title: Biological rep#2, Cells transfected with HDR-CRISPR, T cells

description: Sequencing outsourced to GeneWiz

data_processing:
Mate paired reads were merged using BBmerge from BBmap (v38.76) software. BBmap  was also used for filtering and trimming as follow: merged reads containing the designer nuclease target site were filtered-in, whereas PCR mispriming products reads were filtered-out. Linker sequences, Illumina adapter sequences, targeted elongation sequence and bad quality reads were trimmed.
Selected reads were aligned to the human genome GRCh38 (hg38) using Bowtie2 (v2.3.4.2) and the very-sensitive preset parameters. Aligned reads with good mapping quality (MAPQ >15) were selected. The aligned BAM file was converted into bed file using bedtools (v2.27.1).
Translocated sites were identified using the CAST-Seq pipeline with default parameters, as described on https://github.com/AG-Boerries/CAST-Seq
Assembly: hg38
Supplementary files format and content: matrix table of translocation sites detected with T-CAST pipeline. It includes the genomic coordinates of translocated sites, read coverage.
Library strategy: CAST-seq

source_name: T cells

growth_protocol: Human peripheral blood mononuclear cells (PBMCs) were isolated from leukocyte reduction system chambers by density gradient centrifugation (Ficoll-Paque). PBMCs were kept in RPMI 1640 medium (Life Technologies) supplemented with 10% FCS (Thermo Fisher Scientific) and 1% Penicillin/Streptomycin (Merck) for 4 hours before activation. PBMCs/ T cells were cultured at 37°C with 5% CO2.

extract_protocol:
Cells were harvested 2 days post electroporation and their genomic DNA was extracted using the NucleoSpin® Tissue gDNA extraction kit (Machery Nagel) following the manufacture’s procedure and resuspended in 40 uL of Nuclease-free water.
Library construction was essentially performed as described by Turchiano et. al (Cell Stem Cell, 2021). Briefly, gDNA was fragmented by enzymatic digestion using the NEBNext® Ultra™ II FS DNA Library Prep (NEB) to obtain average fragment lengths of 200-350 bp. The DNA was end repaired and a protruding 3’-A nucleotide was added according to the manufacturer’s instructions  in order to enable the ligation of a linker sequence with a protruding 3’-T. After linker ligation, fragments were purified using the QIAquick PCR Purification Kit (NEB). The region of interes (on-target site) was amplified in two rounds of PCR using Q5® Hot Start High-Fidelity DNA Polymerase (NEB). PCR conditions were: 20 cycles at 95°C for 15 s, 63°C (first reaction) or 68°C (second reaction) for 20 s, 72°C for 20 s. The first reaction was performed with primers complementary to the linker sequence and to a sequence in close proximity to the on-target site (bait primer). Two decoy primers were introduced to reduce full-length amplification of the fragments which contain the on-target sequence without a chromosomal aberration event. The second PCR utilized nested primers to reduce the amount of mis-amplified fragments and to introduce a binding platform for barcoding primers. DNA fragments from the second PCR with a size of 200-500bp were subsequently isolated using the QIAquick® Gel Extraction Kit (Qiagen) and barcoded.
Third PCR introduced the barcoded Illumina adapter for sequencing (NEBNext® Multiplex Oligos for Illumina; Index Primers Sets 1-4). Sequencing was outsourced to service NGS provider Genewiz (part of Azenta Life Sciences) on where it was performed on Illumina HiSeq or NovaSeq devices collecting 2x150 bp paired-end reads.

treatment_protocol: PBMCs were activated 4 hours after thawing in complete RPMI supplemented with IL-2 (100U/uL; Immunotools) using ImmunoCult™ Human CD3/CD28/CD2 T CellActivator (5 uL/1*106; STEMCELL Technologies) and kept at concentration of 2*10E6 cells/mL. Three days post-activation, 1x10E6 PBMCs were electroporated with a 4D-Nucleofector system (Lonza) using the P3 Primary Cell 4D-Nucleofector Kit (Lonza) and the EO-115 program. The DNA mixture contained 30 pmol of the nuclease expressing mRNA transcribed in vitro as previously described (20), 112,5 pmol of sgRNA (Synthego) and 25 pmol of ssODN (Integrated DNA Technologies). After electroporation, complete RPMI medium supplemented with IL-2 (1000U/mL; Immunotools) was used to recover the cells before culturing them in a 96-well Ushaped-bottom plate (Falcon). Cells were harvested 5 days post electroporation.

