title: JC_1_123 (21PG37-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: H2AK119ub,MT,Rep2,CUT&RUN

status: Public on Jan 06 2025

type: SRA

city: La Jolla

first: Zhen

last: Dong

state: California

address: 9420 Athena Circle

department: Department of Signaling and Gene Expression

country: USA

institute: La Jolla Institute for Immunology

library_source: genomic

data_processing:
Trimemd reads were aligned against a combined version of the mouse genome reference (mm10) and the Drosophila melanogaster reference genome (build5.41) using Bowtie2, duplicated reads and unassembled contigs were removed using Picard.
The number of reads aligning to mouse or Drosophila melanogaster chromosomes were obtained using Samtools and were used to calculate normalization factors.
deepTools and UCSC utilities were used to generate the bigwig tracks. To remove the technical noise, averaged IgG signals were removed from the from the CUT&RUN signals using bigwigCompare.
Average tracks per condition were estimated by using BigwigMerge and considering the number of samples. To measure genome-wide changes, we used a 10kb approach, using bedtools map.
Assembly: mm10
Supplementary files format and content: Normalized coverage files in bigWig format
Library strategy: Cut&Run

molecule: genomic DNA

organism: Mus musculus

source_name: myeloid (Cd11b+)

growth_protocol: Cells were isolated from mouse bone marrow and used for experiments immediately

extract_protocol:
Cells were washed twice and immobilized on concanavalin A-coated magnetic beads. Cells were then incubated overnight at 4°C with primary antibody in antibody binding buffer. After washing with dig-wash, cells were incubated with pA-MNase complex in wash buffer for 1 hour at 4°C.
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina. Five nanograms (5 ng) of DNA was used for library preparation, and the libraries were amplified using 13 cycles on the thermocycler. The final libraries were cleaned up using AMPureXP beads, validated using the Agilent High Sensitivity DNA kit, and the concentrations were measured by Qubit.

tag: antibody

tag: cell type

value: myeloid (Cd11b+)

tag: age

value: 18-20 months old


title: ssDRIP_siNT_DMSO_rep2

city: London

first: Chi

last: Zhang

address: 15 Cotswold Road

department: Division of Cancer Therapeutics

country: United Kingdom

institute: The Institute of Cancer Research

description: ssDRIP, replicate 2

data_processing:
library strategy: strand-specific DNA:RNA immunoprecipitation sequencing (ssDRIP-seq)
Pair-end raw reads were aligned to GRCh37 genome assembly using BWA, followed by file format exchange by SAMtools.
The resultant alignment reads were separated by first-in-pair strand into two files corresponding to (+) or (-) strand R-loop (or input) reads using SAMtools flag identifiers.
Peak calling was carried out using MACS2 package using pair-end fragment setting with input and ssDRIP samples. The resultant peaks were served as input for MSPC, and recurrent peaks were filtered using parameters ‘–w 1E-4 –s 1E-8 –c 4’.
Peaks on the same strand and within a distance of 1000 bp were merged using BEDTools, and converted to GTF format using UCSC tools (bedtogenepred and genepredtogtf).
Read counting was conducted using Subread, and raw counts were analysed by DEseq2 using a generalized linear model with an interaction term.
Genome_build: GRCh37
Supplementary_files_format_and_content: Excel table with quantification results, generated by DESeq2

organism: Homo sapiens

source_name: T-47D BRCA cell line

growth_protocol: T-47D (ATCC HTB-133) cells were obtained from ATCC, and were maintained in RPMI-1640 medium supplemented with 10% v/v FBS (PAA), 0.2 Units/ml bovine insulin (Sigma) and 0.5% v/v pen/strep (Gibco).

extract_protocol:
DRIP was performed on T-47D cells using an optimised method previously reported by Halász et al (PMID: 28341774). The best-performing protocol number 5 was adopted. In this experiment, S9.6 antibody from Kerafast (ENH002) was used.
To enable strand-specificity, DRIP product was subjected to second-strand DNA synthesis with uracil incorporation. More specifically, DNA:RNA hybrid was reconstituted in 1× NEB first-strand synthesis buffer (NEB E7525) without the addition of primer and enzyme to a final volume of 20 µl. The product was immediately used as the starting material of NEB’s directional second-strand synthesis method following manufacturer’s instructions (NEB E7550). The resultant DNA was purified using SPRI beads (Thermo Fisher) at a volume ratio of 2.0 and eluted using TE buffer. After quality inspections by BioAnalyzer 2100 (Agilent), the product was sent to BGI, Hong Kong, where strand-specific libraries were constructed using DNB technology.

treatment_protocol: T-47D cells were transfected with 30 nM non-targeting or A3B-targeting siRNA using RNAiMAX reagent (Thermo Fisher) in RPMI-1640 medium supplemented with 10% charcoal-stripped FBS. 48 hours after siRNA transfection, cells were treated with DMSO or 100 nM E2 for 2 hours before proceeding to ssDRIP-seq protocol.

tag: cell line

tag: sirna treatment

value: non-targeting

tag: drug treatment

value: DMSO

tag: molecule subtype

value: DNA:RNA hyprid


title: CAMA, Day20, biol rep3

city: Liège

first: Nor Eddine

last: Sounni

address: avenue de l'Hôpital 11

department: Medical oncology

country: Belgium

institute: Liège University (ULG - ULiège)

library_source: transcriptomic

data_processing:
Sequencing was performed on a Illumina NovaSeq 6000 instrument producing 50 bp paired-end reads running Control Software 1.7.0
Demultiplexing of the samples was perfomed with bcl2fastq v2.20.0.422
Sequence reads were trimmed for adaptor sequence/low quality sequence with Trim galore (version 0.6.6)
Trimmed sequence reads were aligned in paired-end mode to the GRCh38/hg38 reference genome using STAR aligner (version 2.7.9a) and default parameters
Read count extraction was performed using featureCounts (version 2.0.0)
Normalization of the read count was carried out using the DESeq2 R package
Assembly: hg38
Supplementary files format and content: tab-delimited text file including raw counts for each sample
Supplementary files format and content: tab-delimited text file including DESeq2-normalized (median of ratios) counts for each sample, ensembl geneID and gene name

molecule: polyA RNA

growth_protocol: Cell lines were tested by MycoALert Kit (Lonza) to ensure that they were Mycoplasma-free. Cells were grown in red-phenol free DMEM supplemented with 10% FBS, L-glutamine (2 mmol/L), penicillin (100 U/mL), and streptomycin (100 mg/mL) at 37°C, in a 5% CO2 humid atmosphere. All culture reagents were purchased from Gibco/Thermo Fisher.

extract_protocol:
After the end of the treatment, each dish was washed twice with PBS, then a scraper was made in the center of the dish and recovered in 200 μl of PBS. 400 μl of Lysis/binding Buffer from the Roche “High pure RNA isolation Kit (11828665001)” kit was added, and the solution was frozen at −80°. The rest of the extraction was performed according to the protocol of the previously mentioned Roche kit. RNA concentration was measured with the NanoDrop One.
Library preparation has been done with 400ng of input RNA using: NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) followed by NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760) and NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs) (NEB# E6440).

value: epithelial-like cell

tag: genotype

value: WT

tag: treatment

value: 0.3 µM of Palbociclib and 30 nM of Fulvestrant for 20 days

tag: time


title: H2AK119ub,MT,Rep1,CUT&RUN


title: WEEV, 0 mkd, Rep 4

city: Memphis

first: Evan

middle: Peter

last: Williams

state: TN

address: 858 Madison Ave

department: Dept. of Microbiology, Immunology, and Biochemistry

institute: University of Tennessee Health Science Center

data_processing:
CLC Genomics Workbench v 23.0
Sequence reads were trimmed  and filter using default parameters in CLC Genomic Workbench
Trimmed and filter sequence reads were mapped to GRCm39/virus species concatinated genome using default parameters in CLC Genomic Workbench
Read count results were collected in  CLC Genomic Workbench
Read count were normalized and fold change calculated using DESeq2
Assembly: GRCM39 concatinated with lab reference genome of each virus
Supplementary files format and content: tab-delimited text files include total counts for each sample
Supplementary files format and content: tab-delimited text files include total counts, TPM, CPM, and RPKM values for each sample

molecule: total RNA

source_name: Brain

extract_protocol:
Total RNA was isolated using TRIzol
Libraries were constructed using Illumina TruSeq Stranded mRNA

tag: tissue

value: Brain

value: BALB/c

value: Infected, 0 mg/kg/day


title: ssDRIP_siA3B_DMSO_rep1

description: ssDRIP, replicate 1


title: ssDRIP_input_siNT_E2_rep3

description: input, replicate 3

value: estradiol


title: JC_1_122 (21PG37-2)

city: Stockholm

first: Cheng

last: Zhao

state: Stockholm

address: H9 Klinisk vetenskap,171 77 Stockholm

department: Clinical Science

country: Sweden

institute: Karolinska institute

description: Gpig.scRNAseq.counts.all.tsv.gz

library_source: transcriptomic single cell

data_processing:
For the guinea pig single-cell RNA-Seq data, adapters and low-quality reads were removed using Trimgalore with default parameters. Subsequently, high-quality reads were aligned to the guinea pig Ensembl reference genome (v.Cavpor.3.0.105, Cavia porcellus, obtained from the Ensembl website)using the HISAT2 aligner (v 2.2.0) with default settings. Only uniquely mapped reads were retained for gene expression quantification. Raw read counts were tentatively quantified using featureCounts (v1.6.3) based on Ensembl reference annotation.
Considering the incomplete guinea pig reference annotation, we decided to update the guinea pig gene annotation using the following steps: 1. Ensembl transcripts belonging to “lincRNA”, “processed_pseudogene”, “protein_coding”, and “pseudogenes” were selected as the guided annotation. The mapping bam files were used as input for Stringtie (v1.3.3b) for each individual sample. After the initial assembly, the transcripts were merged using 'stringtie --merge' and compared with the guided annotation using 'gffcompare -r'. Transcripts that overlapped with multiple reference genes were excluded, as well as transcripts with a length less than 200 bp and 'class codes' identified by gffcompare equal to ‘e’, ‘s’, ‘x’ were removed in downstream analysis. Transcripts with class codes 'j', 'k', '=', 'm', 'n', 'o', 'p', 'y' were assigned to corresponding reference genes. Novel transcripts with no clear reference annotation were blasted against human and mouse transcripts of protein coding and lncRNA with parameters '-max_target_seqs 1 -outfmt 6 -num_threads 25 -evalue 1e-20 -strand plus -max_hsps 1' to find the most similar human or mouse reference genes. If there were no orthologous genes of matched reference genes in the guinea pig Ensembl annotation, they were added. Other novel transcripts with known orthologous genes in the guinea pig Ensembl annotation were reassigned to known annotated genes based on whether the novel transcripts fell within the nearby loci (± 3 kb) of the current annotation.
Assembly: Cavpor.3.0.105
Supplementary files format and content: tab-delimited text file include raw count for each Sample

organism: Cavia porcellus

source_name: embryo

growth_protocol: Hartley guinea pigs (Charles River Labs, Laval, Québec) were housed in the Animal Care Facility at the CRCHUM, maintained at 21 °C with 30-70 % humidity under a 12 h light cycle, and fed with Teklad Global Guinea Pig Diet 2040 pellets, water, and hay ad libitum.

extract_protocol:
Briefly, embryos were flushed from the oviduct (E3.5) or uterine horns (E4-E5.75) using 5-10 ml of warm M2 medium (MR-015-D, Sigma Aldrich) supplemented with 1 % Penicillin-Streptomycin (15130122, Life Technologies), washed and briefly kept in M2 drops covered with Ovoil TM (10029, Vitrolife) at the incubator at 5 % O2 5 % CO2 at 37.5 °C prior to being fixed in PFA 4 % for 15 min or single cell picking. E6 embryos were collected at E5.75 and incubated in similar conditions for 6 h to reach the desirable embryonic day, as implantation occurs around E6, and obtaining embryos by flushing the uterus was challenging.
Embryos collected from E3-E5.75 were obtained through the flushing female guinea pigs and placed in M2 drops under mineral oil until further processing. Zona pellucida was removed using tyrodes, and subsequent single-cell dissociation was achieved through enzymatic digestion with TrypLE Express (12604-013, Gibco, Life Technologies) followed by isolation using fine glass capillaries. Libraries were prepared using the Smartseq2 protocol, following established procedures 14–16. The quantity and quality of the cDNA libraries were assessed using an Agilent 2100 BioAnalyzer (Agilent Technologies). Approximately 1 ng of cDNA per cell was transformed into a single-cell library using the Nextera XT DNA Library prep kit (Illumina FC-131-1096) and following the manual instructions with slight modifications. In brief, 1 ng of cDNA (in a maximum of 5 µl of sample volume) underwent tagmentation with 2 µl of TD and 1 µl of ATM at 55 °C for 5 min. Upon completion of the program, the reaction was promptly halted by adding 1 µl of 2 % SDS and incubating for 5 min at RT. Amplification was carried out using 3 µl of NMP per sample and adding 1 µl of each dual-indexed (i7 and i5; Illumina) primer. Individual Nextera XT libraries were pooled and then purified using magnetic beads. Indexed sequence libraries were combined for multiplexing (384 samples per lane). The sequencing was performed using the NovoSeq6000 paired-end.

