the manufacturer´s protocol.
Total RNA isolated from tissue as described above was used for NextFlex Small RNA-seq v3 kit (Amplicon). Libraries were prepared according to the manufacturer´s protocol with 3´ adapter ligation overnight at 16 °C, 15 cycles used for PCR amplification and gel purification was performed for size selection.

value: ovotestis

value: WT


title: rco1-delta, H4Ac, ChIP, rep2

value: MATa, his3-delta-1 leu2-delta-0 met15-delta-0 ura3-delta-0 rco1-delta::KANMX6

value: Rco1 deletion


title: sWAT_GDF15KO_fed_ad_libitum_M18

city: Nuthetal

first: Carla

last: Igual Gil

address: Arthur-Scheunert-Allee 114-116

institute: German Institute of Human Nutrition (DIfE)

data_processing:
adapters and low-quality reads have been filtered by BGI
alignment to reference by BGI using Bowtie2 (v2.2.5)
abundance call by BGI using RSEM (v1.2.8)
Assembly: GCF_000001635.27_GRCm39
Supplementary files format and content: excel file, includes raw counts for each sample

source_name: Subcutaneous adipose tissue (sWAT)

extract_protocol:
RNA was isolated following a TRIzol (Thermo Fisher, #15596026)-chloroform extraction and DNase digested following manufacturer instructions (Fisher Scientific, #EN0521)
done by BGI (Yantian District, Shenzhen, China)

value: Subcutaneous adipose tissue (sWAT)

value: male

value: 20 weeks

tag: feeding

value: fed ad libitum


title: ChIP-16h


title: HCC1937-dCas9-KRAB_Rep1__


title: rco1-delta, H4Ac, ChIP, rep1


title: MDAMB231_GWAS_Lane7_NovaSeq

value: Single-cell Expression


title: ChIP-4h


title: sWAT_GDF15KO_fed_ad_libitum_M17


title: sWAT_GDF15KO_fed_ad_libitum_M16


title: MDAMB361-dCas9-KRAB_Rep2__


title: ChIP-0h


title: MDAMB231_GWAS_Lane5_NovaSeq


title: MDAMB231_GWAS_Lane6_NovaSeq


title: sWAT_GDF15KO_fed_ad_libitum_M15


title: MDAMB231_GWAS_Lane4_NovaSeq


title: MDAMB361-dCas9-KRAB_Rep1__


title: Ctrl2-resub

city: London

first: Matthew

last: Berg

state: Ontario

address: 1151 Richmond St

department: Biochemistry

country: Canada

institute: University of Western Ontario

data_processing:
Sequence reads were obtained from Genewiz (South Plainfield, NJ)
Sequenced reads were trimmed for adaptor sequence and then mapped to S. cerevisiae S288C whole genome using STAR v2.5.4b
Raw counts for each sample were obtained using featureCounts v1.6.0
Differentially expressed genes were determined using DESeq2 v1.26.0
Genome_build: S. cerevisiae S288C reference genome (assembly R64-2-1; https://www.yeastgenome.org/)
Supplementary_files_format_and_content: Raw gene counts table for every gene and every sample
Supplementary_files_format_and_content: Normalized counts text files for each gene for each sample

source_name: Ctrl, yeast grown in YPD

growth_protocol: Exponentially growing cultures in YPD were treated for two hours with or without 5 mM TUDCA

extract_protocol:
RNA samples were then extracted using the  MasterPure Yeast RNA purification kit (Lucigen) following manufacturer's protocol
Stranded Illumina TruSeq cDNA libraries with poly dT enrichment were prepared from high quality total RNA (RIN > 8)

treatment_protocol: 5mM TUDCA for two hours

value: MAT{alpha} his3{delta}1 leu2{delta}0 lys2{delta}0 ura3{delta}0

value: Ctrl


title: sWAT_GDF15KO_fed_ad_libitum_M14


title: TUDCA2-resub

source_name: TUDCA, yeast grown in YPD

value: TUDCA


title: ZR751-dCas9-KRAB_Rep2__


title: HFD-Atractylodin 3

value: Liver

value: High fat diet, Atractylodin (10 mg/kg)


title: ZR751-dCas9-KRAB_Rep1__


title: sWAT_GDF15KO_fed_ad_libitum_M13


title: HCC1937-dCas9-KRAB_Rep2__


title: DAA278_sgRNA_NovaSeq


title: MDAMB231_GWAS_Lane3_NovaSeq

source_name: MDAMB231 Cell line


title: MCF7-dCas9-KRAB_Rep2__


title: Ctrl1-resub


title: DAA277_sgRNA_NovaSeq


title: sWAT_WT_fed_ad_libitum_M5


title: TUDCA1-resub


title: MCF7-dCas9-KRAB_Rep1__


title: DAA276_sgRNA_NovaSeq


title: sWAT_WT_fed_ad_libitum_M4


title: sWAT_WT_fed_ad_libitum_M3


title: sWAT_WT_fed_ad_libitum_M2


title: DAA275_sgRNA_NovaSeq


title: KELLY_COMBO_R1

type: RNA

city: Melbourne

first: Janith

last: Seneviratne

state: VIC

address: Peter MacCallum Cancer Centre, 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

description: KELLY cells treated with GSK343 12.8uM and SGC0946 12.8uM for 6h, replicate 1

hyb_protocol: Labeled cRNA was fragmented in fragmentation buffer (5x buffer:200 mM Tris-acetate (pH 8.1)/500nM KOAc/150 mM MgOAc) before hybridization on the array. Fragmented cRNA was hybridized to the microarrays in 90ul hybridization solution. GeneTitan Hybridization, Wash and Stain kit for 3`IVT arrays (Affymetrix) was used for preparing hybridization mixes and processing plate array in GeneTitan.

scan_protocol: The prepared Human Genome U219 array plate was processed in GeneTitan according to manufacturer's instructions

data_processing: Array CEL files, containing the raw probe intensities measured from the microarray, were imported into R using the oligo R package. Raw probe intensity values were then subject to robust multi‐array averaging (RMA) normalisation using the oligo package. PrimeView probes were annotated with ‘hgu219.db’ package annotations alongside the biomaRt package. Genes with multiple microarray probes were collapsed using interquartile range with a custom R script, which removed probes with lower intensities.

label: biotin

source_name: KELLY cells

label_protocol: cRNA synthesis was made using 3`IVT Express kit (Affymetrix) following manufacterer's instructions and starting with 200ng of total RNA

growth_protocol: The human NB cell line SK‐N‐BE(2)‐C (CVCL_0529) were maintained in Dulbecco's Modified Eagle Medium (DMEM) (#10566016 Gibco, Thermo Scientific, NSW, Australia) supplemented with 10% heat inactivated Foetal Bovine Serum (FBS) (Thermo Trace, Noble Park, VIC, Australia). The human NB cell line KELLY (CVCL_2092) was maintained in Roswell Park Memorial Institute 1640 medium (RPMI) (#11875093 Gibco) supplemented with 10% heat inactivated FBS. Cells were seeded in a T25 flask for experiments at 90% confluency.

