title: C102 nucleus accumbens (ACB)

value: Acesulfame potassium (ACE-K)

tag: strain

value: Postnatal day (PN) 80


title: Cell line EO771, untreated, rep2

status: Public on Sep 06 2022

type: SRA

city: Aurora

first: Tonya

last: Brunetti

state: CO

address: 12800 East 19th Avenue

department: Immunology and Microbiology

country: USA

institute: University of Colorado Anschutz Medical Campus

library_source: transcriptomic

data_processing:
Trimming and read cleanup was performed using Cutadapt v2.9 (parameters:  -a AGATCGGAAGAG -A AGATCGGAAGAG -q 30 --minimum-length=10 –pair-filter=any)
Alignment was performed using three different aligners: STAR v2.7.3a (parameters: --outSAMtype BAM SortedByCoordinate, --twopassMode Basic,  --outSAMattributes NH HI NM MD AS nM jM jI XS, --sjdbOverhang 150 ), TopHat v2.1.1 (parameters: --library-type fr-secondstrand), HISAT2 v2.2.1
Alignment correction and cleanup was performed using Opossum v1.0 (parameters: -SoftClipsExist=False --MapCutoff=40 --ProperlyPaired=True)
Variants were called using Platypus v0.8.1 (parameters: --filterDuplicates=0, --minMapQual=0,--minFlank=0, --maxReadLength=500, --minGoodQualBases=10, --minBaseQual=20)
VCF files were normalized using vt v0.5772
SNPs were annotated using variant effect predictor (VEP) against the GRCm38 genome annotation version 102
RNA gene-level and isoform-level quantifications were performed using Salmon v1.3.0 (parameters: --validateMappings)
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files for *quants.sf files containing various raw and normalized counts data
Supplementary files format and content: Excel files for *potential_mhc_binders_9mers_intron_retentions.xlsx contain large spreadsheets of intron retentions and annotations
Supplementary files format and content: Excel files for *miR200c_and_plusDoxyEmptyVector.xlsx contain large spreadsheets of neoantigens and annotations

molecule: polyA RNA

organism: Mus musculus

growth_protocol: cell lines were cultured in RPMI 1640 Medium supplemented with 5% fetal bovine serum (FBS) and 10U/mL Penicillin-Streptomycin. All cells were tested for mycoplasma contamination using the Barbara Davis Center BioResources Core at the University of Colorado

extract_protocol:
RNA using TRIzol (ThermoFisher, Cat.# 15596026) per manufacturer's instructions followed by a RNeasy MinElute Cleanup (Qiagen, Cat.# 74204) per manufacturer's instructions
PolyA Selected Total RNA Library Kit, prepared according to manufacturer’s instructions

tag: cell line

tag: cell type

value: Epithelial-like mammory gland breast carcinoma

tag: treatment

value: untreated


title: C103 nucleus accumbens (ACB)

city: La Jolla

first: Francesca

last: Telese

state: CA

address: 9500 Gilman Drive

department: Psychiatry

institute: UCSD

data_processing:
FastQC: RNA-seq quality control was performed using FastQC
Trimmomatic: Low-quality reads were trimmed by Trimmomatic
STAR: Reads were then aligned to Rattus norvegicus genome Rnor6.0 using STAR
HTSeq: Gene counts were quantified using HTSeq
DEseq2: DEseq2 was then used to perform differential gene expression analysis between control and ACE-K treatment groups across both sexes to identify DEGs affected by ACE-K Treatment, Sex, and Treatment x Sex interactions, or within males and females separately to identify DEGs affected by treatment within each sex
Assembly: Rnor6.0
Supplementary files format and content: csv files including raw counts for each brain region

molecule: total RNA

organism: Rattus norvegicus

source_name: ACB, CTL

extract_protocol:
Total RNA was extracted according to the manufacturer’s instructions using an AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) and checked for purity using the NanoDrop One (Thermo Fisher Scientific, Waltham, MA, USA).
All samples were found to have high purity and were sent to the USC Genome Core for library preparation and RNA sequencing. There, the total RNA was checked for degradation using a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA) to verify the quality for all samples. Libraries were prepared from 1 ug of total RNA using a NuGen Universal Plus mRNA-seq Library Prep Kit (Tecan Genomics Inc. Redwood City, CA, USA). Final library products were quantified using the Qubit 2.0 Fluorometer (Thermo Fisher Scientific Inc., Waltham, MA, USA), and the fragment size distribution was determined with the Bioanalyzer 2100. The libraries were pooled equimolarly, and the final pool was quantified via qPCR using the Kapa Biosystems Library Quantification Kit, according to manufacturer’s instructions. The pool was sequenced using an Illumina NextSeq 550 platform (Illumina, San Diego, CA, USA), in Single-Read 75 cycles format, obtaining about 25 million reads per sample.

tag: tissue

value: Brain

tag: brain region

value: nucleus accumbens

value: CTL (water)

value: Sprague Dawley

tag: Sex

value: Male

tag: age at_sacrifice

tag: body weight_at_pn_80


title: C101 nucleus accumbens (ACB)


title: 12Z_shARID1A_panH4ac_rep1_ChIP

city: Grand Rapids

first: Ronald

middle: L.

last: Chandler

state: MI

department: Obstetrics, Gynecology and Reproductive Biology

institute: Michigan State University

description: Eluted pan-H4ac ChIP DNA (replicate #1) from shARID1A lentiviral particle treated (control) 12Z human endometriotic epithelial cells.

library_source: genomic

data_processing:
Raw reads for IPs and inputs were trimmed with cutadapt (Martin 2011) and Trim Galore! (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) followed by quality control analysis via FastQC (Andrews 2010) and MultiQC (Ewels, Magnusson et al. 2016).
Trimmed reads were aligned to GRCh38.p12 reference genome (Schneider, Graves-Lindsay et al. 2017) via Bowtie2 (Langmead and Salzberg 2012) with flag `--very-sensitive`. Aligned reads were sorted and indexed with samtools (Li, Handsaker et al. 2009).
Molecular complexity was estimated from duplicate rates by ATACseqQC (Ou, Liu et al. 2018) and preseqR (Daley and Smith 2013), and libraries were subsampled to equivalent molecular complexity within an experimental design based on these estimates with samtools.
Picard MarkDuplicates (http://broadinstitute.github.io/picard/) was used to remove PCR duplicates, followed by sorting and indexing.
MACS2 (Zhang, Liu et al. 2008) was used to call peaks on each ChIP replicate against the input chromatin control with FDR < 0.05 threshold. For H2A.Z, narrow peaks were computed with flags `--nomodel --extsize 146` to bypass model building. For pan-H4ac, broad peaks were computed with flags `--nomodel --extsize 146` to bypass model building.
The resulting peaks were repeat-masked by ENCODE blacklist filtering and filtered for non-standard contigs (Amemiya, Kundaje et al. 2019).
A naive overlapping peak set, as defined by ENCODE (Landt, Marinov et al. 2012), was constructed by calling peaks on pooled replicates followed by bedtools intersect (Quinlan and Hall 2010) to select for peaks of at least 50% overlap with each biological replicate.
ChIP-seq differential histone abundance analysis was performed with csaw (Lun and Smyth 2016). First, a consensus peak set was constructed for each differential experiment from the union of replicate-intersecting, filtered MACS2 peak regions called in each condition. ChIP reads were counted in these query regions by csaw, then filtered for low abundance peaks with average log2CPM > -3. When comparing ChIP libraries, any global differences in IP efficiency observed between the two conditions were considered a result of technical bias to ensure a highly conservative analysis. As such, we employed a loess-based local normalization to the peak count matrix, as is implemented in csaw (Lun and Smyth 2016), to assume a symmetrical MA distribution. A design matrix was then constructed from one ‘condition’ variable, without an intercept term. The count matrix and loess offsets were then supplied to edgeR (Robinson, McCarthy et al. 2010) for estimating dispersions and fitting quasi-likelihood generalized linear models for differential abundance hypothesis testing. Nearby query regions were then merged up to 500 bp apart for a maximum merged region width of 5 kb, and the most significant probability was used to represent the merged region. Finally, FDR < 0.05 threshold was used to define significant differentially abundant regions.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Tabular blacklist-filtered broadPeak files reported by MACS2 corresponding to sites of significant H2A.Z and pan-H4ac abundance in 12Z cells from either or both ChIP replicates per condition. Tabular csaw differential H2A.Z and pan-H4ac abundance results tables for shARID1A vs. control conditions, across all tested genome-wide regions per assay.

molecule: genomic DNA

organism: Homo sapiens

source_name: 12Z endometriotic epithelial cells

growth_protocol: Human 12Z endometriotic epithelial cells were cultured in growth media (10% FBS, 1% L-glutamine, 1% Penicillin-Streptomycin).

extract_protocol:
Cells were treated with 1% formaldehyde in growth media for 10 minutes at ambient temperature. Formaldehyde was quenched by the addition of 0.125 M Glycine and incubation for 5 minutes at room temperature, followed by PBS wash and scraping. 1*10^7 crosslinked cells were used for each ChIP, and ChIP was performed in duplicate. Chromatin from crosslinked cells was fractionated by digestion with micrococcal nuclease using the SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling) according to the manufacturer protocol, followed by 30 seconds of sonication. ChIP was then performed according to the SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling) with the addition of 5 mM sodium butyrate to preserve histone acetylation. 1:250 anti-histone H2A.Z (ab4174, abcam) or 1:50 anti-acetyl-histone H4 (06-866, Millipore) was added to each, respective 1.25 mL IP. Crosslinks were reversed with 0.4 mg/mL Proteinase K (ThermoFisher) and 0.2 M NaCl at 65 °C for 2 hours. DNA was purified using the ChIP DNA Clean & Concentrator Kit (Zymo).
Libraries for input and IP samples were prepared by the Van Andel Research Institute Genomics Core. 10 ng of material was used for input samples, and the entire precipitated sample was used for IPs. Libraries were generated using the KAPA Hyper Prep Kit (v5.16) (Kapa Biosystems). Prior to PCR amplification, end-repaired and A-tailed DNA fragments were ligated to IDT for Illumina UDI Adapters (IDT DNA Inc.). Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies), QuantiFluor® dsDNA System (Promega) and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems). Individually indexed libraries were pooled, and 100 bp, single-end sequencing was performed on an Illumina NovaSeq 6000 sequencer using a 100-cycle sequencing kit (Illumina). Each library was sequenced to minimum read depth of 80 million reads per input library and 40 million reads per IP library. Base calling was performed by Illumina NCS v2.0, and NCS output was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.

treatment_protocol: Lentiviral shRNA particles were transduced into 12Z cells at a 100-fold multiplicity of infection, and media was replaced 24 hours later. Cells were harvested 72 hours following shRNA transduction.

value: 12Z endometriotic epithelial cells

tag: treatment/condition

value: shARID1A (lentiviral ARID1A shRNA particles)

tag: antibody


title: C100 nucleus accumbens (ACB)

source_name: ACB, ACE-K


title: Cell line EO771, untreated, rep1


title: 12Z_shARID1A_H2A.Z_rep2_ChIP

description: Eluted H2A.Z ChIP DNA (replicate #2) from shARID1A lentiviral particle treated (control) 12Z human endometriotic epithelial cells.

value: anti-histone H2A.Z (ab4174, abcam)


title: C99 nucleus accumbens (ACB)


title: 12Z_Control_H3.3_rep1_ChIP

description: Eluted H3.3 ChIP DNA (replicate #1) from non-targeting shRNA lentiviral particle treated (control) 12Z human endometriotic epithelial cells.