treatment_protocol: Embryos at each stage were retrieved from at least 3 separate Hartley guinea pig females (~500 grams, 2-3 months of age) between days 3.5 and 5.75 after natural mating.

value: embryo

tag: developmental stage

value: Early blastocyst

value: embryo in vitro day E5.25


title: CAMA, Day20, biol rep1


title: JC_1_121 (21PG37-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: ssDRIP_input_siNT_E2_rep2

description: input, replicate 2


title: T47D, Day5, biol rep1

value: epithelial cells

value: 0.3 µM of Palbociclib and 30 nM of Fulvestrant for 5 days


title: CAMA, Day5, biol rep3


title: WEEV, 0 mkd, Rep 2


title: ssDRIP_input_siNT_E2_rep1

description: input, replicate 1


title: JC_1_120 (21PG37-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: WEEV, 0 mkd, Rep 3


title: JC_1_119 (21PG37-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: WEEV, 0 mkd, Rep 1


title: CAMA, Day5, biol rep2


title: CAMA, Day5, biol rep1


title: ssDRIP_input_siNT_DMSO_rep3

description: input, replicate 3


title: JC_1_124 (21PG37-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_1_12 (21PG39-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: 16 cell

value: embryo in vitro day E4


title: T47D, Untreated, biol rep3

value: Untreated


title: WEEV, 48 mkd, Rep 4

value: Infected, 48 mg/kg/day


title: CAMA, Untreated, biol rep3


title: ssDRIP_input_siNT_DMSO_rep1

description: input, replicate 1

value: non-targeting

value: DMSO


title: WEEV, 48 mkd, Rep 3


title: JC_1_117 (21PG37-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_1_118 (21PG37-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: CAMA, Day20, biol rep2

value: epithelial-like cell

value: WT


title: CAMA, Untreated, biol rep2


title: WEEV, 48 mkd, Rep 1

value: Brain


title: CAMA, Untreated, biol rep1


title: Tet, PB61

city: Paris

first: Victoire

last: Baillet

address: 25-28 rue du Dr Roux

country: France

institute: Institut Pasteur

data_processing:
Reads trimming (removal of sequencing adapters and Q<30 bases), removal of <25nt reads,  cropping to 50bp (Cutadapt v2.10)
Mapping to hg38 in PE mode with the following Bowtie 2 parameters: --very-sensitive -X 2000 --dovetail --no-mixed --no-discordant.
Removal of duplicates (Picard MarkDuplicates v2.23.3) and reads mapping to blacklisted regions and chrM.
Peak calling using MACS2 v2.2.6 with the following parameters: -f BED  --nomodel --shift -100 --extsize 200 --keep-dup all -g hs --call-summits.
Assembly: hg38
Supplementary files format and content: Bigwigs produced with deepTools v3.4.1 (BPM normalization, 10bp bins, ignoring chrX chrY)

source_name: MAIT cells isolated from PBMC

growth_protocol: Freshly isolated PBMC were cultured in RPMI supplemented with 10% FBS, 1% penicillin/streptomycin and 20UI/mL.

extract_protocol:
Nuclei from 90000 sorted MAIT cells were isolated using ATAC-lysis buffer from the Active Motif ATAC-seq Kit following manufacturer's instructions.
Libraries were prepared using the ATAC-seq kit from Active motif according to manufacturer’s instructions. After centrifugation (2800 rpm, 10 min 4°C), nuclei were incubated with the tagmentation master mix in a shaking heat block for 30min at 37°C with agitation at 800rpm. DNA was then purified and amplified for 10 cycles using indexed primers, and size-selected using SPRI bead solution.

treatment_protocol: MR1/5-OP-RU tetramers (NIH) were added the first day of culture at 40pM, and cells were cultured for 6 days. IL-23 or IL-12 (Miltenyi Biotec) were added at the concentration of 20 ng/mL and renewed after 3 days.

value: MAIT cells isolated from PBMC


title: ssDRIP_input_siA3B_E2_rep2

description: input, replicate 2


title: EEEV, 0 mkd, Rep 4

value: BALB/c

value: Infected, 0 mg/kg/day


title: ssDRIP_input_siA3B_E2_rep1

description: input, replicate 1

value: estradiol


title: JC_1_114 (21PG37-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo

value: Early blastocyst


title: EEEV, 0 mkd, Rep 3


title: Tet, PB60


title: ssDRIP_input_siNT_DMSO_rep2

description: input, replicate 2


title: ssDRIP_input_siA3B_DMSO_rep2

description: input, replicate 2


title: JC_1_113 (21PG37-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo in vitro day E5.25


title: EEEV, 0 mkd, Rep 2


title: Tet, PB59


title: ssDRIP_input_siA3B_DMSO_rep3

description: input, replicate 3


title: EEEV, 0 mkd, Rep 1


title: Tet IL23, PB61

value: MR1/5-OP-RU IL-23


title: JC_1_112 (21PG34-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: 16 cell

value: embryo in vitro day E4.5


title: JC_1_116 (21PG37-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: Tet IL23, PB59


title: EEEV, 48 mkd, Rep 3


title: WEEV, 48 mkd, Rep 2


title: ssDRIP_input_siA3B_E2_rep3

description: input, replicate 3


title: EEEV, 48 mkd, Rep 4


title: A3B_SPIseq_siNT_E2_rep2

description: A3B SPI-seq sample for non-targeting siRNA and estradiol-treated cells, replicate 2

data_processing:
library strategy: ssDNA protein immunoprecipitation (SPI)-seq
Single-end raw reads were aligned to GRCh37 genome assembly using BWA, followed by file format exchange by SAMtools.
Peak calling was carried out using MACS2 package, where both input/IP sequence reads were used and the fragment length was set to 200 bp.
The resultant narrow peak files, together with aligned sequence reads, were served as input for DiffBind analysis. EdgeR statistics were applied for quantification of reads.
Genome_build: GRCh37
Supplementary_files_format_and_content: Excel table with quantification results by DiffBind.
Supplementary_files_format_and_content: Bigwig generated by MACS2, scores represent fold enrichment over input control

extract_protocol:
SPI protocol was adapted from the ChIP protocol used by Myer’s Lab at HudsonAlpha (protocol version v011014) which contributed to the ENCODE project. Except that: i), cells were lysed in ChromaTrap lysis buffer that designed for sonication (Porvair Science, 100001), and chromatin fragmentation was carried out on a Covaris E220 instrument with optimised settings for ChIP purpose; 2), ChIP-grade protein A/G beads (Pierce 26162) were used to perform immuno-precipitation experiments; 3), Flag-M2 (Sigma F1804) antibody was used, and the following buffer was used for chromatin binding and washing: 100 mM Tris pH 7.5; 500 mM LiCl; 1% NP-40; 1% sodium deoxycholate; 4), Following ChIP, the immunoprecipitated complex were subjected to denaturing and adapter ligation following the protocol reported by the developers of SPI-seq (PMID: 23249883).
Library was constructed following the protocol reported by the developers of SPI-seq (PMID: 23249883).

treatment_protocol: T-47D cells pretreated with doxycycline for 24 hours were transferred to RPMI-1640 medium supplemented with 10% charcoal-stripped FBS and 1 ug/ml doxycycline 48 hours before treatment. Cells were then treated with DMSO or 100 nM E2 for 2 hours.

tag: strain

value: Non-targeting siRNA


title: A3B_SPIseq_siNT_E2_rep1

description: A3B SPI-seq sample for non-targeting siRNA and estradiol-treated cells, replicate 1


title: JC_1_11 (21PG39-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo in vitro day E4


title: JC_1_115 (21PG37-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_1_110 (21PG34-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: Tet IL23, PB60


title: A3B_SPIseq_siNT_DMSO_rep2

description: A3B SPI-seq sample for non-targeting siRNA and DMSO-treated cells, replicate 2


title: EEEV, 48 mkd, Rep 2

value: Infected, 48 mg/kg/day


title: EEEV, 48 mkd, Rep 1


title: HGSOC (4)

city: Dalian

first: Ning

last: Wang

address: 467 Zhongshan Road, Dalian, P.R.

country: China

institute: the Second Hospital of Dalian Medical University

data_processing:
Real-time Analysis.
Sequence reads were trimmed for adaptor sequence using fastp.
Htseq-count was used to obtain read count extraction,and normalized counts using FPKM.
Assembly: hg38
Supplementary files format and content: processed data.xlsx

source_name: Ovary

extract_protocol:
Quantity and integrity of extracted RNA was assessed by NanoDrop ND-1000 and Agilent 2100 Bioanalyzer, respectively.
RNA libraries for RNA-seq were prepared using  Invitrogen SuperScript™ II Reverse Transcriptase.

value: Ovary

tag: disease

value: high-grade serous ovarian cancer


title: HGSOC (3)


title: JC_1_109 (21PG34-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: HGSOC (2)


title: HGSOC (1)


title: input_siNT_E2_rep2

description: input sample for non-targeting siRNA and estradiol-treated cells, replicate 2


title: JC_1_107 (21PG55-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: Middle blastocyst

value: embryo in vitro day E5.75


title: ssDRIP_input_siA3B_DMSO_rep1

description: input, replicate 1

value: DMSO


title: JC_1_108 (21PG55-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: VEEV, 48 mkd, Rep 3

value: Brain

value: BALB/c


title: JC_1_111 (21PG34-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_1_106 (21PG55-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: input_siNT_E2_rep1

description: input sample for non-targeting siRNA and estradiol-treated cells, replicate 1

value: estradiol


title: Normal (4)

value: Normal


title: input_siNT_DMSO_rep2

description: input sample for non-targeting siRNA and DMSO-treated cells, replicate 2


title: VEEV, 48 mkd, Rep 2


title: Normal (3)


title: JC_1_105 (21PG55-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo


title: JC_1_104 (21PG55-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: Normal (2)


title: Parental

data_processing:
library strategy: WGS
Raw sequences from BGISEQ-500 sequencer were aligned to GRCh38 using BWA.
The resultant bam files were then recalibrated using GATK 4.0.5 mutation calling kit following the ‘best practice’ advised by the developers.
In order to exclude SNVs that are located on either ends of homopolymer DNA sequences and within simple repeating elements, the SNVs passing through GATK filters were further filtered using SNPiR software with perl scripts filter_homopolymer_nucleotides.pl and pblat_candidates_ln.pl scripts only.
Genome_build: GRCh38
Supplementary_files_format_and_content: TAR (of VCF), variant calling results generated by GATK4

growth_protocol: T-47D (ATCC HTB-133) cells were obtained from ATCC, and were maintained in RPMI-1640 medium supplemented with 10% v/v FBS (PAA), 0.2 Units/ml bovine insulin (Sigma) and 0.5% v/v pen/strep (Gibco). Cells were transduced with lentiviral inducible 3×Flag-A3B-P2A-hUGI-HA cassette, which was maintained with 1 µg/ml puromycin (Gibco).

extract_protocol:
Genomic DNA was extracted using Qiagen Genomic-tips 500/G kit following manufacturer’s instructions.
Libraries were constructed by Beijing Genomics Institute Hong Kong, using DNB technology.

treatment_protocol: Expression of ectopic-transduced protein was carried out by induction with 1 µg/ml doxycycline. After 120 hours of incubation, cell colonies were separated and grown in doxycycline-free medium.

