title: PBT_batch5_library4_6donors_CITE

city: San Diego

first: Pandurangan

last: Vijayanand

state: California

address: 9420 Athena Cir, La Jolla

department: Vaccine Discovery

institute: La Jolla Institute for Immunology

description:
10X Genomics_5v2_0
sc_NSCLC_PBT_umi.txt.gz
sc_NSCLC_PBT_annotation.txt.gz
sc_PBT_CD8_umi.txt.gz
sc_PBT_CD8_annotation.txt.gz

data_processing:
Processing of the single-cell (sc)RNA-seq libraries: bcl2fastq () was used to generate FASTQ file with default parameters. count (Cellranger 3.1.0) was used to generate the filtered UMI matrix with default parameters. aggr (Cellranger 3.1.0)  was used to aggregate expression data from individual libraries. Seurat (3.1.5) was used to filter, normalize and scale de UMI matrix. Seurat (3.1.5) was used to cluster cells and assign cell-type identities.
Processing of the sc-T-cell receptor (TCR)-seq libraries: bcl2fastq () was used to generate FASTQ file with default parameters. vdj (Cellranger 3.1.0) was used to generate TCR consensus sequences and annotations, and assign clonotypes to cell barcodes. Custom scripts were used to aggregate libraries.
Processing of the sc-hashtag oligonucleotide (HTO)-seq libraries: bcl2fastq () was used to generate FASTQ file with default parameters. count (Cellranger 3.1.0) was used to generate the filtered UMI matrix with default parameters. Seurat (3.1.5) function MULTIseqDemux and custom scripts (METHODS) were used to classify cell barcodes. Custom scripts were used to aggregate libraries.
Assembly: GRCh37
Supplementary files format and content: sc_PBT_CD4_umi.txt.gz: Matrix with raw UMI counts for the aggregated dataset of CD4+ T cells from Pediatric Brain Tumors (gene expression data). Matrix values are provided as tab-separated values where each column represents a cell (column names are 10x cell barcodes) and each row represents a gene.
Supplementary files format and content: sc_PBT_CD8_umi.txt.gz: Matrix with raw UMI counts for the aggregated dataset of CD8+ T cells from Pediatric Brain Tumors (gene expression data). Matrix values are provided as tab-separated values where each column represents a cell (column names are 10x cell barcodes) and each row represents a gene.
Supplementary files format and content: sc_NSCLC_PBT_umi.txt.gz: Sparse matrix with raw UMI counts for the aggregated dataset of CD4+ and CD8+ T cells from Pediatric Brain Tumors and patients with NSCLC (gene expression data). Sparse matrix values are provided where each column represents a cell (column names are 10x cell barcodes) and each row represents a gene.
Supplementary files format and content: sc_PBT_CD4_annotation.txt.gz: The metadata including all annotations made as detailed before for the aggregated dataset of CD4+ T cells from Pediatric Brain Tumors. Values are provided as tab-separated values where each column represents a metadata annotation (column names are mostly self-explanatory, but any questions about them may be addressed to our GitHub repository; see manuscript) and each row represents a cell barcode. Relevant TCR data-related and Hashtag Oligo (HTO) data-related annotations have been provided in this file as well.
Supplementary files format and content: sc_PBT_CD8_annotation.txt.gz: The metadata including all annotations made as detailed before for the aggregated dataset of CD8+ T cells from Pediatric Brain Tumors. Values are provided as tab-separated values where each column represents a metadata annotation (column names are mostly self-explanatory, but any questions about them may be addressed to our GitHub repository; see manuscript) and each row represents a cell barcode. Relevant TCR data-related and Hashtag Oligo (HTO) data-related annotations have been provided in this file as well.
Supplementary files format and content: sc_NSCLC_PBT_annotation.txt.gz: The metadata including all annotations made as detailed before for the aggregated dataset of CD4+ and CD8+ T cells from Pediatric Brain Tumors and patients with NSCLC. Values are provided as tab-separated values where each column represents a metadata annotation (column names are mostly self-explanatory, but any questions about them may be addressed to our GitHub repository; see manuscript) and each row represents a cell barcode. Relevant TCR data-related and Hashtag Oligo (HTO) data-related annotations have been provided in this file as well.

molecule: protein

source_name: Pediatric brain tumor

extract_protocol:
Tumor-infiltrating T cells were sorted into 1.5 mL tubes containing 500 ul of 1:1 PBS to FBS with 1:100 Recombinant RNAse Inhibitor (Takara Bio 2313B). Following sorting, tubes were filled up to 1.4 mL with PBS and spun at 600xg for 10 minutes. Pellets were resuspended in 35 ul PBS supplemented with 0.04% w/v BSA (Invitrogen) and cells were processed according to manufacturer's recommendations using 10x Genomics' Single Cell Immune Profiling 5'v2 (Dual Index) with Feature Barcoding kit. TCR (VDJ) sequences enriched according to manufacturer's recommendations using 10x Genomics' Single Cell Immune Profiling 5'v2 (Dual Index) with Feature Barcoding kit. HTO (CITE) cDNA was separated from PolyA cDNA through size selection with AMPure XP Purification reagent (Beckman Coulter, A63882)
All Libraries were prepared according to manufacturer's recommendations using 10x Genomics' Single Cell Immune Profiling 5'v2 (Dual Index) with Feature Barcoding kit.
scRNA-Seq, V(D)J library preparation and Cell Surface Protein library preparation

treatment_protocol: Tumors were dissociated into single cell suspensions by trituration, and stained with dead cell discriminating dye, fluorophore-tagged FACS antibodies, and unique anti-human hashtag antibodies against beta2 microglobulin for donor deconvolution. T cells from each donor were FACS-sorted for scRNA-seq using the 10X genomics platform. Experiments were performed on five separate experimental days (5 batches). Two libraries of pooled, live, singlet-gated, CD45+CD3+ T cells were generated from each of the first 3 experiments. And two libraries of pooled, live, singlet-gated cells (one of CD8+ T cells and another of CD4+ T cells), were generated from each of the last 2 experiments.

value: Pediatric brain tumor

value: CD8+ T cells


title: PBT_batch5_library1_6donors_CITE

status: Public on Jan 16 2024

type: SRA

country: USA

description:
10X Genomics_5v2_0
sc_NSCLC_PBT_umi.txt.gz
sc_NSCLC_PBT_annotation.txt.gz
sc_PBT_CD4_umi.txt.gz
sc_PBT_CD4_annotation.txt.gz

library_source: other

organism: Homo sapiens

tag: tissue

tag: cell type

value: CD4+ T cells


title: PBT_batch5_library3_6donors_CITE


title: Monocytes__P09

city: Heidelberg

first: Bruno

last: Steinkraus

state: Baden-Württemberg

address: Im Neuenheimer Feld 583

country: Germany

institute: HUMMINGBIRD DIAGNOSTICS GMBH

library_source: transcriptomic

data_processing:
Raw sequence reads were adapter trimmed and depleted of PCR duplicates based on the UMIs.
Only sequences that had at least one read in at least three samples per blood component type and that were longer than 17 nucleotides were kept.
For 25 cellular fractions (4.6% of derivatives, 25/539) the purification process did not meet the prespecified quality standard (purity > 70% as determined by flow cytometry). These samples were excluded from further analyses. See 'quality filter for processed data'
As additional quality control, the normalized data of the blood component samples was converted to a two-dimensional T-distributed Stochastic Neighbor Embedding (t-SNE) space. When plotting the two embedding vectors against each other, four samples did not cluster with the samples of the same blood component type (0.8% of derivatives, 4/514) and were excluded from further analysis. See 'quality filter for processed data'
The pre-processed sRNA sequences were annotated using the annotation pipelines unitas  and SPORTS. In case of multi-assignments, the annotation was prioritized in the following manner: miRNA > tRNA > rRNA > YRNA > snoRNA > lncRNA > snRNA > piRNA.
Assembly: hg38
Supplementary files format and content: csv files including log2-transformed RPM values per small RNA name for all blood component samples (1 file) and for all whole blood samples (1 file)

molecule: total RNA

source_name: peripheral blood cells

extract_protocol:
The fractional blood derivatives as well as the whole blood samples were directly lysed in Qiazol. For RNA isolation the miRNeasy Serum/Plasma mini kit was combined with minElute columns.
Dual indexed sRNA libraries with unique molecular identifiers (UMIs) adaptors were generated using the QIAseq miRNA Library Kit.

value: peripheral blood cells

value: Monocytes


title: PBT_batch5_library2_6donors_CITE


title: Monocytes__P07


title: PBT_batch4_library2_8donors_CITE


title: PBT_batch4_library1_8donors_CITE


title: Brain, TSC Het, Rep2

city: Nashville

first: Matthew

last: Cottam

state: TN

address: 2213 Garland Avenue South 9465

institute: Vanderbilt University

data_processing:
Raw sequencing reads were trimmed and filtered for quality using Trimgalore v0.6.7.
Trimmed reads were aligned to the hg38 reference genome and counted using STAR v2.7.9a with the `--quantMode GeneCounts` option.
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

molecule: polyA RNA

source_name: BMEC, Astrocytes, Neurons

growth_protocol: Cells were grown for 5 days under continual perfusion.

extract_protocol:
RNA isolation was performed using the Qiagen Rneasy Mini Kit and protocol per manufacturer recommendations
Library preparation was completed using theNEBNext Ultra II Directional RNA Library Prep Kitand protocol (P/N: E7760L) per manufacturer recommendations.
RNA samples underwent mRNA enrichment using oligo(dT) beads, followed by fragmentation using divalent cations under elevated temperature.
First-strand cDNA synthesis was performed using random hexamer primers, while second-strand cDNA synthesis was carried out using DNA Polymerase I and RNase H. End repair, A-tailing, and adapter ligation were performed to generate the final cDNA library.

value: BMEC, Astrocytes, Neurons

tag: genotype

value: TSC Heterozygous Mutation


title: Monocytes__P06


title: Monocytes__P05


title: Monocytes__P04


title: PBT_batch5_library4_6donors_TCR

library_source: transcriptomic single cell


title: PBT_batch5_library2_6donors_TCR


title: PBT_batch5_library3_6donors_TCR


title: Brain, Control, Rep2

value: WT (Control)


title: Brain, Control, Rep1


title: Monocytes__P03


title: PBT_batch5_library1_6donors_TCR


title: PBT_batch4_library2_8donors_TCR


title: Erythrocytes__P12

value: Erythrocytes


title: PBT_batch5_library4_6donors_GEX


title: PBT_batch4_library1_8donors_TCR


title: Monocytes__P01


title: Erythrocytes__P10


title: Monocytes__P08


title: PBT_batch5_library1_6donors_GEX


title: PBT_batch5_library2_6donors_GEX


title: Erythrocytes__P08


title: PBT_batch5_library3_6donors_GEX


title: Erythrocytes__P09


title: Erythrocytes__P07


title: PBT_batch4_library2_8donors_GEX


title: PBT_batch4_library1_8donors_GEX


title: Erythrocytes__P06


title: Erythrocytes__P05


title: Erythrocytes__P03


title: Erythrocytes__P04


title: Monocytes__P02


title: Patient A1 active psoriatic arthritis synovial spatial transcriptomics

city: Erlangen

first: Hashem

last: Mohammadian

address: Ulmenweg 18

department: Department of Medicine 3 - Rheumatology and Immunology

institute: University of Erlangen-Nürnberg

data_processing:
Reads were mapped to the human genome GRCh38 (GENCODE v32/Ensembl 98) using 10x Genomics’ space ranger pipeline (1.2.1) with default settings and manual correction of spots under tissue using Loupe Cell Browser (5.0.1).
Assembly: GRCh38 (GENCODE v32/Ensembl 98)
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: tissue H&E image files (low resolution and high resolution)
Supplementary files format and content: Comma separated tissue positions file
Supplementary files format and content: scale factor json file
Library strategy: Spatial transcriptomics

source_name: synovial joint

extract_protocol:
Unfixed human synovial biopsies were snap frozen in OCT Tissue TEK (Sacura). 10 µm thin sections were cut on a Cryotome FSE (Thermo Fisher)
Spatial transcriptomes was generated according to the Visium Spatial Gene Expression Kit (v1 chemistry, 10x Genomics). An optimisation slide was run for optimal permeabilisation conditions. 6 min was found to be optimal. Spatial transcriptomes were prepared according to the Visisum protocol CG000239 Rev B). Libraries were sequenced as PE150 by Illumina sequencing to >80% saturation by the external provider Novogene.