data_processing:
Raw reads for IPs and inputs were trimmed with cutadapt (Martin 2011) and Trim Galore! (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) followed by quality control analysis via FastQC (Andrews 2010) and MultiQC (Ewels, Magnusson et al. 2016).
Trimmed reads were aligned to GRCh38.p12 reference genome (Schneider, Graves-Lindsay et al. 2017) via Bowtie2 (Langmead and Salzberg 2012) with flag `--very-sensitive`. Aligned reads were sorted and indexed with samtools (Li, Handsaker et al. 2009).
Only properly-paired read fragments were retained for paired-end libraries via samtools view with flag `-f 3` followed by sorting and indexing.
Molecular complexity was estimated from duplicate rates by ATACseqQC (Ou, Liu et al. 2018) and preseqR (Daley and Smith 2013), and libraries were subsampled to equivalent molecular complexity within an experimental design based on these estimates with samtools.
Picard MarkDuplicates (http://broadinstitute.github.io/picard/) was used to remove PCR duplicates, followed by sorting and indexing.
MACS2 (Zhang, Liu et al. 2008) was used to call peaks on each ChIP replicate against the input chromatin control with FDR < 0.05 threshold. For H3.3, broad peaks were computed with flags `--nomodel --extsize 146` to bypass model building. For H2A.Zac, narrow peaks were computed with flags `--nomodel --extsize 146` to bypass model building.
The resulting peaks were repeat-masked by ENCODE blacklist filtering and filtered for non-standard contigs (Amemiya, Kundaje et al. 2019).
A naive overlapping peak set, as defined by ENCODE (Landt, Marinov et al. 2012), was constructed by calling peaks on pooled replicates followed by bedtools intersect (Quinlan and Hall 2010) to select for peaks of at least 50% overlap with each biological replicate.
ChIP-seq differential histone abundance analysis was performed with csaw (Lun and Smyth 2016). First, a consensus peak set was constructed for each differential experiment from the union of replicate-intersecting, filtered MACS2 peak regions called in each condition. ChIP reads were counted in these query regions by csaw, then filtered for low abundance peaks with average log2CPM > -3. When comparing ChIP libraries, any global differences in IP efficiency observed between the two conditions were considered a result of technical bias to ensure a highly conservative analysis. As such, we employed a loess-based local normalization to the peak count matrix, as is implemented in csaw (Lun and Smyth 2016), to assume a symmetrical MA distribution. A design matrix was then constructed from one ‘condition’ variable, without an intercept term. The count matrix and loess offsets were then supplied to edgeR (Robinson, McCarthy et al. 2010) for estimating dispersions and fitting quasi-likelihood generalized linear models for differential abundance hypothesis testing. Nearby query regions were then merged up to 500 bp apart for a maximum merged region width of 5 kb, and the most significant probability was used to represent the merged region. Finally, FDR < 0.05 threshold was used to define significant differentially abundant regions.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Tabular blacklist-filtered broadPeak files reported by MACS2 corresponding to sites of significant H3.3 and H2A.Zac abundance in 12Z cells from either or both ChIP replicates per condition. Tabular csaw differential H3.3 and H2A.Zac abundance results tables for shARID1A vs. control conditions, across all tested genome-wide regions per assay.

extract_protocol:
Cells were treated with 1% formaldehyde in growth media for 10 minutes at ambient temperature. Formaldehyde was quenched by the addition of 0.125 M Glycine and incubation for 5 minutes at room temperature, followed by PBS wash and scraping. 1*10^7 crosslinked cells were used for each ChIP, and ChIP was performed in duplicate. Chromatin from crosslinked cells was fractionated by digestion with micrococcal nuclease using the SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling) according to the manufacturer protocol, followed by 30 seconds of sonication. ChIP was then performed according to the SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling) with the addition of 5 mM sodium butyrate to preserve histone acetylation. 1:125 anti-histone H3.3 (2D7-H1, abnova) or 1:50 anti-histone H2A.Z-acetyl (K4/K7) (D3V1I, Cell Signaling) was added to each, respective 1.25 mL IP. Crosslinks were reversed with 0.4 mg/mL Proteinase K (ThermoFisher) and 0.2 M NaCl at 65 °C for 2 hours. DNA was purified using the ChIP DNA Clean & Concentrator Kit (Zymo).
Libraries for input and IP samples were prepared by the Van Andel Research Institute Genomics Core. 10 ng of material was used for input samples, and the entire precipitated sample was used for IPs. Libraries were generated using the KAPA Hyper Prep Kit (v5.16) (Kapa Biosystems). Prior to PCR amplification, end-repaired and A-tailed DNA fragments were ligated to IDT for Illumina UDI Adapters (IDT DNA Inc.). Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies), QuantiFluor® dsDNA System (Promega) and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems). Individually indexed libraries were pooled, and 50 bp, paired-end sequencing was performed on an Illumina NovaSeq 6000 sequencer using a 100-cycle sequencing kit (Illumina). Each library was sequenced to minimum read depth of 80 million reads per input library and 40 million reads per IP library. Base calling was performed by Illumina NCS v2.0, and NCS output was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.

value: Control (non-targeting shRNA treated)

value: anti-histone H3.3 (2D7-H1, abnova)


title: Dss, replicate 1, scRNA-seq

city: JiNan

first: Shiyang

last: Li

address: Wenhua West Road

country: China

institute: Shandong University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The CellRanger software pipeline(version 6.1.1) was used to align FASTQ sequencing reads to the GRCm38 reference transcriptome, and generating single cell feature counts for each sample
Using Seruat version 3.0, each sample was considered for features shared by 3 or more cells, and cells showing 200 or more genes and less than 8000 genes. Cells with mitochondrial RNA percentages of >40 and nUMI > 40000 were filtered out
Assembly: GRCm38(ftp://ftp.ensembl.org/pub/release-96/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.toplevel.fa.gz)
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: colon

extract_protocol:
Single-cell suspensions were loaded to 10x Chromium to capture 5000 single cells according to the manufacturer’s instructions of 10X Genomics Chromium Single-Cell 3’kit (V3).
Libraries were constructed using Chromium™ Single Cell 3' v2 Reagent Kits following the manufacturer’s protocol

value: colon

value: Dss


title: 12Z_shARID1A_H2A.Z_rep1_ChIP

description: Eluted H2A.Z ChIP DNA (replicate #1) from shARID1A lentiviral particle treated (control) 12Z human endometriotic epithelial cells.


title: Dss, replicate 2, scRNA-seq

description: 10x Genomics


title: Tst-1

city: Changchun

first: Boyin

last: Jia

state: Jilin

address: 2888 Xincheng Street

department: College of Animal Science and Technology

institute: Jilin Agricultural University

data_processing:
CASAVA bcl2fastq-1.8.4 used for basecalling.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq SR Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2500/2000 platform and 50bp single-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas(clean reads) were obtained by removing reads containing poly-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing poly A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw data were calculated. Then, chose a certain range of length from clean reads to do all the downstream analyses. The small RNA tags were mapped to reference sequence by Bowtie without mismatch to analyze their expression and distribution on the reference.
Assembly: miRBase Release 22.1
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Cervus nippon

source_name: testes

extract_protocol:
Tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. A total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext®Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
the small RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Shuangyang

tag: developmental stage

value: juvenile

value: testes

value: male


title: Tst-3

value: adult


title: Tst-2

value: adolescence


title: 12Z_Control_panH4ac_rep2_ChIP

description: Eluted pan-H4ac ChIP DNA (replicate #2) from non-targeting shRNA lentiviral particle treated (control) 12Z human endometriotic epithelial cells.

value: anti-acetyl-histone H4 (06-866, Millipore)


title: C98 nucleus accumbens (ACB)

value: Brain

value: nucleus accumbens

value: Acesulfame potassium (ACE-K)

value: Postnatal day (PN) 80


title: Control, replicate 2, scRNA-seq

description: 10x Genomics

value: control


title: Spl-4

source_name: spleen

value: aged

value: spleen


title: 12Z_Control_panH4ac_rep1_ChIP

description: Eluted pan-H4ac ChIP DNA (replicate #1) from non-targeting shRNA lentiviral particle treated (control) 12Z human endometriotic epithelial cells.

value: 12Z endometriotic epithelial cells

value: Control (non-targeting shRNA treated)


title: C97 nucleus accumbens (ACB)

value: CTL (water)

value: Sprague Dawley

value: Male


title: C96 nucleus accumbens (ACB)


title: 12Z_Control_H2A.Z_rep2_ChIP

description: Eluted H2A.Z ChIP DNA (replicate #2) from non-targeting shRNA lentiviral particle treated (control) 12Z human endometriotic epithelial cells.

value: anti-histone H2A.Z (ab4174, abcam)


title: 12Z_Control_H2A.Zac_rep2_ChIP

description: Eluted H2A.Zac ChIP DNA (replicate #2) from non-targeting shRNA lentiviral particle treated (control) 12Z human endometriotic epithelial cells.

value: anti-histone H2A.Z-acetyl (K4/K7) (D3V1I, Cell Signaling)


title: 12Z_Control_H2A.Z_rep1_ChIP

description: Eluted H2A.Z ChIP DNA (replicate #1) from non-targeting shRNA lentiviral particle treated (control) 12Z human endometriotic epithelial cells.


title: Tst-4

value: Shuangyang

value: testes

value: male


title: 12Z_ChIP_Input [re-analyzed]

description: Reanalyzed sample GSM4623036; Input library from wild-type 12Z cells

data_processing:
Raw reads for IPs and inputs were trimmed with cutadapt (Martin 2011) and Trim Galore! (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) followed by quality control analysis via FastQC (Andrews 2010) and MultiQC (Ewels, Magnusson et al. 2016).
Trimmed reads were aligned to GRCh38.p12 reference genome (Schneider, Graves-Lindsay et al. 2017) via Bowtie2 (Langmead and Salzberg 2012) with flag `--very-sensitive`. Aligned reads were sorted and indexed with samtools (Li, Handsaker et al. 2009).
Picard MarkDuplicates (http://broadinstitute.github.io/picard/) was used to remove PCR duplicates, followed by sorting and indexing.
MACS2 (Zhang, Liu et al. 2008) was used to call broadPeaks on each ChIP replicate against the input chromatin control, with FDR < 0.05 threshold and otherwise default settings.
The resulting peaks were repeat-masked by ENCODE blacklist filtering and filtered for non-standard contigs (Amemiya, Kundaje et al. 2019).
A naive overlapping peak set, as defined by ENCODE (Landt, Marinov et al. 2012), was constructed by calling peaks on pooled replicates followed by bedtools intersect (Quinlan and Hall 2010) to select for peaks of at least 50% overlap with each biological replicate.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Tabular blacklist-filtered broadPeak files reported by MACS2 corresponding to significant CHD4 binding sites in 12Z cells from either or both ChIP replicates.

source_name: 12Z cell line

extract_protocol:
Cells were treated with 1% formaldehyde in growth media for 10 minutes at ambient temperature. Formaldehyde was quenched by the addition of 0.125 M Glycine and incubation for 5 minutes at room temperature, followed by PBS wash and scraping. 1*10^7 crosslinked cells were used for each ChIP, and ChIP was performed in duplicate. Chromatin from crosslinked cells was fractionated by digestion with micrococcal nuclease using the SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling) according to the manufacturer protocol, followed by 30 seconds of sonication. ChIP was then performed according to the SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling). 1:50 anti-CHD4 (D4B7, Cell Signaling) was added to each 1.25 mL IP. Crosslinks were reversed with 0.4 mg/mL Proteinase K (ThermoFisher) and 0.2 M NaCl at 65 °C for 2 hours. DNA was purified using the ChIP DNA Clean & Concentrator Kit (Zymo).
Libraries for input and IP samples were prepared by the Van Andel Research Institute Genomics Core. 10 ng of material was used for input samples, and the entire precipitated sample was used for IPs. Libraries were generated using the KAPA Hyper Prep Kit (v5.16) (Kapa Biosystems). Prior to PCR amplification, end-repaired and A-tailed DNA fragments were ligated to IDT for Illumina UDI Adapters (IDT DNA Inc.). Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies), QuantiFluor® dsDNA System (Promega) and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems). Individually indexed libraries were pooled, and 100 bp, single-end sequencing was performed on an Illumina NovaSeq 6000 sequencer using a 100-cycle sequencing kit (Illumina). Each library was sequenced to minimum read depth of 80 million reads per input library and 40 million reads per IP library. Base calling was performed by Illumina NCS v2.0, and NCS output was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.

value: 12Z cell line

value: Wild-type


title: 12Z_CHD4_rep2_ChIP

description: Eluted CHD4 ChIP DNA (replicate #2) from wild-type 12Z human endometriotic epithelial cells.

value: anti-CHD4 (D4B7, Cell Signaling)


title: Msc-4

source_name: skeletal muscle

value: skeletal muscle


title: Spl-2

value: adolescence


title: B cells, VC 4 days, pSTAT3, IL-21 6h, bio rep 2 [ChIP-seq]

city: Columbus

first: Chan-Wang

middle: Jerry

last: Lio

state: Ohio

address: 460 W 12th Ave

institute: Ohio State University

data_processing:
Bowtie2 (v2.4.2)
Samtools (v1.10)
Deeptools (v3.5.1)
Assembly: mm10
Supplementary files format and content: Bigwig

source_name: Spleen

growth_protocol: Naïve B cells were co-cultured with irradiated 40LB stromal cells in the presence of recombinant mouse interleukin-4 (1ng/mL; Peprotech) in complete media (RPMI1640, 10% fetal bovine serum, 2mM GlutaMax, 1x non-essential amino acid, 1mM sodium pyruvate, 10mM HEPES, 50 ug/mL gentamicin, and 55 uM 2-mercaptoethanol). Cells were incubated at 37°C with 5% CO2 for 4 days.