extract_protocol: Medium was aspirated, cells were trypsinised and pelleted. Cells were washed three times in PBS. Total RNA extraction was performed using the PureLink RNA Mini kit (#12183025 Thermofisher), quantitation and quality control were performed via nanodrop. RNA from treated samples were then subject to microarray profiling via the PrimeView Human Genome U219 Array (#901605 Applied Biosystems) according to manufacturer instructions, by the Ramaciotti Centre for Genomics (UNSW, Australia).

treatment_protocol: Following an initial 24 h of incubation after cell seeding, drug treatments were made in fresh DMEM or RPMI 1640 medium supplemented with 10% FBS. Cell culture medium was replaced with medium containing either DMSO, 12.8 μM SGC0946, 12.8 μM GSK343 or a combination of both drugs. Treated cells were incubated for 6 h at 37°C and 5% CO2

tag: model

value: KELLY

value: COMBO

tag: replicate


title: KELLY_SGC0946_R2

description: KELLY cells treated with SGC0946 12.8uM for 6h, replicate 2


title: brachial_non-draining_rep2

city: San Francisco

first: Kevin

middle: Y

last: Chen

address: 513 Parnassus Ave

department: Microbiology and Immunology

institute: UCSF

data_processing:
ATAC-seq reads from two biological replicates for each sample were mapped to the mouse genome (mm39 assembly) using Bowtie 1.3.1.
Redundant reads were removed using FastUniq.
Customized Python scripts were used to calculate the fragment length of each pair of uniquely mapped paired-end (PE) reads. Only one mapped read to each unique region of the genome that was less than 175 bp was kept and used in peak calling.
Regions of open chromatin were identified by MACS (version 1.4.2) using a p-value threshold of 1x10−5. Only peaks detected in both replicates were used in downstream analysis.
Peak intensities (“tags” column) were normalized as tags per 10 million reads (RP10M) in the original library. The annotation was carried out using PAPST and the heatmap creation utilized deeptools 3.5.4.
Assembly: mm39
Supplementary files format and content: bigWig, BED peaks

source_name: lymph node

extract_protocol:
ATAC-seq was performed according to a published Omni-ATAC protocol. 5-8x103 sorted lymph node FRCs from popliteal or brachial lymph nodes were centrifuged at 500 r.c.f. for 5 min at 4°C in a fixed-angle centrifuge. Cell pellets were lysed and tagmented in one step by resuspending in 25 ul of tagmentation reaction mix containing 0.02% digitonin, 0.1% Tween-20, and 100 nM Tn5 transposase in tagmentation buffer (10 mM Tris-HCl, 5 mM MgCl2, and 10% dimethyl formamide). Transposition reactions were incubated at 37 °C for 60 min in a thermocycler. Reactions were cleaned up with Zymo DNA Clean and Concentrator 5 columns (Zymo Research).
ATAC-seq libraries were prepared following the protocol described in Buenrostro et al., 2015. A series of SPRI-bead size selections were performed to generate libraries with a target library size between 300-400bp which primarily represents sub-nucleosomal and mono-nucleosomal peaks. Library concentrations were determined using UV Qubit fluorometer. Libraries size distributions were validated using the Agilent High Sensitivity DNA kit.

value: lymph node

tag: cell type

value: fibroblastic reticular cell

value: LCMV footpad infection


title: KELLY_SGC0946_R1

description: KELLY cells treated with SGC0946 12.8uM for 6h, replicate 1

tag: treatment


title: popliteal_inflamed_rep2

value: WT


title: brachial_non-draining_rep1


title: DAA273_sgRNA_NovaSeq

city: Dallas

first: Yihan

last: Wang

address: 5323 Harry Hines Blvd.

institute: UT Southwestern


title: KELLY_GSK343_R2

description: KELLY cells treated with GSK343 12.8uM for 6h, replicate 2


title: sWAT_WT_fed_ad_libitum_M6

tag: age


title: popliteal_inflamed_rep1


title: KELLY_GSK343_R1

description: KELLY cells treated with GSK343 12.8uM for 6h, replicate 1


title: KELLY_COMBO_R2

description: KELLY cells treated with GSK343 12.8uM and SGC0946 12.8uM for 6h, replicate 2


title: optic tectum batch 8, replica 2, scRNAseq

description:
10x Genomics
dr_7dpf_tectum9_S2

data_processing:
Demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0
Assembly: GRCz11 genome assembly (Ensembl release 98)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: optic tectum

extract_protocol:
The optic tectum and torus longitudinalis of 6 and 7 dpf larvae were carefully dissected under a stereoscope. Cell dissociation was performed using the Papain Dissociation System (Worthington Biochemical Corporation).
libraries according to the manufacturer’s instructions (Chromium Single Cell 3′ Reagent Kit v3, 10x Genomics).
single-cell 3′ barcoded cDNA

value: optic tectum

value: 7 day post fertilization

value: all cells

value: wild type

value: no treatment


title: sWAT_GDF15KO_fed_ad_libitum_F17

value: Subcutaneous adipose tissue (sWAT)

value: female

value: 20 weeks

value: fed ad libitum


title: DAA271_sgRNA_NovaSeq

value: Single-cell Expression


title: KELLY_DMSO_R2

description: KELLY cells treated with DMSO for 6h, replicate 2

value: DMSO


title: MDAMB361_GWAS_SM_Lane8_NovaSeq

data_processing:
Basecalls performed 10x Cellranger v6 and fba v0.0.6
Mapping and combining the libraries with 10x Cellranger
Genome_build: hg38
processed_data_files_format_and_content: Single cell process h5


title: optic tectum batch 8, replica 1, scRNAseq

description:
10x Genomics
dr_6dpf_tectum9_S1


title: KELLY_DMSO_R1

description: KELLY cells treated with DMSO for 6h, replicate 1

value: KELLY


title: DAA274_sgRNA_NovaSeq


title: sWAT_GDF15KO_fed_ad_libitum_F16


title: optic tectum batch 7, scRNAseq

description:
10x Genomics
dr_6dpf_tectum8_S1

value: 6 day post fertilization


title: BE2C_COMBO_R2

description: SK-N-BE(2)-C cells treated with GSK343 12.8uM and SGC0946 12.8uM for 6h, replicate 2

source_name: SK-N-BE(2)-C cells

value: COMBO


title: MDAMB361_GWAS_SM_Lane7_NovaSeq


title: sWAT_GDF15KO_fed_ad_libitum_F15


title: optic tectum batch 6, replica 2, scRNAseq

description:
10x Genomics
dr_6dpf_tectum7_S2


title: BE2C_COMBO_R1

description: SK-N-BE(2)-C cells treated with GSK343 12.8uM and SGC0946 12.8uM for 6h, replicate 1