value: synovial joint

tag: disease

value: psoriatic arthritis


title: Patient A2 active psoriatic arthritis synovial spatial transcriptomics


title: Patient A4 healthy synovial spatial transcriptomics

value: healthy


title: Patient A3 healthy synovial spatial transcriptomics


title: Erythrocytes__P02


title: Synovia of RA patient ST10

data_processing:
The Salmon (v 1.5.2) index was generated using the GRCh38 human genome (GENCODE v38/Ensembl 104) with --type quasi -k 31
Transcript quantification was performed using Salmon (v 1.5.2) with --validateMapping, --useVBOpt and –seqBias
Transcript quantifications were converted to gene-level counts in R using the tximport (v 1.24.0)
DESeq2 (v 1.36.0) was used to correct for library size using “avgTxLength” (normalized_counts)
The “rlog” from DESeq22 (v 1.36.0) for regularised log transformation was used for count transformation (rlog_trnasformed_counts)
Assembly: GRCh38
Supplementary files format and content: Salmon quantification results in .tar format
Supplementary files format and content: tab-delimited text file include raw counts for each sample
Supplementary files format and content: tab-delimited text file include normalized counts for each sample
Supplementary files format and content: tab-delimited text file include rlog transformed counts for each sample

source_name: synovia

extract_protocol:
Total RNA was extracted from synovial biopsies using the RNeasy kit and an RNase-free DNase set (Qiagen)
Library preparation, QC and 150PE Illumina sequencing services were provided by the external provider Novogene in accordance to the ENCODE guidelines for RNA-Seq (revised version Dec 2016). 30G of data were sequenced per sample.

value: synovia

value: rheumatoid arthritis

tag: Sex

value: female


title: Erythrocytes__P01


title: Erythrocytes__P11


title: Eosinophils__P12

value: Eosinophils


title: Synovia of RA patient ST9

value: male


title: Eosinophils__P11


title: Eosinophils__P09


title: Synovia of RA patient ST7


title: Synovia of RA patient ST6

tag: Sex:


title: Eosinophils__P08


title: Eosinophils__P07


title: Synovia of RA patient ST4


title: Synovia of RA patient ST5


title: Eosinophils__P06


title: Synovia of RA patient ST3


title: Eosinophils__P05


title: Synovia of RA patient ST2


title: Synovia of RA patient ST1


title: Synovia of PsA patient ST9


title: Eosinophils__P02


title: Eosinophils__P01


title: Synovia of PsA patient ST8


title: CD8__P12


title: Synovia of PsA patient ST7


title: CD8__P09


title: Synovia of RA patient ST8


title: CD8__P08


title: Synovia of PsA patient ST6


title: Synovia of PsA patient ST4


title: CD8__P11


title: Synovia of PsA patient ST5


title: CD8__P10


title: m6A-TNF3_S9

city: Izmir

first: Bünyamin

last: Akgül

state: Urla

address: Gulbahce Campus

department: Molecular Biology and Genetics

country: Turkey

institute: Izmir Institute of Technology

data_processing:
Data were analysed by Eclipse Bioinnovations according to their standard m6A-eCLIP analysis pipeline
Demultiplexing by umi_tools
Quality check with fatqc
Adaptor trimming by Cutadopt
Reference genome aligment by STAR
Identification of cluster of reads by CLIPper
Crosslink sites at a single nucleotide resolution by PureCLIP
Assembly: UCSC version GRCh38/hg38

source_name: HeLa cells

growth_protocol: HeLa cells were routinely cultured in RPMI medium supplemented with 10% FBS

extract_protocol:
Total RNA was extracted by TRIzol Reagent
RNA samples were subjected m6A e-CLIP protocol

treatment_protocol: Hela cells were treated with 0.1% DMSO and 75ng/ml TNF-alpha for 24h.

value: cervix epithelial

tag: passages

tag: treatment

value: 0.1% DMSO and 75ng/ml TNF-alpha


title: Synovia of PsA patient ST3


title: CD8__P05

value: CD8+ T cells


title: CD8__P07

value: peripheral blood cells


title: Synovia of PsA patient ST2


title: CD8__P04


title: m6A-TNF1_S7


title: CD8__P06


title: Eosinophils__P04

tag: quality filter_for_processed_data

value: does NOT pass cellsorting purity filter


title: CD8__P03


title: Thrombocytes__P06

value: Thrombocytes


title: m6A-TNF2_S8


title: NSCLC_batch1_library4B_CD8_5donors_CITE

description: 10X Genomics_5v2_0

source_name: Non-small cell lung cancer

treatment_protocol: Tumors from 10 patients were dispersed into single cell suspensions by a combination of mechanical and enzymatic dissociation, and stained with dead cell discriminating dye, fluorophore-tagged FACS antibodies, unique anti-human hashtag antibodies against beta2 microglobulin, for donor deconvolution. T cells from each donor were FACS-sorted for scRNA-seq using the 10X genomics platform. Two and four libraries of pooled, live, singlet-gated, CD45+CD3+CD4+ T cells and CD45+CD3+CD8+ T cells were generated respectively from the 10 donors.

value: Non-small cell lung cancer


title: NSCLC_batch1_library4A_CD8_5donors_CITE

description: 10X Genomics_5v2_0


title: CD8__P02


title: CD8__P01


title: NSCLC_batch1_library3_CD4_5donors_CITE

description: 10X Genomics_5v2_0

value: CD4+ T cells


title: CD4__P12


title: NSCLC_batch1_library2B_CD8_5donors_CITE

description: 10X Genomics_5v2_0


title: CD4__P11


title: NSCLC_batch1_library2A_CD8_5donors_CITE

description: 10X Genomics_5v2_0


title: CD4__P10


title: CD4__P09


title: NSCLC_batch1_library1_CD4_5donors_CITE

description: 10X Genomics_5v2_0


title: NSCLC_batch1_library4B_CD8_5donors_TCR

description: 10X Genomics_5v2_0


title: NSCLC_batch1_library3_CD4_5donors_TCR

description: 10X Genomics_5v2_0


title: CD4__P06


title: CD4__P07


title: NSCLC_batch1_library4A_CD8_5donors_TCR

description: 10X Genomics_5v2_0


title: CD4__P05


title: CD4__P04


title: CD4__P01


title: NSCLC_batch1_library2A_CD8_5donors_TCR

description: 10X Genomics_5v2_0


title: NSCLC_batch1_library4B_CD8_5donors_GEX

description: 10X Genomics_5v2_0


title: Basophils__P12

value: Basophils


title: CD4__P02


title: Basophils__P11


title: NSCLC_batch1_library4A_CD8_5donors_GEX

description: 10X Genomics_5v2_0


title: NSCLC_batch1_library2B_CD8_5donors_TCR

description: 10X Genomics_5v2_0


title: NSCLC_batch1_library3_CD4_5donors_GEX

description: 10X Genomics_5v2_0


title: NSCLC_batch1_library1_CD4_5donors_TCR

description: 10X Genomics_5v2_0


title: NSCLC_batch1_library2A_CD8_5donors_GEX

description: 10X Genomics_5v2_0


title: NSCLC_batch1_library2B_CD8_5donors_GEX

description: 10X Genomics_5v2_0


title: Basophils__P08


title: PBT_batch3_library2_9donors_CITE

description: 10X Genomics_5v2_0

value: Pediatric brain tumor

value: CD45+CD3+ T cells


title: Basophils__P07


title: CD4__P08


title: PBT_batch3_library1_9donors_CITE

description: 10X Genomics_5v2_0


title: Basophils__P06


title: PBT_batch2_library2_8donors_CITE

description: 10X Genomics_5v2_0


title: Basophils__P05


title: PBT_batch1_library2_7donors_CITE

description: 10X Genomics_5v2_0


title: Basophils__P04


title: PBT_batch2_library1_8donors_CITE

description: 10X Genomics_5v2_0


title: Basophils__P03


title: Basophils__P02


title: PBT_batch1_library1_7donors_CITE

description: 10X Genomics_5v2_0


title: Basophils__P01


title: PBT_batch3_library2_9donors_TCR

description: 10X Genomics_5v2_0


title: PBT_batch3_library1_9donors_TCR

description: 10X Genomics_5v2_0


title: PBT_batch2_library1_8donors_TCR

description: 10X Genomics_5v2_0


title: B_cells__P11

value: B cells


title: Basophils__P09


title: Basophils__P10


title: NSCLC_batch1_library1_CD4_5donors_GEX

description: 10X Genomics_5v2_0


title: B_cells__P10


title: PBT_batch1_library1_7donors_TCR

description: 10X Genomics_5v2_0


title: B_cells__P09


title: B_cells__P08


title: PBT_batch1_library2_7donors_TCR

description: 10X Genomics_5v2_0


title: PBT_batch3_library2_9donors_GEX

description: 10X Genomics_5v2_0


title: B_cells__P07


title: B_cells__P04


title: B_cells__P05


title: B_cells__P06


title: B_cells__P03


title: PBT_batch2_library2_8donors_GEX

description: 10X Genomics_5v2_0


title: PBT_batch2_library1_8donors_GEX

description: 10X Genomics_5v2_0


title: PBT_batch1_library1_7donors_GEX

description: 10X Genomics_5v2_0


title: B_cells__P02


title: COR-9633-D2

city: Ithaca

first: Jennifer

middle: K

last: Grenier

state: NY

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

data_processing:
cellranger mkfastq was used to generate fastq files by the sequencing facility
Because some samples were sequenced on different (or multiple) Illumina sequencers with different read lengths, all reads were trimmed for analysis and for upload to GEO (R1=28bp, R2=55bp). Samples are annotated with the number of different sequencer models used (NextSeq, HiSeq, and NovaSeq) and final fastq files are annotated by the instrument that generated the majority of reads.
cellranger count (v6) was used to generate raw count tables (h5 files), with the following parameters: --expect-cells=5000 --r1-length=28 --r2-length=55 --nosecondary
Assembly: 10x Genomics reference: refdata-gex-GRCh38-2020-A
Supplementary files format and content: h5

source_name: PBMCs

extract_protocol:
Whole blood was collected in EDTA tubes before and 24h after a cardiopulmonary exercise test (CPET) for each subject in the study. PBMCs were isolated with SepMate tubes  and cryopreserved with 1-10 x10^6 cells per vial. Frozen PBMCs were recovered following the 10x Genomics Demonstrated Protocol: Fresh Frozen Human Peripheral Blood Mononuclear Cells for Single Cell RNA Sequencing (CG00039) and resuspended in 1x PBS containing 0.04% BSA. For a target of 5,000 cells per final library, 8,000 cells were loaded onto the 10x Chromium chip.
Libraries were constructed using the Chromium Single Cell 3ʹ v3 kit (10x Genomics)

value: PBMCs

tag: collection day

tag: disease state

value: control

value: F

tag: age bin

tag: chromium batch

value: batch 15

tag: number of sequencer models used


title: COR-9633-D1


title: PBT_batch2_library2_8donors_TCR

description: 10X Genomics_5v2_0


title: B_cells__P12


title: B_cells__P01


title: COR-4209-D2

value: M

value: batch 17


title: COR-4209-D1


title: COR-4617-D2


title: COR-9868-D2

value: case


title: COR-6711-D1

value: batch 14


title: COR-9868-D1


title: COR-4617-D1


title: PBT_batch3_library1_9donors_GEX

description: 10X Genomics_5v2_0


title: COR-7717-D1

value: batch 16


title: COR-6711-D2


title: COR-7717-D2


title: PBT_batch1_library2_7donors_GEX

description: 10X Genomics_5v2_0


title: COR-5797-D1

value: batch 18


title: COR-5797-D2


title: COR-8625-D2


title: COR-3722-D2


title: il102

city: Hangzhou

first: Jiajia

last: Wang

address: 866 Yuhangtang Road

country: China

institute: Zhejiang University

data_processing:
Illumina Casava 2.19 software used for base-calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

source_name: human MSCs

growth_protocol: Human umbilical cord mesenchymal stem cells (MSC) were culture in MEM-α medium, 10% fetal bovine serum, human FGF (20 ng/mL) and human EGF (20 ng/mL).

extract_protocol:
RNA from MSCs were treated with rhIL-10 or not were extracted using TRIZOL (Life Technologies) followed by purification using an RNeasy Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MSCs were treated with rhIL-10 or not for 8 h.

value: Human umbilical cord MSCs

tag: agent


title: COR-9643-D2


title: il103


title: ctrl3

value: ctrl


title: COR-8111-D1


title: COR-5087-D2


title: COR-9643-D1


title: COR-5087-D1


title: COR-3195-D2


title: mouse  skin with  UVB  irradiation, replicate 3

type: RNA

city: shanghai

first: xu

last: peng

state: Please select region, state or province

address: shanghai  dongchuan road 500号

institute: east china  normal  university

description: mouse (C57BL/6) skin with  UVB  irradiation, replicate 1

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE V2.0 (8*60K,Design ID:028005) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray  Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area  61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set  to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1  (Agilent) using default parameters to obtain background subtracted and spatially  detrended Processed Signal intensities as the raw data. Raw data were normalized  in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2  samples flagged as Detected were maintained.

organism: Mus musculus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color  Low RNA Input Linear Amplification PLUS kit (Agilent) according to the  manufacturer's instructions, followed by RNAeasy column purification (QIAGEN,  Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop  ND-1000 Spectrophotometer