extract_protocol:
Cells were fixed with 1% formaldehyde (ThermoFisher) in media at 1 × 106 cells/ml for 10 mins at room temperature with constant nutation. Fixation was quenched with 125 mM glycine for 5 min on ice. After being washed twice with PBS, cell pellets were snap-frozen with liquid nitrogen and stored at −80 °C until nuclei preparation. To extract chromatin, nuclei were isolated using lysis buffer (50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, and 0.25% Triton X-100) and were washed once with wash buffer (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, and 0.5 mM EGTA), followed by two washes with shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, and 0.1% SDS) without disturbing pellets. Pellets were then resuspended in shearing buffer and the chromatin was sheared using Bioruptor Pico (Diagenode) for 7 cycles (30 sec on, 30 sec off) at 4 °C. After precleared with ProteinA dynabeads (ThermoFisher), 20 μg of chromatin was diluted to a final of 500uL RIPA buffer (50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 1 mM EDTA, 1% NP40, 0.1% SDS, and 0.5% sodium deoxycholate) and incubated with 1 μg rabbit monoclonal anti-phsopho-STAT3 (Tyr705) antibody (clone D3A7, Cell Signaling Technology) overnight at 4°C with constant rotation. To capture the antibody-bound chromatin, the samples were incubated with 30 μl of precleaned Protein A Dynabeads for 2 hours at 4 °C. The beads were washed twice with RIPA buffer and once with TE buffer (10 mM Tris-HCl pH 8.0 and 1 mM EDTA). All washes were incubated for 5 min at 4 °C with constant rotation. After the last wash, samples were eluted twice with 100 μl elution buffer (100 mM NaHCO3,1% SDS, and 0.5 mg/ml RNase A). To decrosslink, proteinase K (0.5 mg/ml; Ambion) and NaCl (200 mM) were added to the eluted samples, followed by the incubation at 65 °C overnight. The samples were purified using DNA Clean & Concentrator-5 (Zymo Research).
Sequencing libraries were prepared using NEB Ultra II kits according to the standard protocol (NEB).

treatment_protocol: Cells were treated with vehicle or with 100 ug/mL L-ascorbic acid 2-phosphate at the beginning of culture

value: Spleen

value: B cells

tag: chip antibody

value: pSTAT3 (CST D3A7)

value: VC, IL-21 6h


title: C93 nucleus accumbens (ACB)

value: Brain

value: nucleus accumbens

value: CTL (water)

value: Postnatal day (PN) 80


title: C92 nucleus accumbens (ACB)

value: Acesulfame potassium (ACE-K)

value: Sprague Dawley

value: Male


title: C94 nucleus accumbens (ACB)


title: 12Z_CHD4_rep1_ChIP

description: Eluted CHD4 ChIP DNA (replicate #1) from wild-type 12Z human endometriotic epithelial cells.

value: 12Z endometriotic epithelial cells


title: Msc-2

value: Shuangyang

value: male


title: Msc-3

value: adult


title: B cells, VC 4 days, pSTAT3, IL-21 6h, bio rep 1 [ChIP-seq]


title: C91 nucleus accumbens (ACB)


title: B cells, mock 4 days, pSTAT3, IL-21 6h, bio rep 2 [ChIP-seq]

value: Untreated, IL-21 6h


title: C122 dorsal hippocampus (dHP)

source_name: dHP, ACE-K

value: hippocampus

value: Female


title: Msc-1

value: juvenile

value: skeletal muscle


title: Spl-3

value: spleen


title: Control, replicate 1, scRNA-seq

description: 10x Genomics

value: colon

value: control


title: B cells, mock 4 days, pSTAT3, IL-21 6h, bio rep 1 [ChIP-seq]

value: Spleen

value: B cells

value: pSTAT3 (CST D3A7)


title: C95 nucleus accumbens (ACB)

value: Brain

value: nucleus accumbens

value: CTL (water)

value: Sprague Dawley

value: Postnatal day (PN) 80


title: Human pancreatic beta cell replicate 2

city: Philadelphia

first: Chun

last: Su

state: PA

address: 3615 Civic Center Blvd

institute: Children's Hospital of Philadelphia

description: gender: male, female, female

data_processing:
Bases were called using Illumina bcl2fastq2 conversion v2.29
Paired-end reads from two replicates were pre-processed using the HICUP pipeline v0.7.4, with bowtie as aligner and hg19 as the reference genome. The alignment .bam file were parsed to .pairs format using pairtools v0.3.0 and pairix v0.3.7, and eventually converted to pre-binned Hi-C matrix in .cool format by cooler v 0.8.10 with multiple resolutions (1kbp, 2kbp, 4kbp, 5kbp, 10kbp, 40kbp) and normalized with ICE method.
Genome_build: hg19
Supplementary_files_format_and_content: .cool files

extract_protocol:
Dissociated cells were resuspended in 2% FBS/1XDPBS at 5 × 106 cells per ml. Cells were sorted using the FACSAriaII (BD Biosciences) (nozzle size 100 μm, low flow rate, sample injection chamber set at 4 °C) through various gating schemes such that beta cells are HPi1(HICO-4F9)+ HPa3(HIC3-2D12)- HIC1-1C10 (HPx2)- NTPDase3+, alpha cells are HPi1(HICO-4F9)+ HPa3(HIC3-2D12)+ HIC1-1C10 (HPx2)- NTPDase3-, and acinar cells are HPi1(HICO-4F9)- HPa3(HIC3-2D12)- HIC1-1C10 (HPx2)+ NTPDase3-
Hi-C library preparation on FACS-sorted pancreatic cells was performed using the Arima-HiC kit (Arima Genomics Inc; cat# A410030), according to the manufacturer’s protocols. Briefly, cells were crosslinked using formaldehyde. Crosslinked cells were then subject to the Arima-HiC protocol, which utilizes multiple restriction enzymes to digest chromatin. Arima-HiC sequencing libraries were prepared by first shearing purified proximally-ligated DNA and then size-selecting 200-600 bp DNA fragments using AmpureXP beads (Beckman Coulter; cat# A63882). The size-selected fragments were then enriched using Enrichment Beads (provided in Arima-HiC kit), and then converted into Illumina-compatible sequencing libraries with the Swift Accel-NGS 2S Plus DNA Library Kit (Swift, 21024) and Swift 2S Indexing Kit (Swift, 26148).  The purified, PCR-amplified DNA underwent standard QC (qPCR, Bioanalyzer, and KAPA Library Quantification (Roche, KK4824)) and was sequenced with unique single indexes on the Illumina NovaSeq 6000 Sequencing System at 2x101 base pairs.
Arima Hi-C

value: Human pancreatic beta cell

tag: donor id

value: HPAP040, HPAP045, HPAP066

tag: disease state

value: No HX diabetes

tag: age

tag: restriction enzyme

value: DpnII [^GATC] Arima [G^ANTC]


title: Human pancreatic alpha cell replicate 2

description: gender: male, female, female

value: Human pancreatic alpha cell


title: Human pancreatic beta cell replicate 1

description: gender: male, female, female


title: Spl-1

value: Shuangyang

value: juvenile

value: male


title: B cells, VC 4 days, pSTAT3, unstimulated [ChIP-seq]

tag: strain

value: VC, unstimulated


title: lvr-4

source_name: liver

value: aged

value: liver


title: C121 dorsal hippocampus (dHP)

source_name: dHP, CTL

value: hippocampus

value: Female


title: C120 dorsal hippocampus (dHP)

value: Brain

value: Acesulfame potassium (ACE-K)


title: B cells, mock 4 days, pSTAT3, unstimulated [ChIP-seq]

value: Spleen

tag: cell type

value: B cells

value: pSTAT3 (CST D3A7)

value: Untreated, unstimulated


title: Human pancreatic alpha cell replicate 1

description: gender: male, female, female

value: HPAP040, HPAP045, HPAP066

value: No HX diabetes


title: Human pancreatic acinar cell replicate 2

description: gender: male, female, female, male

value: Human pancreatic acinar cell

value: HPAP040, HPAP054, HPAP066, HPAP072

value: DpnII [^GATC] Arima [G^ANTC]


title: C119 dorsal hippocampus (dHP)

tag: treatment

value: CTL (water)

value: Sprague Dawley

value: Postnatal day (PN) 80


title: lvr-1

value: Shuangyang

value: juvenile

tag: tissue

value: liver

value: male


title: C118 dorsal hippocampus (dHP)

value: Brain

tag: brain region

value: hippocampus

value: Acesulfame potassium (ACE-K)

value: Female


title: lvr-2

value: adolescence

tag: Sex


title: Human pancreatic acinar cell replicate 1

description: gender: male, female, female, male


title: siOASL-T/I-HUVEC rep2 (RNA-seq)

city: Seoul

first: GooTaeg

last: Oh

address: 52, Ewhayeodae-gil

department: Department of Life Sciences

country: South Korea

institute: Ewha Womans University

data_processing:
The sequence reads were counted by StringTie-2.1.3b and genes showing <10 read counts total were pre-filtered.
DESeq2 was used to obtain normalized count and identify differentially expressed genes in siCTL or siOASL transfected HUVECs (TNFα/IFNγ).
For performing downstream analysis such as drawing heatmap, the count data was rlog-transformed using DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: RNA_normalized_count.txt.gz, RNA_transformed_count.txt.gz

source_name: HUVEC

growth_protocol: HUVECs were obtained from the American Type Culture Collection (Manassas, VA). HUVECs were cultured in EGM-2 BulletKit (Lonza, CC-3162) medium containing 10% FBS, 2mM L-glutamine, and penicillin (10,000 Units/mL)/streptomycin (10,000 ug/mL) and used at passage 7-10 for experiments. Cells were routinely maintained in a humidified chamber at 37℃ and 5% CO2.

extract_protocol:
HUVECs were stimulated for 3hours and total RNA was manually extracted using Trizol reagent and purified by ethanol precipitation. TruSeq Stranded Total RNA LT Sample Prep Kit (Gold) was used with total RNA for the construction of sequencing libraries.
TruSeq Stranded Total RNA LT Sample Prep Kit (Gold) was used for the construction of sequencing libraries and total RNA libraries were processed following standard Illumina protocols.

treatment_protocol: Two replicates of siRNA-transfected HUVECs per group were treated with or without TNFα and IFNγ added in the serum-free EGM-2 for 3hours.

value: Human umbilical vein endothelial cell (HUVEC)

value: TNFalpha and IFNgamma

tag: genotype

value: OASL knockdown


title: lng-4

source_name: lung

value: aged

value: lung


title: Multiome_ATAC_Lin–RORgt+MHCII+

city: New York

first: Chrysothemis

last: Brown

state: NY

department: Immunology Program, Sloan Kettering Institute

institute: Memorial Sloan Kettering Cancer Center

description: single-cell ATAC-seq of  Lin–RORgt+MHCII+ cells from mesenteric lymph nodes of two-week-old mice

library_source: genomic single cell

data_processing:
Single-cell RNA-seq and ATAC-seq FASTQ files were aligned to mm10 and counted by Cell Ranger ARC v2.0.0 with default parameters.
The barcodes were filtered based on the number of RNA-seq transcripts (>1k and <50k), the number of detected genes (>500 and <6k), and the fraction of mitochondrial transcripts (<15%). Barcodes were further filtered based on the number of ATAC-seq fragments (3.5 < log10{nFrags} < 4.5) and TSS enrichment score (>4). Arrow files were created from the scATAC-seq fragments using ArchR v1.0.1, and doublets were identified and removed with default parameters.
The multiome scATAC-seq data analysis was restricted to the cells in clusters 1-16 of the multiome scRNA-seq results.
LSI was performed on 100K top variable 500bp tiles identified after 10 iterations of ‘IterativeLSI’ by ArchR. Tiles from non-standard chromosomes, chrM, and chrY were not included in this analysis.
Cells were clustered (k=30, resolution=1.2) and visualized with UMAP (nNeighbors=30) using 30 LSI components.
Assembly: mm10
Supplementary files format and content: The ATAC fragments (BED-like tabular file) contains ATAC-seq fragments captured by the assay.
Supplementary files format and content: The tabix index of the fragment intervals facilitates random access to records from an arbitrary genomic interval.
Supplementary files format and content: The scATAC-seq results (tab-delimited tsv table) include clusters and UMAP.