title: MDAMB361_GWAS_SM_Lane6_NovaSeq


title: sWAT_GDF15KO_fed_ad_libitum_F14


title: sWAT_WT_fed_ad_libitum_M1

value: male


title: optic tectum batch 6, replica 1, scRNAseq

description:
10x Genomics
dr_6dpf_tectum7_S1


title: MDAMB361_GWAS_SM_Lane5_NovaSeq


title: BE2C_SGC0946_R2

description: SK-N-BE(2)-C cells treated with SGC0946 12.8uM for 6h, replicate 2


title: optic tectum batch 5, replica 2, scRNAseq

description:
10x Genomics
dr_6dpf_tectum6_S2


title: sWAT_GDF15KO_fed_ad_libitum_F18


title: DAA272_sgRNA_NovaSeq


title: BE2C_SGC0946_R1

description: SK-N-BE(2)-C cells treated with SGC0946 12.8uM for 6h, replicate 1


title: sWAT_WT_fed_ad_libitum_F6


title: MDAMB361_GWAS_SM_Lane4_NovaSeq


title: BE2C_GSK343_R2

description: SK-N-BE(2)-C cells treated with GSK343 12.8uM for 6h, replicate 2


title: MDAMB361_GWAS_SM_Lane3_NovaSeq


title: optic tectum batch 5, replica 1, scRNAseq

description:
10x Genomics
dr_6dpf_tectum6_S1


title: sWAT_WT_fed_ad_libitum_F5


title: optic tectum batch 4, scRNAseq

description:
10x Genomics
dr_7dpf_tectum4_S1


title: MDAMB361_GWAS_SM_Lane2_NovaSeq

data_processing:
Basecalls performed 10x Cellranger v6 and fba v0.0.6
Mapping and combining the libraries with 10x Cellranger
Genome_build: hg38
processed_data_files_format_and_content: Singel cell process h5


title: sWAT_WT_fed_ad_libitum_F4


title: optic tectum batch 3, scRNAseq

description:
10x Genomics
dr_7dpf_tectum3_S1


title: BE2C_DMSO_R2

description: SK-N-BE(2)-C cells treated with DMSO for 6h, replicate 2


title: optic tectum batch 2, scRNAseq

description:
10x Genomics
dr_7dpf_tectum2_S1


title: MDAMB361_GWAS_SM_Lane1_NovaSeq

data_processing:
Basecalls performed 10x Cellranger v6 and fba v0.0.6
Mapping and combining the libraries with 10x Cellranger
Genome_build: hg38
processed_data_files_format_and_content: Sinlge cell process h5


title: BE2C_DMSO_R1

description: SK-N-BE(2)-C cells treated with DMSO for 6h, replicate 1


title: H9 hESC shLuc

city: New York

first: Jianlong

state: New York

department: Department of Medicine

institute: Columbia University Irving Medical Center

description: Hi-C seq of H9 hESC shLuc

data_processing:
Paired-end reads were combined and pre-processed by Trim Galore (v.0.6.3) and Cutadapt programs.
Hi-C labrary reads were processed using HiC-Pro (v3.0.0) and aligned to the hg19 reference genome using Bowtie2.
All valid pairs of contacts were generated after filter and remove duplicates in HiC-Pro.
Valid contact read pairs of samples were applied to obtain the correlation coefficient matrices using Homer (v4.11) and PC1 values were exported in bedgraph
Genome_build: hg19
Supplementary_files_format_and_content: Valid pairs; bedgraph

source_name: H9 hESC shLuc

growth_protocol: Human ES cells were maintained on irradiated inactivated MEFs in human ES cell medium composed of DMEM/F12 (Cellgro, Mediatech) containing 20% Knockout serum (Invitrogen), penicillin/streptomycin, L-glutamine, non-essential amino acids, β-merceptoethanol (β-ME, sigma), and bFGF (R&D Systems).

extract_protocol:
Human embryonic cells were washed with PBS and fixed with 2% formaldehyde for 10min at RT.
Hi-C samples were prepared with the Arima Hi-C Kit, and libraries were preapred with the KAPA HyperPrep Kits following the manufacturer’s instructions

treatment_protocol: Human ES cells were infected with shLuc and shDDX18 Virus, samples are collected at day 4.

tag: cell types

value: human ESC

tag: tatreatment

value: shLuc


title: sWAT_GDF15KO_fed_ad_libitum_F13

tag: Sex


title: H9 hESC shDDX18

description: Hi-C seq of H9 hESC shDDX18

source_name: H9 hESC shDDX18

tag: strain


title: sWAT_WT_fed_ad_libitum_F2

tag: tissue

value: WT


title: sWAT_WT_fed_ad_libitum_F1


title: Human brain prefrontal cortex BA10, Control sample5

status: Public on Nov 12 2024

city: New Orleans

first: Yun

last: Gong

address: 3720 Clio St

institute: Tulane University

data_processing:
The fastq files from Stereo-seq were processed following the standard pipeline (https://github.com/STOmics/SAW)
Assembly: hg38
Supplementary files format and content: The .tissue.gef data is the tissue bin resolution and the .cellbin.gef data is the cellbin resolution

source_name: Brain

extract_protocol:
The BA10 area from 12 postmortem human brains were harvested and immediately flash frozen, embedded with OCT medium in liquid nitrogen, and then stored at -80°C until ready for the Stereo-seq pipeline. the tissue section on the Stereo-seq chip (10 mm x 10 mm) was incubated at 37°C for 5 mins, and subsequently fixed in pre-cooled methanol (Cat # 34860, Sigma) at -20°C for 30 mins. Once the fixation was completed, the chip was placed under a ventilation hood to allow residual methanol to air dry. The tissue section on the chip was then stained with nucleic acid reagent (Cat # Q10212, 0.5% v/v, Invitrogen) for 5 mins and subsequently washed with 0.1X SSC buffer (Cat # AM9770, 0.05 U/mL RNase inhibitor, Ambion). Stereo-seq transcriptomics chip-captured RNAs from the permeated tissue were then reverse transcribed for 3 hours at 42°C.
The tissue was removed and the cDNAs were released from the chip using the transcriptomics reagent kit (Cat # 111KT114, STOmics America Ltd). After the cDNA obtained was size-selected, amplified, and purified, the concentration was quantified by Qubit dsDNA HS assay kit (Cat # Q32854, Invitrogen). Next, 20 ng of cDNA from each sample were used for library construction using the library preparation kit (Cat # 111KL114, STOmics America Ltd) and subsequently for DNB generation.

value: Brain

tag: tissue type

value: control

value: Human brain cells


title: optic tectum batch 1, scRNAseq

city: Martinsried

first: Inbal

institute: Max Planck Institute for Biological Intelligence

description:
10x Genomics
dr_7dpf_tectum1_S1

value: optic tectum

value: 7 day post fertilization

value: all cells

value: wild type

value: no treatment


title: Human brian prefrontal cortex BA10, Control sample4


title: Human brian prefrontal cortex BA10, AD sample6

value: AD


title: Human brian prefrontal cortex BA10, Control sample1


title: Human brain prefrontal cortex BA10, Control sample6


title: Human brian prefrontal cortex BA10, AD sample5


title: Human brian prefrontal cortex BA10, Control sample2


title: mE14_10m_B1_T2

city: Los Angeles

first: Marty

middle: G

address: 615 Charles E Young Dr S

department: Biological Chemistry

institute: University of California, Los Angeles

description: E14 mESCs were treated with 10 uM BrdU for varying timepoints to label newly replicated chromatin, nuclei were isolated and treated with EcoGII for footprinting of protein-DNA contacts, and DNA was purified and prepared into PacBio SMRTbell libraries for sequencing on the PacBio Sequel II platform.