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n  AM1556 ) following the manufacturer's instructions.

treatment_protocol: The 6-8 week old mice were divided into two groups, a dark-treated (con) and UVB-treated group, with 3 mice in each group. The hair on the back of each mouse was shaved, and after two days, the mice in the UVB-treated group were anesthetized and placed in a UVB irradiation meter to irradiate the back of the mouse with UVB at a dose of 180mj/cm2. Three times a week, irradiation for 2 weeks,The darkened group did not receive UVB exposure.

value: skin

value: male

tag: strain


title: mouse  skin without UVB  irradiation, replicate 3

description: mouse (C57BL/6) skin without UVB  irradiation, replicate 1


title: mouse  skin with  UVB  irradiation, replicate 1


title: mouse  skin with  UVB  irradiation, replicate 2

description: mouse(C57BL/6)  skin with  UVB  irradiation, replicate 1


title: mouse  skin without UVB  irradiation, replicate 1

description: mouse(C57BL/6)  skin without UVB  irradiation, replicate 1


title: mouse  skin without UVB  irradiation, replicate 2


title: COR-8625-D1


title: COR-3717-D1


title: il101


title: COR-8111-D2


title: Pupal abdominal epidermis, H3 antibody, CUT&RUN, control

city: Ciudad de Buenos Aires

first: Nicolas

last: Frankel

state: Buenos Aires

address: Ciudad Universitaria

department: FMBC

country: Argentina

institute: CONICET

library_source: genomic

data_processing:
*library strategy: CUT&RUN
Adapters were removed from fastq files with bbduk.sh.
Adapter-corrected reads were aligned to the D. melanogaster reference genome dm6 using BWA, producing SAM files.
SAM files were compressed to BAM format using samtools.
Duplicate reads in BAM files were identified and marked using MarkDuplicates from the Picard suite.
BAM files were filtered based on MAPQ values (>=20) and sam flags 4, 256, 1024 and 2048 with samtools. Only properly paired reads were retained (sam flag 2).
H3K27ac experiments were normalized with bamCompare from the DeepTools suite (Ramírez et al. 2016) with --scaleFactorsMethod SES and a bin size of 1. The IgG was provided as the background file and the resulting normalized files were averaged base-by-base to generate an average signal bigWig file across replicates. We generated this file only for the X chromosome, were the regulatory region of svb is located.
Assembly: dm6
Supplementary files format and content: bigWig file with H3K27ac enrichment signal across the X chromosome.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Pupal abdominal epidermis

extract_protocol:
For each replicate (n=2) we removed abdominal cuticles from 10 pupae 38-45 hAPF. We generated two replicates for the histone H3K27ac antibody (39134, Active Motif) and one control replicate for the Normal Rabbit IgG antibody (Cat. 2729S, Cell Signaling). Both antibodies were used at a 1:100 dilution. After dissection, we washed pupal abdomens by replacing PBS with 1ml of Wash+ buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine with Roche complete EDTA-free protease inhibitor) and centrifuging twice at 12000 g for 5 minutes. We resuspended pupal abdomens in 15 ul of BioMag Plus Concanavalin-A-conjugated magnetic beads (ConA beads, Polysciences Inc.) and followed a CUT&RUN protocol for Drosophila tissues (https://dx.doi.org/10.17504/protocols.io.umfeu3n).
Libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB) following  instructions,  but with the following changes: (i) adaptors were diluted 1:10 in water for adaptor ligation (step 2),  (ii) the size selection of the adaptor-ligated DNA in step 3A was omitted (we proceeded directly to step 3B) and (iii) we performed 14 cycles of PCR with 10 seconds of annealing/extension for enrichment of short DNA fragments. Libraries were sequenced on a NovaSeq 6000 system with 150 bp PE reads.

value: Pupal abdominal epidermis

value: WT

value: H3 antibody


title: COR-6913-D2

value: PBMCs


title: COR-3195-D1


title: COR-3717-D2


title: Pupal abdominal epidermis, H3K27ac antibody, CUT&RUN, replicate 1

value: H3K27ac antibody


title: Pupal abdominal epidermis, H3K27ac antibody, CUT&RUN, replicate 2


title: COR-7804-D2

description: COR.6604.D2 col in rawCounts.txt file

data_processing:
Illumina pipeline software was used for base calling.
Sequenced reads were trimmed for 3' adaptor sequence and low-quality sequence and filtered to remove reads < 50nt with TrimGalore/cutadapt.
Processed reads were mapped to the reference genome/transcriptome with STAR using --quantMode GeneCounts to generate raw counts per gene.
Raw counts were analyzed in R with DEseq2.
Assembly: hg38 (Ensembl genes)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNA was isolated with Trizol, with an extra chloroform extraction to remove residual phenol and addition of glyco-blue as a carrier to promote RNA precipitation. RNA concentration was determined with a HS RNA Qubit assay (ThermoFisher) and integrity assessed on a Fragment Analyzer.
Directional RNA-seq libraries were prepared from 25ng total RNA using the NEBNext Directional Ultra II RNA Library Prep Kit for Illumina (New England Biolabs), with initial polyA+ isolation.

treatment_protocol: Whole blood was collected in EDTA tubes 24h after subjects completed a cardiopulmonary exercise test (CPET). PBMCs were isolated using SepMate tubes  and cryopreserved with 1-10 x10^6 cells per vial. Frozen PBMCs were recovered following the 10x Genomics Demonstrated Protocol: Fresh Frozen Human Peripheral Blood Mononuclear Cells for Single Cell RNA Sequencing (CG00039). Classical monocytes were isolated using the Miltenyi Biotec Classical Monocyte Isolation Kit (130-117-337) and CD14 MicroBeads (130-050-201).

value: control


title: COR-2960-D2

description: COR.4361.D2 col in rawCounts.txt file


title: ctrl1


title: ctrl2


title: COR-6604-D2

description: COR.9359.D2 col in rawCounts.txt file


title: COR-6913-D1


title: 293T-seq

city: Shanghai

first: Haizhu

last: Zhang

address: No. 131 Dong'an Road, Xuhui District

department: Institutes of Biomedical Sciences

institute: Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 or mm10 whole genome using bowtie2 v2.2.6 with parameters with the parameters -X2000 and -m1.
Remove mitochondrial DNA with removeChrom.py
Peak calling with macs2 v 2.2.1
Motif finding with homer(findMotifsGenome.pl)
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files were generated using macs2

source_name: 293T cells

growth_protocol: Human cell line 293T was maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and Pen-Strep (100 U / ml penicillin, 100 mg / ml streptomycin) at 37℃, 5% CO2.

extract_protocol:
Cells were harvested and wash once with cold 1x PBS buffer, and then resuspended in 1 mL cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 1mM PMSF). This cell lysis reaction was incubated on ice for 10 min.
DNA libraries were prepared for sequencing using TruePrepTM DNA Library Prep Kit V2 for Illumina.

tag: cell line


title: KO  UVB   TUMOR

description: UVB induced  skin  tumor of P2RY6-/- mice

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE V2.0 (8*60K,Design ID:074809) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

source_name: P2RY6-/-  UVB   TUMOR

treatment_protocol: Twenty pairs of two-month-old P2ry6+/+ and P2ry6-/- mice were housed in SPF conditions with free access to food and tap water. In order to induce epidermal hyperplasia, the dorsal skins of mice were shaved, followed by UVB irradiation at a dose of 180mJ/cm2, administered three times per week for two consecutive weeks.   In order to induce skin tumor formation, mice were irradiated with 180mJ/cm2 UVB for initial ten weeks, increasing 10mJ/cm2 every week to the dose of 300mJ/cm2 at week 22 and keeping it until to week 40. The tumors on the backs of the mice were counted weekly after becoming visible. The incidence of mouse tumors and multiplicity of tumors were also calculated.

tag: tissue

value: skin  tumor


title: COR-5655-D2

description: COR.2960.D2 col in rawCounts.txt file

tag: cell type


title: COR-1726-D2

description: COR.1726.D2 col in rawCounts.txt file


title: COR-4361-D2

description: COR.5655.D2 col in rawCounts.txt file


title: Hela-60 ATAC-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 or mm10 whole genome using bowtie2 v2.2.6 with parameters with the parameters -X2000 and -m1.
Remove mitochondrial DNA with removeChrom.py
Peak calling with macs2 v 2.2.1
Motif finding with homer(findMotifsGenome.pl)
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: narrowPeak files were generated using macs2

growth_protocol: Human cell lines HeLa, HepG2 and MCF-7 were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and Pen-Strep (100 U / ml penicillin, 100 mg / ml streptomycin) at 37℃, 5% CO2. Mouse C2C12 were cultured in DMEM supplemented with 10% FBS, 2 mM -glutamine, 100 U/ml penicillin and 100 g of streptomycin (1% Pen/Strep) at 37℃, 5% CO2. For myogenic differentiation, cells were shifted to DMEM containing 2% horse serum (differentiation medium).

treatment_protocol:
1.Final concentration of 20 ng/mL TNF-α was added into the cell culture medium and HeLa cells were incubated in 37 °C for 15 min, 30 min and 60 min. Cells were harvested in cold 1x PBS buffer and counted.
2.When the density of MCF7 cells was up to 70%, DMEM was changed to Phenol Red-free DMEM with 2.5% FBS for 24 h and then Phenol Red-free DMEM only for 24 h. Final concentration of 100 nM 17β-estradiol(E2) and 2 uM 4-hydroxytamoxifen(4-HT) were added into the cell culture medium, cells were incubated in 37 °C for 2 h. Cells were harvested in cold 1x PBS buffer and counted.

value: HeLa

value: 20ng/mL TNF-α for 60min


title: EVT_D8, TFAP2C_OE_noDox, rep2

city: Austin

first: Mijeong

last: Kim

address: 2506 Speedway, NMS 4.246

institute: The University of Texas at Austin

data_processing:
Paired-end or single reads were aligned to human transcript (hg38) using Salmon mapper (v1.4.0)
Expression levels of each gene were calculated using R library tximport as transcripts per million (TPM), and the count of each gene was quantified and normalized by R package DEseq2.
Assembly: hg38
Supplementary files format and content: Count information in excel files

source_name: Placenta

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (74136) following the manufacturer’s instructions.
mRNA was enriched from total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490). RNA-seq libraries were generated with 300 ng of total RNA using NEBNext Ultra II RNA Library Prep with (E7775) and NEBNext Multiplex Oligos for Illumina (E7600S) following the manufacturer’s protocol.

value: Placenta

value: Human trophoblast stem cells

value: TFAP2C overexpression no Dox


title: EVT_D8, TFAP2C_OE_noDox, rep1


title: WT  UVB  TUMOR

description: UVB induced  skin  tumor of P2RY6+/+ mice

source_name: P2RY6+/+ UVB  TUMOR

tag: genotype


title: COR-1433-D2

description: COR.1433.D2 col in rawCounts.txt file

value: case


title: Hela-15 ATAC-seq

value: 20ng/mL TNF-α for 15min


title: MCF7-4HT ATAC-seq

source_name: MCF7 cells

value: 2 uM 4-hydroxytamoxifen(4-HT)


title: Hela-0 ATAC-seq


title: EVT_D8, TFAP2C_KD, rep2

value: TFAP2C KD


title: EVT_D8, TFAP2C_OE_Dox, rep2

value: TFAP2C overexpression with Dox


title: EVT_D8, TFAP2C_KD, rep1


title: COR-9359-D2

description: COR.7804.D2 col in rawCounts.txt file


title: EVT_D8, NRIP1_KD, rep2

value: NRIP1 KD


title: EVT_D8, NRIP1_KD, rep1


title: EVT_D8, ZNF439_KD, rep2

value: ZNF439 KD


title: mESC, synHPRT1RnoCpG integrated on chr3, clone 2, rep 1, RNA-Seq

city: New York

first: Brendan

middle: R.