source_name: Mesenteric Lymph Node (MLN)

extract_protocol:
Mesenteric lymph nodes of 2-week-old Rorc(CreERT2)Venus mice were pooled from 16 biological replicates and processed. Cells were depleted of Lineage (TCRb, TCRgd, CD19, B220, NK1.1)+ cells via staining with biotinylated antibodies followed by magnetic bead negative selection. Cells were incubated with anti-CD16/32 in sorting buffer (2% FBS in PBS) for 10 minutes at 4°C to block binding to Fc receptors. Extracellular antigens were stained for 30 minutes at 4°C in sorting buffer (2% FBS, 2mM EDTA, in PBS). Cells were washed and resuspended in sorting buffer with SYTOX blue (Invitrogen) for exclusion of dead cells. Live, CD45+Lin(TCRb, TCRgd CD19)–RORgt(Venus)+ MHCII+ cells were then sort purified. Cells were sorted into cRPMI, before being pelleted and resuspended in RPMI-2% FBS.
Single Cell Multiome ATAC + Gene Expression was performed with 10X genomics system using Chromium Next GEM Single Cell Multiome Reagent Kit A (catalog no. 1000282) and ATAC Kit A (catalog no. 1000280) following Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide and demonstrated protocol - Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing. Briefly, >50,000 cells (viability 95%) were lysed for 4min and resuspended in Diluted Nuclei Buffer (10x Genomics, PN- 2000207). Lysis efficiency and nuclei concentration was evaluated on Countess II automatic cell counter by trypan blue staining.  9,660 nuclei were loaded per transposition reaction, targeting recovery of 6,000 nuclei after encapsulation. After the transposition reaction, nuclei were encapsulated and barcoded. Next-generation sequencing libraries were constructed following User Guide, which were sequenced on an Illumina NovaSeq 6000 system.

value: Mesenteric Lymph Node (MLN)

value: two weeks


title: RBM20-3

city: Nashville

first: Lance

last: Riley

state: TN

address: 9445 MRB4, 2213 Garland Ave

department: Biomedical Engineering

institute: Vanderbilt University

data_processing:
Sequenced reads were mapped using HISAT2 and gene counts were quantified using Htseq-count
Gene counts were quantified using HTseq-count
Differential gene expression was determined using DESeq2 using Cook's outliers to filter out low expression and alpha = 0.05 to for significance.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw counts for every gene and every sample.
Supplementary_files_format_and_content: Matrix table with DEseq2 counts for every gene and every sample.

source_name: Tibialis anterior muscle

growth_protocol: iMSBmal1fl/fl mice were maintained in 12L:12D conditions in a AAALAC approved facility until 12-16 weeks of age.

extract_protocol:
Tibialis anterior muscles were isolated and flash frozen in liquid nitrogen. Muscles were pulverized under liquid nitrogen to prevent fiber type sampling bias then homogenized in Trizol before RNA was extracted with a Qiagen RNeasy kit using the standard protocol. RNA was treated with TURBO DNase (Ambion) to remove genomic DNA.
Libraries were prepared using KAPA Stranded RNAseq Kits with RiboErase according to standard protocols.

treatment_protocol: iMSBmal1fl/fl mice were treated with 2 mg day-1 tamoxifen via intraperitonial injections for five days to induce recombination. 4 weeks after recombination, mice were injected evenly throughout the entire TA muscle with AAV. Muscles were collected 4 weeks after AAV injection.

value: Skeletal muscle


title: siOASL-T/I-HUVEC rep1 (RNA-seq)


title: C116 dorsal hippocampus (dHP)

value: Sprague Dawley

tag: age at_sacrifice

value: Postnatal day (PN) 80

tag: body weight_at_pn_80


title: lng-3

value: Shuangyang

value: adult


title: Multiome_RNA_Lin–RORgt+MHCII+

description: single-cell gene expression of  Lin–RORgt+MHCII+ cells from mesenteric lymph nodes of two-week-old mice

data_processing:
Single-cell RNA-seq and ATAC-seq FASTQ files were aligned to mm10 and counted by Cell Ranger ARC v2.0.0 with default parameters.
The barcodes were filtered based on the number of RNA-seq transcripts (>1k and <50k), the number of detected genes (>500 and <6k), and the fraction of mitochondrial transcripts (<15%). Barcodes were further filtered based on the number of ATAC-seq fragments (3.5 < log10{nFrags} < 4.5) and TSS enrichment score (>4). Arrow files were created from the scATAC-seq fragments using ArchR v1.0.1, and doublets were identified and removed with default parameters. Finally, any genes detected in <2 cells in the scRNA-seq data were discarded.
The filtered count matrix was library-size normalized, log-transformed and then centered and scaled using Seurat v4.0.4. PCA was performed on the scaled data.
PhenoGraph clustering was performed using the first 30 PCs with k=30 nearest neighbors. Cell clustering was visualized using UMAP, computed from the nearest neighbor graph built by PhenoGraph.
Assembly: mm10
Supplementary files format and content: The count matrix (tab-delimited tsv matrix) contains raw gene expression values.
Supplementary files format and content: The scRNA-seq results (tab-delimited tsv table) include clusters, annotations, and UMAP.


title: siCTL-T/I-HUVEC rep2 (RNA-seq)

value: Control


title: RBM20-2


title: C117 dorsal hippocampus (dHP)

value: Brain

value: hippocampus

value: CTL (water)


title: RBM20-1


title: lng-2

value: adolescence

value: male


title: lvr-3

value: liver


title: lng-1

value: juvenile


title: siCTL-T/I-HUVEC rep1 (RNA-seq)

value: Human umbilical vein endothelial cell (HUVEC)

value: TNFalpha and IFNgamma


title: C115 dorsal hippocampus (dHP)

value: Female


title: C114 dorsal hippocampus (dHP)

value: Acesulfame potassium (ACE-K)


title: ChIP-seq_RH30-QC6352-Abcam.H3K9me3-02

city: Memphis

first: Hongjian

last: Jin

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

data_processing:
ChIP-seq raw reads were first trimmed low-quality ends using trim-galore (0.4.4; default parameter) and then aligned to the human reference genomes (hg19) using BWA (version 0.7.12; default parameter) and duplicated reads were then marked with Picard (version 1.65), with only nonduplicated reads kept by samtools (version 1.3.1, parameter ‘‘-q 1 -F 1024’’. For data quality control and to estimate the fragment size, the nonduplicated version of SPP (version 1.11) was used to calculate the relative strand correlation value with support of R (version 3.5.1). To visualize ChIP-seq data on the integrated genome viewer (IGV) (version 2.3.82), we utilized genomeCoverageBed (bedtools 2.25.0) to obtain genome-wide coverage in BEDGRAPH file format and then converted it to bigwig file format by bedGraphToBigWig. The bigwig files were scaled to 15 million reads to allow comparison across samples.
MACS2 (version 2.1.1 20160309) was used to call narrow peaks with option “nomodel” and “extsize” defined as fragment size estimated by SPP and a FDR corrected p-value cutoff of 0.05. SICER (version 1.1, with parameters of redundancy threshold 1, window size 200 bp, effective genome fraction 0.86, gap size 600 bp, FDR 0.00001 with fragment size defined above) was used for broad peak/domain calling. Enriched regions were identified by comparing the ChIP library file to input library file. Peak regions were defined to be the union of peak intervals from ChIP replicates. Genomic feature annotation of peaks was carried out by annotatePeaks.pl, a program from HOMER suite (v4.8.3, http://homer.salk.edu/homer/).
genomeCoverageBed (bedtools 2.25.0) was used to produce genome-wide coverage in BEDGRAPH file and then converted it to bigwig file by bedGraphToBigWig. The bigwig files were scaled to 15 million reads to allow comparison across samples. To show average of several replicates as a single track in the browser, the bigwig files were merged to a single average bigwig file using UCSC tools bigWigtoBedGraph, bigWigMerge and bedGraphToBigWig.
ChIPseqSpikeInFree normalization for H3K9me3 and H3K36me3. ChIPseqSpikeInFree(version 1.2.3 )  was used to calculate scaling factor (S) for every sample (Si). The effective ChIP-seq library size for sample i was then calculated as Ni * Si, where Ni is the original library size. The effective library size was then used to normalize the read count from sample i during the downstream differential analysis, bigwig and heatmap visualization.
Genome_build: hg19(GRCh37)
Supplementary_files_format_and_content: bigwig

source_name: cell line

growth_protocol: RH30 cells were cultured with RPMI 1640 media supplemented with 100 U/mlpenicillin/streptomycin and 10% fetal bovine serum. Cells were maintained at 37 °C in an atmosphere of 5% CO2.

extract_protocol:
1 x 10e7 of Rh30 cells treated with DMSO control or 200 nM of QC6352 for 48 hr were cross-linked with freshly prepared 1% formaldehyde (final concentration) for 10 min and quenched with 125 mM glycine (final concentration) for 5 min at room temperature. Cells were washed once with Dulbecco's Phosphate-Buffered Saline (DPBS). 5-8 ml of ice-cold cell lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl and 0.5% NP-40 with 1 tablet protease inhibitor cocktail) were added to cells. The cells were scraped with a cell scraper and transferred into 50-ml conical tubes on ice. Cell pellets were collected by centrifugation at 2,000 rpm for 5 minutes at 4 °C. The pellets were resuspended in cell lysis buffer and incubated on ice for 10 min. Cells were passed through a 20-gauge needle 20 times. The nuclei were collected by centrifugation at 2,000 rpm at 4 °C for 5 minutes. The nuclear pellets were resuspended and lysed with 250 μl RIPA buffer (1X PBS, 1% NP-40, 0.5% sodium deoxycholate and 0.1% SDS with 1 tablet protease inhibitor cocktail). The lysates were sonicated for at least 30 min (30 sec on/30 sec off) using Bioruptor Pico (Diagenode, Inc., Denville, NJ) and centrifuged at 14,000 rpm in a microfuge for 15 minutes at 4 °C. The supernatant was collected and the sonicated DNA fragments were examined by electrophoresis on a 1% agarose gel. The sonicated samples with enrichment of fragments between 100 to 500 bp range were used for the chromatin immunoprecipitation (ChIP) after removing 50 μL from each sample as input. The primary antibodies H3K9me3 (Millipore, 07-442), H3K36me3 (RevMab, 31-1051-00), H3K4me1 (Abcam, ab8895) and H3K27ac (Abcam, ab4729) were coupled with 25 μL magnetic beads (Dynabeads M-280 Sheep Anti-Rabbit IgG, Invitrogen 11203D) overnight in the cold room at 4 °C, washed three times with PBS/BSA (1X PBS/5 mg/ml BSA (fraction V)) at 4°C, then incubated with sonicated DNA chromatin samples overnight in the cold room at 4°C. The beads containing immuno-bound chromatin were collected by placing the microfuge tube on a magnet rack. The beads were extensively washed with LiCl washing buffer (100 mM Tris pH 7.5/500 mM LiCl/1% NP-40/1% sodium deoxycholate) 5 times and TE buffer (10 mM Tris-HCl pH 7.5 and 0.1 mM Na2EDTA) once. Bound chromatin was eluted by IP elution buffer (1% SDS and 0.1 M NaHCO3) and reverse-crosslinked at 65°C overnight. DNAs were purified using Mini-Elute PCR Purification Kit (Qiagen, Valencia, CA) after treatment with RNase A and proteinase K. ChIP enrichment DNAs were submitted for library preparation and sequencing.
5-10 ng of DNA was using to prepare libraries by the NEBNext ChIP-Seq Library Prep Reagent Set for Illumina with NEBNext Q5 Hot Start HiFi PCR Master Mix according to the manufacturer’s instructions (New England Biolabs). Completed ChIP-seq libraries were analyzed for insert size distribution on a 2100 BioAnalyzer High Sensitivity kit (Agilent) or Caliper LabChip GX DNA High Sensitivity Reagent Kit (Perkin Elmer). All libraries were quantified using the Quant-iT PicoGreen dsDNA assay (Life Technologies), Kapa Library Quantification kit (Kapa Biosystems).

treatment_protocol: RH30 cells were treated with QC6352 200nM for 48h.