tag: lentiviral construct

tag: sample group

value: parantal control


title: VEEV, 0 mkd, Rep 4

value: Infected, 0 mg/kg/day


title: JC_1_103 (21PG55-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: Normal (1)


title: A3B_SPIseq_siNT_DMSO_rep1

description: A3B SPI-seq sample for non-targeting siRNA and DMSO-treated cells, replicate 1


title: VEEV, 0 mkd, Rep 3


title: M_plus_3

value: inducible 3xFlag-A3B**-P2A-hUGI-HA (inactive A3B enzyme)

value: 1 ug/ml doxycycline-induced, followed by clonal seperation

value: M+ group of colony


title: JC_1_102 (21PG55-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: SK_N_BE2_shNC_3

city: Chengdu

first: Wang

last: Zhaokun

address: Chuanda Road Section 2

institute: Sichuan university

data_processing:
Hisat2 v2.0.5
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 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

extract_protocol:
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Neuroblastoma

value: WT


title: M_plus_2


title: VEEV, 0 mkd, Rep 2


title: JC_1_101 (21PG55-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: VEEV, 0 mkd, Rep 1


title: JC_1_100 (21PG55-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: M_plus_1


title: SK_N_BE2_shNC_1


title: PBS, 48 mkd, Rep 4

value: Uninfected, 48 mg/kg/day


title: A_plus_5

value: inducible 3xFlag-A3B-P2A-hUGI-HA

value: A+ group of colony


title: JC_1_10 (21PG39-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: 16 cell

value: embryo in vitro day E4


title: SK_N_BE2_shL5_3

value: TSPYL5 knockdown


title: PBS, 48 mkd, Rep 3

value: Brain

value: BALB/c


title: input_siNT_DMSO_rep1

description: input sample for non-targeting siRNA and DMSO-treated cells, replicate 1

value: Non-targeting siRNA

value: DMSO


title: SK_N_BE2_shL5_2


title: A_plus_4


title: JC_1_1 (21PG50-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo

value: 8 cell

value: embryo in vitro day E3.5


title: PBS, 48 mkd, Rep 2


title: A_plus_3

value: 1 ug/ml doxycycline-induced, followed by clonal seperation


title: input_siA3B_E2_rep2

description: input, replicate 2

data_processing:
library strategy: DSBCapture-seq
Raw reads were aligned to GRCh37 genome assembly using BWA and processed by SAMtools.
MACS2 was used to perform peak calling, with modelled narrow peak settings and an extended fragment length of 200 bp.
For quantification, EdgeR analysis was performed using DiffBind.
Genome_build: GRCh37
Supplementary_files_format_and_content: Exel table of quantification results generated by DiffBind

extract_protocol:
DSBCapture was conducted following a previous report (PMID:27525976) except that Covaris E220 was used for fragmenting adapter-ligated DNA with the following settings: duty factor 10%; peak incident power 75 watts; cycles per burst 1000; time 50 seconds; temperature 4 ºC.
Library was constructed using DSBCapture developer’s protocol (PMID:27525976).

value: A3B-targeting siRNA

value: estradiol


title: A_plus_2


title: SK_N_SH_shL5_3

source_name: SK-N-SH

value: SK-N-SH

value: Neuroblastoma


title: SK_N_BE2_shL5_1


title: PBS, 48 mkd, Rep 1

value: Uninfected, 48 mg/kg/day


title: Epiblast female WT 2

first: Laurène

last: Syx

address: 11 rue Pierre et Marie Curie

department: Centre de recherche

institute: Institut Curie

data_processing:
the first eight base pairs of the reads were trimmed using the FASTX-Toolkit v0.0.13
Adapter sequences were removed with Cutadapt v1.3 and reads shorter than 16 bp were discarded.
The cleaned sequences were aligned to the mouse reference genome (mm10) using Bismark v0.12.5 with Bowtie2-2.1.0 and the default parameters.
Only the reads that mapped uniquely to the genome were conserved. Methylation calls were extracted after duplicate removal.
Only CG dinucleotides covered by a minimum of ten reads were conserved for the remainder of the analysis.
Assembly: mm10
Supplementary files format and content: text file with number of methylated and unmethylated CG

growth_protocol: natural matings, no embryo culture

extract_protocol: Illumina manufacturer protocol

tag: lineage

value: Epiblast

tag: embryonic day

value: XX


title: input_siA3B_E2_rep1

description: input, replicate 1


title: A_plus_1

value: inducible 3xFlag-A3B-P2A-hUGI-HA

value: A+ group of colony


title: SK_N_BE2_shNC_2

tag: cell type

value: WT


title: DSBCapture_siNT_E2_rep2

description: DSBCapture-seq, replicate 2

value: non-targeting siRNA


title: Epiblast female WT 1


title: A_minus_3

value: non-induced, follow by clonal seperation

value: A- group of colony


title: DSBCapture_siNT_E2_rep1

description: DSBCapture-seq, replicate 1


title: SK_N_SH_shNC_3


title: SK_N_SH_shL5_1

value: TSPYL5 knockdown


title: A_minus_2


title: DSBCapture_siNT_DMSO_rep2

description: DSBCapture-seq, replicate 2

value: DMSO


title: A_minus_1


title: SK_N_SH_shNC_1


title: DSBCapture_siA3B_E2_rep2

description: DSBCapture-seq, replicate 2


title: ssDRIP-seq

description: strand-specific DRIP enriched DNA:RNA hybrid

data_processing:
library strategy: DRIP-seq
Pair-end raw reads were aligned to GRCh37 genome assembly using BWA, followed by file format exchange by SAMtools.
The resultant alignment reads were separated by first-in-pair strand into two files corresponding to (+) or (-) strand R-loop (or input) reads using SAMtools flag identifiers.
Peak calling was carried out using MACS2 package using paired input/IP sequences using the following command: ‘macs2 callpeak -c $INPUT -t $DRIP -g hs -n $NAME -f BAMPE –keep-dup auto -m 5 50 –bdg –SPMR’.
Signal tracks were composed using bdgcmp tool from MACS2 package using ‘fold enrichment (FE) over control’ method. The resultant peaks were filtered against a ‘black list’ of regions defined by the ENCODE project (PMID: 22955616).
Genome_build: GRCh37
Supplementary_files_format_and_content: Peak text files generated by MACS2 software
Supplementary_files_format_and_content: bigwig files generated by macs2, score represent fold enrichment over input control

value: BRCA cell line

tag: sample type

value: DNA:RNA hybrid


title: DSBCapture_siNT_DMSO_rep1

description: DSBCapture-seq, replicate 1

tag: cell line


title: SK_N_SH_shNC_2


title: Input

description: Total DNA input control

value: total DNA


title: PWS_Tet1c_NT_r3 [bisulfite_neurons]

status: Public on Jan 05 2025

city: Durham

first: Charles

last: Gersbach

state: North Carolina

address: 101 Science Dr.

department: Biomedical Engineering

institute: Duke University

description:
Library name: PWS_Tet1c_NT_r3
del_NonTargeting_r3

data_processing:
Raw reads were trimmed using Trimmomatic to remove low quality reads and adapters with the following settings: HEADCROP: 25; ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10; TRAILING: 20; SLIDINGWINDOW:4:15; MINLEN:40
Bismark was used to create a bisulphite-converted reference genome from the hg19 genome build. Trimmed, paired-end reads were aligned to the genome and analysed with Bismark version 0.22.3. The output coverage files were used to determine percentage of methylated cytosine for each CpG site in the amplicon.
Bismark coverage (cov) files were retrieved, and cov files were filtered for CpG sites located on chr15 within the target amplicon (24 CpG sites total) and compiled into a filtered methylation table for all samples. Methylation coverage and counts at CpG sites within the target amplicon were then compared between treatments.
Assembly: hg19
Supplementary files format and content: Comma-separated methylation coverage table.

growth_protocol: iPSCs were maintained in StemCell mTeSR or mTeSR Plus, with ROCK inhibitor (Y-27632) after seeding or passaging.

extract_protocol:
For bisulphite sequencing of iPSCs and neurons, genomic DNA was extracted from cultured cells with the Qiagen DNeasy Blood and Tissue kit (Qiagen, 69504) or the Zymo QuickDNA Miniprep kit (Zymo D3024). gDNA was stored at -80C. 250ng of gDNA were input into the bisulphite conversion reaction. For bisulphite conversion and purification, we used the Zymo EZ DNA Methylation Gold kit as instructed (Zymo, D5005).
2uL of bisulphite-converted gDNA was used as input for PCR as described above, with an annealing temperature of 57C. PCR1 reactions were then cleaned with Ampure XP beads (Beckman, A63881) at a ratio of 1.8x. 1/10th of PCR1 was used as input for PCR2 with Q5 polymerase. PCR2 added i5 and i7 barcodes and P5 and P7 overhangs for dual-index Illumina short read sequencing. PCR2 products were purified with Ampure XP beads. Products were visualized via electrophoresis on an Agilent TapeStation 4200 and quantified with Qubit dsDNA HS assay kit (Invitrogen, Q32851) on a Qubit fluorometer (Invitrogen). Libraries were pooled and sequenced on an Illumina Miseq instrument with a Miseq v3 600 cycle kit (Illumina, MS-102-3003) with read lengths of 250x250.

treatment_protocol: Stable polyclonal Tet1-dCas9 or VP64-dCas9-VP64 cell lines were established by transducing with lentivirus and selecting for transgene-expressing cassette with 1.5 ug/mL blasticidin for 5 days. Then, cells were transduced with gRNA lentivirus and selected for gRNA-expressing cassette with puromycin (1ug/mL) for 3 days.

value: iPSC

value: PWS deletion

value: Tet1v4 + NT gRNA


title: DSBCapture_siA3B_E2_rep1

description: DSBCapture-seq, replicate 1

tag: sirna treatment

value: A3B-targeting siRNA

value: estradiol


title: WT_Tet1c_NT_r2 [bisulfite_neurons]

description:
Library name: WT_Tet1c_NT_r2
ctrl_NonTargeting_r2


title: WT_Tet1c_NT_r1 [bisulfite_neurons]

description:
Library name: WT_Tet1c_NT_r1
ctrl_NonTargeting_r1


title: ∆PWS iPSC Tet1v4 mat3 gRNA rep3

description:
Library name: PWS_Tet1c_G4363_r3
dPWS_G4363_r3

data_processing:
Raw reads were trimmed using Trimmomatic to remove low quality reads and adapters with the following settings: HEADCROP: 25; ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10; TRAILING: 20; SLIDINGWINDOW:4:15; MINLEN:40
Bismark was used to create a bisulphite-converted reference genome from the hg19 genome build. Trimmed, paired-end reads were aligned to the genome and analysed with Bismark version 0.22.3. The output coverage files were used to determine percentage of methylated cytosine for each CpG site in the amplicon.
Bismark coverage (cov) files were retrieved, and cov files were filtered for CpG sites located on chr15 within the target amplicon (24 CpG sites total) and compiled into a filtered methylation table for all samples. Methylation coverage and counts at CpG sites within the target amplicon were then compared between treatments.
Assembly: hg19
Supplementary files format and content: Comma-separated methylation coverage tables.

value: Tet1v4 + mat3 gRNA


title: ∆PWS iPSC Tet1v4 mat3 gRNA rep1

description:
Library name: PWS_Tet1c_G4363_r1
dPWS_G4363_r1


title: ∆PWS iPSC Tet1v4 NT gRNA rep3

description:
Library name: PWS_Tet1c_NT_r3
dPWS_NonTargeting_r3


title: ∆PWS iPSC Tet1v4 NT gRNA rep1

description:
Library name: PWS_Tet1c_NT_r1
dPWS_NonTargeting_r1


title: ∆PWS iPSC Tet1v4 NT gRNA rep2

description:
Library name: PWS_Tet1c_NT_r2
dPWS_NonTargeting_r2


title: PWS_Tet1c_G4363_r3 [bisulfite_neurons]

description:
Library name: PWS_Tet1c_G4363_r3
del_Targeting_r3


title: PWS_Tet1c_G4363_r2 [bisulfite_neurons]

description:
Library name: PWS_Tet1c_G4363_r2
del_Targeting_r2


title: ∆PWS iPSC VP64 NT gRNA rep2

description:
Library name: PWS_VP64_nt_r2
del-VP64-nt-set1-r2

value: VP64 + NT gRNA


title: ∆PWS iPSC VP64 NT gRNA rep1

description:
Library name: PWS_VP64_nt_r1
del-VP64-nt-set1-r1


title: PWS_Tet1c_NT_r1 [bisulfite_neurons]

description:
Library name: PWS_Tet1c_NT_r1
del_NonTargeting_r1


title: WT iPSC VP64 NT gRNA rep3

description:
Library name: WT_VP64_nt_r3
ctrl-VP64-nt-set1-r3


title: WT iPSC VP64 NT gRNA rep2

description:
Library name: WT_VP64_nt_r2
ctrl-VP64-nt-set1-r2


title: WT iPSC VP64 NT gRNA rep1

description:
Library name: WT_VP64_nt_r1
ctrl-VP64-nt-set1-r1


title: SK_N_SH_shL5_2

value: SK-N-SH

value: Neuroblastoma


title: ∆PWS iPSC Tet1v4 mat3 gRNA rep2

description:
Library name: PWS_Tet1c_G4363_r2
dPWS_G4363_r2


title: VP64 sorted low GFP rep2 [VP64-sublib]