last: Camellato

state: New York

address: 435 E 30th St

department: Institute for Systems Genetics

institute: NYU Langone Health

data_processing:
Demultiplexing and fastq generation was performed using Illumina bcl2fastq v2.20
STAR (v2.5.2a) was used to align reads, without providing a gene annotation file, to custom references in which the synthetic HPRT1 and HPRT1R sequences were present on separate chromosomes or inserted at their specific integration sites in the GRCm38/mm10  genome (produced using the reform tool, https://gencore.bio.nyu.edu/reform/).
Samtools (v1.9) was used to sort and index bam files.
Coverage tracks were produced in bigWig format using bamCoerage (deepTools v3.5.0) with options: --binSize 10 --smoothLength 100 --normalizeUsing RPGC --effectiveGenomeSize 2652783500
Assembly: GRCm38/mm10  + HPRT1/HPRT1R, GRCm38/mm10 reformed with HPRT1/HPRT1R custom genomes
Supplementary files format and content: bigWig - coverage depth tracks for visualiztion

source_name: BL6xCAST with synHPRT1RnoCpG integrated on chr3

growth_protocol: Cells were cultured in 80/20 medium, which consists of 80% 2i medium (1:1 mixture of Advanced DMEM/F12 (ThermoFisher 12634010) and Neurobasal-A (ThermoFisher 10888022) supplemented with 1% N2 Supplement (ThermoFisher 17502048), 2% B27 Supplement (ThermoFisher 17504044), 1% GlutaMAX™ (ThermoFisher 35050061), 1% Pen-Strep (ThermoFisher 15140122), 0.1 mM 2-mercaptoethanol (Sigma M3148), 1,250 U/mL LIF (ESGRO ESG1107l), 3 μM CHIR99021 (R&D Systems 4423), and 1 μM PD0325901 (Sigma PZ0162)), and 20% mESC medium (KnockOut™ DMEM (ThermoFisher 10829018) supplemented with 15% FBS (BenchMark 100106), 0.1 mM 2-mercaptoethanol, 1% GlutaMAX™, 1% MEM non-essential amino acids (ThermoFisher 11140050), 1% nucleosides (EMD Millipore ES-008-D), 1% Pen-Strep, and 1,250 U/mL LIF). mESCs were maintained on plates coated with 0.1% gelatin (EMD Millipore ES-006-B) at 37oC in a humidified incubator with 5% CO2.

extract_protocol:
Cells were grown to medium confluency in 6-well plates. Cells were harvested by washing once with PBS, disso-ciating into single-cell suspending with TrypLE Express (ThermoFisher 12604013) and then neutralizing with mESC media. Cells were pelleted at 500 rcf for 5 minutes and RNA was isolated using Qiagen RNeasy Plus Mini kit, resuspending in 350 μL buffer RLT Plus + β-mercaptoethanol, with homogenization using QIAshredder columns (Qiagen 79654).
RNA-seq libraries were prepared from 1 μg total RNA using QIAseq FastSelect -rRNA HMR (Qiagen 334386) and QIAseq Stranded RNA kits (Qiagen 180743) according to the manufacturer’s protocol.

value: Embryonic stem cells


title: mESC, synHPRT1RnoCpG integrated on chrX, clone 2, rep 2, RNA-Seq

source_name: BL6xCAST with synHPRT1RnoCpG integrated on chrX


title: mESC, synHPRT1RnoCpG integrated on chr3, clone 2, rep 2, RNA-Seq


title: mESC, synHPRT1RnoCpG integrated on chr3, clone 1, rep 2, RNA-Seq


title: mESC, synHPRT1RnoCpG integrated on chr3, clone 1, rep 1, RNA-Seq


title: MCF7-E2  ATAC-seq

value: 100 nM 17β-estradiol(E2) and


title: mESC, synHPRT1RnoCpG integrated on chrX, clone 2, rep 1, RNA-Seq


title: EVT_D8, ZNF439_KD, rep1


title: MCF7-C ATAC-seq


title: EVT_D8, ASCL2_KD, rep2

value: ASCL2 KD


title: Hela-30 ATAC-seq

value: 20ng/mL TNF-α for 30min


title: mESC, synHPRT1RnoCpG integrated on chrX, clone 1, rep 2, RNA-Seq


title: EVT_D8, ASCL2_KD, rep1


title: EVT_D8, TFAP2C_OE_Dox, rep1


title: mESC, synHPRT1RnoCpG integrated on chrX, clone 1, rep 1, RNA-Seq


title: EVT_D8, DLX6_KD, rep1

value: DLX6 KD


title: mESC, synHPRT1R integrated on chr3, clone 2, rep 2, RNA-Seq


title: EVT_D8, DLX5_KD, rep2

value: DLX5 KD


title: EVT_D8, DLX6_KD, rep2


title: mESC, synHPRT1R integrated on chr3, clone 2, rep 1, RNA-Seq

source_name: BL6xCAST with synHPRT1R integrated on chr3


title: EVT_D8, Control_KD, rep2

value: non-targeting shRNA-expressing


title: mESC, synHPRT1R integrated on chr3, clone 1, rep 2, RNA-Seq


title: mESC, synHPRT1R integrated on chr3, clone 1, rep 1, RNA-Seq


title: EVT_D8, DLX5_KD, rep1

value: Placenta


title: mESC, synHPRT1R integrated on chrX, clone 2, rep 1, RNA-Seq

source_name: BL6xCAST with synHPRT1R integrated on chrX


title: mESC, synHPRT1R integrated on chrX, clone 2, rep 2, RNA-Seq


title: EVT_D8, Control_KD, rep1

value: Human trophoblast stem cells


title: mESC, synHPRT1R integrated on chrX, clone 1, rep 2, RNA-Seq


title: mESC, synHPRT1R integrated on chrX, clone 1, rep 1, RNA-Seq


title: EVT_D8, Input

description: Input

data_processing:
Sequenced reads were mapped to human genome (hg38) using Bowtie (v2.4.5).
Peaks were called using MACS3 peak caller with default parameters.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include information regarding chromosome, peak start, peak end, peak score, and peak center for each peak

extract_protocol:
ChIP and bioChIP were performed by cross-linking the target TF to genomic DNA using a 1% formaldehyde solution. Immunoprecipitated DNA was sequenced using Illumina sequencers.
Pull-downed DNAs were applied for the generation of sequencing libraries using the NEBNext Ultra II DNA Library Prep Kit (E7103L) and NEBNext Multiplex Oligos for Illumina (E7600S) following the manufacturer’s protocol.

tag: chip target

value: none (Input)


title: TSC, Input

description: Input


title: EVT_D3, Input

description: Input


title: mESC, synHPRT1 integrated on chrX, clone 2, rep 1, RNA-Seq

source_name: BL6xCAST with synHPRT1 integrated on chrX


title: EVT_D8, NRIP1, bioChIP-seq

description:
Chromatin IP against NRIP1
NRIP1_EVT_D8.peak

value: Chromatin IP against NRIP1


title: mESC, synHPRT1 integrated on chrX, clone 2, rep 2, RNA-Seq


title: EVT_D8, DLX5, ChIP-seq, rep2

description:
Chromatin IP against DLX5
DLX5_EVT_D8_comb.peak

value: Chromatin IP against DLX5


title: mESC, synHPRT1 integrated on chrX, clone 1, rep 2, RNA-Seq


title: EVT_D8, DLX5, ChIP-seq, rep1


title: EVT_D8, ASCL2, ChIP-seq, rep2

description:
Chromatin IP against ASCL2
ASCL2_EVT_D8_comb.peak

value: Chromatin IP against ASCL2


title: mESC, synHPRT1RnoCpG integrated on chr3, clone 2, PolII ChIP, rep 2

data_processing:
Demultiplexing and fastq generation was performed using Illumina bcl2fastq v2.20
bowtie2 (v2.2.9) was used to align reads to custom references in which the synthetic HPRT1 and HPRT1R sequences were present on separate chromosomes or inserted at their specific integration sites in the GRCm38/mm10  genome (produced using the reform tool, https://gencore.bio.nyu.edu/reform/).
Samtools (v1.9) was used to sort and index bam files.
Coverage tracks were produced in bigWig format using bamCoerage (deepTools v3.5.0) with options: --binSize 10 --smoothLength 100 --normalizeUsing RPGC --effectiveGenomeSize 2652783500
Assembly: GRCm38/mm10  + HPRT1/HPRT1R, GRCm38/mm10 reformed with HPRT1/HPRT1R custom genomes
Supplementary files format and content: bigWig - coverage depth tracks for visualiztion

extract_protocol:
Cells were grown to medium confluency in 6-well plates. Cells were harvested by washing once with PBS, disso-ciating into single-cell suspending with TrypLE Express (ThermoFisher 12604013) and then neutralizing with mESC media. Crosslinking was performed by adding formaldehyde to a final concentration of 0.1% (v/v), and cells were incubated at room temperature for 5 minutes with occasional mixing by in-version. Crosslinking was stopped by quenching with 125 mM glycine, incubating at room temperature for 5 minutes with occasional mixing by inversion. DMSO was added to a final concentration of 10% (v/v) and cells were frozen in aliquots of ~106 cells.
~10^6 crosslinked and frozen mESCs were thawed and processed for CUT&RUN using the CUTANA™ ChIC/CUT&RUN kit (EpiCy-pher 14-1048) according to the manufacturer’s protocol. Antibodies were all used at 0.5 μg: rabbit IgG negative control (EpiCypher 13-0042), H3K4me3 (EpiCypher 13-0041), H3K27ac (EpiCypher 13-0045), H3K27me3 (Active Motif 39055, RRID: AB_2561020), Pol II (Santa Cruz Biotechnology sc-56767). Sequencing libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (New England Biolabs E7645L) according to the manufacturer's protocol.


title: EVT_D8, ASCL2, ChIP-seq, rep1


title: mESC, synHPRT1RnoCpG integrated on chr3, clone 2, H3K27me3 ChIP, rep 2


title: EVT_D8, DLX6, ChIP-seq, rep2

description:
Chromatin IP against DLX6
DLX6_EVT_D8_comb.peak

value: Chromatin IP against DLX6


title: mESC, synHPRT1RnoCpG integrated on chr3, clone 2, H3K27ac ChIP, rep 2


title: EVT_D5, DLX6, ChIP-seq

description:
Chromatin IP against DLX6
DLX6_EVT_D5.peak


title: mESC, synHPRT1RnoCpG integrated on chr3, clone 2, PolII ChIP, rep 1


title: EVT_D2, DLX6, ChIP-seq

description:
Chromatin IP against DLX6
DLX6_EVT_D2.peak


title: mESC, synHPRT1RnoCpG integrated on chr3, clone 2, H3K4me3 ChIP, rep 1


title: mESC, synHPRT1RnoCpG integrated on chr3, clone 2, H3K27me3 ChIP, rep 1


title: TSC, DLX6, ChIP-seq

description:
Chromatin IP against DLX6
DLX6_TSC.peak


title: mESC, synHPRT1RnoCpG integrated on chr3, clone 2, H3K27ac ChIP, rep 1


title: mESC, synHPRT1RnoCpG integrated on chr3, clone 1, PolII ChIP, rep 2


title: EVT_D5, TFAP2C, ChIP-seq

description:
Chromatin IP against TFAP2C
TFAP2C_EVT_D5.peak

value: Chromatin IP against TFAP2C


title: mESC, synHPRT1RnoCpG integrated on chr3, clone 1, H3K4me3 ChIP, rep 2


title: EVT_D2, TFAP2C, ChIP-seq

description:
Chromatin IP against TFAP2C
TFAP2C_EVT_D2.peak


title: EVT_D8, TFAP2C, ChIP-seq

description:
Chromatin IP against TFAP2C
TFAP2C_EVT_D8.peak


title: mESC, synHPRT1RnoCpG integrated on chr3, clone 1, H3K27me3 ChIP, rep 2


title: EVT_D8, ATAC-seq

description:
ATAC-seq
ATAC_EVT_D8.peak


title: TSC, ATAC-seq

description:
ATAC-seq
ATAC_TSC.peak


title: mESC, synHPRT1RnoCpG integrated on chr3, clone 1, PolII ChIP, rep 1


title: mESC, synHPRT1 integrated on chrX, clone 1, rep 1, RNA-Seq


title: EVT_D8, H3K27ac, ChIP-seq, rep3

description:
Chromatin IP against H3K27ac
H3K27ac_EVT_D8_comb.peak

value: Chromatin IP against H3K27ac


title: mESC, synHPRT1RnoCpG integrated on chr3, clone 1, H3K27me3 ChIP, rep 1


title: mESC, synHPRT1RnoCpG integrated on chr3, clone 1, H3K4me3 ChIP, rep 1


title: mESC, synHPRT1RnoCpG integrated on chr3, clone 2, H3K4me3 ChIP, rep 2


title: TSC, H3K4me3, ChIP-seq

description:
Chromatin IP against H3K4me3
H3K4me3_TSC.peak

value: Chromatin IP against H3K4me3


title: EVT_D8, H3K4me3, ChIP-seq

description:
Chromatin IP against H3K4me3
H3K4me3_EVT_D8.peak


title: mESC, synHPRT1RnoCpG integrated on chr3, clone 1, H3K27ac ChIP, rep 1

value: Embryonic stem cells


title: EVT_D8, DLX6, ChIP-seq, rep1


title: mESC, synHPRT1RnoCpG integrated on chr3, clone 1, H3K27ac ChIP, rep 2


title: EVT_D8, H3K27ac, ChIP-seq, rep1


title: mESC, synHPRT1RnoCpG integrated on chrX, clone 2, PolII ChIP, rep 2


title: EVT_D8, H3K27ac, ChIP-seq, rep2


title: EVT_D3, H3K27ac, ChIP-seq, rep3

description:
Chromatin IP against H3K27ac
H3K27ac_EVT_D3_comb.peak


title: mESC, synHPRT1RnoCpG integrated on chrX, clone 2, H3K27me3 ChIP, rep 2


title: mESC, synHPRT1RnoCpG integrated on chrX, clone 2, H3K27ac ChIP, rep 2


title: EVT_D3, H3K27ac, ChIP-seq, rep2


title: EVT_D3, H3K27ac, ChIP-seq, rep1


title: mESC, synHPRT1RnoCpG integrated on chrX, clone 2, PolII ChIP, rep 1


title: mESC, synHPRT1RnoCpG integrated on chrX, clone 2, H3K4me3 ChIP, rep 1


title: PHIKZ non-infected cells, repl.2

city: Würzburg

first: Jörg

last: Vogel

address: Josef-Schneider-Straße 2

department: Institute for Molecular Infection Biology

institute: Würzburg University

data_processing:
FASTQ files were demultiplexes with bcl2fastq2 v2.20.0.422 (Illumina).
Reads were trimmed with cutadapt 1.15 (Martin 2011)
Reads mapped to genomics sequences NC_002516 (PAO1) and NC_004629 (ΦKZ) and quantified and normalized by RPKM with READemption 0.4.3 (Förstner et al. 2014).
Assembly: NC_002516 and NC_004629
Supplementary files format and content: wig files contain the read coverage normalized to min.