data_processing:
Reads are demultiplexed using lima to produce a .bam file for subreads for each sample.
Circular consensus sequences (CCS) were generated for each sample using ccs to produce a corresponding .bam file per sample.
Supplementary files format and content: Processed data is shared in .pickle format.
Library strategy: Replication-Aware Single-molecule Accessibility Mapping (RASAM)

source_name: mESCs

growth_protocol: K562 cells (ATCC) were grown for at least three days in standard media containing RPMI 1640 + L-Glutamine (Hyclone) supplemented with 10% Fetal Bovine Serum (Gibco) and 1% Penicillin-Streptomycin (Gibco). mESC E14 cells were grown on 0.2% gelatin and maintained in standard media containing DMEM + Glutamax (ThermoFisher 10566-016), 15% Fetal Bovine Serum (ThermoFisher SH30071.03), 1X Non-Essential Amino Acids (ThermoFisher 11140-50), 1 mM Sodium Pyruvate (ThermoFisher 11360-070), 0.128mM 2-Mercaptoethanol (BioRad 1610710XTU), and 1X Leukemia Inhibitory Factor (purified and gifted by Barbara Panning Lab at UCSF). mESCs were passaged every 1-2 days using TrypLE Express Enzyme (1X) (12605010). Media was changed daily when cells were not passaged. All cell lines were regularly tested negative for mycoplasma contamination. Standard media was added to mESC E14 or K562 cells with a final concentration of 10 uM BrdU (abcam ab142567). Cells were incubated in BrdU-containing media for between 5 minutes and 24 hours. After labeling, mESC E14 plates were rinsed three times with 1x PBS and collected using TrypLE Express Enzyme (1X) (12605010). K562s were collected and spun down (300xg, 5 minutes) immediately after labeling.

extract_protocol:
To the methylation reaction, 2.65 uL 10% SDS and 2.65 uL of 20 mg/mL Proteinase K (Thermo Scientific AM2548) were added and incubated at 65oC for at least 2 hours and up to overnight. To extract the DNA, an equal volume of Phenol-Chloroform was added and mixed vigorously by shaking. The samples were then spun at max speed for 2 min and the aqueous portion was removed. To the aqueous extraction, 0.1x volumes of 3M NaOAc, 1 uL GlycoBlue, and 3x volumes of cold 100% EtOH were added, mixed by inversion and incubated overnight at -20oC or for 2 hours at -80oC. Samples were then spun at max speed for 30 minutes at 4oC, washed with 500 uL 70% EtOH, spun again at max speed for 2 minutes at 4oC. The resulting pellet was air dried and resuspended in 40 uL EB.
Purified DNA from mESCs and K562s was sheared using a Covaris g-tube (520079) in a 5424 rotor at 7,000 RPM for 6 passes for a target size between 6,000 and 8,000 bp. Sheared DNA was used as input for the PacBio HiFi SMRTbell Library Preparation protocol using the SMRTbell Express Template Prep Kit 2.0. Briefly, samples underwent removal of single stranded overhangs, DNA damage repair, end-repair, A-tailing, barcoded SMRTbell adapter ligation, and exonuclease cleanup according to manufacturer’s protocol followed by a 1X AMPure PB bead cleanup. Final sample concentration was measured via Qubit High Sensitivity DNA Assay and library size was measured on an Agilent Bioanalyzer DNA chip. Libraries were sequenced on PacBio Sequel II 8M SMRTcells.

treatment_protocol: Briefly, all nuclei were collected by centrifugation (300xg, 5 min), washed in ice cold 1X PBS, spun again (300xg, 5 min), and resuspended in 1 mL Nuclear Isolation Buffer (20mM HEPES, 10mM KCl, 1mM MgCl2, 0.1% Triton X-100, 20% Glycerol, and 1X Protease Inhibitor (Roche 4693132001)) per 10 million cells by gently pipetting 5x with a wide-bore pipette tip. The suspension was incubated on ice for 5 minutes, and nuclei were pelleted (600xg, 4oC, 5 min), washed with Buffer M (15mM Tris-HCl pH 8.0, 15 mM NaCl, 60mM KCl, 0.5mM Spermidine), and spun once again (600xg, 4oC, 5 min). Nuclei were resuspended in 200 uL of Methylation Reaction Buffer (Buffer M containing 1mM S-adenosylmethionine (SAM; New England BioLabs B9003S)). 10uL high-concentration EcoGII was added per 1e6 nuclei and the nuclei suspension was incubated at 37oC for 30 minutes. An additional 1 uL of 32 mM SAM was supplemented after 15 minutes. Any unmethylated controls were treated similarly with the addition of SAM, but EcoGII was excluded from those reactions.

value: mESCs

value: EcoGII treated; 10m BrdU


title: Human brain prefrontal cortex BA10, AD sample4


title: Human brain prefrontal cortex BA10, Control sample3


title: BE2C_GSK343_R1

description: SK-N-BE(2)-C cells treated with GSK343 12.8uM for 6h, replicate 1


title: Human brain prefrontal cortex BA10, AD sample3


title: wild-type heart, 96 hours after cryoinjury_1

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl zebrafish genome version danRer11 (Ensembl release 104) with STAR 2.7.10a
Aligned reads were filtered to remove: duplicates with Picard 3.0.0 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5, multiple testing adjusted p-value < 0.05, and -0.585 < log2FC > 0.585. The Ensemble annotation was enriched with UniProt data (Activities at the Universal Protein Resource (UniProt)).
Assembly: danRer11
Supplementary files format and content: library-size normlized count matrix

source_name: heart ventricle (border zone and injured area)

extract_protocol:
A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (RNase-Free DNase Set, Qiagen)
4µg of total RNA was used as input for VAHTS Stranded mRNA-seq V6 Library preparation following manufacture’s protocol (Vazyme).

value: cardiac cryoinjury


title: wild-type heart, 96 hours after cryoinjury_3

value: heart ventricle (border zone and injured area)


title: sWAT_WT_fed_ad_libitum_F3

value: Subcutaneous adipose tissue (sWAT)