description:
Library name: 287-low-r2
287_L_R2

data_processing:
FASTQ files were aligned to custom indexes (generated from the bowtie2-build function) using Bowtie 2. Counts for each gRNA were extracted and used for further analysis. All enrichment analysis was done with R. Individual gRNA enrichment was determined using the DESeq2 package to compare between high and low conditions for each screen.
Differentially-enriched gRNAs were gRNAs were identified via DESeq2 using an adjusted p-value cutoff of 0.05.
Assembly: hg19
Supplementary files format and content: DESeq2 results table and sequencing counts for each condition.
Library strategy: CRISPR Screen

source_name: iPSC

extract_protocol:
Cells were harvested for sorting 14 d after transduction of the gRNA sub-library. Cells were washed once with 1x PBS, dissociated using Accutase, filtered through a 30 μm CellTrics filter (Sysmex, 04-004-2326) and resuspended in FACS Buffer (0.5% BSA (Sigma, A7906), 2 mM EDTA (Sigma, E7889) in PBS). The highest and lowest 10% of cells were sorted based on GFP expression and 0.4 x 10^6 cells were sorted into each bin. Sorting was done with a SH800 FACS Cell Sorter (Sony Biotechnology).
After sorting, genomic DNA was harvested with the DNeasy Blood and Tissue Kit (Qiagen, 69506). The gRNA libraries were amplified from each gDNA sample across 100 μL PCR reactions using Q5 hot start polymerase (NEB, M0493) with 1 μg of gDNA per reaction. The PCR amplification was done according to the manufacturer’s instructions, using 25 cycles at an annealing temperature of 60 °C with the following primers 18: Fwd: 5′-AATGATACGGCGACCACCGAGATCTACACAATTTCTTGGGTAGTTTGCAGTT Rev: 5′-CAAGCAGAAGACGGCATACGAGAT-(6-bp index sequence)- GACTCGGTGCCACTTTTTCAA The amplified libraries were purified with Agencourt AMPure XP beads (Beckman Coulter, A63881) using double size selection of 0.65× and then 1× the original volume. Each sample was quantified after purification with the Qubit dsDNA High Sensitivity assay kit (Thermo Fisher, Q32854). Samples were pooled and sequenced on a MiSeq (Illumina) with 21-bp paired-end sequencing using the following custom read and index primers: Read1: 5′-GATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCG Index: 5′-GCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTC Read2: 5’ - GTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAAC

treatment_protocol: The screen was performed in triplicate with independent transductions. For each replicate, 1.7 x 10^6 matSNRPN-2A-GFP Tet1cdCas9 or VP64dCas9VP64 iPSCs were dissociated using Accutase (Stemcell Tech, 7920) and transduced in suspension in a matrigel-coated 10-cm dish in mTesR (Stemcell Tech 85850) supplemented with 10 μM Rock Inhibitor (Y-27632, Stemcell Tech, 72304). Cells were transduced at a MOI of 0.2 to obtain one gRNA per cell and ~580-fold coverage of the gRNA sub-library. The medium was changed to fresh mTesR without Rock Inhibitor 18-20 h after transduction. Antibiotic selection was started 30 h after transduction by adding 1 μg/mL puromycin (Sigma, P8833) directly to the plates without changing the medium. The cells were fed daily and passaged as necessary maintaining library coverage until harvest.

value: matSNRPN-GFP RVR iPSCs

value: low GFP


title: VEEV, 48 mkd, Rep 1

value: Brain

value: BALB/c

value: Infected, 48 mg/kg/day


title: VP64 sorted low GFP rep1 [VP64-sublib]

description:
Library name: 287-low-r1
287_L_R1


title: ∆PWS iPSC VP64 mat1 gRNA rep3

description:
Library name: PWS_VP64_mat1_r3
del-VP64-G5117-set1-r3

value: VP64 + mat1 gRNA


title: VP64 sorted low GFP rep1

description:
Library name: 287_Low_R1
R1.lo

data_processing:
FASTQ files were aligned to custom indexes (generated from the bowtie2-build function) using Bowtie 2. Counts for each gRNA were extracted and used for further analysis. All enrichment analysis was done with R. Individual gRNA enrichment was determined using the DESeq2 package to compare between high and low conditions for each screen. Only forward read (read 1) of paired-end sequenced sequencing files was used for data processing and enrichment analysis.
Differentially-enriched gRNAs were gRNAs were identified via DESeq2 using an adjusted p-value cutoff of 0.05.
Assembly: hg19
Supplementary files format and content: DESeq2 results table and sequencing counts for each condition.
Library strategy: CRISPR Screen

extract_protocol:
Each screen was performed in triplicate with independent transductions. For each replicate, 24 x 10^6  SNRPN-2A-GFP VP64dCas9VP64 (maternal) or dCas9KRAB (paternal) iPSCs were dissociated using Accutase (Stemcell Tech, 7920) and transduced in suspension across five matrigel-coated 15-cm dishes in mTesR (Stemcell Tech 85850) supplemented with 10 μM Rock Inhibitor (Y-27632, Stemcell Tech, 72304). Cells were transduced at a MOI of 0.2 to obtain one gRNA per cell and ~430-fold coverage of the gRNA library. The medium was changed to fresh mTesR without Rock Inhibitor 18-20 h after transduction. Antibiotic selection was started 30 h after transduction by adding 1 μg/mL puromycin (Sigma, P8833) directly to the plates without changing the medium. The cells were fed daily and passaged as necessary maintaining library coverage until harvest. Cells were harvested for sorting 9 d after transduction of the gRNA library for all screens.
Cells were washed once with 1x PBS, dissociated using Accutase, filtered through a 30 μm CellTrics filter (Sysmex, 04-004-2326) and resuspended in FACS Buffer (0.5% BSA (Sigma, A7906), 2 mM EDTA (Sigma, E7889) in PBS). Before sorting, an aliquot of 4.8 x 10^6 cells were taken to represent a bulk unsorted population. The highest and lowest 10% of cells were sorted based on GFP expression and 4.8 x 10^6 cells were sorted into each bin. Sorting was done with a SH800 FACS Cell Sorter (Sony Biotechnology).

tag: sorting


title: VP64 sorted high GFP rep3

description:
Library name: 287_High_R3
R3.hi

value: high GFP


title: VP64 sorted high GFP rep1

description:
Library name: 287_High_R1
R1.hi


title: ∆PWS iPSC VP64 mat1 gRNA rep2

description:
Library name: PWS_VP64_mat1_r2
del-VP64-G5117-set1-r2


title: ∆PWS iPSC VP64 mat1 gRNA rep1

description:
Library name: PWS_VP64_mat1_r1
del-VP64-G5117-set1-r1


title: ∆PWS iPSC VP64 NT gRNA rep3

description:
Library name: PWS_VP64_nt_r3
del-VP64-nt-set1-r3


title: WT iPSC Tet1v4 NT gRNA rep2

description:
Library name: WT_Tet1c_NT_r2
WT_NonTargeting_r2

value: WT


title: Tet1c sorted high GFP rep3

description:
Library name: 154-high-r3
154_H_R3

value: iPSC


title: WT iPSC Tet1v4 NT gRNA rep3

description:
Library name: WT_Tet1c_NT_r3
WT_NonTargeting_r3


title: WT iPSC Tet1v4 NT gRNA rep1

description:
Library name: WT_Tet1c_NT_r1
WT_NonTargeting_r1


title: Tet1c sorted high GFP rep2

description:
Library name: 154-high-r2
154_H_R2


title: VP64 sorted high GFP rep3 [VP64-sublib]

description:
Library name: 287-high-r3
287_H_R3


title: KRAB sorted low GFP rep3

description:
Library name: 289_Low_R3
R3_lo

data_processing:
FASTQ files were aligned to custom indexes (generated from the bowtie2-build function) using Bowtie 2. Counts for each gRNA were extracted and used for further analysis. All enrichment analysis was done with R. Individual gRNA enrichment was determined using the DESeq2 package to compare between high and low conditions for each screen. Only forward read (read 1) of paired-end sequenced sequencing files was used for data processing and enrichment analysis.
Differentially-enriched gRNAs were identified via DESeq2 using an adjusted p-value cutoff of 0.05.
Assembly: hg19
Supplementary files format and content: DESeq2 results table and sequencing counts for each condition.
Library strategy: CRISPR Screen

value: patSNRPN-GFP RVR iPSCs


title: VP64 sorted low GFP rep2

description:
Library name: 287_Low_R2
R2.lo


title: VP64 sorted low GFP rep3 [VP64-sublib]

description:
Library name: 287-low-r3
287_L_R3


title: VP64 sorted high GFP rep2 [VP64-sublib]

description:
Library name: 287-high-r2
287_H_R2


title: PWS_Tet1c_NT_r2 [bisulfite_neurons]

description:
Library name: PWS_Tet1c_NT_r2
del_NonTargeting_r2

value: PWS deletion

value: Tet1v4 + NT gRNA


title: PWS_Tet1c_G4363_r1 [bisulfite_neurons]

description:
Library name: PWS_Tet1c_G4363_r1
del_Targeting_r1


title: VP64 sorted high GFP rep1 [VP64-sublib]

description:
Library name: 287-high-r1
287_H_R1


title: VP64 sorted high GFP rep2

description:
Library name: 287_High_R2
R2.hi


title: Tet1c sorted low GFP rep2

description:
Library name: 154-low-r2
154_L_R2


title: Tet1c sorted low GFP rep3

description:
Library name: 154-low-r3
154_L_R3


title: KRAB sorted high GFP rep1

description:
Library name: 289_High_R1
R1_hi


title: Tet1c sorted low GFP rep1

description:
Library name: 154-low-r1
154_L_R1


title: mycelium, 4-phenoxybenzoic acid, 3 day, flask rep3

city: Nanjing

first: Paul

last: Daly

state: Jiangsu

address: 50 Zhongling St

institute: Jiangsu Academy of Agricultural Sciences

description: Library name: p_PBA_f3_3d

data_processing:
Raw data (raw reads) in Fastq format were first processed through in-house Perl scripts where clean reads were obtained by removing reads containing adapter, reads containing poly-N and low-quality reads from raw data. At the same time, Q20, Q30, and GC content of the clean data were calculated. The reference genome and gene model annotation files that were used were those deposited at NCBI as part of Bioproject accession PRJNA992906. FeatureCounts v1.5.0-p3 was used to count the read numbers mapped to each gene, and then FPKM (Fragments Per Kilobase of transcript sequenced per Million mapped reads) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: The reference genome and gene model annotation files that were used were those deposited at NCBI as part of Bioproject accession PRJNA992906.
Supplementary files format and content: WF8_LMCs_gene_count.txt is a tab-delimited text file and contains count data for all genes from all samples.
Supplementary files format and content: WF8_LMCs_gene_fpkm.txt  is a tab-delimited text file and contains FPKM data for all genes from all samples.

organism: Trichoderma cf. simile

source_name: mycelium

growth_protocol: The T. cf. simile WF8 strain used in this work was isolated from decaying wood around Xiaolongtan coal mine in Yunnan Province, and was maintained on PDA slants at 4°C and as a spore glycerol stock at -80°C.

extract_protocol:
The mycelium samples were ground in liquid nitrogen, and the RNA was extracted using TRIzol reagent. Residual DNA was removed from the RNA samples by using a DNase treatment. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, USA).
The mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, and fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of the 3’ ends of the DNA fragments, adaptors with hairpin loop structure were ligated to prepare for hybridization. To select cDNA fragments preferentially of 370~420 bp in length, the library fragments were purified with the AMPure XP system (Beckman Coulter, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. The PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform, and 150 bp paired-end reads were generated.

treatment_protocol: For liquid cultures, a 6 mm diameter agar plug from the growing edge of a colony on the SMA plate was inoculated into a 250 mL flask containing 100 mL of Sabouraud maltose broth (SMB) (40 g maltose and 10 g peptone per liter) and shaken at 180 RPM and 29 °C for 60 h in the dark. After the 60 h incubation, the cultures were supplemented with one of three lignite model compounds (phenetole (PE, SCR; 99%; Cat# 30144370, PubChem CID: 7674), 4-phenoxybenzoic acid  (4-PBA, Macklin; 99%; Cat# P817102, PubChem CID: 75182), or 9,10-dibutoxyanthracene (9-10-DBO, Macklin; 95%; Cat# D843625, PubChem CID: 21987539)) and three potential co-inducers or co-factors of lignite-degrading enzymes (copper and manganese metals and the aromatic veratryl alcohol). Stock solutions of the powder of 4-phenoxybenzoic acid and 9,10-dibutoxyanthracene were prepared by dissolving in dichloromethane (DCM) at a concentration of 0.2 g·L−1  and sterilized by a 0.22 μm nylon membrane filter. The phenetole is a liquid at room temperature, and was not dissolved in any solvent. The stock solutions of CuSO4 and MnSO4 were autoclaved at 121℃ for 20 min, and the stock solution of veratryl alcohol was sterilized by a 0.22 μm PES filter. For the RNA-seq experiment, the final concentration of 4-phenoxybenzoic acid and 9,10-dibutoxyanthracene was 10 mg ·L−1 and 5 mg ·L−1, respectively. The phenetole was added directly to the cultures at a final concentration of 200 mg ·L−1.  Mycelial samples for RNA-seq were collected after 1 d and 3 d after adding the LMCs to the cultures. The cultures were filtered using nylon, and the mycelium was washed with MM to remove excess culture medium, flash frozen in liquid nitrogen, and stored at -80°C before the RNA was extracted.