tag: cell line

value: QC6352 200nM treatment

value: H3K9Me3 (Abcam,ab8898 )


title: Kdn-4

source_name: kidney

value: kidney

tag: breed

value: aged


title: C113 dorsal hippocampus (dHP)

value: Sprague Dawley

value: Postnatal day (PN) 80


title: GFP-2

value: Skeletal muscle

value: AAV-GFP


title: C112 dorsal hippocampus (dHP)

value: Brain

value: hippocampus


title: Kdn-3

value: Shuangyang

tag: developmental stage

value: adult

value: male


title: GFP-1


title: Kdn-2

value: adolescence


title: ChIP-seq_RH30-QC6352-Abcam.H3K9me3-01

tag: chip antibody


title: TAC+NT rep4

city: Iowa City

first: Long-Sheng

last: Song

state: IA

address: 285 Newton Rd

department: Internal Medicine

institute: University of Iowa

description:
Pressure overload, JP2NT virus
NT-TAC4

data_processing:
Raw files were uploaded into Illumina's BaseSpace hub (basespace.illumina.com) and quality assessed with the FastQC Version 1.0.0 App.
Sequences were trimmed to 125bp by cutting 10bp from the 5'-end and 16bp from the 3'end using the FASTQ Toolkit Version 2.2.0 App.
Trimmed fisrt strand sequences were aligned to mus musculus mm10 genome using the RNA-Seq Alignment App (v2.0.2) that includes STAR 2.6.1a  and Salmon Quantification 0.11.2.
The BaseSpace RNA-Seq Differential Expression App (v1.0.1) was used for determine pairwise differential gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: comma separated file containing sequence reads counts

source_name: Ventricular Tissue

extract_protocol:
Ventricles were removed, rinsed in cold saline and flash frozen in liquid nitrogen. Total RNA was harvested using an RNeasy Plus mini kit (QIAGEN).
polyA RNA was enriched and stranded libraries were prepared for sequencing using Illumina's TruSeq Stranded mRNA sample preparation kit
Paired-end libraries were sequenced on an Illumina NovaSeq 6000 sequencer using a single lane and SP Flow cell for 200 cycles.

treatment_protocol: Male mice (9-10-weeks-old) underwent sham or TAC surgery. Two weeks later, mice were injected via tail vein with AAV2/9 viruses expressing GFP or JP2NT. Heart tissue was isolated six weeks later (8 weeks after surgery).

value: cardiac

tag: surgery

value: transaortic constriction (TAC)


title: ChIP-seq_RH30-Ctrl-Abcam.H3K9me3-02

value: DMSO 0.1% treatment


title: Kdn-1

value: juvenile


title: C110 dorsal hippocampus (dHP)

value: Acesulfame potassium (ACE-K)

value: Female


title: ChIP-seq_RH30-Ctrl-Abcam.H3K9me3-01

value: H3K9Me3 (Abcam,ab8898 )


title: TAC+NT rep3

description:
Pressure overload, JP2NT virus
NT-TAC3


title: ChIP-seq_RH30-QC6352-Millipore.H3K9me3-02

value: QC6352 200nM treatment

value: H3K9Me3 (Millipore, 07-442)


title: C108 dorsal hippocampus (dHP)

value: Sprague Dawley

value: Postnatal day (PN) 80


title: C109 dorsal hippocampus (dHP)

value: Brain

value: CTL (water)


title: GFP-3

value: Skeletal muscle

value: AAV-GFP


title: TAC+NT rep1

description:
Pressure overload, JP2NT virus
NT-TAC1


title: TAC+NT rep2

description:
Pressure overload, JP2NT virus
NT-TAC2


title: Hrt-2

source_name: heart

value: Shuangyang

value: heart

value: male


title: Sham+NT rep3

description:
Control operated, JP2NT virus
NT-Sham3

value: cardiac

value: sham


title: ChIP-seq_RH30-Ctrl-Millipore.H3K9me3-02

value: DMSO 0.1% treatment


title: Hrt-3

value: adult


title: Sham+NT rep2

description:
Control operated, JP2NT virus
NT-Sham2


title: Hrt-1

value: juvenile


title: ChIP-seq_RH30-Ctrl-Millipore.H3K9me3-01


title: C107 dorsal hippocampus (dHP)

value: hippocampus

value: Female


title: C105 dorsal hippocampus (dHP)

value: Male


title: Brn-3

source_name: brain

value: brain


title: Brn-4

value: aged


title: Sham+NT rep1

description:
Control operated, JP2NT virus
NT-Sham1


title: C111 dorsal hippocampus (dHP)

value: Brain

value: Sprague Dawley

value: Postnatal day (PN) 80


title: ChIP-seq_RH30-QC6352-Millipore.H3K9me3-01

value: QC6352 200nM treatment

value: H3K9Me3 (Millipore, 07-442)


title: Hrt-4

value: Shuangyang

value: heart


title: C104 dorsal hippocampus (dHP)

value: Acesulfame potassium (ACE-K)


title: Brn-2

value: adolescence

value: male


title: ChIP-seq_RH30-Ctrl-INPUT-04

value: DMSO 0.1% treatment


title: Brn-1

value: juvenile


title: C103 dorsal hippocampus (dHP)

value: hippocampus

value: CTL (water)


title: TAC+GFP  rep2

description:
Pressure overload, control virus
GFP-TAC2

value: cardiac

value: transaortic constriction (TAC)


title: C102 dorsal hippocampus (dHP)

value: Male


title: ChIP-seq_RH30-QC6352-H3K36me3-02


title: C106 dorsal hippocampus (dHP)

value: Brain


title: Atl-4

source_name: antler

value: aged

value: antler


title: C101 dorsal hippocampus (dHP)

value: Sprague Dawley

value: Postnatal day (PN) 80


title: TAC+GFP rep1

description:
Pressure overload, control virus
GFP-TAC1


title: Atl-3

value: Shuangyang

value: adult


title: ChIP-seq_RH30-QC6352-INPUT-04

value: QC6352 200nM treatment


title: Sham+GFP rep3

description:
Control operated, control virus
GFP-Sham3

value: sham


title: ChIP-seq_RH30-QC6352-INPUT-03


title: TAC+GFP rep4

description:
Pressure overload, control virus
GFP-TAC4


title: C100 dorsal hippocampus (dHP)

value: Acesulfame potassium (ACE-K)


title: ChIP-seq_RH30-QC6352-H3K36me3-01


title: Atl-1

value: male


title: Atl-2

value: adolescence


title: Sham+GFP rep2

description:
Control operated, control virus
GFP-Sham2


title: C98 dorsal hippocampus (dHP)

value: hippocampus


title: C99 dorsal hippocampus (dHP)

value: CTL (water)


title: TAC+GFP  rep3

description:
Pressure overload, control virus
GFP-TAC3

value: cardiac


title: ChIP-seq_RH30-Ctrl-H3K36me3-02

value: DMSO 0.1% treatment


title: Adr-4

source_name: adrenal

value: adrenal


title: Sham+GFP rep1

description:
Control operated, control virus
GFP-Sham1


title: ChIP-seq_RH30-Ctrl-H3K36me3-01


title: ChIP-seq_RH30-QC6352-H3K27Ac-02

value: H3K27Ac (Abcam, ab4729)


title: ChIP-seq_RH30-Ctrl-INPUT-03


title: Day4_B_VC_rep3_RNA

data_processing:
STAR (v 2.7.0)
limma (v3.12)
Genome_build: GRCm38
Supplementary_files_format_and_content: Counts

extract_protocol:
RNA was isolated using Qiagen RNeasy kit. The quality of RNA was assayed using TapeStation (Agilent) to ensure all samples are of high quality (RIN > 9.5)
Libraries were constructed using NEBNext Ultra II Directional RNA Library Prep Kit according to the manufacturer’s protocol and barcoded using the NEBNext Multiplex (unique dual index) Oligos

value: B cell


title: Adr-2


title: Adr-3


title: Day4_B_VC_rep2_RNA


title: C95 dorsal hippocampus (dHP)

value: Brain

value: Male


title: C94 dorsal hippocampus (dHP)

value: Sprague Dawley

value: Postnatal day (PN) 80


title: ChIP-seq_RH30-Ctrl-H3K27Ac-02


title: ChIP-seq_RH30-QC6352-H3K27Ac-01


title: C96 dorsal hippocampus (dHP)


title: Adr-1

value: Shuangyang

value: juvenile


title: Day4_B_mock_rep3_RNA


title: C93 dorsal hippocampus (dHP)


title: ChIP-seq_RH30-Ctrl-H3K27Ac-01


title: DKO B cells, VC 4 days, bio rep 2 [E_DKO_VC]

data_processing:
Guppy (v6.1.2)
Porechop (v0.2.4)
Nanofilt (v2.8.0)
nanoEM
minimap2 (v2.24)
samtools (v1.15.1)
Assembly: mm10
Supplementary files format and content: TSV (initial methylation call data)
Supplementary files format and content: BedGraph

extract_protocol:
DNA was isolated with Qiagen Blood and Tissue kit.
Purified genomic DNA was bisulfite converted and used as template for PCR. PCR products were pooled and barcoded using  the EXP-NBD104 kit from Oxford Nanopore, followed by ligation of adapters from the SQK-LSK-110 kit.
Bisulfite treatment followed by Nanopore sequencing with barcodes

value: Spleen

value: B cells

value: Tet2/3 DKO

value: VC


title: Day4_B_mock_rep2_RNA


title: Day4_B_mock_rep1_RNA


title: DKO B cells, mock 4 days, bio rep 2 [E_DKO_Mock]

value: Untreated


title: C92 dorsal hippocampus (dHP)

value: hippocampus

value: Acesulfame potassium (ACE-K)


title: C97 dorsal hippocampus (dHP)

value: CTL (water)


title: DKO B cells, VC 4 days, bio rep 1 [D_DKO_VC]


title: ChIP-seq_RH30-QC6352-H3K4me1-02

value: QC6352 200nM treatment

value: H3K4me1 (Abcam, ab8895)


title: Naive_B_rep3_RNA

value: B cell

value: Unstimulated


title: ChIP-seq_RH30-Ctrl-H3K4me1-02

value: DMSO 0.1% treatment


title: ChIP-seq_RH30-QC6352-H3K4me1-01


title: C91 dorsal hippocampus (dHP)

value: Brain

value: Sprague Dawley

value: Male


title: WT B cells, VC 4 days, bio rep 3 [C_WT_VC_CT]

value: Tet2/3 WT


title: DKO B cells, mock 4 days, bio rep 1 [D_DKO_Mock]

value: Spleen


title: Naive_B_rep2_RNA


title: ChIP-seq_RH30-QC6352-INPUT-01


title: Naive_B_rep1_RNA


title: ChIP-seq_RH30-Ctrl-INPUT-02


title: WT B cells, VC 4 days, bio rep 2 [B_WT_VC]

value: B cells


title: Day4_B_VC_rep1_5hmC

data_processing:
Library strategy: 5hmC
Bowtie2 (v2.4.2)
Samtools (v1.10)
Deeptools (v3.5.1)
HOMER (v4.8)
DiffBind (v2.0.2)
Genome_build: mm10
Supplementary_files_format_and_content: Txt (peaks), Bigwig

extract_protocol:
DNA was isolated with Qiagen Blood and Tissue kit.
DNA was quantified with Qubit (ThermoFisher) and sonicated to around 150-200bp using Bioruptor Pico (Diagenode). 5hmC enrichment analysis was performed using the HMCP kit (Cambridge Epigenetix) based on the addition of azido-glucose to 5hmC by T4-beta-glucosyltransferase following the manufacturer’s instruction.