value: female

value: 20 weeks

value: fed ad libitum


title: flt1 mutant heart, 96 hours after cryoinjury_3


title: wild-type heart, 96 hours after cryoinjury_2


title: flt1 mutant heart, 96 hours after cryoinjury_2


title: Human brain prefrontal cortex BA10, AD sample2

value: Brain


title: WT, replicate 3, IgG

first: danhong

last: wu

address: 3rd Floor, Building 2, 801 Heqing Road, Shanghai

department: Department of Neurology

institute: Shanghai Fifth People’s Hospital, Fudan University

data_processing:
cRIP enrichment control and library quality control, raw reads were quality controlled using Q30 aacRIP enrichment control and library quality control, raw reads were quality controlled using Q30 and FastQC. Adapter trimming of 3' sequences and removal of low quality reads were performed using Cutadapt software (v1.9.3) to generate clean reads. A post-alignment filter was applied to exclude alignments to mitochondrial DNA (chrM) and mismatched mating pairsnd FastQC
Clean reads were then aligned to the mouse genome (mm10) using Hisat2 software (v2.04).
To identify acetylated sites, we evaluated the enrichment of clean reads in acRIP, input and IgG control samples. MACS software (v1.4.2) was used to detect regions of significant read enrichment in the acRIP samples, with adjustments made to optimize the analysis of transcript-mapped reads (e.g., disabling the shift model and local lambda, and setting the sequencing read length to 150 bp).Input samples were used as controls during peak calling. The enriched regions were identified as acetylated sites and ac4C peaks were generated in bed or bam format for further analysis.
only peaks located on protein-coding exons were selected for further analysis. Additional filters were applied, including an adjusted p-value threshold of <0.05 and a fold enrichment (FE) greater than 1. Peaks with a false discovery rate (FDR)-adjusted p-value <0.05 were considered statistically significant. For IgG control peaks, a calibration step was performed to exclude non-specific IgG binding peaks, retaining only those with no coordinate overlap. Fold enrichment (FE) was calculated by dividing the difference between the acRIP and IgG peaks by the input peak.
Assembly: mm10
Supplementary files format and content: Column A ~ E: the coordinates of the acetylated RNA sites in bed format, please ref http://genome.ucsc.edu/FAQ/FAQformat.html#format1. Column F: the length of the acetylated RNA sites Column G ~ H: the transcript id and gene symbol of acetylated RNA. Column I ~ K: the enrichment results calculated by MACS. Column L ~ S: the annotation of the acetylated gene.
Supplementary files format and content: The table contains information about the mRNA acetylation modification peaks identified for each sample

source_name: Hippocampus

extract_protocol:
A total of 10 to 50 micrograms of RNA was subjected to immunoprecipitation using the GenSeq acRIP Kit (GenSeq Inc.) in accordance with the manufacturer's instructions. In summary, total RNA was randomly fragmented to a length of approximately 200 nt using RNA fragmentation reagents. The anti-ac4C antibody or control IgG (sc-2027, Santa Cruz) was conjugated to Protein A/G Dynabeads (Share-Bio, SB-PR001) in PBS and incubated for one hour at room temperature. Subsequently, the RNA fragments were incubated with the bead-conjugated antibodies, which were rotated at 4°C for four hours. Subsequently, the RNA/antibody complexes were subjected to multiple rounds of washing in order to remove any unbound materials. The captured RNA was subsequently eluted from the complexes and purified to ensure its suitability for subsequent analysis. Ribosomal RNA (rRNA) depletion was performed on the RNA samples using the NEBNext rRNA Depletion Kit (New England Biolabs, Inc.).
RNA libraries for immunoprecipitation (IP) and input samples were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc.) in accordance with the standard protocol. The quality of the libraries was evaluated using the Agilent 2100 Bioanalyzer (Agilent), and sequencing was conducted on the NovaSeq platform (Illumina).

value: Hippocampus

value: WT

tag: group

value: IgG


title: WT, replicate 3, IP

value: IP


title: flt1 mutant heart, 96 hours after cryoinjury_1


title: WT, replicate 2, IgG


title: WT, replicate 2, IP


title: WT, replicate 1, IgG


title: WT, replicate 2, Input

value: Input


title: WT, replicate 1, IP


title: WT, replicate 1, Input


title: 5xFAD, replicate 3, IgG


title: 5xFAD, replicate 3, Input


title: 5xFAD, replicate 2, IgG


title: 5xFAD, replicate 2, IP


title: 5xFAD, replicate 1, IgG


title: 5xFAD, replicate 2, Input


title: 5xFAD, replicate 1, Input


title: Human brain prefrontal cortex BA10, AD sample1

value: Human brain cells


title: 5xFAD, replicate 3, IP


title: 5xFAD, replicate 1, IP


title: shRNA-2

city: Shanghai

first: Hong

last: Zhang

address: 600 Yishan Road

department: Shanghai Diabetes Institute

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

data_processing:
The cleaned reads were aligned to the index file of the mm10 genome generated by HISAT2 version 2.0.5. Read counts for each gene were calculated by HTSeq-count
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Mouse pancreatic β-cells

growth_protocol: Min6 cells were seeded in 12-well plates  and cultured in DMEM (Gibco, 12100-046) supplemented with 15% fetal bovine serum and 1% penicillin-streptozotocin in the humidified incubator at 37℃ with 5% CO2

extract_protocol:
Total RNA was extracted from Min6 cells via TRIzol reagent (Thermo Fisher).
RNA libraries were constructed using VAHTS® Universal V6 RNA-seq Library Prep Kit for Illumina Vazyme, according to the manufacturer’s protocol, and paired-end reads were obtained on the NovaSeq 6000 platform.

treatment_protocol: Min6 cells were infected with Il22ra1 knockdown adenovirus (sh-Il22ra1) or control adenovirus (sh-ctrl) at 37℃ for 48h and 0.3mM PA for 24h, and then harvested.

tag: cell line

value: Min6 cells

value: Mouse pancreatic beta-cells

value: Adenovirus sh-Il22ra2+PA


title: shRNA-4

tag: genotype

value: Adenovirus sh-Il22ra4+PA


title: shRNA-6

value: Adenovirus sh-Il22ra6+PA


title: shRNA-1

value: Adenovirus sh-Il22ra1+PA


title: GFP-6

value: Adenovirus sh-ctrl+PA


title: GFP-5


title: shRNA-3

value: Adenovirus sh-Il22ra3+PA


title: GFP-4


title: WT, replicate 3, Input


title: shRNA-5

value: Adenovirus sh-Il22ra5+PA


title: GFP-2


title: GFP-1


title: GFP-3


title: Cre-6

description: Ins2Cre mice

source_name: islets

extract_protocol:
Total RNA was extracted from islets via TRIzol reagent (Thermo Fisher).
RNA libraries were constructed using VAHTS® Universal V6 RNA-seq Library Prep Kit for Illumina Vazyme, according to the manufacturer’s protocol, and paired-end reads were obtained on the NovaSeq 6000 platform.

value: islets

value: Ins2Cre mice


title: Cre-5

description: Ins2Cre mice


title: Cre-3

description: Ins2Cre mice


title: Cre-4

description: Ins2Cre mice


title: BKO-6

description: Il22ra1βKO mice

value: Il22ra1{beta}KO mice


title: Cre-2

description: Ins2Cre mice


title: BKO-5

description: Il22ra1βKO mice


title: IgG + BTKi 4

city: Cambridge

first: Timothy

middle: R

last: Hammond

state: MA

address: 350 Water Street

institute: Sanofi

data_processing:
Omicsoft Aligner 4 (OSA4); ArrayStudio_V10.0
Assembly: Mouse.mm10 (ENSEMBL.R89)
Supplementary files format and content: FPKM counts matrix

source_name: microglia

extract_protocol:
Qiazol
TruSeq stranded mRNA library prep Kit

value: microglia

value: IgG + BTKi


title: BKO-1

description: Il22ra1βKO mice


title: IgG + BTKi 3


title: BKO-3

description: Il22ra1βKO mice


title: BKO-4

description: Il22ra1βKO mice


title: BKO-2

description: Il22ra1βKO mice


title: IgG + BTKi 1


title: IgG + BTKi 2


title: IgG 4

value: IgG


title: IgG 3


title: Vehicle 4

value: Vehicle


title: IgG 1


title: Vehicle 3


title: IgG 2


title: Cre-1

description: Ins2Cre mice


title: MAVS_Veh.rep1

city: Tokyo

first: Shunsuke

last: Kitajima

address: 3-8-31 Ariake, Koto

country: Japan

institute: Japanese Foundation for Cancer Research

data_processing:
Raw reads were trimmed using  Trimmomatic.
Trimmed reads are mapped to the mouse GRCm38 genome with HISAT2.
Transcript is assembled by StringTie with aligned reads.
Assembly: mm10
Supplementary files format and content: A tab-delimited text file includes raw read counts.