organism: Pseudomonas aeruginosa PAO1

source_name: bacterial cells

growth_protocol: PAO1 was grown to OD600 0.3 in LB media. Cells were washed and inoculated 1:3 in M9 minimal media and grown to OD600 0.5. Cells were infected with 15 MOI ΦKZ phage.

extract_protocol:
RNA was extracted with PCI, chloroform, and precipitated with Ethanol/0.3 M NaOAc pH 6.5. RNA was DNase digested.
100 ng RNA was used for rRNA depletion with RiboCop rRNA Depletion Kit for Mixed Bacterial Samples (META, Lexogen). RNA quality was assessed by 2100 Bioanalyzer with the RNA 6000 pico kit (Agilent Technologies). Libraries were prepared with CORALL RNA-Seq Library Prep Kit (Lexogen). PCR amplification was conducted for 14 cycles. Libraries were pooled and spiked with 1% PhiX control library.

treatment_protocol: After indicated time points, cells were lysed with 1% SDS and 0.3 M NaOAc pH 5.2 at 64 °C for 5 min.

value: bacterial cells

value: bacteria

value: wt

value: M9 minimal media, non-infected cells


title: PHIKZ infected cells after 8 min, repl.2

value: M9 minimal media, 8 min post infection with PHIKZ


title: mESC, synHPRT1RnoCpG integrated on chrX, clone 2, H3K27me3 ChIP, rep 1


title: mESC, synHPRT1RnoCpG integrated on chrX, clone 2, H3K27ac ChIP, rep 1


title: TSC, H3K27ac, ChIP-seq, rep1

description:
Chromatin IP against H3K27ac
H3K27ac_TSC_comb.peak


title: mESC, synHPRT1RnoCpG integrated on chrX, clone 1, PolII ChIP, rep 2


title: PHIKZ infected cells after 6 min, repl.2

value: M9 minimal media, 6 min post infection with PHIKZ


title: mESC, synHPRT1RnoCpG integrated on chrX, clone 1, H3K4me3 ChIP, rep 2


title: PHIKZ infected cells after 4 min, repl.2

value: M9 minimal media, 4 min post infection with PHIKZ


title: mESC, synHPRT1RnoCpG integrated on chrX, clone 1, H3K27me3 ChIP, rep 2


title: PHIKZ infected cells after 2 min, repl.2

value: M9 minimal media, 2 min post infection with PHIKZ


title: mESC, synHPRT1RnoCpG integrated on chrX, clone 1, H3K4me3 ChIP, rep 1


title: mESC, synHPRT1RnoCpG integrated on chrX, clone 2, H3K4me3 ChIP, rep 2


title: PHIKZ infected cells after 10 min, repl.2

value: M9 minimal media, 10 min post infection with PHIKZ


title: mESC, synHPRT1RnoCpG integrated on chrX, clone 1, H3K27me3 ChIP, rep 1


title: mESC, synHPRT1RnoCpG integrated on chrX, clone 1, PolII ChIP, rep 1


title: mESC, synHPRT1RnoCpG integrated on chrX, clone 1, H3K27ac ChIP, rep 1


title: mESC, synHPRT1RnoCpG integrated on chrX, clone 1, H3K27ac ChIP, rep 2


title: Cas9-treat3

first: Wei

last: Liu

state: Shanghai

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

institute: Chinese Academy of Sciences

description:
small RNA
miRNA_cas9_treament_expression.txt

data_processing:
We used cutadapt to clip adaptor and filter low quality reads. Reads failing to match the adaptor or reads with lengths shorter than 17 nt were discarded. Redundant sequences were collapsed as useful reads for further analysis. Then, we aligned the reads to reference sequences by bowtie. To assess the expression levels of the miRNAs, the 3’ ends of miRNA with ≤ 3 nt deletions or additional sequences derived from pri-miRNAs were counted as miRNAs. The miRNA expression level was normalized by size factor from DEseq2.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file of miRNA expression normalized by RPM(reads of per million mapped reads)

source_name: Extracellular vesicle

extract_protocol:
Frozen plasma samples were thawed in thermostat water bath for 2 min at 37 °C and then centrifuged at 2,500 × g for 15 min at 4 °C to remove precipitated proteins and lipids. ~0.5-1 ml plasma was used as the starting material for each EVs isolation by exoRNeasy Midi kit (Qiagen; Cat#77144) according to the manufacturer’s instructions. For EV-RNA extraction, 1 ml Trizol reagent (Invitrogen; Cat#15596026) was added to the column and centrifuged at 3,000 × g for 1 min. Total EV-RNA was isolated by Trizol reagent according to manufacturer’s recommendations.
A total amount of 0.5-1 ng RNA per sample was used as input material for the RNA sample preparations. The cDNA libraries establishment of small RNAs included adaptor ligation, adapter depletion, first-strand cDNA synthesis, Cas9/sgRNA in vitro cleavage treatment, PCR amplification and gel purification.

treatment_protocol: For each blood collection, 2 ml venous blood was collected into 10 ml BD K2EDTA Vacutainer tubes to prevent coagulation. The anticoagulant-treated blood samples were immediately inverted several times and transferred to 2 ml conical tubes (Eppendorf; Cat# 0030120094). To obtain plasma, blood samples were centrifuged at 1,300 × g for 10 min at room temperature (RT). The upper layer containing plasma was transferred to new tubes and centrifuged twice at 2,500 × g for 15 min at RT to obtain platelet poor plasma (PPP). Each plasma supernatant was carefully transferred to 1 ml fresh tubes and then stored at -80 °C until further use.

value: Blood plasma

value: Cas9 treatment


title: Cas9-treat4


title: PHIKZ infected cells after 8 min, repl.1


title: mESC, synHPRT1R integrated on chr3, clone 2, PolII ChIP, rep 2


title: Cas9-treat2


title: mESC, synHPRT1R integrated on chr3, clone 2, H3K27me3 ChIP, rep 2


title: Cas9-treat1


title: TSC, H3K27ac, ChIP-seq, rep2

value: Placenta

value: Human trophoblast stem cells


title: Cas9-ctrl4

value: Control


title: PHIKZ infected cells after 2 min, repl.1


title: mESC, synHPRT1R integrated on chr3, clone 2, H3K27me3 ChIP, rep 1


title: mESC, synHPRT1R integrated on chr3, clone 2, PolII ChIP, rep 1


title: mESC, synHPRT1R integrated on chr3, clone 2, H3K27ac ChIP, rep 2


title: mESC, synHPRT1R integrated on chr3, clone 2, H3K4me3 ChIP, rep 1


title: mESC, synHPRT1R integrated on chr3, clone 1, PolII ChIP, rep 2


title: Cas9-ctrl3


title: mESC, synHPRT1R integrated on chr3, clone 1, H3K4me3 ChIP, rep 2


title: PHIKZ infected cells after 10 min, repl.1


title: PHIKZ non-infected cells, repl. 1


title: mESC, synHPRT1R integrated on chr3, clone 1, H3K27me3 ChIP, rep 2


title: mESC, synHPRT1R integrated on chr3, clone 2, H3K4me3 ChIP, rep 2


title: mESC, synHPRT1R integrated on chr3, clone 1, H3K4me3 ChIP, rep 1


title: Cas9-ctrl1


title: mESC, synHPRT1R integrated on chr3, clone 1, PolII ChIP, rep 1


title: Cas9-ctrl2


title: mESC, synHPRT1R integrated on chr3, clone 1, H3K27ac ChIP, rep 2


title: Noncrosslink

growth_protocol: Human cell lines 293T were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and Pen-Strep (100 U / ml penicillin, 100 mg / ml streptomycin) at 37℃, 5% CO2.

extract_protocol:
Cells were harvested and wash once with cold 1x PBS buffer, and then resuspended in 1 mL lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 1mM PMSF). This cell lysis reaction was incubated at room temperature for 10 min.
DNA libraries were prepared for sequencing using TruePrepTM DNA Library Prep Kit V2 for Illumina.

treatment_protocol: In the group with crosslinking, 293T cells were fixed with 1% formaldehyde for 10 min and quenched with 0.125 M glycine for 5 min at room temperature. After permeabilization with lysis buffer, the transposed reaction was performed. Then, a reverse-crosslinking solution was added (with final concentration of 50 mM Tris–Cl, 1 mM EDTA, 1% SDS, 0.2 M NaCl, 5 ng/mL proteinase K). The mixture was incubated with shaking in a heat block at 65 °C, at 1,000 rpm overnight for the crosslinking reversion. After purification, DNA libraries were prepared and sequencing was performed. In the group without crosslinking, living cells were prepared following the original ATAC-seq protocol.

tag: sample type

value: non-crosslink


title: PHIKZ infected cells after 6 min, repl.1


title: mESC, synHPRT1R integrated on chr3, clone 1, H3K27me3 ChIP, rep 1


title: mESC, synHPRT1R integrated on chr3, clone 1, H3K27ac ChIP, rep 1


title: mESC, synHPRT1R integrated on chrX, clone 2, PolII ChIP, rep 2


title: siTP53_STV_2

city: Graz

first: Andreas

last: Prokesch

state: Styria

address: Harrachgasse 21/7

department: Institute of Cell Biology, Histology, and Embryology

country: Austria

institute: Medical University Graz

data_processing:
sequenced data were aligned to the UCSC hg38 genome
Assembly: UCSC hg38
Supplementary files format and content: Data was analyzed by Dr. Tom and .xlsx file with TPM values of all genes was extracted
Supplementary files format and content: DEseq2 was used for differential expression detection

source_name: SGBS

growth_protocol: SGBS cells were maintained and differentiated to mature adipocytes as described in Wabitsch et al., Int J Obes, 2001

extract_protocol:
RNA was isolated with SV Total RNA Isolation System (Promega, Z3105) according to manufactureres protocol.
BGI Strand-Specific mRNA Library Preparation (DNBSEQ)
Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

treatment_protocol: Fully differentiated SGBS cells were transfected with 100 nM of siCtrl or sip53 (Thermo Fisher Scientific, Waltham, MA, United States) by using Lipofectamine RNAiMax (Thermo Fisher Scientific, Waltham, MA, United States) following the provider`s instructions. After transfection, ells were cultivated 24 h in normal and 24 h in starvation medium (HBSS and HEPES) before harvest.

value: SGBS

value: fibroblast

value: adipogenic differentiation and starvation


title: siTP53_STV_3


title: Crosslink

value: crosslink


title: PHIKZ infected cells after 4 min, repl.1

value: bacterial cells

value: bacteria

value: wt


title: mESC, synHPRT1R integrated on chr3, clone 2, H3K27ac ChIP, rep 1

value: Embryonic stem cells


title: mESC, synHPRT1R integrated on chrX, clone 2, H3K4me3 ChIP, rep 2


title: mESC, synHPRT1R integrated on chrX, clone 2, H3K27ac ChIP, rep 2


title: mESC, synHPRT1R integrated on chrX, clone 2, PolII ChIP, rep 1


title: mESC, synHPRT1R integrated on chrX, clone 2, H3K27me3 ChIP, rep 2


title: siCrtl_STV_2

value: siCrtl


title: E2-EP300

growth_protocol: Cell lines 293T were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and Pen-Strep (100 U / ml penicillin, 100 mg / ml streptomycin) at 37℃, 5% CO2.

extract_protocol:
Cells were harvested and wash once with cold 1x PBS buffer, and then resuspended in 1 mL cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 1mM PMSF). This cell lysis reaction was incubated on ice for 10 min.
DNA libraries were prepared for sequencing using TruePrepTM DNA Library Prep Kit V2 for Illumina（）.

treatment_protocol: 1.ATAC-seq was applied to 293T, HeLa, HepG2 and MCF7 cell line. 2.ATAC-seq was applied to mouse liver rhythm model.3. ChIP-seq was applied to different cells with different treatment.