tag: sample type


title: Day4_B_VC_rep2_5hmC


title: Day4_B_mock_rep2_5hmC


title: ChIP-seq_RH30-Ctrl-INPUT-01


title: WT B cells, mock 4 days, bio rep 2 [B_WT_mock]


title: ChIP-seq_RH30-Ctrl-H3K4me1-01


title: WT B cells, VC 4 days, bio rep 1 [A_WT_VC]


title: Cut_and_Run_RH30-QC6352-Pax3Foxo1-003

data_processing:
Library strategy: CUT&RUN
ChIP-seq raw reads were first trimmed low-quality ends using trim-galore (0.4.4; default parameter) and then aligned to the human reference genomes (hg19) using BWA (version 0.7.12; default parameter) and duplicated reads were then marked with Picard (version 1.65), with only nonduplicated reads kept by samtools (version 1.3.1, parameter ‘‘-q 1 -F 1024’’. For data quality control and to estimate the fragment size, the nonduplicated version of SPP (version 1.11) was used to calculate the relative strand correlation value with support of R (version 3.5.1). To visualize ChIP-seq data on the integrated genome viewer (IGV) (version 2.3.82), we utilized genomeCoverageBed (bedtools 2.25.0) to obtain genome-wide coverage in BEDGRAPH file format and then converted it to bigwig file format by bedGraphToBigWig. The bigwig files were scaled to 15 million reads to allow comparison across samples.
MACS2 (version 2.1.1 20160309) was used to call narrow peaks  using macs2 callpeak -f BEDPE --keep dup all -p 0.05 with IP library file  and IGG file.
genomeCoverageBed (bedtools 2.25.0) was used to produce genome-wide coverage in BEDGRAPH file and then converted it to bigwig file by bedGraphToBigWig. The bigwig files were scaled to 15 million reads to allow comparison across samples.
Genome_build: hg19(GRCh37)
Supplementary_files_format_and_content: bigwig

extract_protocol:
The CUT&RUN library DNAs of Rh30 with and without QC6352 200 nM treatments were prepared by following the protocol as described previously papper with minor modifications. Briefly, 200,000 Rh30 cells treated with and without QC6352 treatment were washed 3 times with CUT&RUN washing buffer (20 mM HEPES at pH 7.5, 150 mM NaCl, 0.5 mM spermidine (S2501-5G, Sigma-Aldrich), 1× protease inhibitor cocktails (11836170001, Roche) and then transferred to a 1.5-ml tube containing 50 µL of washing buffer. Cells were then collected with concanavalin A-coated beads (BP531, Bangs laboratories) and incubated with antibodies (1:100), normal rabbit IgG (CS200581, Millipore),  rabbit anti-KDM4B (A301-478A, Bethyl Laboratories) and mouse anti-PAX3-FOXO1 (a gift from Dr. Taosheng Chen) overnight at 4 °C in the antibody incubation buffer (20 mM HEPES at pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1× protease inhibitor cocktails, 2 mM EDTA and 0.02% digitonin). The samples with mouse anti-PAX3-FOXO1 antibody were washed 3 times with washing buffer and incubated with rabbit anti-mouse secondary antibody (ab6709, Abcam) overnight at 4 °C. After unbound antibodies were washed away, 140 μg/ml protein A-MNase (pA-MN; a gift from Dr. Steven Henikoff) was added at a 1:280 ratio and incubated for 1 hr at 4 °C. After washing, 3 μl of 100 mM CaCl2 was added to activate pA-MN for 30 min at 4 °C and then stopped by adding same volume of 2× STOP buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% digitonin, 100 µg/ml RNase A and 50 µg/ml glycogen). The protein–DNA complexes were released by 10-min incubation at 37°C followed by centrifugation at 16,000 g for 5 min at 4 °C. After transferring the supernatant to a new 1.5 ml Eppendorf tube, 2 μl of 10% (wt/vol) SDS and 1.5 μl of proteinase K (20 mg/ml) were added and incubated for 1 hr at 50 °C. DNA was then precipitated by phenol/chloroform/isoamylalcohol followed by ethanol precipitation with glycogen and then dissolved in water.
Sequencing libraries were prepared using an Accel-NGS 1S plus DNA library preparation kit (10096, Swift Biosciences) and Accel-NGS 1S plus combinatorial Dual Indexing Kit (18096, Swift Biosciences) for Illumina platforms according to the manufacturer's instructions. The PCR products were cleaned up with SPRIselect beads and quantified using Qubit dsDNA HS assay kit (Q32854, Thermo fisher).


title: ChIP-seq_RH30-QC6352-INPUT-02


title: Day4_B_mock_rep1_5hmC


title: Cut_and_Run_RH30-QC6352-Pax3Foxo1-001


title: Cut_and_Run_RH30-QC6352-Pax3Foxo1-002


title: RPMI8226 cells, GST, 6 h, rep3

city: Madison

first: Hae Yeun

last: Chang

state: WI

address: 1111 Highland ave., WIMR II

institute: UW-Madison

data_processing:
The fastQC program is used to verify raw data quality of the Illumina reads.
The raw sequence reads were mapped to the genome using Subjunc aligner from Subread
The alignment bam files were compared against the gene annotation GTF file, and raw counts for each gene were generated using the featureCounts tool from Subread
The raw counts data were normalized using voom method from the R Limma package, then used for differential expression analysis.
Assembly: hg19 human genome and Ensembl gene annotations (v75)
Supplementary files format and content: txt file including gene counts for all 6 samples

growth_protocol: RPMI8226 were cultured at 37°C/5% CO2 in RPMI1640 containing 10% FBS, 2% glutamax (Gibco) + 1% penicillin/streptomycin.

extract_protocol:
RNA was harvested using Trizol (Thermo-Fisher). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq strand specific mRNA sample preparation system (Illumina) following manufacturer's protocols.

treatment_protocol: RPMI8226 cells were treated with GST-PTR1 or GST control for 6 hours in 3 biological replicates.

value: Multiple myeloma

value: WT

value: GST 100 nM, 6 h


title: RPMI8226 cells, GST-PTR1, 6 h, rep3

value: GST-PTR1 100 nM, 6 h


title: RPMI8226 cells, GST-PTR1, 6 h, rep2


title: RPMI8226 cells, GST-PTR1, 6 h, rep1


title: WT B cells, mock 4 days, bio rep 3 [C_WT_Mock]

value: Untreated


title: DR3261

city: Ningbo

first: Peng

last: Shu

state: Zhejiang

address: No1288 of Lushan East Street,Beilun District

department: Molecular laboratory

institute: Bielun People's Hospital,Ningbo

data_processing:
The rRNA   sequences were removed and the effective reads were mapped with the reference genome.
After obtaining transcriptome assembly, lncRNAs expression were detected
Difference analysis was performed by using R version 3.6.1 (http://www.r-project.org/).
A heat map and volcano map wereused to show differences in exosomal lncRNA expression between groups, which enrich in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: venous blood

growth_protocol: 5 patients were randomly selected from each group, and exosome was extracted from 2-mL plasma sample using ExoQuick exosome precipitation solution (EXOQ5A-1, SBI, USA).

extract_protocol:
Total RNA was extracted from plasma exosomes using QIAGEN miRNeasy Micr Kit (217084,  QIAGEN, Germany).
RNA-Seq libraries were constructed using KAPA RNA HyperPrep Kit Illumina®  (Illumina, USA) and sequenced using HiSeq X10 PE150 mode (Illumina, USA).

value: venous blood

value: plasma

tag: age

tag: disease state

value: T2DM and DR


title: DR3263


title: Day4_B_VC_rep2_Input

tag: strain

value: B cell

value: Input


title: Cut_and_Run_RH30-Ctrl-Pax3Foxo1-003

value: DMSO 0.1% treatment


title: RPMI8226 cells, GST, 6 h, rep1

tag: cell type


title: Day4_B_VC_rep1_Input

tag: treatment


title: DR3169

tag: tissue


title: Cut_and_Run_RH30-Ctrl-Pax3Foxo1-002


title: DR3118

value: Female


title: Cut_and_Run_RH30-Ctrl-Pax3Foxo1-001


title: Naive_B_rep2_5hmC

value: Unstimulated


title: Cut_and_Run_RH30-QC6352-KDM4B-003

value: QC6352 200nM treatment


title: Day4_B_mock_rep2_Input


title: WT B cells, mock 4 days, bio rep 1 [A_WT_mock]

value: Tet2/3 WT


title: Naive_B_rep1_5hmC


title: siOASL-T/I-HUVEC rep2 (miRNA-seq)

data_processing:
The sequence reads were counted by miRDeep2 and miRNA showing <10 read counts total were pre-filtered.
DESeq2 was used to obtain normalized count and identify differentially expressed miRNA in siCTL or siOASL transfected HUVECs (TNFα/IFNγ).
For performing downstream analysis such as drawing heatmap, the count data was rlog-transformed using DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: miRNA_normalized_count.txt.gz, miRNA_transformed_count.txt.gz

growth_protocol: HUVECs obtained from the American Type Culture Collection (Manassas, VA). HUVECs were cultured in EGM-2 BulletKit (Lonza, CC-3162) medium containing 10% FBS, 2mM L-glutamine, and penicillin (10,000 Units/mL)/streptomycin (10,000 ug/mL) and used at passage 7-10 for experiments. Cells were routinely maintained in a humidified chamber at 37℃ and 5% CO2.

extract_protocol:
HUVECs were stimulated  for 3hours and total RNA was manually extracted using Trizol reagent. TruSeq Stranded Small RNA Library Prep Kit was used for the construction of small RNA sequencing libraries.
RNA libraries were prepared by TruSeq Small RNA Library Prep kit for sequencing using standard Illumina protocols.

treatment_protocol: Two replicates of siRNA-transfected HUVECs per group were treated with TNFα and IFNγ added in the serum-free EGM-2 for 3hours.

value: Human umbilical vein endothelial cell (HUVEC)

value: TNFalpha and IFNgamma for 3 hrs

value: OASL knockdown


title: DR3111


title: siOASL-T/I-HUVEC rep1 (miRNA-seq)


title: Cut_and_Run_RH30-QC6352KDM4B-002


title: DR3098

value: Male


title: Day4_B_mock_rep1_Input


title: DR3028


title: siCTL-T/I-HUVEC rep2 (miRNA-seq)

value: Control


title: DR3044


title: Naive_B_rep2_Input


title: siCTL-T/I-HUVEC rep1 (miRNA-seq)


title: Cut_and_Run_RH30-QC6352-KDM4B-001


title: Ahr HKO+EtOH, liver 3

first: Sang Geon

last: Kim

state: Seoul

address: San56-1, Sillim-dong, Kwanak-gu

department: College of Pharmacy

institute: Seoul National University

description:
Expression_Profile.mm10.gene.txt
ALKO-EtOH-L15

data_processing:
FastQC v0.11.7 used for base-calling and quality check
Trimmomatic 0.38 performs trimming and alignment with various parameters for illumina paired-end or single-end.
HISAT2 version 2.1.0, Bowtie2 2.3.4.1 is a tool that quickly and accurately maps high throughput sequencing data to the reference genome.
StringTie version1.3.4d is a tool that assembles sequencing information mapped to a reference to quickly and accurately generate potential transcripts.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include Read_Count, FPKM (normalized value), and TPM (normalized value) values for each samples

extract_protocol:
Liver were removed and total RNA concentration was calculated by Quant-IT RiboGreen (Thermo Fisher Scientific, R11490). To assess the integrity of the total RNA, samples were run on the Tape Station RNA screen tape (Agilent Technologies, 5067-5576). TruSeq Stranded mRNA LT Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

value: Ahr HKO

value: EtOH


title: KD1340, replicate 3, scRNAseq

city: Kaohsiung

first: Kuang-Den

last: Chen

address: 123, Ta-Pei Rd., Niao-Sung Dist.

department: Translational Research Center in Biomedical Sicences

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: peripheral blood

extract_protocol:
RNA samples of mononuclear/polymorphnuclear cells are harvested by Tri-zol (Invritrogen, Inc. Faraday Avenue, Carlsbad, CA). (500 μl Tri-zol/600 μl cell lyses buffer for each 1 × 105 cell)
Single-cell RNA-Seq libraries were prepared using GemCode Single-Cell 3’ Gel Bead and Library Kit (now sold as P/N 120262, 1000009, 120267, 10x Genomics). GEM-RT was performed in a Veriti 96-Well Thermal Cycler 2020/7/29 Version1 (Applied Biosystems; Model#: 9902)at 53 °C for 45 min, 85 °C for 5 min, and held at 4 °C.

value: WBC

value: peripheral blood

value: Kawasaki disease


title: Cut_and_Run_RH30-Ctrl-KDM4B-003


title: Cut_and_Run_RH30-Ctrl-KDM4B-002


title: DR3019

value: venous blood

value: plasma


title: Ahr HKO+EtOH, liver 2

description:
Expression_Profile.mm10.gene.txt
ALKO-EtOH-L07


title: DR2015

value: Female


title: Ahr HKO+EtOH, liver 1

description:
Expression_Profile.mm10.gene.txt
ALKO-EtOH-L04


title: scPACS

city: Boston

first: Zhaorong

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

data_processing:
The I1 fastq file includes the cell barcodes and R1/R2 include the UMI and cDNA sequences. The sample is aligned to GRCm38 transcriptome and quantified using Kallisto and Bustools.
Assembly: GRCm38
Supplementary files format and content: RDS file which includes the Seurat object of the single cell RNA-Seq analysis results, along with the raw counts and normalized counts. In order to read in the data, use readRDS('Dataset.rds') command in R.