value: mycelium

value: WF8 strain


title: mycelium, 4-phenoxybenzoic acid, 1 day, flask rep2

description: Library name: p_PBA_f2_1d


title: mycelium, 4-phenoxybenzoic acid, 3 day, flask rep2

description: Library name: p_PBA_f2_3d


title: KRAB sorted low GFP rep1

description:
Library name: 289_Low_R1
R1_lo


title: Tet1c sorted high GFP rep1

description:
Library name: 154-high-r1
154_H_R1


title: mycelium, 4-phenoxybenzoic acid, 3 day, flask rep1

description: Library name: p_PBA_f1_3d


title: KRAB sorted low GFP rep2

description:
Library name: 289_Low_R2
R2_lo


title: KRAB sorted high GFP rep3

description:
Library name: 289_High_R3
R3_hi


title: mycelium, phenetole, 1 day, flask rep3

description: Library name: PE_f3_1d


title: KRAB sorted high GFP rep2

description:
Library name: 289_High_R2
R2_hi


title: VP64 sorted low GFP rep3

description:
Library name: 287_Low_R3
R3.lo


title: mycelium, phenetole, 3 day, flask rep3

description: Library name: PE_f3_3d


title: mycelium, phenetole, 3 day, flask rep2

description: Library name: PE_f2_3d


title: mycelium, phenetole, 3 day, flask rep1

description: Library name: PE_f1_3d


title: mycelium, 9-10-dibutoxyanthracene, 3 day, flask rep3

description: Library name: P9_10_O_f3_3d


title: mycelium, 9-10-dibutoxyanthracene, 3 day, flask rep1

description: Library name: P9_10_O_f1_3d


title: mycelium, 9-10-dibutoxyanthracene, 1 day, flask rep2

description: Library name: P9_10_O_f2_1d


title: mycelium, 4-phenoxybenzoic acid, 1 day, flask rep3

description: Library name: p_PBA_f3_1d


title: mycelium, 4-phenoxybenzoic acid, 1 day, flask rep1

description: Library name: p_PBA_f1_1d


title: mycelium, phenetole, 1 day, flask rep2

description: Library name: PE_f2_1d


title: mycelium, control, 1 day, flask rep3

description: Library name: CK_f3_1d


title: mycelium, control, 1 day, flask rep2

description: Library name: CK_f2_1d


title: mycelium, control, 3 day, flask rep2

description: Library name: CK_f2_3d


title: Root_PSBI3_1

city: Jeddah

first: Sabiha

last: Parween

address: Thuwal

department: Hirt lab

country: Saudi Arabia

institute: KAUST

description: Salt Bacteria I treated Root Plant 3

data_processing:
The reads were aligned to the reference genome of O. sativa Japonica cv. Nipponbare (IRGSP-1.0) and gene model annotation files were downloaded from RAP-DB (https://rapdb.dna.affrc.go.jp/). The obtained bam files were further converted in to gff files to analyse the data further. The number of reads in the alignments that overlap with gene features were counted with feature Counts v1.5.0-p3.
Assembly: O. sativa Japonica cv. Nipponbare
Supplementary files format and content: Normalized_data.csv

organism: Oryza sativa

source_name: Root

growth_protocol: Oryza sativa plants were grown in growth chambers at 27/25°C (day/night) with a 12:12 h light/dark cycle, the light intensity of 200 µmol photons m−2 s−1, and 70% humidity. For RNASeq analysis,  and flash-frozen in liquid N2 before RNA extraction. Total RNA was extracted from roots and shoots of 6-day-old mock and AK164, AK171 colonized plants using Direct-zol RNA Miniprep Plus Kit following the manufacturer’s instructions (ZYMO RESEARCH; USA). RNA libraries were prepared for sequencing using ....protocol. RNA-seq was carried out on three independent biological replicates.

extract_protocol:
After 24h, the shoots and roots were collected separately
Meta-transcriptome library preparation (strand specific library)

treatment_protocol: The 5-days-old seedlings were transferred to buckets containing Hoagland solution supplemented with 0 or 100 mM NaCl.

value: Root

value: Salt Bacteria I


title: mycelium, control, 3 day, flask rep1

description: Library name: CK_f1_3d


title: Root_PSBI1_1

description: Salt Bacteria I treated Root Plant 1


title: mycelium, control, 1 day, flask rep1

description: Library name: CK_f1_1d


title: Shoot_PSBI3_1

description: Salt Bacteria I treated Shoot Plant 3

source_name: Shoot

value: Shoot


title: mycelium, phenetole, 1 day, flask rep1

description: Library name: PE_f1_1d


title: Root_PBI3_1

description: Bacteria I treated Root Plant 3

value: Bacteria I


title: Root_PBI2_1

description: Bacteria I treated Root Plant 2


title: pDC from TLR7ko mice, biological rep 2

type: RNA

first: Trever

last: Greene

state: CA

address: 9500 Gilman Dr,

institute: University of California San Diego

hyb_protocol: Affymetrix GeneChip WT Terminal Labeling and Hybridization Manual

scan_protocol: Array scanning was performed according to manufacturer (Affymetrix) instructions

data_processing: Bioconductor Oligo package (Carvalho & Irizarry et al 2010) was used for preprocessing data (RMA normalization). Expression sets were then filtered using genefilter (Gentleman et al 2018) to exclude values with low expression or variance, as well as probes that did not correspond to an ENTREZ entry.

label: biotin

source_name: pDC

label_protocol: Extracted RNA was labeled and hybridized to Affymetrix Mouse Transcriptome Array 1.0 (MTA-1.0; one array per subject) according to the manufacturer’s instructions. WT cDNA Synthesis and Amplification kit and WT Sense Target Labelling and Control Reagents (Affymetrix) were used

extract_protocol: Qiagen Rneasy Micro Kit

treatment_protocol: Mixed bone marrow chimeras were infected with LCMV Cl13, and WT or TLR7ko pDC were isolated from the spleens of these mice at day 8 post infection prior to RNA extraction.

value: spleen


title: mycelium, 9-10-dibutoxyanthracene, 1 day, flask rep3

description: Library name: P9_10_O_f3_1d


title: Root_PBI1_1

description: Bacteria I treated Root Plant 1


title: mycelium, 9-10-dibutoxyanthracene, 3 day, flask rep2

description: Library name: P9_10_O_f2_3d


title: mycelium, 9-10-dibutoxyanthracene, 1 day, flask rep1

description: Library name: P9_10_O_f1_1d


title: pDC from WT mice, biological rep 2


title: Shoot_PBI1_1

description: Bacteria I treated Shoot Plant 1


title: mycelium, control, 3 day, flask rep3

description: Library name: CK_f3_3d


title: Root_PSBII3_1

description: Salt Bacteria II treated Root Plant 3

value: Salt Bacteria II


title: pDC from TLR7ko mice, biological rep 1


title: Root_PSBII2_1

description: Salt Bacteria II treated Root Plant 2


title: Root_PSBI2_1

description: Salt Bacteria I treated Root Plant 2


title: Shoot_PSBII1_1

description: Salt Bacteria II treated Shoot Plant 1


title: Shoot_PSBI1_1

description: Salt Bacteria I treated Shoot Plant 1


title: Shoot_PBI3_1

description: Bacteria I treated Shoot Plant 3


title: Root_PBII3_1

description: Bacteria II treated Root Plant 3

value: Bacteria II


title: Shoot_PBI2_1

description: Bacteria I treated Shoot Plant 2


title: Root_PSBII1_1

description: Salt Bacteria II treated Root Plant 1


title: VEEV, 48 mkd, Rep 4

data_processing:
CLC Genomics Workbench v 23.0
Sequence reads were trimmed  and filter using default parameters in CLC Genomic Workbench
Trimmed and filter sequence reads were mapped to GRCm39/virus species concatinated genome using default parameters in CLC Genomic Workbench
Read count results were collected in  CLC Genomic Workbench
Read count were normalized and fold change calculated using DESeq2
Assembly: GRCM39 concatinated with lab reference genome of each virus
Supplementary files format and content: tab-delimited text files include total counts for each sample
Supplementary files format and content: tab-delimited text files include total counts, TPM, CPM, and RPKM values for each sample

value: Brain

value: BALB/c

value: Infected, 48 mg/kg/day


title: Shoot_PSBII3_1

description: Salt Bacteria II treated Shoot Plant 3


title: Shoot_PBII1_1

description: Bacteria II treated Shoot Plant 1


title: Root_PS3_1

description: Salt treated Root Plant 3

value: Salt


title: Shoot_PSBII2_1

description: Salt Bacteria II treated Shoot Plant 2


title: Root_PS2_1

description: Salt treated Root Plant 2


title: Root_PS1_1

description: Salt treated Root Plant 1


title: Shoot_PS2_1

description: Salt treated Shoot Plant 2


title: Root_P2_1

description: Normal Condition Root Plant 2

value: Normal Condition


title: Shoot_PSBI2_1

description: Salt Bacteria I treated Shoot Plant 2


title: Root_PBII2_1

description: Bacteria II treated Root Plant 2


title: Shoot_PBII3_1

description: Bacteria II treated Shoot Plant 3


title: Root_PBII1_1

description: Bacteria II treated Root Plant 1


title: Shoot_PBII2_1

description: Bacteria II treated Shoot Plant 2


title: Shoot_PS3_1

description: Salt treated Shoot Plant 3


title: ∆PWS iPSC VP64 mat1 gRNA rep3 [ATAC-seq]

description:
Library name: PWS_VP64_mat1_r3
PWS_VP64_mat1_r3

data_processing:
Raw reads were trimmed using Trimmomatic to remove adapters.
Trimmed reads were aligned to hg19 genome using Bowtie2. Reads mapping to ENCODE blacklisted regions were removed, and duplicated reads were removed with Picard MarkDuplicates. Peaks were called using MACS2. bamCoverage was used to generate rpkm-normalized bigwig files from deduplicated bam files for visualization.
Union peak set was generated from narrowPeak files of all samples for each effector (VP64 or Tet1). Counts files were generated using the featureCounts function.
Differential peak analysis was determined with DESeq2 on the feature counts files, where gene counts are fitted into negative binomial generalized linear models (GLMs) and Wald statistics to determine significantly differentially expressed genes, with an adjusted p-value threshold of p<0.01.
Assembly: hg19
Supplementary files format and content: featurecounts table (read counts for each peak) in csv file.

extract_protocol:
14 days after gRNA virus transduction, cells were harvested with Accutase, pelleted, and the ATAC-seq protocol from Corces et al. 2017 was followed with 45,000 cells per sample with the following alterations: KAPA polymerase (Roche, KK2101) was used in the PCR step, following reaction condition recommendations for KAPA polymerase. Libraries were sequenced with 2x25 paired-end reads with a coverage of 50 million reads per sample.
ATAC libraries were prepared according to Corces et al. 2017 Omni-ATAC protocol, with KAPA polymerase as the polymerase used for library PCR.

value: iPSC

value: VP64 + mat1 gRNA


title: ∆PWS iPSC VP64 mat1 gRNA rep1 [ATAC-seq]

description:
Library name: PWS_VP64_mat1_r1
PWS_VP64_mat1_r1

value: PWS deletion


title: Root_P1_1

description: Normal Condition Root Plant 1


title: ∆PWS iPSC VP64 NT gRNA rep3 [ATAC-seq]

description:
Library name: PWS_VP64_nt_r3
PWS_VP64_nt_r3

value: VP64 + NT gRNA


title: Shoot_P2_1

description: Normal Condition Shoot Plant 2


title: WT iPSC VP64 NT gRNA rep1 [ATAC-seq]

description:
Library name: WT_VP64_nt_r1
WT_VP64_nt_r1

value: WT


title: ∆PWS iPSC Tet1v4 mat3 gRNA rep3

description: Library name: PWS_Tet1_mat3_rep3

data_processing:
Raw reads were trimmed using Trimmomatic to remove adapters.
Trimmed reads were aligned to hg19 genome using STAR aligner.
Gene counts were obtained with featureCounts from the subread package (v1.4.6-p4) using the comprehensive gene annotation in Gencode v22.
Differential expression analysis was determined with DESeq2 where gene counts are fitted into negative binomial generalized linear models (GLMs) and Wald statistics to determine significantly differentially expressed genes.
Assembly: hg19
Supplementary files format and content: featurecounts table (gene counts) in csv file.