tag: antibody


title: 4HT-HDAC1


title: mESC, synHPRT1R integrated on chrX, clone 2, H3K4me3 ChIP, rep 1


title: mESC, synHPRT1R integrated on chrX, clone 2, H3K27me3 ChIP, rep 1


title: CTRL-HDAC1

value: input


title: Interlobular_hTERT_2.

city: Copenhagen

first: Mikkel

last: Morsing

state: Nørrebro

address: Blegdamsvej 3b

department: Department of Cellular and Molecular Medicine and Danish Stem Cell Center

country: Denmark

institute: University of Copenhagen

data_processing:
Used SOAPnuke software to filter reads
Data processing included removing adaptors, removing reads in which unknown bases(N) are more than 1% and low-quality reads from raw reads.
After reads filtering, we map clean reads to reference genome using HISAT
Assembly: hg19

source_name: Female normal breast

extract_protocol:
Total RNA was extracted using Trizol (Thermo Fischer) and a spin column method according to the manufacturer’s instructions (Zymo Research)
DNAse treated total RNA samples were sent to BGI, Hong Kong for RNA-seq. There, total RNA was enriched for mRNAs using oligo dT magnetic beads. The mRNAs were fragmented and reverse transcribed to double-strand cDNA by random-hexamer primers. The synthesized cDNA was subjected to end-repair and was then 3’Adenylated. Adaptors were ligated to the ends of these 3’ Adenylated cDNA fragments. The ligation products were purified and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer, splint oligo and DNA ligase, followed by sequencing on the DNBseq platform resulting in on average ~30 million reads per sample.

value: Female normal breast

value: hTERT immortalized

value: Fibroblast


title: mESC, synHPRT1R integrated on chrX, clone 2, H3K27ac ChIP, rep 1


title: siTP53_STV_1


title: Lobular_hTERT_2.


title: mESC, synHPRT1R integrated on chrX, clone 1, PolII ChIP, rep 2


title: Interlobular_hTERT_1.


title: mESC, synHPRT1R integrated on chrX, clone 1, H3K4me3 ChIP, rep 2


title: mESC, synHPRT1R integrated on chrX, clone 1, H3K27me3 ChIP, rep 2


title: HeLa-1-15min

source_name: HeLa

value: HeLa


title: CTRL-EP300


title: HeLa-1-0min


title: mESC, synHPRT1R integrated on chrX, clone 1, H3K27ac ChIP, rep 2


title: Lobular_hTERT_1.


title: mESC, synHPRT1R integrated on chrX, clone 1, H3K4me3 ChIP, rep 1


title: GA ATAC-seq

description: In one of my ATAC-seq experiment, 293T cells were crosslinked, permeabilized and incubated with transposons. After tagmentation with transposons, the mixture was incubated with Q Sepharose for 10 min and shortly centrifuged. The supernatant was collected into a new tube as FT (flow-through). The Q Sepharose was then washed with 20 mM, 100 mM, 200 mM, 300 mM, 500 mM, 700 mM, and 1000 mM NaCl successively. The supernatant was collected into new tubes. At last the Q Sepharose was resuspended with 20 mM NaCl as the last group.   GA   represent the Q Sepharose group. This sample is related to those samples in my last submission (GSE164299)


title: mESC, synHPRT1R integrated on chrX, clone 1, PolII ChIP, rep 1


title: siCrtl_STV_3


title: L1EHB2200219--siACSL5_2260_2, ACSL5 KO

first: jun yi

last: Xu

address: 160 Pujian Rd

institute: Shanghaijiaotong university

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.
Then clean reads were separately aligned to hg38 with orientation mode using HISAT2  software
The mapped reads of each sample were assembled by StringTie  in a reference-based approach
differential expression analysis was performed using the DESeq2
Assembly: GRCh38
Supplementary files format and content: Tab-delimited sheet includes tpm of each sample
Supplementary files format and content: Tab-delimited sheet includes count of each sample

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies).
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions (Illumina, San Diego, CA)

value: Pancreatic tumor cells

value: ACSL5 knockdown


title: mESC, synHPRT1R integrated on chrX, clone 1, H3K27me3 ChIP, rep 1


title: L1EHB2200220--siACSL5_2260_3, ACSL5 KO


title: mESC, synHPRT1R integrated on chrX, clone 1, H3K27ac ChIP, rep 1


title: mESC, synHPRT1 integrated on chrX, clone 2, PolII ChIP, rep 2


title: L1EHB2200218--siACSL5_2260_1, ACSL5 KO


title: mESC, synHPRT1 integrated on chrX, clone 2, H3K4me3 ChIP, rep 2


title: mESC, synHPRT1 integrated on chrX, clone 2, H3K27me3 ChIP, rep 2


title: MCF7 ATAC-seq


title: mESC, synHPRT1 integrated on chrX, clone 2, H3K27ac ChIP, rep 2


title: L1EHB2200217--siACSL5_CY3_3, WT

value: WT


title: mESC, synHPRT1 integrated on chrX, clone 2, PolII ChIP, rep 1


title: HeLa ATAC-seq

source_name: HeLa cells


title: HepG2 ATAC-seq

source_name: HepG2 cells


title: 293T ATAC-seq

source_name: 293T cells


title: mESC, synHPRT1 integrated on chrX, clone 2, H3K27ac ChIP, rep 1


title: mESC, synHPRT1 integrated on chrX, clone 2, H3K27me3 ChIP, rep 1


title: mESC, synHPRT1 integrated on chrX, clone 2, H3K4me3 ChIP, rep 1


title: L1EHB2200216--siACSL5_CY3_2, WT


title: L1EHB2200215--siACSL5_CY3_1, WT


title: mESC, synHPRT1 integrated on chrX, clone 1, PolII ChIP, rep 2


title: iRBD56

data_processing:
We used cutadapt to clip adaptor and filter low quality reads. Reads failing to match the adaptor or reads with lengths shorter than 17 nt were discarded. Redundant sequences were collapsed as useful reads for further analysis. Then, we aligned the reads to reference sequences by bowtie. To assess the expression levels of the miRNAs, the 3’ ends of miRNA with ≤ 3 nt deletions or additional sequences derived from pri-miRNAs were counted as miRNAs. The miRNA expression level was normalized by size factor from DEseq2.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include log2-transformed normalized read counts for each sample

value: Blood plasma

value: iRBD


title: iRBD54


title: iRBD55


title: mESC, synHPRT1 integrated on chrX, clone 1, H3K4me3 ChIP, rep 1


title: mESC, synHPRT1 integrated on chrX, clone 1, H3K27me3 ChIP, rep 2


title: mESC, synHPRT1 integrated on chrX, clone 1, H3K4me3 ChIP, rep 2


title: mESC, synHPRT1 integrated on chrX, clone 1, H3K27ac ChIP, rep 2


title: iRBD53


title: mESC, synHPRT1 integrated on chrX, clone 1, H3K27me3 ChIP, rep 1


title: iRBD52


title: mESC, synHPRT1 integrated on chrX, clone 1, H3K27ac ChIP, rep 1


title: hippocampus, dKO, biol rep 3

city: Philadelphia

first: Naiara

last: Akizu

state: PA

address: 3501 Civic Center Blvd

department: Pathology And Lab Medicine

institute: Children's Hospital of Philadelphia

data_processing:
Adapter and poor quality sequences were trimmed and cleaned mRNA reads mapped to the Mus musculus GRCm38 reference genome using STAR (v2.7.3a).
Reads were counted using FeatureCounts from the subread package (v2.0.1) with parameters: -p -C -O.
Differential gene expression analysis was performed with DEseq2 (V1.38.3) excluding genes with less than five reads, and all genes from chromosome X and Y. Differential expression was performed using a linear model and as factor the genotypes.
Assembly: GRCm38
Supplementary files format and content: Coverage files in BigWig format

source_name: hippocampus

growth_protocol: 20 day old mice were euthanized and cortex, hippocampus and cerebellum were dissected on ice, fast frozen, and stored in -80˚C until RNA extraction.

extract_protocol:
On the day of RNA extraction, 50-100mg tissue from each sample was lysed in 1ml TRIzol (Invitrogen, #15596026) according to the manufacturer’s recommendations.
mRNA-seq libraries were generated at Novogene and sequenced on an Illumina NovaSeq 6000 platform with 2x150 PE configuration at an average of 15 million reads per sample.

value: hippocampus

value: Ampd2-/- and Ampd3-/- double knock out

tag: time

value: Day 20


title: hippocampus, dKO, biol rep 2


title: hippocampus, dKO, biol rep 1


title: hippocampus, Ctrl, biol rep 3


title: mESC, synHPRT1RnoCpG integrated on chr3, clone 2, rep 1

data_processing:
Demultiplexing and fastq generation was performed using Illumina bcl2fastq v2.20
bowtie2 (v2.2.9) was used to align reads to custom references in which the synthetic HPRT1 and HPRT1R sequences were present on separate chromosomes or inserted at their specific integration sites in the GRCm38/mm10  genome (produced using the reform tool, https://gencore.bio.nyu.edu/reform/).
Samtools (v1.9) was used to sort and index bam files.
Coverage tracks were produced in bigWig format using bamCoerage (deepTools v3.5.0) with options: --binSize 10 --smoothLength 100 --normalizeUsing RPGC --effectiveGenomeSize 2652783500
Assembly: GRCm38/mm10  + HPRT1/HPRT1R/HPRT1RnoCpG, GRCm38/mm10 reformed with HPRT1/HPRT1R/HPRT1RnoCpG custom genomes
Supplementary files format and content: bigWig - coverage depth tracks for visualiztion

extract_protocol:
Cells were grown to medium confluency in 6-well plates. Cells were harvested by washing once with PBS, disso-ciating into single-cell suspending with TrypLE Express (ThermoFisher 12604013) and then neutralizing with mESC media. Cells were counted and 50,000 were taken for tagmentation. Cells were pelleted at 500 rcf for 5 minutes at 4oC, washed with 50 μL cold PBS, resuspended in 50 μL cold ATAC lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630), spun down at 500 rcf for 10 mins at 4oC, resuspended in 50 μL TDE mix.
Tagmentation was performed at 37oC on a rotator for 30 mins and DNA was purified using the DNA Clean and Concentrator 5 kit (Zymo Research D4004). PCR was performed as previously described (Buenrostro, J.D., et al., Curr Protoc Mol Biol, 2015) using barcoded primers for 10 total cycles.


title: mESC, synHPRT1RnoCpG integrated on chr3, clone 2, rep 2


title: hippocampus, Ctrl, biol rep 2


title: mESC, synHPRT1RnoCpG integrated on chr3, clone 1, rep 2


title: mESC, synHPRT1RnoCpG integrated on chrX, clone 2, rep 1


title: mESC, synHPRT1RnoCpG integrated on chr3, clone 1, rep 1


title: mESC, synHPRT1RnoCpG integrated on chrX, clone 2, rep 2


title: iRBD49


title: mESC, synHPRT1 integrated on chrX, clone 1, PolII ChIP, rep 1


title: cortex, dKO, biol rep 3

source_name: cortex

value: cortex


title: mESC, synHPRT1RnoCpG integrated on chrX, clone 1, rep 2


title: mESC, synHPRT1RnoCpG integrated on chrX, clone 1, rep 1


title: mESC, synHPRT1R integrated on chr3, clone 2, rep 2


title: hippocampus, Ctrl, biol rep 1


title: mESC, synHPRT1R integrated on chr3, clone 2, rep 1


title: mESC, synHPRT1R integrated on chr3, clone 1, rep 1


title: cortex, dKO, biol rep 2


title: mESC, synHPRT1R integrated on chr3, clone 1, rep 2


title: mESC, synHPRT1R integrated on chrX, clone 2, rep 2


title: iRBD46


title: iRBD45


title: mESC, synHPRT1R integrated on chrX, clone 2, rep 1


title: mESC, synHPRT1R integrated on chrX, clone 1, rep 2


title: iRBD50


title: iRBD43


title: iRBD48


title: iRBD44


title: cortex, Ctrl, biol rep 3


title: mESC, synHPRT1 integrated on chrX, clone 2, rep 1


title: cortex, Ctrl, biol rep 2


title: iRBD47


title: iRBD42


title: iRBD51


title: mESC, synHPRT1 integrated on chrX, clone 1, rep 2


title: mESC, synHPRT1 integrated on chrX, clone 1, rep 1


title: cerebellum, dKO, biol rep 3

source_name: cerebellum

value: cerebellum


title: Liver, Vehicle 24 w, Rep 7 [16251]

city: Hørsholm

first: Henrik

last: Hansen

address: Hørsholm Kongevej 11

department: Histology & NGS

institute: Gubra

data_processing:
Reads were aligned to the GRCm38 Ensembl Mus musculus genome and counted using STAR v.2.7.0f with default settings.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text file contaning raw counts from each sample

source_name: Liver

extract_protocol:
Liver tissue (Chow mice, GAN DIO-NASH mice, and chow-reversal mice) were collected and snap-frozen in liquid nitrogen. RNA was isolated using the NucleoSpin® kit (MACHEREY-NAGEL).
RNA sequence libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, USA) and sequenced on the NextSeq 500 (Illumina) with NextSeq 500/550 High Output Kit V2 (75 CYS, Illumina, San Diego, USA).