source_name: scPACS

extract_protocol:
Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, and washed in PBS.
SMART-seq3

treatment_protocol: Induction of EAE in mice. EAE was induced by injecting 150 µg of MOG35-55 diluted in 100 µL of PBS emulsified in 100 µL of CFA per mouse.

value: WT C57Bl/6


title: Ahr HKO+con, liver 1

description:
Expression_Profile.mm10.gene.txt
ALKO-con-L02

value: con


title: Ahr HKO+con, liver 2

description:
Expression_Profile.mm10.gene.txt
ALKO-con-L06


title: Ahr HKO+con, liver 3

description:
Expression_Profile.mm10.gene.txt
ALKO-con-L07


title: Cut_and_Run_RH30-QC6352-IGG-003

value: QC6352 200nM treatment

value: IgG


title: Cut_and_Run_RH30-QC6352-IGG-001


title: Cut_and_Run_RH30-QC6352-IGG-002


title: WT+EtOH, liver 2

description:
Expression_Profile.mm10.gene.txt
WT-EtOH-L05

value: WT


title: Cut_and_Run_RH30-Ctrl-IGG-003

value: DMSO 0.1% treatment


title: Cut_and_Run_RH30-Ctrl-IGG-002


title: ATAC-seq_Sp7+_osteoblasts_rep2

city: Bunkyo-ku

first: Hironori

last: Hojo

state: Tokyo

address: 7-3-1 Hongo

department: Center for Disease Biology and Integrative Medicine

country: Japan

institute: The University of Tokyo

data_processing:
DNA-sequence information was aligned to the unmasked mouse genome by bowtie
Peak calling was performed by two-sample analysis on CisGenome software (Ji et al., 2008) with a P-value cutoff of 10-5 comparing with the negative control
In the analysis with ATAC_Col2, ATAC_Col10 and ATAC_Sp7 data sets, to identify the cell-type specific and shared regions, we selected ATAC-seq peaks with the ATAC-seq normalized peak intensity based on the following criteria: raw fe > 30, fold change > 5, and p-value < 0.05, for cell-type specific regions. The differential accessible regions were called as below. C2: C2-Cho-distinct peaks; C10: C10-Cho-distinct peaks; S7: S7-Ob-distinct peaks; C2C10: peaks with high intensity in both C2-Cho and C10-Cho but not in S7-Ob; C10S7: peaks with high intensity in both C10-Cho and S7-Ob but not in C2-Cho; C2S7: peaks with high intensity in both C2-Cho and S7-Ob but not in C10-Cho. These peaks were listed in "ATAC_C2_C10_Sp7_peaks.xlsx”
In the analysis with ATAC_POB_Runx2_cHetKO and ATAC_POB_Runx2_cHomKO data sets, to identify the differential binding regions between the genotypes, DiffBind was applied with the following parameters "summits = 150" in the step of "dba.count" to resize peaks. To obtain statistically different chromatin-accessible regions, we selected the peaks based on FDR < 0.05. The differential accessible regions were listed in “ATAC_Runx2KO_peaks. xlsx”
In the analysis with ATAC_3T3cells data sets, to identify Runx2-responsive and osteoblast induction-responsive regions, DiffBind was applied with the following parameters "summits = 250" in the step of "dba.count" to resize peaks. Pairwise comparison was performed among ATAC-seq profiles of day 0 GFP expression samples, day 0 Runx2 expression samples, day 3 GFP expression samples, day 3 Runx2 expression samples, and no expression samples (None). The Runx2-responsive and the osteoblast induction-responsive regions were selected as ATAC-seq peaks whose intensity was statistically upregulated by both Runx2 expression and osteogenic induction on day 3, based on the following criteria: FDR < 0.05, fold change > 4. The Runx2-responsive regions were listed in “ATAC_3T3_Runx2_responsive_regions.xlsx”.
Genome_build: mm9
Supplementary_files_format_and_content: peak files

source_name: P1 calvaria osteoblasts

extract_protocol:
Rib chondrocytes were manually dissected from the neonatal mouse ribs. The ribs were initially digested in 2 mg/mL Pronase (53702, EMD Millipore Corporation) for 30 min at 37 °C, washed three times with phosphate buffered saline (PBS), and then digested in 0.2% collagenase D (1088858, Roche Applied Science) for 3 h at 37 °C. Calvarial osteoblasts were manually dissected from osteoblast-enriched partial calvarias consisting of the frontal bone and a rostral part of the parietal bone. The partial calvarias were digested in five changes of 0.1% collagenase D and 0.2% dispase for 10 min each at 37 °C.   Cultured 3T3 cells were digested in trypsin-EDTA solution 1X (Wako, 206-17291) for 5 to 15 min at  37 °C.
ChIP-seq libraries were constructed using a ThruPLEX®-FD Prep Kit (R40012, Rubicon Genomics) according to the manufacturer′s instructions. ATAC-seq libraries were constructed as previously described (Buenrostro et al., 2013).

treatment_protocol: For in vitro cell culture, osteogenic medium contains 10% FBS/DMEM supplemented with 50 μg/ml ascorbic acid phosphate, 10 mM β-glycerophosphate, and 100 ng/ml rhBMP‑2

value: Sp7-EGFP-positive calvarial osteoblasts at P1

value: Sp7-EGFP tg


title: RPMI8226 cells, GST, 6 h, rep2

value: Multiple myeloma

value: GST 100 nM, 6 h


title: Naive_B_rep1_Input

source_name: Spleen

value: B cell

value: Unstimulated

value: Input


title: Cut_and_Run_RH30-Ctrl-IGG-001


title: ATAC-seq_Sp7+_osteoblasts_rep1


title: ATAC-seq_Col10+_chondrocytes_rep3

source_name: P1 rib chondrocytes

value: Col10a1-mCherry-positive rib hypertrophic chondrocytes at P1

value: ICR

value: Col10a1-mCherry tg


title: WT+EtOH, liver 1

description:
Expression_Profile.mm10.gene.txt
WT-EtOH-L04

source_name: liver

value: liver

value: EtOH


title: ATAC-RH30-shKDM4B-814-2

data_processing:
The ATAC-seq raw reads were aligned to the human reference genome (hg19) using BWA (version 0.7.12-r1039) to and then marked duplicated reads with Picard (version 1.65), with only high-quality reads kept by samtools (version 1.3.1, parameter ‘‘-q 1 -F 1024’’). Reads mapping to mitochondrial DNA were excluded from the analysis. All mapped reads were offset by +4 bp for the + strand and -5 bp for the  – strand
Subsample 150 million of reads per sample from Bam file with Samtools for peak calling. Peaks were called for each sample using MACS2 (version 2.1.1 20160309)   with parameters “-q 0.01 --nomodel --extsize 200 –shift 100 ".
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak

growth_protocol: LHCN cells were cultured in medium with four parts Dulbecco's modified Eagle's medium to one part medium 199 supplemented with 15% fetal bovine serum, 0.02 M HEPES, Basic FGF 10 ng/ml , 2.5ng/ml HGF, 0.055 µg/ml dexamethasone , 0.03 µg/mlzinc sulphate (ZnSO4)  and 1.4 µg/mlvitamin B12 , 60 U/ml penicillin/streptomycin on dishes coated with 0.1% porcine skin gelatin. RH30 cells were cultured with RPMI 1640 media supplemented with 100 U/mlpenicillin/streptomycin and 10% fetal bovine serum.All cells were maintained at 37 °C in an atmosphere of 5% CO2.

extract_protocol:
Fresh cultured LHCN or RH30 cells (100,000 per sample) with or without various treatments were harvested and washed with 150ml cold Dulbecco's Phosphate-Buffered Saline (DPBS) containing protease inhibitor (PI). Nuclei were collected by centrifuging at 500g for 10 minutes at 4°C after cell pellets were resuspended in lysis buffer (10 mM Tris-Cl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 containing 0.1% NP-40 and PI. Nuclei were incubated with Tn5 transposon enzyme in transposase reaction mix buffer (Illumina) for 30 min at 37°C. DNAs were purified from transposition sample by using Min-Elute PCR purification kit (Qiagen, Valencia, CA) and measured by Qubit.
Polymerase chain reaction (PCR) was performed to amplify with High-Fidelity 2X PCR Master Mix [72°C/5mins+ 98 °C /30 s +12 × (98 °C /10 s + 63 °C /30 s + 72 °C /60 s) + 72 °C /5 min]. The libraries were purified using Min-Elute PCR purification kit (Qiagen, Valencia, CA). ATAC-seq libraries followed by pair-end sequencing on HiSeq4000 (Illumina) in the Hartwell Center at St Jude Children's Research Hospital.

treatment_protocol: LHCN cells were overexpressed PAX3-FOXO1 or empty vector for 72 hours. RH30 cells were treated with QC6352 200nm or 0.1% DMSO or transduced with shRNA control or KDM4B for 72 hours.

value: RH30 transduced with shKDM4B-814


title: WT+con, liver 3

description:
Expression_Profile.mm10.gene.txt
WT-con-L07

value: con


title: ATAC-RH30-shKDM4B-814-1


title: WT+con, liver 2

description:
Expression_Profile.mm10.gene.txt
WT-con-L06


title: Cut_and_Run_RH30-Ctrl-KDM4B-001


title: ATAC-seq_Col10+_chondrocytes_rep2


title: WT+con, liver 1

description:
Expression_Profile.mm10.gene.txt
WT-con-L03


title: ATAC-RH30-shKDM4B-813-2

value: RH30 transduced with shKDM4B-813


title: ATAC-RH30-shKDM4B-813-1


title: ATAC-seq_Col10+_chondrocytes_rep1


title: P2ry14WT-Eos-5

city: Research Triangle Park

first: Donald

middle: Nelson

last: Cook

state: NC

address: 111 T.W. Alexander Drive

department: IIDL

institute: NIEHS

data_processing:
Raw reads were filtered to retain only those with average base quality score >20.
Reads were aligned to mm10 via STAR v2.5 (parameters: --alignSJoverhangMin 8 --limitBAMsortRAM 55000000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical).
Read counts per gene were determined by Subread featureCounts v1.5.0-p1 (parameters: -s0).
Coverage tracks were generated by STAR v2.5 (parameters: --outWigStrand Unstranded --outWigNorm None), normalized by DESeq2 size factors, then converted to bigWig format via UCSC utility bedGraphToBigWig.
Genome_build: mm10
Supplementary_files_format_and_content: normalized depth tracks in bigWig format; RNAseq counts per gene in tab-delimited text format

source_name: WT_lung eosinophils

extract_protocol:
RNA was isolated using TRizol Plus reagent, followed by DNase treatment and additional cleanup step using PureLink RNA Mini kit (Thermo Fisher Scientific) according to the manufacturer's instructions.
Libraries were constructed via Illumina TruSeq RNA sample prep kit.

treatment_protocol: Mice were sensitized twice, week apart, by oropharyngeal instillation of 50 µg OVA and 20 μg protease from Aspergillus oryzae. Seven days after the second sensitization, mice were challenged by exposing them to an aerosol of 1% OVA and lung eosinophils were purified using FACS sorting 16 h later.

value: male

value: FACS-purified lung eosinophils

tag: treatment condition

value: OVA/Aspergillus asthma model, 16 hrs after OVA challenge


title: WT+EtOH, liver 3

description:
Expression_Profile.mm10.gene.txt
WT-EtOH-L07

value: WT


title: RNA-seq_Col10+_chondrocytes_rep3

data_processing:
Trimmed the sequences by Trimomatic-0.33
Aligned the sequence to the mouse genome reference sequence mm9 byby Tophat-2.1.0
Quantification of gene expression and differentially expressed gene analysis were performed using Cufflinks/Cuffdiff 2.2.1
The data from Cufflinks/Cuffdiff 2.2.1 were output as fragments per kilobase of transcript per million mapped reads (FPKM) values
For comparison analysis among Col2a1-ECFP chondrocytes, Col10a1-mCherry chondrocytes with calvaria osteoblasts sorted from Sp7-GFP mice at P1, public data set for RNA-seq data of Sp7-GFP osteoblast (GSM1976262, GSM1976263, GSM1976264) was used for Cufflinks/Cuffdiff analysis
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values

extract_protocol:
Rib chondrocytes were manually dissected from the neonatal mouse ribs. The ribs were initially digested in 2 mg/mL Pronase (53702, EMD Millipore Corporation) for 30 min at 37 °C, washed three times with phosphate buffered saline (PBS), and then digested in 0.2% collagenase D (1088858, Roche Applied Science) for 3 h at 37 °C. Calvarial osteoblasts were manually dissected from osteoblast-enriched partial calvarias consisting of the frontal bone and a rostral part of the parietal bone. The partial calvarias were digested in five changes of 0.1% collagenase D and 0.2% dispase for 10 min each at 37 °C.
For RNA-seq with rib chondrocytes sorted from Col2a1-ECFP and Col10a1-mCherry mice at P1, 100 ng of total RNA was subjected to analysis. RNA libraries were constructed using a Tru-Seq Illumina kit (RS-122-2001, Illumina) with some modifications. For RNA-seq for with Runx2_cHet_KO cells and Runx2_cHom_KO cells from calvaria, 1.7 ng of total RNA was subjected to the analysis. RNA libraries were constructed using a SMARTer Stranded Total RNA-Seq Kit v2 Pico Input Mammalian (634411, Takara).