growth_protocol: iPSCs were maintained in StemCell mTeSR Plus, with ROCK inhibitor (Y-27632) after seeding or passaging.

extract_protocol:
14 days after gRNA virus transduction, cells were harvested with Accutase, pelleted, and total RNA was extracted using Norgen Total RNA Plus Micro kit. Total RNA was submitted to Genewiz (Azenta) for library prep and total RNA sequencing.
RNA libraries were prepared by Genewiz/Azenta Life Sciences. Total RNA library was constructed with rRNA depletion method.

value: Tet1v4 + mat3 gRNA


title: ∆PWS iPSC VP64 NT gRNA rep2 [ATAC-seq]

description:
Library name: PWS_VP64_nt_r2
PWS_VP64_nt_r2


title: ∆PWS iPSC VP64 mat1 gRNA rep2 [ATAC-seq]

description:
Library name: PWS_VP64_mat1_r2
PWS_VP64_mat1_r2


title: Shoot_PS1_1

description: Salt treated Shoot Plant 1


title: Shoot_P1_1

description: Normal Condition Shoot Plant 1


title: Root_P3_1

description: Normal Condition Root Plant 3

value: Root


title: ∆PWS iPSC Tet1v4 mat3 gRNA rep2

description: Library name: PWS_Tet1_mat3_rep2


title: WT iPSC VP64 NT gRNA rep3 [ATAC-seq]

description:
Library name: WT_VP64_nt_r3
WT_VP64_nt_r3


title: ∆PWS iPSC Tet1v4 NT gRNA rep3

description: Library name: PWS_Tet1_NT_rep3

value: Tet1v4 + NT gRNA


title: ∆PWS iPSC Tet1v4 mat3 gRNA rep1

description: Library name: PWS_Tet1_mat3_rep1


title: ∆PWS iPSC Tet1v4 NT gRNA rep2

description: Library name: PWS_Tet1_NT_rep2


title: ∆PWS iPSC VP64 mat1 gRNA rep2

description: Library name: PWS_VP64_mat1_r2


title: ∆PWS iPSC VP64 NT gRNA rep1

description: Library name: PWS_VP64_nt_r1


title: ∆PWS iPSC VP64 NT gRNA rep2

description: Library name: PWS_VP64_nt_r2


title: ∆PWS iPSC VP64 mat1 gRNA rep3

description: Library name: PWS_VP64_mat1_r3


title: ∆PWS iPSC VP64 NT gRNA rep1 [ATAC-seq]

description:
Library name: PWS_VP64_nt_r1
PWS_VP64_nt_r1


title: Shoot_P3_1

description: Normal Condition Shoot Plant 3

value: Shoot


title: WT iPSC Tet1v4 NT gRNA rep1

description: Library name: WT_Tet1_NT_rep1


title: WT iPSC VP64 NT gRNA rep2 [ATAC-seq]

description:
Library name: WT_VP64_nt_r2
WT_VP64_nt_r2


title: WT iPSC VP64 NT gRNA rep3

description: Library name: WT_VP64_nt_r3


title: WT iPSC Tet1v4 NT gRNA rep3

description: Library name: WT_Tet1_NT_rep3


title: WT iPSC VP64 NT gRNA rep1

description: Library name: WT_VP64_nt_r1


title: WT iPSC Tet1v4 NT gRNA rep2

description: Library name: WT_Tet1_NT_rep2


title: WT iPSC VP64 NT gRNA rep2

description: Library name: WT_VP64_nt_r2


title: WT IgG high salt rep 6

first: Jessica

middle: A

last: Downs

address: 237 Fulham Road

data_processing:
Fastq reads were trimmed using TrimGalore (v0.6.6) using the options--trim-n--paired.
The human CHM13-T2Tv1.1 (GenBank GCA_009914755.3) and S. cerevisiae S288C (GenBank GCA_000146045.2) assemblies were combined into one FASTA file, then trimmed reads were mapped using Bowtie2 (v2.4.2) using the parameters --local --very-sensitive-local --no-unal --no-mixed --no-discordant --dovetail --soft-clipped-unmapped-tlen --non-deterministic --phred33 -I 50 -X 1500.
Reads with more than 3 mismatches were removed with Sambamba (v0.5.0), and their corresponding mates were removed with Picard tools (v2.23.8).
Sam files were converted to bam with SAMtools (v1.11). Reads mapped to the CHM13-T2Tv1.1 assembly were extracted using BAMtools (v2.5.1) split. Low and high salt BAM files from each sample were merged, sorted, and indexed using SAMtools.Uniquely mapped reads were extracted using sambamba (v0.5.0).
Bigwig files were made using Deeptools (v3.1.3) bamCoverage --extendReads --maxFragmentLength 1500 --binSize 10 –outFileFormat bigwig and normalised by total number of mapped reads.
Briefly, for k-mer analysis, reads that mapped to the peri/centromere in the CHM13-T2Tv1.1 assembly were extracted, deduplicated, trimmed and interleaved (L+H salt separately) using bedtools (v2.29.2), BBmap (v38.84) and trimmomatic (v0.39) packages. 51-mers that occur at least twice in each replicate were counted and dumped using kmc (v3.2.1). K-mers not counted in specific replicates were given an arbitrary count of 1, to allow average and fold change calculations. k-mer counts were normalised by dividing by the total base count (in reads that map to the whole genome), before average and fold change calculation. Adjusted p-values were calculated between groups using the genefilter (v1.80.0) package, with a BH-adjustment. Enriched k-mers were defined as those with at least 3 replicates having a normalised k-mer count > 2e-09, and an adjusted p-value < 0.1.
Bowtie2 (v2.4.2) was used to map these enriched k-mers back to the CHM13-T2Tv1.1 genome, using the specific parameters -f -k 5000 --score-min C,0,0
Bigwig files were generated from enriched k-mer bam files using deepTools (v3.5.1) bamCoverage tool using the following parameters --binSize 1 --scaleFactor 1
Assembly: T2T-CHM13v1.1
Supplementary files format and content: Bigwig files showing CUT&RUN read coverage for reads mapped uniquely (no multimapping) to the T2T-CHM13v1.1 reference genome.
Supplementary files format and content: Bigwig files showing mapping locations of k-mers (up to 5000 exact matches per k-mer) after being mapped to the T2T-CHM13v1.1 reference genome.
Library strategy: CUT&RUN

growth_protocol: hTERT-RPE1 cells were cultured in Dulbecco Modified Minimal Essential Medium (DMEM)/F-12 (Sigma) supplemented with 10% FBS (Gibco), 200µM glutamax (Gibco), 0.26% sodium bicarbonate (Gibco), and 1% penicillin/streptomycin (P/S)(Sigma). Cells were maintained at 37oC in a humified incubator with 5% CO2

extract_protocol:
CUT&RUN was performed according to the CUT&RUN Assay Kit protocol (Cell Signaling Technology) with the following modifications. Cells were detached with Accutase (Sigma). 200,000 cells were collected per experiment and pelleted by centrifugation for 5 minutes at 600 x g. Beads were incubated in primary antibody on a nutator overnight at 4°C. MNase digestion was carried out at 0°C in an ice water bath for 30 minutes. Salt fractionation and DNA purification were carried out according to the CUT&RUN.salt protocol (PMID: 29386331). Briefly, after STOP buffer addition, samples were incubated at 4°C for 1 hour to release low-salt fragments. Beads were resuspended in low salt buffer (175mM NaCl, 10mM EDTA, 2mM EGTA, 0.1% TritonX-100, 20μg/mL glycogen), rocked at 4°C for 1 hour, centrifuged for 5 minutes at 16,000 x g, and the supernatant containing the low salt fraction was collected. High salt buffer (825mM NaCl, 10mM EDTA, 2mM EGTA, 0.1% TritonX-100, 20μg/mL glycogen) was added to beads dropwise with gentle vortexing. Samples were again rocked at 4°C for 1 hour, centrifuged for 5 minutes at 16,000 x g, and the supernatant containing the high salt fraction was collected. Low salt fractions were adjusted to 500mM NaCl. RNAse A (Thermo Fisher Scientific) was added to all fractions and samples were incubated at 37°C for 20 minutes. SDS (sodium dodecyl sulfate) and Proteinase K (Cell Signaling Technology) were added and samples were incubated at 50°C for 1 hour. DNA was extracted using phenol/chloroform and precipitated in 100% ethanol as described.
CUT&RUN libraries were constructed using the NEB Ultra II DNA library prep kit for Illumina with at least 12 cycles of PCR amplification. Libraries were profiled using the Agilent TapeStation D1000 high sensitivity ScreenTape on the Agilent 4150 TapeStation System

value: Retinal pigment epithelial

tag: cut&run antibody


title: WT IgG low salt rep 5

tag: genotype


title: ∆PWS iPSC Tet1v4 NT gRNA rep1

description: Library name: PWS_Tet1_NT_rep1

tag: treatment


title: WT IgG high salt rep 5


title: WT PBRM1 low salt rep 3

description:
WT_PBRM1_LH_r3.bw
PBRM1_enriched_kmers.bw

value: PBRM1 (Active Motif 61381)


title: WT IgG high salt rep 4


title: WT PBRM1 low salt rep 2

description:
WT_PBRM1_LH_r2.bw
PBRM1_enriched_kmers.bw


title: WT PBRM1 high salt rep 1

description:
WT_PBRM1_LH_r1.bw
PBRM1_enriched_kmers.bw


title: WT PBRM1 low salt rep 1


title: MOLE_SVR24_B_cells_3p

city: Darlinghurst

first: Timothy

middle: John

last: Peters

state: NSW

address: 384 Victoria St

department: Immunology

country: Australia

institute: Garvan Institute of Medical Research

data_processing:
Raw sequencing files binary base call (bcl) files were demultiplexed and converted to Fastq using bcl2fastq (v2.19.0.316) (Illumina). Alignment and barcode counting were performed using cell ranger (v6.0.2) (10X Genomics). Gene expression reads were aligned to human genome reference GRCh38 (hg38). Gene expression count matrices were exported by cell barcode linked to a polyclonal or clonal annotation (as determined above) using R. Single cell gene expression counts were normalized using SAVER with default values. Single cells were excluded if the library size or number of expressed genes fell below 2 median absolute deviations, or if mitochondrial reads accounted for more than 20% of the reads. Polyclonal naïve and B cell memory clusters were determined using landmark genes IGHM, IGHG1, IGHD, TCL1A. Differentially expressed genes were determined using limma on log normalised values. Bonferroni correction was applied to each set of p-values, to determine the family-wise error rate (FWER). Statistically significant differentially expressed genes were defined as FWER <0.05.
Assembly: GRCh38.p12
Supplementary files format and content: tsv.gz
Supplementary files format and content: mtx.gz

source_name: B cell

extract_protocol:
PBMCs were thawed and washed in 2% FCS/PBS and incubated with Fc block for 20 min on ice. PBMCs were stained with eF780 Fixable Viability Dye (ThermoFisher Scientific) and a cocktail of antibodies (see Key resources table) for 30 mins on ice. Anti-idiotypic monoclonal antibody G6, specific for F-allele IGHV1-69 heavy chains, was fluorescently labelled using the Alexa Fluor 488 Antibody Labelling kit (Life Technologies). After staining, cells were washed and fixed in 2% formaldehyde (5% formalin, Sigma) for 15 min on ice. Total B cells (CD19+CD20+) from PBMC were sorted at the clearance (HCV-) timepoint.
Single cell V(D)J  and RNA-sequencing at the clearance (HCV-) timepoint was performed using Repertoire and Gene Expression by Sequencing (RAGE-Seq) using droplet based capture of approximately 10,000 cells using 10X Genomics Chromium 3’ system as described. In brief, following reverse transcription and before fragmentation, two extra PCR cycles were performed and full length cDNA equally spilt for short-read gene expression library generation (Illumina) and targeted V(D)J capture followed by long-read library generation (Oxford Nanopore Technologies, ONT). Short-read gene expression libraries were sequenced on a NovaSeq 6000 (Illumina) at 50,000 mean reads per cell.