source_name: Cell line-derived subcutaneous tumor

growth_protocol: 1 x 107 393P cells in PBS were subcutaneously injected into the flank of 8-week-old male 129-Elite mice (129S2/SvPasCrl, Charles River Laboratories).

extract_protocol:
RNA extraction was performed using QIAGEN RNeasy Mini Kit and RNase-Free DNase Set.
Libraries were prepared using TruSeq stranded mRNA LT Sample Prep Kit according to the manufacturer’s instruction.

treatment_protocol: MPS1 inhibitor (BAY-1217389) was formulated in 50% PEG 400, 10% ethanol and 40% water. 393P tumors in mice were treated with 5 mg/kg MPS1 inhibitor twice daily for 2 days, and the tumors were harvested the following day.

value: Cell line-derived subcutaneous tumor

value: Lung cancer

value: MAVS reconstituted

value: Control


title: MAVS_MPS1i.rep3


title: MAVS_Veh.rep2


title: Luc_Veh.rep1

value: MAVS knockout


title: Vehicle 1


title: MAVS_Veh.rep3


title: Luc_MPS1i.rep1


title: Luc_Veh.rep3


title: Vehicle 2


title: Luc_Veh.rep2


title: Luc_MPS1i.rep2


title: MAVS_MPS1i.rep1


title: Hippocampus, WT, replicate 3

data_processing:
The quality of the sequencing data was evaluated using Q30 metrics. Low-quality reads and 3' adapter sequences were removed using the Cutadapt software (version 1.9.3).
The remaining high-quality reads were then aligned to the reference genome using the HISAT2 software (v2.0.4). The raw counts were generated using HTSeq software (version 0.9.1).
Transcripts per kilobase million (TPM) were calculated to assess similarities and differences between samples.
The identification of differentially expressed genes (DEGs) was conducted using the edgeR (v3.16.5) software, which involved the normalization of raw counts and the calculation of fold change between the two sample groups. A gene was considered to be differentially expressed if the p-value was less than 0.05 and the fold change was greater than or equal to 2.
Assembly: mm10
Supplementary files format and content: Column A: gene_id, the gene identifier. Column B ~ G: counts of all samples of the gene. Column H ~ M: normalized counts by edgeR. Column N ~ W: annotation of the genes.
Supplementary files format and content: The table contains the mRNA raw count and normalized counts identified by each sample

extract_protocol:
total RNA was initially subjected to ribosomal RNA (rRNA) depletion through the use of the GenSeq® rRNA Removal Kit (GenSeq, Inc.), in accordance with the instructions provided by the manufacturer. Subsequently, the rRNA-depleted samples were processed for library construction using the GenSeq® Low Input RNA Library Prep Kit (GenSeq, Inc.).
The quality and quantity of the library were evaluated using the Agilent Bioanalyzer 2100 system (Agilent Technologies, Inc., USA). The sequencing was conducted on an Illumina NovaSeq platform, resulting in the generation of 150 bp paired-end reads.

value: Hippocampus

value: WT


title: Hippocampus, WT, replicate 1


title: Luc_MPS1i.rep3


title: MAVS_MPS1i.rep2


title: Hippocampus, WT, replicate 2


title: Hippocampus, 5xFAD, replicate 3


title: Hippocampus, 5xFAD, replicate 1


title: H1944.MPS1i.rep2

data_processing:
Mapping and peakcall were conducted by ENCODE ATAC-seq pipeline.
Reads were mapped to the human GRCh38 genome using Bowtie2.
Peak calling was performed using MACS2 with the following parameters; -p 0.01 --shift -75 --extsize 150 --nomodel -B --SPMR --keep-dup all --call-summits.
Reads on peaks were counted using featureCounts.
Assembly: hg38
Supplementary files format and content: A tab-delimited text file includes raw read counts for merged peaks and annotations generated using HOMER.

growth_protocol: NCI-H1944 cells were cultured in RPMI 1640 supplemented with 10% FBS, 1x penicillin-streptomycin, and 2.5 μg/ml plasmocin prophylactic.

extract_protocol:
Approximately 50,000 cells were lysed and transposition reaction was performed with the Tn5 Transposase at 37°C for 30 minutes. The reaction liquid was purified with Qiagen MinElute PCR Purification Kit.
Five cycles of PCR with custom Nextera PCR primers74 were conducted using NEBNext Q5 Hot Start HiFi PCR Master Mix (New England Biolabs). The additional number of PCR cycles was determined by qPCR of the partly amplified products. The PCR products were purified with Agencourt AMPure XP beads (Beckman Coulter: A63881), using double size selection (left ratio: 1.4x, right ratio: 0.5x) according to the manufacturer’s protocol.

treatment_protocol: Cells were treated with MPS1i (100 nM, BAY-1217389), or DMSO as a control, for 48 hr, washed out the drug, and then cultured for 24 hr.


title: Cortex, XPro1595 CPZ3, rep12

city: Athens

first: Lesley

last: Probert

state: Attiki

address: Vassilisis Sofias 127

department: Immunology

country: Greece

institute: Hellenic Pasteur Institute

description: 10x Genomics

data_processing:
CellRanger software (v5.0.1) was used to quantify the gene counts counting introns and exons. Ambient RNA was corrected using CellBender (v0.3.0) and Doublets were then removed using DoubletFinder (v 2.0.2). Seurat  was used for further filterinf of low quality nuclei and data was normalised and integrated using LIGER (v 0.5.0). Cells were annotated using enrichment of cell-type specific markers.
Assembly: mm10
Supplementary files format and content: RDS files

molecule: nuclear RNA

source_name: Cortex

extract_protocol:
Brain cortex tissue was suspended in 500 µL homogenization buffer (Nuclei Isolation Kit, Sigma-Aldrich, NUC201) and homogenised in a pre-cooled 2 mL dounce homogeniser. The homogenate was filtered through a cell strainer cap (70μM) and centrifuged at 600g for 5 min. Thereafter, nuclei were subjected to an additional clean-up step by resuspending in freshly prepared nuclei wash buffer and density centrifugation for the gradient of the layered nuclei/29% iodixanol solution at 5000g for 15 mins at 4 °C. Nuclei pellets were collected. SnRNA-Seq performed in samples processed as per 10× Genomics Chromium Single Cell Reagent Kits Protocol (chemistry: Single Cell 3′ v2). The samples were processed to target 10,000 nuclei per sample.
SnRNA-Seq was performed according to the manufacturers instructions (10× Genomics Chromium Single Cell 3' v3). The samples were processed to target 10,000 nuclei per sample. Briefly, 12 cycles of cDNA amplification were performed, and 12 cycles of final indexing PCR. cDNA concentrations were measured using Qubit dsDNA HS Assay Kit (ThermoFisher, Q32851). cDNA and library preparations were assessed using the Bioanalyzer High-Sensitivity DNA Kit. All samples were pooled to equimolar concentration and sequenced together on an Illumina NovaSeq 6000.