title: Day4_B_VC_rep1_RNA


title: RNA-seq_Col10+_chondrocytes_rep1


title: ATAC-RH30-shCtrl-1

value: RH30 transduced with shCtrlRNA


title: ATAC-RH30-shCtrl-2


title: RNA-seq_Col10+_chondrocytes_rep2


title: P2ry14WT-Eos-3

tag: Sex


title: P2ry14WT-Eos-2


title: ATAC-RH30-QC6352-2

value: RH30 treated with 200nM QC6352


title: P2ry14WT-Eos-4


title: RNA-seq_Col2+_chondrocytes_rep3

value: Col2a1-ECFP-positive rib chondrocytes at P1

tag: genotype

value: Col2a1-ECFP tg


title: RNA-seq_Col2+_chondrocytes_rep2


title: ATAC-RH30-DMSO-2

value: RH30 treated with 0.1 % DMSO


title: RNA-seq_Col2+_chondrocytes_rep1


title: ATAC-RH30-QC6352-1


title: P2ry14WT-Eos-1


title: L1 overexpression condition replicate-3

city: New Haven

first: Takehiro

last: Takahashi

state: Connecticut

address: 300 Cedar Street TAC S630

institute: Yale University

description:
L1_sgRNA_3
NIH3T3_transient_L1OE_normalized_counts.xlxs

data_processing:
Sequenced reads were aligned using STAR (STAR/2.5.3a-foss-2016b, mm10 assembly) with parameters: --runThreadN 20 --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 35129075129 --outFilterMultimapNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.02 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 for mapping host genes.
For endogenous retroelements, ERVMAP (Tokuyama et al., 2018; Treger et al., 2019) and RepEnrich2 (Criscione et al., 2014) were used using modules, Python/2.7.13-foss-2016b, Bowtie2/2.2.9-foss-2016b, BEDTools/2.27.1-foss-2016b and SAMtools/1.9-foss-2016b using repeatmasker mm10 assembly.
Counts were counted using BEDTools (BEDTools/2.27.1-foss-2016b) (Quinlan and Hall, 2010), coverageBed function, and normalized using DESeq2 (Love et al., 2014).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: NIH3T3_L1OE_normalized_counts.xlsx: Matrix table of normalized counts for cellular genes, uniquely mappable endogenous retrovirus (ERVs), and endogenous retroelements from Repenrich.

source_name: NIH3T3 cells

extract_protocol:
Total RNA was extracted using RNeasy Kit (Qiagen).
Library was constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina (E7770).

value: Fibroblast cell line

tag: sgrna

value: targeting LINE1 promoter

tag: time point

value: 48-hour post transfection of sgRNA-encoding plasmid


title: P2ry14KO-Eos-5

source_name: P2ry14-null_lung eosinophils


title: P2ry14KO-Eos-3


title: L1 overexpression condition replicate-2

description:
L1_sgRNA_2
NIH3T3_transient_L1OE_normalized_counts.xlxs

tag: cell line


title: AR2, biol rep 2

city: Beijing

first: Baoli

last: Lin

address: No.7 Beinong Road, Shigezhuang Street

institute: College of Landscape Architecture, Beijing Agricultural College

description: AR is a healthy red leaf sample from a bud mutation branches of Acer pictum subsp. mono.(15-20 days ahead of color change) we found.

data_processing:
AP Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using AP genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using AP genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using AP genomic benchwork
Assembly: without reference genome
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Acer pictum subsp. mono

source_name: leaf cells

growth_protocol: Both wild-type branch leaves and mutant branch leaves of Acer pictum subsp. mono grow in the wild under natural conditions.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Two leaves grown in the wild in their natural state were collected and stored in an ultra-low temperature refrigerator at -80 degrees Celsius without any treatment.

value: leaf cells

value: Day 0


title: AG3, biol rep 3

description: AG is a healthy green leaf sample from a bud mutation branches of Acer pictum subsp. mono (15-20 days ahead of color change) we found.


title: AR3, biol rep 3


title: P2ry14KO-Eos-2


title: ATAC-LHCN-P3F1-OE-2

source_name: cell line

value: LHCN

value: LHCN overexpress Pax3-Foxo1


title: L1 overexpression condition replicate-1

description:
L1_sgRNA_1
NIH3T3_transient_L1OE_normalized_counts.xlxs


title: AG2, biol rep 2


title: ATAC-LHCN-Ctrl-2

value: LHCN overexpress empty vector


title: P2ry14KO-Eos-1

value: male


title: Scramble condition replicate-2

description:
Scr_sgRNA_2
NIH3T3_transient_L1OE_normalized_counts.xlxs

value: Scramble


title: ATAC-LHCN-Ctrl-1


title: AG1, biol rep 1


title: embryonic brain immune cells

status: Public on Sep 05 2022

city: Chongqing

first: jiangyong

last: he

address: Tiansheng Li Street of Beibei District

institute: southwest university

description: one sample from zebrafish brain tissue

data_processing:
The scRNA-seq data were aligned to the zebrafish reference genome (Danio rerio, GRCz11) by Cell Ranger 5.0.0. The resulting matrix was inputted into Seurat v3 for quality control, filtration, dimensionality reduction, clustering analysis and differential expressed genes analysis
Genome_build: GRCz11
Supplementary_files_format_and_content: Matrix table with gene counts for every gene and every sample

organism: Danio rerio

source_name: brain immune cells

extract_protocol:
Briefly, 4 dpf WT Tg(coro1a:DsRed) transgenic zebrafish were anesthetized with 0.02% tricaine, and 200 brains were freshly isolated in ice-cold dPBS and incubated with papain (10U/mL) at 30 ℃ for 20 min. After centrifuging with 800 rpm and a brief washing, the digested tissue were resuspended with 5% FBS (dissolved in dPBS) and passed through 1.2 um and 0.5 um glass pipette 7 times, respectively. Then, samples were filtered with a 70 um Cell Strainer to gain single cell suspension. Coro1a-DsRed+ cells were collected on a flow cytometry (Moflo XDP, Beckman) in preparation for single-cell sequencing
The 10x RNA-seq libraries were constructed using Chromium single cell gene expression platform and Chromium Single Cell 3’ Reagent Kits (v3.1 chemistry PN-1000121) according to the manufacture`s protocol

value: brain

value: 4 dpf


title: Scramble condition replicate-1

description:
Scr_sgRNA_1
NIH3T3_transient_L1OE_normalized_counts.xlxs


title: PBAT wildtype blastocyst

city: Fukuoka

first: Wan Kin

last: Au Yeung

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

department: Department of Molecular and Structural Biology

institute: Kyushu University

data_processing:
Low quality bases in the 3’ portion (Q <30) and adapter sequences were removed from raw reads by Trim-Galore! v0.3.3 and trimmed reads were mapped to mouse genome mm10 by Bismark v0.20.0 with options ‘--bowtie2 --pbat -D 75’. For allelic-specific analysis, trimmed reads were mapped to N-masked mm10 genome using published SNP data of JF1 strain. Allelic reads were selected using SNPsplit v0.3.2.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: The CpG coverage files of maternal/paternal genome are space-delimited, 1-based genomic coordinates for every covered CpG dinucleotide in the experiment and are in the following format: <chromosome> <CpG position>  <number of methylated cytosines> <number of unmethylated cytosines> <methylation level (0to1)>.

source_name: blastocyst

growth_protocol: All animal experiments were performed under the ethical guidelines of Kyushu University. All mice used in this manuscript were aged 4 weeks or older and were euthanized by CO2 asphyxiation.

extract_protocol:
Cells were lyzed by proteinase K and 2% SDS. Cell extract was directly applied to library construction.
Libraries were constructed using the post-bisulfite adapter tagging method (Miura et al., 2012; Au Yeung et al., 2019). Pooled  blastocysts were spiked with 1% unmethylated lambda phage DNA (Promega). Libraries were amplified with KAPA library amplification kit (KAPA) for 4 cycles using primers AATGATACGGCGACCACCGAGATCTACAC and CAAGCAGAAGACGGCATACGAGAT. Libraries were sequenced on HiSeq 1500 and NovaSeq 6000 (Illumina) (HiSeq: HCS v2.2.68 and RTA v1.18.66.3; NovaSeq: NVCS v1.6.0 and RTA v3.4.4) using TruSeq SBS kit v3-HS and NovaSeq S1 reagent kit v1 (Illumina) according to manufacturer’s protocols

treatment_protocol: Superovulated C57BL/6 MII oocytes were in vitro fertilized by JF1 inseminated sperm. Fertilized zygotes were culture in KSOM medium. Mature blastocysts were collected at 96 hours post fertilization.

value: C57BL/6 (maternal), JF1 (paternal)

tag: Stage

value: blastocyst

value: wildtype


title: ATAC-RH30-DMSO-1


title: Spin_PBS_1

city: Guangzhou

first: Xiaoyun

last: Wang

state: Guangdong

address: 190 Kaiyuan Avenue, Huangpu

department: Infection and Immunity

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

description: The whole-body were sampled from pool of five 5-7-day-old female mosquitoes

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house Perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data. At the same time, Q20, Q30, GC-content, and sequence duplication levels of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
For RNA-seq data, the adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the Aedes aegypti genome sequence (NCBI: GCF_002204515.2_AaegL5.0). Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome.
For RNA-seq clean data, the mapped reads were assembled with the Bowtie2 software (version 2.2.5).
For RNA-seq clean data, after detecting transcriptome library was eligible, The library preparations were sequenced on a platform of MGISEQ-2000. The FPKM（Fragments Per Kilobase of transcript per Million fragments mapped）value representing the expression level of transcripts was calculated.
For RNA-seq clean data, differential expression analysis of the control and treated groups was performed using the DESeq2 (version 1.6.3). DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value < 0.001 found by DESeq2 were assigned as differentially expressed.
Genome_build: Aedes aegypti genome sequence (NCBI:GCF_002204515.2_AaegL5.0).
Supplementary_files_format_and_content: Tab-delimited text file (.txt) includes raw read counts for the RNA-seq data

organism: Aedes aegypti

source_name: Whole body

growth_protocol: Mosquitoes were maintained under standard insectary conditions of 27 ± 1°C, 12:12 h photoperiods, and 80 ± 5% humidity.

extract_protocol:
Total RNA from the pool of five female mosquitoes in the control and spinetoram-treated group with and without DENV-2 infection was extracted by using the TRIzol reagent according to the manufacturer’s protocol (Invitrogen, California, USA).
To construct the library for the MGISEQ-2000, total RNA was used for library construction using the MGIEasy RNA Directional Library Prep Kit (MGI). Next, paired-end sequencing was performed using the MGISEQ-2000 sequencing instrument, according to the manufacturer’s instructions, yielding 150-bp paired-end reads.

treatment_protocol: The third-instar larvae (L3, N = 100 per treatment) were separated into four 500 mL plastic pots with 200 mL of water and turtle food for survival rate analysis. The larvae were exposed to different concentrations of spinetoram (0, 2, 10, 20 and 50 μg/L) for 36 h, and were then transferred to dechlorinated water after the treatments. Two to three-day-old surviving Ae. aegypti female mosquitoes were infected with DENV-2 via intrathoracic injection. Mosquitoes were anesthetized on ice and injected with 100 nL of DENV-2 stock or PBS using a Nanoject II injector (Drummond Scientific, Broomall, PA, USA).

value: 5-7-day-old female adult

tag: culture environment

value: Feed on 10% sucrose water

value: with Spinetoram exposure and PBS injection

tag: replicate

value: female

value: whole body


title: ATAC-LHCN-P3F1-OE-1