value: Liver

tag: treatment

value: Vehicle 24 w


title: Liver, Chow-reversal 24 w, Rep 8 [16253]

value: Chow-reversal 24 w


title: mESC, synHPRT1 integrated on chrX, clone 2, rep 2

value: Embryonic stem cells


title: Liver, Chow-reversal 8 w, Rep 7 [16247]

value: Chow-reversal 8 w


title: Liver, Vehicle 16 w, Rep 8 [16248]

value: Vehicle 16 w


title: cerebellum, dKO, biol rep 2


title: cortex, dKO, biol rep 1


title: cortex, Ctrl, biol rep 1


title: Liver, Chow-reversal 16 w, Rep 8 [16250]

value: Chow-reversal 16 w


title: Liver, Vehicle 8 w, Rep 9 [16245]

value: Vehicle 8 w


title: mESC, synHPRT1R integrated on chrX, clone 1, rep 1


title: iRBD40


title: iRBD41


title: cerebellum, dKO, biol rep 1


title: Liver, Chow-reversal 24 w, Rep 7 [16243]


title: cerebellum, Ctrl, biol rep 3


title: Liver, Chow Vehicle 24 w, Rep 8 [16244]

value: Chow Vehicle 24 w


title: iRBD38


title: cerebellum, Ctrl, biol rep 1

value: WT


title: Liver, Chow Vehicle 24 w, Rep 7 [16234]


title: Liver, Vehicle 24 w, Rep 6 [16241]


title: Liver, Chow-reversal 8 w, Rep 6 [16237]


title: Liver, Vehicle 8 w, Rep 8 [16235]


title: cerebellum, Ctrl, biol rep 2


title: iRBD37

value: Blood plasma


title: Liver, Vehicle 16 w, Rep 7 [16238]


title: iRBD36

value: iRBD


title: iRBD35


title: Liver, Chow-reversal 24 w, Rep 6 [16233]


title: BMDM_LA_2h, scATAC-seq

city: Los Angeles

first: Stephen

last: Smale

state: Ca

address: 6-730 MRL 675 Charles E. Young Drive South

department: MIMG

institute: University of California Los Angeles

library_source: genomic single cell

data_processing:
scATAC-seq libraries were sequenced paired-end at 100 cycle in an Illumina NovaSeq 6000 S1 platform.
FASTQ files were generated from binary base call files using Cell Ranger ATAC v.2.0.0 mkfastq command
FASTQ files were used to aligned to the mm10 mouse reference genome using Cell Ranger ATAC (v2.0.0 ‘cellranger-atac count’) with default settings.
Used "cellranger-atac count" for Read alignment, barcode counting and peak calling
Final analysis were perfomed in R, Signac,  Seurat and ggplot2 softwares.
Assembly: mm10
Supplementary files format and content: "filtered_peak_bc_matrix.h5" file contains the filtered peak-barcode matrix from produced by Cell Ranger ATAC V2 pipeline, which is suitable for analysis with  Signac in R.
Supplementary files format and content: "fragments.tsv.gz" file contains information about each DNA fragment . This includes the genomic coordinates of each fragment and the corresponding cell barcode.
Supplementary files format and content: "fragments.tsv.gz.tbi" file  contains index information and allows for quick access to the compressed scATAC-seq fragment data in "fragments.tsv.gz" files during downstream analysis.
Supplementary files format and content: "singlecell.csv" file contains a matrix of chromatin accessibility across cells, with barcodes for cell identification, genomic loci of open chromatin, quality metrics and metadata for each cell, which is useful for down stream analysis in R using Signac.
Supplementary files format and content: "web_summary.html" file is HTML-formatted report that details key metrics from scATAC-seq data analysis by Cell Ranger V2. This includes information about sequencing depth, peak detection, and library quality, which can be viewed in a web browser for easy assessment

source_name: primary macrophages

growth_protocol: Bone marrow precursors were grown in M-CSF conditioned media and FBS for 6 days prior to stimulation as described in Purbey et al., 2017 (PMID:28930658).

extract_protocol:
The transposition reaction was prepared by mixing about 12000 nuclei (to finally recover about 8000 nuclei) prepared from unstimulated and stimulated samples with ATAC Buffer and Enzyme and incubated for 30 min at 37 °C as per 10X scATAC-seq guide (CG000496 Rev B). Nuclei preparation: Both untreated and stimulated cells were washed twice with DPBS ( Thermo Fisher, Cat # 14190144) and incubated with 1ml Accutase (Sigma Aldrich, Cat # A6968) for 8 minutes at 37 0C and then diluted with additional 2 ml of DPBS + 0.04% BSA. Single cell suspension was prepared by gently dislodging by splashing and pipetting the DPBS (3-4 times). The resuspended cells were pelleted in a 5 ml Eppendorf tube (300g for 5 min at 4 0C) and then washed with 1ml of DPBS + 0.04% BSA. The pellet was flicked resuspended in 50ul DPBS + 0.04% BSA and then lysed with 200 ul nuclei lysis buffer (10 mM Tris-HCl “pH 7.4”, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween 20, 0.1% NP-40 substitute, 0.01% digitonin and 1% bovine serum albumin “BSA; Thermo Fisher, Cat# AM2616”) by pipetting 8 times and vortexing for 10 sec and by incubating for 8 minutes on ice (with gentle flicking of the cells every 2 mins). The pellet was washed with 1 ml of chilled wash buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% Tween 20 and 1% BSA) by pipetting 5-6 times. Nuclei were pelleted at 500gfor 5 min at 4 °C, and the supernatant was removed carefully without disrupting the nuclei pellet. Assuming, about 50% loss during the procedure, nuclei were resuspended into 60 ul of chilled 1X Nuclei Buffer (10x Genomics).
libraries were constructed Chromium Next GEM Single Cell ATAC Reagent kits v2 (10X Genomics) according to manufactuer's instruction.

treatment_protocol: BMDM on day 6 was stimulated with 100ng/ ml final concentration of Lipid A (Sigma Aldrich, Cat# L6895-1MG)

value: Bone Marrow

value: mouse bone marrow derived macrophages (BMDM)

value: Lipid A for 2 hours


title: iRBD33


title: Pam3_2h_r4

data_processing:
ATAC-seq libraries were sequenced on an Illumina HiSeq 2000.
Adapter sequences were removed with cutadapt -a CTGTCTCTTATA -m 23 and all fastq files were mapped using Bowtie2.
The reads were excluded from downstream analysis if unmapped to index genome, multiple alignments, in duplicate, aligned to mitochondrial genome. or contiguous sequences.
Genomic sites enriched with aligned reads were identified and called peaks by using MACS2. The called peaks from each sample were merged to generate a combined probe list using HOMER.
All the sorted bam files were imported into seqMonk for quantification. Raw reads among each combined probe site were converted to reads per kilobases of the probe and per million reads of total read counts (RPKM).
Assembly: mm9
Supplementary files format and content: bedGraph files for each sample were generated from sorted bam files using HOMER to represent the reads coverage genome-widely.

source_name: bone marrow

growth_protocol: Bone marrow precursors were grown in CMG media containing FBS for 6 days prior to stimulation.

extract_protocol:
50,000 mature BMDM were centrifuged and washed with PBS once. The cell pellet was resuspended with cold hypotonic lysis buffer. The lysate was centrifuged and the supernatant was discarded. The crude nuclei were treated with transposition reaction mix (50ul) containing 2.5ul Tn5 transposase (Nextera) and incubated in a 37oC thermomixer with 1000RPM mixing for 30 minutes. The transposed DNA was then cleaned up with a Qiagen Minelute PCR Purification Kit.
The transposed DNA was amplified by a non-saturating PCR containing primer 1 and barcode primer 2 provided in the published protocols by Buenrostro et al. The amplified DNA was size selected on the gel from 100bp to 1000bp and purified with a Qiagen QIAquick Gel Extraction Kit. The selected DNA library was quantified by Qubit and Agilent Bioanalyzer High-Sensitivity DNA Analysis Kit.

treatment_protocol: Bone-marrow derived macrophages were stimulated with Lipid A (100 ng/mL), Pam3CSK4 (100ng/mL) or Poly (I:C) (100 µM) for 0 or 2 hours.

value: bone marrow

value: bone marrow-derived macrophages

value: wild-type


title: BMDM_LA_0h, scATAC-seq

value: untreated


title: Liver, Vehicle 8 w, Rep 7 [16227]

value: Liver


title: Liver, Vehicle 24 w, Rep 5 [16231]

value: Vehicle 24 w


title: Liver, Vehicle 16 w, Rep 6 [16228]


title: Liver, Vehicle 8 w, Rep 6 [16225]


title: Liver, Chow Vehicle 24 w, Rep 6 [16224]


title: iRBD39


title: Liver, Chow-reversal 24 w, Rep 5 [16223]

value: Chow-reversal 24 w


title: iRBD32


title: Liver, Chow-reversal 16 w, Rep 6 [16230]


title: LipidA_2h_r4


title: Colonic C3-expressing cells, scRNASeq

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Raw sequencing data in the form of binary files were converted into FASTQ files using the mkfastq command from CellRanger v6.1.0.
The FASTQ files were demultiplexed into gene expression libraries using CellRanger’s count command, and only reads mapping unambiguously and with less than 2 mismatches were kept
reads were mapped to the mouse mm10 transcriptome using CellRanger
Duplicate reads, those mapping to multiple regions or having a low alignment score (MAPQ < 10) were filtered out
A final gene expression matrix with genes in rows and cells in columns was then constructed
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: colon

extract_protocol:
Colons from one male and one female C3IRES-tdTomato C57BL/6 mice were collected, and single cell suspensions were prepared. Live C3-expressing cells were sorted as DAPI-tdTomato+ using FACSAria (BD) into DMEM containing 10% FBS. A total of ~10,000 C3-expressing cells from each mouse were collected and pooled together.
Samples were loaded into Chip G per the user guide from 10x Genomics. The Chip G was then run on a 10x Chromium Controller. 100ul of GEM emulsion was taken from the chip, and inspected visually for inconsistencies in the recovered volume, the uniformity of the emulsion, or the relative amount of partitioning oil, and incubated at RT in a thermocycler (45 min at 53C, 5 min at 85C, then held at 4C until the next step). The emulsion was then broken by adding 125ul of Recovery Agent. The cDNA was then purified using Dynabeads MyOne SILANE. Per the 10x 3’v3.1 user guide, the 35ul of the purified cDNA was mixed with 15ul 10x cDNA primers (PN 200089) and 50ul of 10xAmp Mix (PN 2000047), then amplified on a thermocycler (98C for 3 minutes, [98C for 15 seconds, 63C for 20 seconds, 72C for 60 seconds], 12 repeats of the bracketed steps, 72C for 60 seconds, then held at 4 C. The amplified cDNA was then purified and separated based on size using a 0.6x Beckman Coulter SPRIselect Reagent cleanup. The larger bound fragments in the bead pellet containing transcript-derived cDNA were eluted in 35ul of Qiagen Buffer EB for use in Gene Expression library construction. Library size was measured by an Agilent Bioanalyzer 2100 High Sensitivity DNA assay and quantified using a Qubit dsDNA HS Assay kit on a Qubit 4.0 Fluorometer. A portion of the transcript-derived cDNA was fragmented, ligated to an Illumina Read 2 Sequencing Adaptor, and indexed with a unique 10x T Set A index, yielding the GEX library. 50ng of the transcript-derived cDNA was mixed with nuclease-free water up to a volume of 20ul, then mixed with 15ul of nuclease-free water, 5ul of 10x Fragmentation Buffer (PN 2000091), and 10ul of 10x Fragmentation Enzyme (PN 2000090), loaded onto a thermocycler, and incubated at 32C for 2 minutes, then 65 C for 35 minutes, and then held at 4 C. The fragmented product was purified with a 0.6x SPRI, with 75ul of the supernatant saved. The supernatant was purified with a 0.8x SPRI, with the pellet-bound DNA saved and eluted in 50uL. All 50ul of eluted sample was mixed with 20ul 10x Ligation Buffer (PN 2000092), 10ul DNA ligase (PN 220110), and 20ul of Adaptor Oligos (2000094), then incubated on a thermocycler at 20C for 15min. This product was purified using a 0.8x SPRI cleanup, with the pellet-bound DNA saved and eluted in 30ul. These 30ul were then mixed with 20ul of a unique 10X T Set A index and 50ul of 10x Amp Mix, then incubated on a thermocycler at 98 C for 45 seconds, [98C for 20 seconds, 54C for 30 seconds, 72C for 20 seconds], 13 repeats of the bracketed steps, 72C for 60 seconds, then held at 4C. The sample was then purified with a 0.6x SPRI, saving and transferring 150ul of the supernatant. The transferred supernatant was purified with a 0.8x SPRI and the pellet-bound DNA was eluted in 35ul. The finished library was measured on an Agilent BioAnalyzer and quantified on a Qubit 4.0. This library was then sequenced on an Illumina Novaseq SP 100, yielding approximately ~366M reads in the GEX.