value: Cortex


title: Cortex, XPro1595 CPZ3, rep13

description: 10x Genomics


title: Cortex, XPro1595 CPZ3, rep11

description: 10x Genomics


title: Cortex, XPro1595 CPZ3, rep14

description: 10x Genomics


title: Cortex, XPro1595 CPZ3, rep9

description: 10x Genomics


title: Cortex, XPro1595 CPZ3, rep15

description: 10x Genomics


title: H1944.MPS1i.rep1


title: H1944.DMSO.rep2

value: DMSO


title: Hippocampus, 5xFAD, replicate 2


title: H1944.DMSO.rep1


title: Cortex, XPro1595 CPZ3, rep8

description: 10x Genomics


title: Cortex, XPro1595 CPZ3, rep6

description: 10x Genomics


title: H1944.DKO.DMSO.rep2

data_processing:
Raw reads were trimmed and quality-filtered using the Trim Galore, Trimmomatic, and cutadapt software.
Trimmed reads were then mapped to the human GRCh38 genome using STAR.
Reads on annotated genes were counted using featureCounts.
Assembly: hg38
Supplementary files format and content: A tab-delimited text file includes raw read counts.

growth_protocol: NCI-H1944 and NCI-H647 cells were cultured in RPMI 1640 supplemented with 10% FBS, 1x penicillin-streptomycin, and 2.5 μg/ml plasmocin prophylactic.

extract_protocol:
RNA extraction was performed using QIAGEN RNeasy Mini Kit and RNase-Free DNase Set.
After poly (A) + RNA enrichment by NEBNext Poly(A) mRNA Magnetic Isolation Module, double-stranded cDNA libraries were prepared using QIAseq FastSelect -rRNA HMR Kit , QIAseq Stranded RNA Lib Kit UDI, and DNBSEQ MGIEasy Universal Library Conversion Kit according to the manufacturer’s instruction.

value: STING/MAVS knockout


title: Cortex, XPro1595 CPZ3, rep2

description: 10x Genomics


title: Cortex, XPro1595 CPZ3, rep5

description: 10x Genomics


title: Cortex, XPro1595 CPZ3, rep7

description: 10x Genomics


title: H1944.DKO.MPS1i.rep1


title: H1944.DKO.MPS1i.rep2


title: H1944.SCR.MPS1i.rep2


title: Cortex, saline CPZ3, rep12

description: 10x Genomics

value: Saline-treated


title: H1944.MAVSsg.DMSO.rep2


title: H1944.STINGsg.MPS1i.rep1

value: STING knockout


title: Cortex, saline CPZ3, rep15

description: 10x Genomics


title: Cortex, saline CPZ3, rep10

description: 10x Genomics


title: Cortex, XPro1595 CPZ3, rep10

description: 10x Genomics


title: Cortex, XPro1595 CPZ3, rep3

description: 10x Genomics


title: H1944.MAVSsg.MPS1i.rep1


title: Cortex, XPro1595 CPZ3, rep1

description: 10x Genomics


title: Cortex, saline CPZ3, rep13

description: 10x Genomics


title: Cortex, XPro1595 CPZ3, rep4

description: 10x Genomics


title: H1944.STINGsg.MPS1i.rep2


title: H1944.MAVSsg.MPS1i.rep2


title: Cortex, saline CPZ3, rep14

description: 10x Genomics


title: Cortex, saline CPZ3, rep9

description: 10x Genomics


title: H1944.DKO.DMSO.rep1


title: Cortex, saline CPZ3, rep8

description: 10x Genomics


title: H1944.MAVSsg.DMSO.rep1


title: H1944.STINGsg.DMSO.rep1


title: H1944.STINGsg.DMSO.rep2


title: Cortex, saline CPZ3, rep11

description: 10x Genomics


title: H1944.SCR.DMSO.rep2


title: H1944.SCR.DMSO.rep1


title: Cortex, saline CPZ3, rep6

description: 10x Genomics


title: Cortex, saline CPZ3, rep7

description: 10x Genomics


title: H1944.MPS1i.J2

data_processing:
Raw reads were trimmed and quality-filtered using the Trim Galore, Trimmomatic, and cutadapt software.
Trimmed reads were then mapped to the human GRCh38 genome using STAR.
Reads on non-exonic regions (exonic regions described in GENCODE Comprehensive gene annotation release 44 were eliminated) were counted using featureCounts, and the peaks derived from non-exonic regions in which average TPM (DMSO and MPS1i) is more than 2.5 defined as dsRNA-peaks.
Assembly: hg38
Supplementary files format and content: A tab-delimited text file includes raw read counts for dsRNA peaks and annotations generated using HOMER.

extract_protocol:
Cells were collected in ice-cold PBS and lysed in RIP buffer with protease inhibitors. Ten percent of the lysate was used for total RNA Input, while the rest was used for dsRNA immunoprecipitation with the J2 antibody. RNA was purified using TRIZOL and the QIAGEN miRNeasy Mini Kit.
RNA-seq libraries were prepared using SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian, and DNBSEQ MGIEasy Universal Library Conversion Kit according to the manufacturer’s instruction.


title: Cortex, saline CPZ3, rep5

description: 10x Genomics


title: Cortex, saline CPZ3, rep4

description: 10x Genomics


title: Cortex, saline CPZ3, rep2

description: 10x Genomics


title: Cortex, saline CPZ3, rep3

description: 10x Genomics


title: H1944.DMSO.Input


title: Cortex, naïve, rep15

description: 10x Genomics

value: Naïve


title: H1944.IFNAR1sg.IFNb.J2.rep1

treatment_protocol: Cells were treated with MPS1i (100 nM, BAY-1217389), or DMSO as a control, for 48 hr, washed out the drug, and then cultured for 24 hr with or without recombinant IFNb (5ng/ml).