value: B cell


title: WT IgG low salt rep 4


title: WT PBRM1 high salt rep 3


title: ∆PWS iPSC VP64 mat1 gRNA rep1

description: Library name: PWS_VP64_mat1_r1


title: WT PBRM1 high salt rep 2


title: ∆PWS iPSC VP64 NT gRNA rep3

description: Library name: PWS_VP64_nt_r3


title: NKX2-3-3_1

city: guangzhou

first: xiaoyu

last: wu

state: guangdong

address: huangpu road

institute: jinan university

data_processing:
The fragmented RNA pieces were used to construct library by Hieff NGS® Ultima Dual-mode mRNA Library Prep Kit and sequenced with Illumina Novaseq™ 6000
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Human colorectal cancer

extract_protocol:
Total RNA was extracted using TRIzol reagent (Life technologies) according to the manufacturer manual. The RNA concentration and integrity were evaluated by NanoDrop 2000.
TPCs derived from CRC patients with liver metastasis were infected with Guide RNA of NKX2-3 for 48 h and selected by puromycin (2 mg/mL).

value: Human colorectal cancer

value: TPCs

value: stromal cell

value: NKX2-3 knockdown

value: Transfection of knockdown lentivirus


title: NKX2-3-2_1


title: Hypoxia-enhanced kidney organoids

city: Ulsan

first: Tae-Eun

last: Park

address: 50, UNIST-gil, Eonyang-eup, Ulju-gun

country: South Korea

institute: Ulsan National Institute of Science and Technology (UNIST)

data_processing:
Raw sequencing data of FASTQ files were performed quality control and aligned to GRCh38 human reference genome using Cell Ranger (v7.0.1) (10X Genomics).
Assembly: GRCh38
Supplementary files format and content: Tab-separatedvalues (tsv) files and matrix files

source_name: hiPSC-derived kidney organoids

extract_protocol:
To obtain single cells from kidney organoids, detached organoids were harvested by gentle pipetting and then dissociated using Accutase for 20 min. Isolated cells were washed and resuspended in PBS containing 0.04% BSA.
Cells were prepared according to manufacturer’s protocol (10X Genomics). Sequencing libraries were constructed using 10X Chromium Next GEM Single Cell 3' reagent kit v3.1 (10X Genomics).

value: hiPSC-derived kidney organoids

value: hypoxia


title: NKX2-3-1_1


title: SCR-3_1

value: Transfection of Negative control lentivirus


title: SCR-1_1


title: U-2 OS, PPARG-EGFP,cut&tag, rep3

city: Hangzhou

first: Tianyu

last: Guo

state: Zhejiang

address: 866 Yuhangtang Road

institute: Zhejiang University

data_processing:
*library strategy: CUT&TAG
The sequences were processed using fastq.
The clean reads were aligned to hg38 with BWA mem algorithm.
Peaks were called using macs2 callpeak -f BEDPE -g hs.
Assembly: hg38
Supplementary files format and content: BEDPE, BigWig

source_name: U-2 OS

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37℃ at 5% CO2.

extract_protocol:
CUT&TAG sequencing sample preparation was performed using reagent in Hyperactive In Situ ChIP Library Prep Kit for Illumina (pG-Tn5).
CUT&TAG sequencing sample preparation and library construction was performed using Hyperactive In Situ ChIP Library Prep Kit for Illumina (pG-Tn5) (Vazyme, China), VAHTS DNA Clean Beads (Vazyme, China) and TruePrep Index kit V2 for Illumina (Vazyme, China) according to the manufacturer’s instruction.

value: U-2 OS

tag: chip antibody

value: GFP Polyclonal antibody (Invitrogen, A11122)

value: osteosarcoma


title: WT IgG low salt rep 6

value: WT


title: RPE1 PBRM1 KO B16 rep 1

description:
RPE1_normalised_reads.csv
RPE1_centromere_TE_normalised_read_counts.csv

data_processing:
Fastq reads were trimmed using TrimGalore --trim-n --paired (fastqc0.11.9).
Residual ribosomal RNA reads were removed using Ribodetector with -e norRNA setting (v0.2.7) and strandedness was detected using RSeQC (v4.0.0).
Reads were aligned to the T2T-CHM13v2.0 genome using STAR alignment software (v2.7.6a) --outFilterMultimapNmax 10
Reads mapping to genes were quantified using HTSeqCount (v0.12.4) --stranded=reverse --nonunique=none
Differential analysis of gene expression was calculated in R using DESeq2 (v1.38.3).
For TEs, reads were aligned to the T2T-CHM13v2.0 genome using STAR alignment software (v2.7.6a) --outFilterMultimapNmax 100 --winAnchorMultimapNmax 100
Reads uniquely mapping to TEs were quantified using TElocal (v1.1.1) --stranded reverse --mode uniq using chm13v2.0_GENCODEv35_CAT_Liftoff.vep.gtf  to count the genes and the provided prebuilt indices to map to TEs at a locus level (T2T_CHM13_v2_rmsk_TE.gtf.locInd)
Differential analysis of TE expression was calculated in R using DESeq2 (v1.38.0)
Assembly: T2T-CHM13v2.0
Supplementary files format and content: csv files showing normalised reads calculated using DESeq2 (v1.38.3).
Supplementary files format and content: csv files showing normalised reads of TEs in the peri/centromere - normalised counts were calculated using DESeq2 (v1.38.0), and TEs in peri/centromere were extracted using bedtools (v2.29.2)

growth_protocol: hTERT-RPE1 cells were cultured in Dulbecco Modified Minimal Essential Medium (DMEM)/F-12 (Sigma) supplemented with 10% FBS (Gibco), 200µM glutamax (Gibco), 0.26% sodium bicarbonate (Gibco), and 1% penicillin/streptomycin (P/S)(Sigma). 1BR3-hTERT cells were cultured in  Dulbecco Modified Eagle medium (DMEM) (Sigma), supplemented with 10% FBS (Gibco) and 1% penicillin/streptomycin (P/S)(Sigma). Cells were maintained at 37oC in a humified incubator with 5% CO2

extract_protocol:
Pellets were harvested by scraping cells in ice-cold PBS following by centrifugation at 7,500 x g for 10 minutes. Pellets were resuspended in 500µL TRIzol reagent (Invitrogen) and total RNA was extracted using a Direct-zol RNA miniprep kit (Zymo Research) according to the manufacturer’s protocol. RNA concentration and quality was confirmed with the Agilent High sensitivity RNA ScreenTape, using the Agilent 4150 TapeStation System.
Library preparation was performed by Novogene Corporation Ltd, using the Novogene NGS Stranded RNA Library Prep Set (PT044) and an in-house protocol for 250~300 bp insert strand specific library preparation. 50 million 150bp paired-end stranded reads were sequenced on an Illumina NovaSeq 6000 using an S4 flow cell.
RNA-seq with rRNA removal to include ncRNAs and lncRNAs

value: Retinal pigment epithelium


title: RPE1 PBRM1 KO B16 rep 2


title: RPE1 PBRM1 KO B3 rep 2


title: U-2 OS, PPARG-EGFP,cut&tag, rep1


title: RPE1 PBRM1 KO B3 rep 1


title: RPE1 WT rep 3


title: RPE1 WT rep 1


title: RPE1 WT rep 2


title: 1BR3 WT rep 3

description:
1BR3_normalised_reads.csv
1BR3_centromere_TE_normalised_read_counts.csv

value: Skin fibroblast


title: 1BR3 PBRM1 KO B3 rep 1


title: 1BR3 PBRM1 KO B5 rep 2


title: SMARCA4KO SMARCA4 high salt rep 3

value: Retinal pigment epithelial

value: SMARCA4 (Abcam ab110641)


title: SMARCA4KO SMARCA4 low salt rep 3


title: SMARCA4KO SMARCA4 high salt rep 2


title: 1BR3 WT rep 1


title: SMARCA4KO SMARCA4 low salt rep 2


title: 1BR3 WT rep 2


title: SCR-2_1

tag: tissue


title: U-2 OS, PPARG-EGFP,cut&tag, rep2


title: SMARCA4KO SMARCA4 high salt rep 1


title: SMARCA4KO SMARCA4 low salt rep 1


title: Normal kidney organoids

value: normoxia


title: PBRM1KO IgG high salt rep 3


title: PBRM1KO IgG low salt rep 3


title: PBRM1KO IgG high salt rep 2


title: PBRM1KO IgG high salt rep 1


title: PBRM1KO SMARCA4 high salt rep 3


title: PBRM1KO IgG low salt rep 6

data_processing:
Fastq reads were trimmed using TrimGalore (v0.6.6) using the options--trim-n--paired.
The human CHM13-T2Tv1.1 (GenBank GCA_009914755.3) and S. cerevisiae S288C (GenBank GCA_000146045.2) assemblies were combined into one FASTA file, then trimmed reads were mapped using Bowtie2 (v2.4.2) using the parameters --local --very-sensitive-local --no-unal --no-mixed --no-discordant --dovetail --soft-clipped-unmapped-tlen --non-deterministic --phred33 -I 50 -X 1500.
Reads with more than 3 mismatches were removed with Sambamba (v0.5.0), and their corresponding mates were removed with Picard tools (v2.23.8).
Sam files were converted to bam with SAMtools (v1.11). Reads mapped to the CHM13-T2Tv1.1 assembly were extracted using BAMtools (v2.5.1) split. Low and high salt BAM files from each sample were merged, sorted, and indexed using SAMtools. Uniquely mapped reads were extracted using sambamba (v0.5.0).
Bigwig files were made using Deeptools (v3.1.3) bamCoverage --extendReads --maxFragmentLength 1500 --binSize 10 –outFileFormat bigwig and normalised by total number of mapped reads.
Briefly, for k-mer analysis, reads that mapped to the peri/centromere in the CHM13-T2Tv1.1 assembly were extracted, deduplicated, trimmed and interleaved (L+H salt separately) using bedtools (v2.29.2), BBmap (v38.84) and trimmomatic (v0.39) packages. 51-mers that occur at least twice in each replicate were counted and dumped using kmc (v3.2.1). K-mers not counted in specific replicates were given an arbitrary count of 1, to allow average and fold change calculations. k-mer counts were normalised by dividing by the total base count (in reads that map to the whole genome), before average and fold change calculation. Adjusted p-values were calculated between groups using the genefilter (v1.80.0) package, with a BH-adjustment. Enriched k-mers were defined as those with at least 3 replicates having a normalised k-mer count > 2e-09, and an adjusted p-value < 0.1.
Bowtie2 (v2.4.2) was used to map these enriched k-mers back to the CHM13-T2Tv1.1 genome, using the specific parameters -f -k 5000 --score-min C,0,0
Bigwig files were generated from enriched k-mer bam files using deepTools (v3.5.1) bamCoverage tool using the following parameters --binSize 1 --scaleFactor 1
Assembly: T2T-CHM13v1.1
Supplementary files format and content: Bigwig files showing CUT&RUN read coverage for reads mapped uniquely (no multimapping) to the T2T-CHM13v1.1 reference genome.
Supplementary files format and content: Bigwig files showing mapping locations of k-mers (up to 5000 exact matches per k-mer) after being mapped to the T2T-CHM13v1.1 reference genome.
Library strategy: CUT&RUN

source_name: Retina

value: Retina


title: PBRM1KO IgG low salt rep 1


title: 1BR3 PBRM1 KO B5 rep 1


title: PBRM1KO SMARCA4 low salt rep 3


title: 1BR3 PBRM1 KO B3 rep 2


title: PBRM1KO IgG high salt rep 6


title: PBRM1KO SMARCA4 low salt rep 2


title: PBRM1KO IgG low salt rep 5


title: PBRM1KO SMARCA4 high salt rep 2


title: PDBAG1-3

first: Xingxing

last: Li

address: 123 Tianfei Road

institute: Women’s Hospital of Nanjing Medical University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)
Removing reads containing sequencing adapter;
Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%;
Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
Assembly: Genome_build: GRCh38.p12
Supplementary files format and content: The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by RSEM (v1.2.12) .

source_name: Breast cancer tissue

growth_protocol: Cells were grown in Dulbecco’s Modified Eagle’s Medium (Gibco, USA) supplemented with 10% FBS and 1% penicillin-streptomycin mixture and incubated at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from treated MDA-MB-231 cells by using TRIzol reagent (Thermo Fisher Scientific).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with vehicle and 30μM PDBAG1 for 24 hours.