value: colon

value: C3-tdTomato reporter mouse line (C3IRES-tdTomato C57BL/6)


title: Liver, Vehicle 24 w, Rep 4 [16221]


title: iRBD31


title: Liver, Chow-reversal 16 w, Rep 5 [16220]

value: Chow-reversal 16 w


title: PolyIC_2h_r4


title: iRBD34


title: iRBD30


title: unstimulated_r3


title: iRBD29


title: Liver, Vehicle 8 w, Rep 5 [16215]

value: Vehicle 8 w


title: Liver, Chow-reversal 8 w, Rep 5 [16217]

value: Chow-reversal 8 w


title: Pam3_2h_r3


title: iRBD28

value: Blood plasma


title: Liver, Chow Vehicle 24 w, Rep 5 [16214]

value: Chow Vehicle 24 w


title: Yeast, synHPRT1R integrated on chrXI, rep 2, RNA-Seq

data_processing:
Demultiplexing and fastq generation was performed using Illumina bcl2fastq v2.20
STAR (v2.5.2a) was used to align reads, without providing a gene annotation file, to custom references in which the synthetic HPRT1 and HPRT1R sequences were present on separate chromosomes or inserted at their specific integration sites in the SacCer_April2011/sacCer3 genome (produced using the reform tool, https://gencore.bio.nyu.edu/reform/).
Samtools (v1.9) was used to sort and index bam files.
Coverage tracks were produced in bigWig format using bamCoerage (deepTools v3.5.0) with options: -bs 1 --scaleFactor (-)TMM --filterRNAstrand forward/reverse. Scale factors for TMM normalization were calcualted using edgeR.
Assembly: SacCer_April2011/sacCer3 + HPRT1/HPRT1R, SacCer_April2011/sacCer3 reformed with HPRT1/HPRT1R custom genomes
Supplementary files format and content: bigWig - coverage depth tracks for visualiztion

organism: Saccharomyces cerevisiae

source_name: BY4741 with synHPRT1R integrated on chrXI

growth_protocol: Yeast were cultured overnight at 30C in SC-Leu for YAC strains and YPD for integrated strains. In the morning, cultures were diluted to OD 0.1 and cultured for another 6 hours to reach  mid-log phase at an OD of ~0.6.

extract_protocol:
Yeast were pelleted at 3,000 rcf for 5 minutes, washed once with water, pelleted again at 3,000 rcf for 5 minutes, and cell pellets were frozen at -80oC. Frozen pellets were resuspended in 200 μL lysis buffer (50 mM Tris-HCl pH 8, 100 mM NaCl) and lysed by disruption with an equal volume of acid washed glass beads, vortexing 10 x 15 seconds. 300 μL lysis buffer was added and samples were mixed by inversion followed by a short centrifugation to collect all liquid in the tube. 450 μL of supernatant was mixed with an equal volume of phenol:chloroform:isoamyl alcohol, vortexed for 1 minute, and centrifuged at max speed for 5 minutes. 350 μL of the aqueous layer was then mixed with an equal volume of phenol:chloroform:isoamyl alcohol, vortexed for 1 minute, and centrifuged at max speed for 5 minutes. RNA was precipitated from 300 μL of the aqueous phase by adding 30 μL of 3 M NaOAc and 800 μL of cold 99.5% ethanol, briefly vortexing, and centrifuging at max speed for 10 minutes. The pellet was rinsed with 70% ethanol and dried at room temperature before dissolving in 100 μL of RNase-free DNase set (Qiagen 79254) and incubating at room temperature for 10 minutes to remove DNA. RNA was purified using the RNeasy Plus Mini kit (Qiagen 74136) and eluted in 30 μL RNase-free water.
RNA-seq libraries were prepared from 1 μg total RNA using the QIAseq FastSelect -rRNA Yeast kit (Qiagen 334217) and QIAseq Stranded RNA Library kit (Qiagen 180743) according to the manufacturer’s protocol.

value: Yeast


title: LipidA_2h_r3


title: Liver, Chow-reversal 24 w, Rep 4 [16213]


title: Liver, Chow-reversal 16 w, Rep 7 [16240]


title: iRBD26

value: iRBD


title: PolyIC_2h_r3


title: iRBD25


title: Liver, Chow-reversal 16 w, Rep 4 [16210]


title: Liver, Vehicle 24 w, Rep 3 [16211]


title: unstimulated_r2


title: Liver, Vehicle 16 w, Rep 4 [16208]

value: Vehicle 16 w


title: Yeast, synHPRT1 integrated on chrXI, rep 2, RNA-Seq

source_name: BY4741 with synHPRT1 integrated on chrXI


title: Liver, Vehicle 16 w, Rep 5 [16218]


title: Yeast, synHPRT1R YAC, rep 1, RNA-Seq

source_name: BY4741 with synHPRT1R YAC


title: Pam3_2h_r2

value: bone marrow


title: iRBD24

source_name: Extracellular vesicle


title: Yeast, synHPRT1 integrated on chrXI, rep 1, RNA-Seq


title: Liver, Chow-reversal 8 w, Rep 4 [16207]


title: iRBD23


title: iRBD22


title: iRBD27


title: Yeast, synHPRT1R integrated on chrXI, rep 1, RNA-Seq


title: Yeast, synHPRT1 YAC, rep 2, RNA-Seq

source_name: BY4741 with synHPRT1 YAC


title: Yeast, synHPRT1R YAC, rep 2, RNA-Seq


title: PolyIC_2h_r2

value: bone marrow-derived macrophages


title: Pam3_2h_r1

value: wild-type


title: Liver, Chow-reversal 24 w, Rep 3 [16203]


title: Yeast, synHPRT1 YAC, rep 1, RNA-Seq


title: Liver, Chow Vehicle 24 w, Rep 4 [16204]


title: iRBD20


title: Yeast, synHPRT1R integrated on chrXI, H3K4me3 ChIP, rep 2

data_processing:
Demultiplexing and fastq generation was performed using Illumina bcl2fastq v2.20
bowtie2 (v2.2.9) was used to align reads to custom references in which the synthetic HPRT1 and HPRT1R sequences were present on separate chromosomes or inserted at their specific integration sites in the SacCer_April2011/sacCer3 genome (produced using the reform tool, https://gencore.bio.nyu.edu/reform/).
Samtools (v1.9) was used to sort and index bam files.
Coverage tracks were produced in bigWig format using bamCoerage (deepTools v3.5.0) with options: -bs 1 --normalizeUsing RPGC --effectiveGenomeSize 12100000.
Signal enrichment peaks were called using macs2 (v2.1.0) callpeak with options: --nomodel -f BAMPE -g 1.2e7 --keep-dup all
Assembly: SacCer_April2011/sacCer3 + HPRT1/HPRT1R, SacCer_April2011/sacCer3 reformed with HPRT1/HPRT1R custom genomes
Supplementary files format and content: bigWig - coverage depth tracks for visualiztion
Supplementary files format and content: narrowPeak - called peaks of ChIP-seq signal enrichment (for H3K4me3 ChIP only)

extract_protocol:
Cells were pelleted at 3,000 rcf for 5 minutes, washed twice with water, and resuspended in spheroplasting buffer (1.4 M Sorbitol, 40 mM HEPES-KOH pH 7.5, 0.5 mM MgCl2, 0.5 mM 2-mercaptoethanol). Spheroplasting was performed by adding 0.125 U/μL Zymolyase (Zymo Research E1004) and incubating at 37oC for 45 minutes on a rotator. Nuclei were prepared as previously described (Orsi, G.A., et al., Curr Protoc Mol Biol, 2015). Resuspended nuclei were split into aliquots of ~108 nuclei each and snap frozen in liquid nitrogen.
~10^8 frozen nuclei were thawed and processed for CUT&RUN using the CUTANA™ ChIC/CUT&RUN kit (EpiCy-pher 14-1048) according to the manufacturer’s protocol. Antibodies were  used at 0.5 μg: rabbit IgG negative control (EpiCypher 13-0042), H3K4me3 (EpiCypher 13-0041). Sequencing libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (New England Biolabs E7645L) according to the manufacturer's protocol.


title: Liver, Vehicle 24 w, Rep 2 [16201]


title: iRBD19


title: Yeast, synHPRT1R integrated on chrXI, IgG ChIP, rep 1


title: Liver, Chow-reversal 16 w, Rep 3 [16200]


title: LipidA_2h_r2


title: iRBD18


title: WT_clone_0h_r2

data_processing:
ATAC-seq libraries were sequenced on an Illumina NovaSeq 6000 SP.
Adapter sequences were removed with cutadapt -a CTGTCTCTTATA -m 23 and all fastq files were mapped using Bowtie2.
The reads were excluded from downstream analysis if unmapped to index genome, multiple alignments, in duplicate, aligned to mitochondrial genome. or contiguous sequences.
Genomic sites enriched with aligned reads were identified and called peaks by using MACS2. The called peaks from each sample were merged to generate a combined probe list using HOMER.
All the sorted bam files were imported into seqMonk for quantification. Raw reads among each combined probe site were converted to reads per kilobases of the probe and per million reads of total read counts (RPKM).
Assembly: mm9
Supplementary files format and content: bedGraph files for each sample were generated from sorted bam files using HOMER to represent the reads coverage genome-widely.

source_name: macrophage cell line

growth_protocol: J2 immortalized bone-marrow derived macrophages were grown in CMG media containing FBS prior to stimulation.

extract_protocol:
50,000 macrophages were centrifuged and washed with PBS once. The cell pellet was resuspended with cold hypotonic lysis buffer. The lysate was centrifuged and the supernatant was discarded. The crude nuclei were treated with transposition reaction mix (50ul) containing 2.5ul Tn5 transposase (Nextera) and incubated in a 37oC thermomixer with 1000RPM mixing for 30 minutes. The transposed DNA was then cleaned up with a Qiagen Minelute PCR Purification Kit.
The transposed DNA was amplified by a non-saturating PCR containing primer 1 and barcode primer 2 provided in the published protocols by Buenrostro et al. The amplified DNA was size selected on the gel from 100bp to 1000bp and purified with a Qiagen QIAquick Gel Extraction Kit. The selected DNA library was quantified by Qubit and Agilent Bioanalyzer High-Sensitivity DNA Analysis Kit.

treatment_protocol: Immortalized macrophages were stimulated with lipid-A for 0 or 2 hours.

value: macrophage cell line

value: J2 virus immortalized bone marrow-derived macrophage, single cloned

value: unstimulated


title: Yeast, synHPRT1R integrated on chrXI, H3K4me3 ChIP, rep 1


title: WT_clone_2h_r2

value: 2-hour Lipid A


title: Liver, Vehicle 16 w, Rep 3 [16198]

value: Liver


title: WT_clone_2h_r1


title: Liver, Vehicle 8 w, Rep 4 [16205]


title: WT_clone_0h_r1


title: Yeast, synHPRT1R YAC, IgG ChIP, rep 2


title: iRBD17


title: Liver, Chow-reversal 8 w, Rep 3 [16197]


title: iRBD21


title: C9_DKO_clone_2h_r1


title: PolyIC_2h_r1


title: Liver, Vehicle 8 w, Rep 3 [16195]


title: Yeast, synHPRT1R integrated on chrXI, IgG ChIP, rep 2


title: iRBD15


title: iRBD16


title: Liver, Chow Vehicle 24 w, Rep 3 [16194]


title: C9_DKO_clone_0h_r1


title: Liver, Chow-reversal 24 w, Rep 2 [16193]

value: Chow-reversal 24 w


title: iRBD14


title: iRBD13


title: Yeast, synHPRT1R YAC, IgG ChIP, rep 1


title: Yeast, synHPRT1R YAC, H3K4me3, rep 2


title: C2_DKO_clone_2h_r2


title: Yeast, synHPRT1R YAC, H3K4me3 ChIP, rep 1


title: Liver, Chow-reversal 16 w, Rep 2 [16190]

value: Chow-reversal 16 w


title: iRBD12


title: C2_DKO_clone_2h_r1


title: Liver, Vehicle 16 w, Rep 2 [16188]


title: Yeast, synHPRT1 integrated on chrXI, IgG ChIP, rep 2


title: C2_DKO_clone_0h_r2


title: iRBD11


title: Yeast, synHPRT1 integrated on chrXI, IgG ChIP, rep 1


title: iRBD10


title: Liver, Chow-reversal 8 w, Rep 2 [16187]


title: Yeast, synHPRT1 integrated on chrXI, H3K4me3 ChIP, rep 2


title: C2_DKO_clone_0h_r1