value: IFNAR1 knockout

value: IFNb recombinant protein


title: H1944.IFNAR1sg.MPS1i.J2.rep1


title: H1944.DMSO.J2


title: H1944.MPS1i.Input


title: Cortex, saline CPZ3, rep1

description: 10x Genomics


title: Cortex, naïve, rep13

description: 10x Genomics


title: H1944.IFNAR1sg.DMSO.J2.rep2


title: H1944.IFNAR1sg.IFNb.J2.rep2


title: Cortex, naïve, rep14

description: 10x Genomics


title: Cortex, naïve, rep12

description: 10x Genomics


title: H1944.IFNAR1sg.DMSO.J2.rep1


title: H1944.SCR.MPS1i.rep1


title: Cortex, naïve, rep11

description: 10x Genomics


title: H1944.SCR.IFNb.J2.rep2


title: Cortex, naïve, rep10

description: 10x Genomics


title: H1944.SCR.IFNb.J2.rep1


title: H1944.SCR.MPS1i.J2.rep2


title: Cortex, naïve, rep9

description: 10x Genomics


title: Cortex, naïve, rep8

description: 10x Genomics


title: H1944.IFNAR1sg.MPS1i.J2.rep2


title: H1944.SCR.MPS1i.J2.rep1


title: H1944.SCR.DMSO.J2.rep2


title: Cortex, naïve, rep6

description: 10x Genomics


title: Cortex, naïve, rep5

description: 10x Genomics


title: Cortex, naïve, rep3

description: 10x Genomics


title: Cortex, naïve, rep2

description: 10x Genomics


title: H647.MPS1i.rep1

data_processing:
NCI-H647: Raw reads were trimmed and quality-filtered using the Trim Galore, Trimmomatic, and cutadapt software.Trimmed reads were then mapped to the human GRCh38 genome using STAR.Reads on annotated genes were counted using featureCounts.
NCI-H1944: Raw reads were trimmed using  Trimmomatic. Trimmed reads are mapped to the human GRCh38 genome with HISAT2. Transcript is assembled by StringTie with aligned reads.
Assembly: hg38
Supplementary files format and content: A tab-delimited text file includes raw read counts.

extract_protocol:
RNA extraction was performed using QIAGEN RNeasy Mini Kit and RNase-Free DNase Set.
NCI-H647: Libraries were prepared using QIAseq FastSelect -rRNA HMR Kit , QIAseq Stranded RNA Lib Kit UDI, and DNBSEQ MGIEasy Universal Library Conversion Kit according to the manufacturer’s instruction. NCI-H1944: Libraries were prepared using TruSeq stranded mRNA LT Sample Prep Kit according to the manufacturer’s instruction.


title: H647.DMSO.rep2


title: H647.MPS1i.rep2


title: Cortex, naïve, rep4

description: 10x Genomics


title: lung adenocarcinoma cells, aged KP mouse, rep 4, L004

first: Yingqian

middle: Ada

last: Zhan

address: 430 East 67th Street

department: EPIGENETICS RESEARCH CENTER

institute: MSKCC

data_processing:
The Bismark pipeline was adopted to map bisulfite-treated EPIC sequencing reads and determine cytosine methylation states.
Trim Galore v0.6.4 was used to remove raw reads with low-quality (less than 20) and adapter sequences.
The trimmed sequence reads were C(G) to T(A) converted and mapped to similarly converted reference human genome (mm10) using default Bowtie 2 settings within Bismark.
Duplicated reads were discarded. The remaining alignments were then used for cytosine methylation calling by Bismark methylation extractor.
bigWig files were generated using bedGraphToBigWig from kentUtils.
Assembly: mm10
Supplementary files format and content: bigWig for cytosine read coverage and methylation rate
Supplementary files format and content: bsseq object in rds format for cytosine read counts on all samples
Library strategy: Enzymatic Methyl-seq (EM-Seq)

source_name: Primary mouse lung tumor tissue

growth_protocol: Samples were obtained from primary mouse tissues. All mice were housed in non-pathogenic conditions, controlled temperature (20–25 °C), and a 12-hour light–dark cycle with 30-70% relative humidity. Food and water were provided ad libitum.

extract_protocol:
Genomic DNA was purified using DNeasy Blood & Tissue Kit (Qiagen, #69504), following manufacturer's protocol.
NEB Next Enzymatic Methyl-seq (EM-seq, New England Biolabs, #E7120S) was used to identify 5-methylcytosine and 5-hydroxymethylcytosine bases and sequencing libraries were constructed by NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, #E7645S), following the manufacturer’s protocol.

treatment_protocol: No treatment has been performed.

value: Primary mouse lung tumor tissue

value: lung tumor cells

value: LSL-KrasG12D/+; Trp53fl/fl


title: lung adenocarcinoma cells, aged KP mouse, rep 3, L004


title: lung adenocarcinoma cells, young KP mouse, rep 6, L004


title: Cortex, naïve, rep1

description: 10x Genomics


title: Genomic DNA methylation from 201516340036_R05C01

type: genomic

city: Barcelona

first: Joan

address: Carrer del Doctor Aiguader, 88

country: Spain

institute: Hospital del Mar Research Institute

hyb_protocol: The bisulfite converted DNA was processed and hybridized to the 450K or EPIC BeadChip (Illumina, Inc.), according to the manufacturer's instructions.

scan_protocol: The BeadChip images were scanned on the iScan system and the data was extracted into GenomeStudio software v2011.1, using default analysis settings.

data_processing: Idat files were loaded with Minfi. CpGs with a detection rate lower than 99% (detection p-value > 0.05) or having a beadcount lower than 1% in at least 5% of samples were excluded. Additionally, CpGs at multi-hit or single-nucleotide polymorphism locations (MethylToSNP) were also excluded. Samples having a call-rate lower than 95% or sex mismatch were excluded. DNA methylation was expressed as beta values and we applied preprocessnoob and BMIQ normalizations

label: Cy5 and Cy3

source_name: Blood DNA

label_protocol: Bisulfite conversion was performed using 500 ng genomic DNA input using the EZ DNA Methylation Gold Kit (Zymo Research)

extract_protocol: DNA was extracted from whole peripheral blood collected in 10mL EDTA tubes during the first 24h after stroke onset.

value: Blood DNA

value: female

value: no


title: Genomic DNA methylation from 201516340051_R06C01


title: Genomic DNA methylation from 201516340036_R02C01

value: male

value: yes


title: Genomic DNA methylation from 201516330035_R06C01


title: Genomic DNA methylation from 201516340036_R06C01


title: lung adenocarcinoma cells, young KP mouse, rep 7, L004


title: Genomic DNA methylation from 201516330035_R05C01


title: lung adenocarcinoma cells, young KP mouse, rep 3, L004


title: Genomic DNA methylation from 201516330035_R04C01


title: lung adenocarcinoma cells, aged KP mouse, rep 1, L004


title: Genomic DNA methylation from 201516330035_R02C01


title: lung adenocarcinoma cells, young KP mouse, rep 2, L004


title: H1944.SCR.DMSO.J2.rep1

value: WT


title: lung adenocarcinoma cells, aged KP mouse, rep 2, L004


title: Cortex, naïve, rep7

description: 10x Genomics

value: Cortex


title: Genomic DNA methylation from 201516330029_R05C01


title: H647.DMSO.rep1

value: DMSO


title: lung adenocarcinoma cells, young KP mouse, rep 1, L004


title: Genomic DNA methylation from 201516330029_R03C01


title: lung adenocarcinoma cells, aged KP mouse, rep 4, L003


title: Genomic DNA methylation from 201516330029_R04C01


title: lung adenocarcinoma cells, aged KP mouse, rep 3, L003


title: Genomic DNA methylation from 201516310048_R07C01


title: Genomic DNA methylation from 201516330028_R03C01


title: lung adenocarcinoma cells, young KP mouse, rep 7, L003