value: Breast cancer tissue


title: PBRM1KO IgG high salt rep 4

institute: The Institute of Cancer Research


title: PBRM1KO IgG high salt rep 5


title: PBRM1KO IgG low salt rep 4


title: PBRM1KO SMARCA4 high salt rep 1


title: PBRM1KO H3K9me3 high salt rep 3


title: PBRM1KO H3K9me3 low salt rep 3


title: PBRM1KO SMARCA4 low salt rep 1


title: PBRM1KO H3K9me3 low salt rep 2


title: PDBAG1-1


title: WT IgG high salt rep 3

description:
WT_IgG_LH_r3.bw
IgG_vs_H3K27me3_enriched_kmers.bw


title: PBRM1KO IgG low salt rep 2


title: PBRM1KO H3K9me3 high salt rep 1


title: PBRM1KO H3K9me3 high salt rep 2


title: PBRM1KO H3K9me3 low salt rep 1


title: Vehicle-3

value: vehicle


title: PBRM1KO H3K9me2 high salt rep 3

value: H3K9me2 (Millipore 05-1249)


title: WT IgG low salt rep 3


title: Vehicle-2


title: PBRM1KO H3K9me2 low salt rep 3


title: PBRM1KO H3K9me2 high salt rep 2


title: WT IgG low salt rep 2

description:
WT_IgG_LH_r2.bw
IgG_vs_H3K27me3_enriched_kmers.bw


title: PBRM1KO H3K9me2 low salt rep 2


title: Vehicle-1


title: PBRM1KO H3K9me2 high salt rep 1


title: PBRM1KO H3K9me2 low salt rep 1


title: PDBAG1-2


title: WT IgG high salt rep 8


title: WT IgG low salt rep 1

description:
WT_IgG_LH_r1.bw
IgG_vs_H3K27me3_enriched_kmers.bw


title: Sora-3

first: Shuowang

address: Yuhang Tang Street No.866

description: Library name: sora-3

data_processing:
The libraries were sequenced on an Illumina NovaSeq 6000 platform, generating 150 bp paired-end reads. Approximately 40M raw reads for each sample were produced. The raw reads in FASTQ format were first processed using fastp to remove low-quality reads, thereby obtaining the clean reads. Subsequently, approximately 40 clean reads for each sample were retained for further analyses. These clean reads were then mapped to the reference genome using HISAT2. The FPKM (Fragments Per Kilobase of transcript per Million mapped reads) of each gene was calculated, and the read counts of each gene were obtained by HTSeq-count. PCA (Principal Component Analysis) was performed using R (v 3.2.0) to evaluate the biological duplication of the samples.
Differential expression analysis was performed using DESeq2. Q value < 0.05 and a fold change > 2 or < 0.5 were set as the thresholds for identifying significantly differentially expressed genes (DEGs). Hierarchical cluster analysis of DEGs was conducted using R (v 3.2.0) to illustrate the expression patterns of genes across different groups and samples. Additionally, a radar map of the top 30 genes was generated using the R package ggradar to visualize the expression levels of up-regulated and down-regulated DEGs.
Based on the hypergeometric distribution, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, Reactome, and WikiPathways enrichment analyses of differentially expressed genes (DEGs) were performed to identify significantly enriched terms using R (v 3.2.0). R (v 3.2.0) was also utilized to generate column diagrams, chord diagrams, and bubble diagrams to visualize the significantly enriched terms.
Gene Set Enrichment Analysis (GSEA) was performed using GSEA software. A predefined gene set was used, and the genes were ranked based on the degree of differential expression between the two types of samples. The analysis then tested whether the predefined gene set was significantly enriched at the top or bottom of the ranking list.
Assembly: GRCm39
Supplementary files format and content: txt format inculde the FPKM and row gene counts for each sample

source_name: Hep1-6 tumor tissue

extract_protocol:
Total RNA was extracted using TRIzol reagent (9109, TaKaRa, Kusatsu, Shiga, Japan) and reverse transcribed into cDNA using a cDNA synthesis kit (RR047A, TaKaRa) according to the manufacturer’s instructions.
RNA purity and quantification were assessed using a NanoDrop 2000 Spectrophotometer (Thermo Scientific, USA), while RNA integrity was evaluated with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The transcriptome library was constructed following the manufacturer's instructions using the VAHTS Universal V5 RNA-seq Library Prep Kit.

value: Hep1-6 tumor tissue

value: sorafenib treated


title: WT IgG low salt rep 8


title: Sora-2

description: Library name: sora-2


title: WT IgG high salt rep 7


title: Ctrl-4

description: Library name: ctrl-4

value: control


title: WT H3K9me3 high salt rep 3


title: WT H3K9me3 low salt rep 3


title: WT IgG low salt rep 7


title: WT H3K27me3 low salt rep 3


title: Ctrl-3

description: Library name: ctrl-3


title: WT H3K27me3 high salt rep 2


title: WT H3K9me3 low salt rep 2


title: WT H3K9me3 high salt rep 1


title: WT IgG high salt rep 2


title: Ctrl-1

description: Library name: ctrl-1


title: WT H3K9me3 low salt rep 1


title: WT H3K9me2 high salt rep 3


title: Sora-4

description: Library name: sora-4


title: WT H3K27me3 low salt rep 2


title: WT IgG high salt rep 1


title: sora-3

source_name: Treg cell

value: Treg cell

value: sorafenib


title: WT H3K27me3 high salt rep 1


title: WT H3K9me2 low salt rep 3


title: WT H3K9me2 low salt rep 2


title: WT H3K27me3 low salt rep 1


title: sora-1


title: sora-2


title: WT H3K9me2 high salt rep 2


title: WT H3K27me3 high salt rep 3


title: WT H3K9me2 high salt rep 1


title: WT CENPB high salt rep 3

description:
WT_CENPB_LH_r3.bw
CENPB_vs_IgG_enriched_kmers.bw

value: CENPB (Abcam ab25734)


title: WT H3K9me2 low salt rep 1


title: ∆PWS iPSC Tet1v4 mat3 gRNA rep1 [ATAC-seq]

description:
Library name: PWS_Tet1c_G4363_r2
PWS_Tet1c_mat3_r2

value: iPSC

value: PWS deletion

value: Tet1v4 + mat3 gRNA


title: WT CENPB low salt rep 3

value: WT


title: ∆PWS iPSC Tet1v4 NT gRNA rep3 [ATAC-seq]

description:
Library name: PWS_Tet1c_NT_r3
PWS_Tet1c_NT_r3

value: Tet1v4 + NT gRNA


title: control-3


title: ∆PWS iPSC Tet1v4 NT gRNA rep2 [ATAC-seq]

description:
Library name: PWS_Tet1c_NT_r2
PWS_Tet1c_NT_r2


title: control-2


title: WT CENPB high salt rep 2

description:
WT_CENPB_LH_r2.bw
CENPB_vs_IgG_enriched_kmers.bw

value: Retinal pigment epithelial


title: ∆PWS iPSC Tet1v4 NT gRNA rep1 [ATAC-seq]

description:
Library name: PWS_Tet1c_NT_r1
PWS_Tet1c_NT_r1


title: control-1


title: WT CENPB low salt rep 2


title: WT iPSC Tet1v4 NT gRNA rep1 [ATAC-seq]

description:
Library name: WT_Tet1c_NT_r1
WT_Tet1c_NT_r1


title: Positive control cell sample K4me3 K met stat panel [CR]

description: Library name: pos-K4me3

data_processing:
Sequencing data were processed using CUT&RUNTools 2.0, and peaks for H3K4me3 signal were annotated using MACS2 narrow peak calling.
Data were visualised in a genome viewer as cpm-normalized bigwig files.
Assembly: hg19
Supplementary files format and content: cpm-normalized bigwig
Library strategy: CUT&Run

extract_protocol:
2 weeks after gRNA virus transduction, cells were harvested with Accutase, and cell concentration and cell number were assessed with a Countess II cell counter (Invitrogen) and Trypan Blue (Invitrogen).
Library preparation was completed using the CUT&RUN Library Prep Kit with primer set 1 (Epicypher 14-1001). Libraries were sequenced on an Illumina Nextseq 2000 with a coverage of at least 5 million reads per sample.

value: assay control


title: Inf_Smoke_D

city: RTP

first: Xiaojiang

last: Xu

address: 111 T. W. Alexander Dr.,

institute: NIEHS

description: Illumina

data_processing:
Reads were aligned to the UCSC mm10 reference genome using STAR with default parameters. The quantification results from featureCounts were then analyzed with the Bioconductor package DESeq2
Assembly: mm10
Supplementary files format and content: Excel

source_name: Stomach

growth_protocol: Mice were housed in regular growth conditions

extract_protocol:
RNA was extracted in TRIzol (ThermoFisher) and precipitated from the aqueous phase using 1.5 volumes of 100% ethanol. The mixture was transferred to an RNA isolation column (Omega Bio-Tek), and the remaining steps were followed according to the manufacturer’s recommendations. Reverse transcription followed by qPCR was performed in the same reaction using the Universal Probes One-Step PCR kit (Bio-Rad Laboratories) and the TaqMan primers: Ppib (Mm00478295_m1), Aqp5 (Mm00437578_m1), and Gkn3 (Mm01183934_m1) (all from Thermofisher).
Libraries were prepared using a NEB ultraII directional kit (New England Biolabs), and 40 million paired-end reads were collected per library using an Illumina HiSeq (Illumina)

treatment_protocol: Infected mice were exposed to smoke from Marlboro Red cigarettes in whole-body inhalation chambers using the Gram’s Universal smoke machine (Gram Research). Puff volume was 87ml, with a 5-second inhale and 3-second exhale. Mainstream smoke was pumped into the chamber while sidestream fresh air was constantly provided. Chamber total flow rate was 4.3 L/min. The mice were exposed for approximately 2 hours/day, with each cigarette burning for approximately 7 minutes with a 5-minute break between cigarettes; the mice were exposed to 10 cigarettes/day. Mock-infected and H. pylori-infected control mice were exposed to filtered air in parallel with the smoke-exposed groups. Mice were exposed 5 days/week for 2 months.

value: Stomach

value: C57BL/6J WT

value: Helicobacter pylori PMSS4 + smoke


title: WT CENPB high salt rep 1

description:
WT_CENPB_LH_r1.bw
CENPB_vs_IgG_enriched_kmers.bw


title: Negative control IgG K met stat panel [CR]

description: Library name: NC-IgG-neg


title: Inf_Smoke_C

description: Illumina


title: ∆PWS iPSC Tet1v4 mat3 gRNA rep2 [CR]

description: Library name: 18-dPWS-Tet1-mat3


title: WT CENPB low salt rep 1


title: ∆PWS iPSC Tet1v4 NT gRNA rep2 [CR]

description: Library name: 15-dPWS-Tet1-NT


title: Inf_Smoke_A

description: Illumina


title: ∆PWS iPSC Tet1v4 mat3 gRNA rep1 [CR]

description: Library name: 17-dPWS-Tet1-mat3


title: Inf_Air_E

description: Illumina

value: Helicobacter pylori PMSS3


title: ∆PWS iPSC Tet1v4 mat3 gRNA rep2 [ATAC-seq]

description:
Library name: PWS_Tet1c_G4363_r3
PWS_Tet1c_mat3_r3


title: ∆PWS iPSC Tet1v4 NT gRNA rep1 [CR]

description: Library name: 13-dPWS-Tet1-NT


title: WT SMARCA4 high salt rep 3

description:
WT_SMARCA4_LH_r3.bw
SMARCA4_vs_IgG_enriched_kmers.bw

value: SMARCA4 (Abcam ab110641)


title: ∆PWS iPSC VP64 mat1 gRNA rep1 [CR]

description: Library name: 07-dPWS-VP64-mat1

value: VP64 + mat1 gRNA


title: ∆PWS iPSC VP64 mat1 gRNA rep2 [CR]

description: Library name: 08-dPWS-VP64-mat1


title: Inf_Air_B

description: Illumina

value: Helicobacter pylori PMSS2


title: WT SMARCA4 low salt rep 3


title: WT H3K9me3 high salt rep 2

value: Retina


title: WT iPSC Tet1v4 NT gRNA rep2 [ATAC-seq]

description:
Library name: WT_Tet1c_NT_r2
WT_Tet1c_NT_r2


title: Inf_Air_A

description: Illumina

value: Helicobacter pylori PMSS1


title: ∆PWS iPSC VP64 NT gRNA rep2 [CR]

description: Library name: 06-dPWS-VP64-NT

value: VP64 + NT gRNA


title: WT SMARCA4 high salt rep 2

description:
WT_SMARCA4_LH_r2.bw
SMARCA4_vs_IgG_enriched_kmers.bw


title: WT SMARCA4 low salt rep 2


title: ∆PWS iPSC VP64 NT gRNA rep1 [CR]

description: Library name: 05-dPWS-VP64-NT

value: iPSC


title: WT iPSC VP64 NT gRNA rep1 [CR]

description: Library name: 01-WT-VP64-NT


title: WT SMARCA4 low salt rep 1

description:
WT_SMARCA4_LH_r1.bw
SMARCA4_vs_IgG_enriched_kmers.bw


title: WT iPSC Tet1v4 NT gRNA rep2 [CR]

description: Library name: 12-WT-Tet1-NT


title: WT iPSC Tet1v4 NT gRNA rep1 [CR]

description: Library name: 11-WT-Tet1-NT


title: WT iPSC VP64 NT gRNA rep2 [CR]

description: Library name: 02-WT-VP64-NT