value: T cells

value: Electroporated with HDR-CRISPR expressing IVT mRNA + sgRNA


title: slr1-RNA_seq-2

status: Public on Aug 11 2023

type: SRA

city: Wuhan

first: Qi

last: Li

address: Lion Rock Street

department: Hongshan District

country: China

institute: Huazhong Agricultural University

library_source: transcriptomic

data_processing:
The RNA-seq clean data were mapped against the rice genome(MSU version 7.0) with the corre_x0002_sponding annotation by hisat2 using default parameters
FeatureCounts (version 2.0.0) and DESeq2 (version 1.38.3) were used to calculate DEGs
Assembly: MSU version 7.0 rice genome
Supplementary files format and content:output from DESeq

molecule: total RNA

organism: Oryza sativa Japonica Group

source_name: seedling

growth_protocol: Seedlings were grown in one-half-strength Murashige and Skoog medium under 14-h light/10-h dark cycles at 28/24 °C

extract_protocol:
Total RNA was extracted from the indicated tissues using TRIzol reagent (Invitrogen, USA) according to the manufac_x0002_turer’s protocol.
RNA-seq libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit and sequenced (paired-end, 2 x 150 bp).

treatment_protocol: In chemical treatment experiments, 100 uM GA (Sigma, G1025) was supplied to seedlings through the roots for various durations.

tag: tissue

value: seedling

tag: genotype

value: SLR1 knockout


title: RPE1, non-methylated, replicate 1

city: Helsinki

first: Konsta

last: Karttunen

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

data_processing:
FastQC v.0.11.9 was used for quality control and determination of read lengths of raw data.
Two technical replicates were combined before alignment.
Raw reads were mapped with bowtie2 v.2.4.1 (bowtie2 --maxins 1000) to the reference genome.
Picard v.2.23.4 was used to remove duplicates (MarkDuplicates -REMOVE_DUPLICATES false -ASSUME_SORTED true)
Samtools v.1.7 was used to filter non-concordant reads and reads with a MAPQ of smaller than 20 (samtools view -F 1024 -b -q 20).
Peaks were called with MACS2 v.2.2.7.1 with the STARR input library as control (macs2 callpeak -f BAMPE -g hs).
Peaks overlapping with ENCODE blacklisted regions were removed from the narrowPeak and summit files with bedtools v.2.29.2 (bedtools subtract -A).
Genome read coverage was calculated with bedtools v.2.29.2 (bedtools coverage –pc -bg) and bedGraphToBigWig v377 was used to create a bigwig file.
A RPKM normalized bigwig file was created with deepTools v.3.5.0 (bamCoverage --binSize 50 --normalizeUsing RPKM --effectiveGenomeSize 2913022398).
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak
Library strategy: STARR-seq

organism: Homo sapiens

growth_protocol: As described in (Sahu et al., Nat. Gen. 2022).

extract_protocol:
Extraction was performed as described in (Sahu et al., Nat. Gen. 2022).
Library was prepared as described in (Sahu et al., Nat. Gen. 2022).

tag: cell line

tag: cell type

value: Retinal pigment epithelium


title: Biological rep#2, Cells transfected with Cas9, T cells

city: Freiburg

first: Claudio

last: Mussolino

address: Breisacherstr. 115

country: Germany

institute: Institute for Transfusion Medicine and Gene Therapy

description: Sequencing outsourced to GeneWiz

library_source: genomic

molecule: genomic DNA

tag: treatment

value: Electroporated with Cas9 expressing IVT mRNA + sgRNA


title: slr1-RNA_seq-1


title: WD49422

city: Stanford

first: Tomek

last: Swigut

state: CA

address: 265 Campus Dr

department: Chemical and Systems Biology

country: USA

institute: Stanford University

data_processing:
salmon quant
Assembly: GRCm39 and gencode_M31 gene models
Supplementary files format and content: salmon quant.genes.sf with pseudocounts and TPM

source_name: Skin

growth_protocol: melanocytes were isolated from foreskin human tissue and cultured in the presence of serum-free medium 254 supplemented with 1x human melanocyte growth supplement

extract_protocol:
Total RNA was isolated from melanocytes using an RNA isolation kit (Zymo Research) following manufacturer’s instructions
RNA Sequencing libraries were prepared using Ovation Ultralow System (Nugen/Tecan) following manufacturer’s instructions

value: Skin

tag: group

value: darkly pigmented

value: melanocyte

value: WT

value: growth medium


title: WD49421

value: Lightly pigmented


title: Biological rep#2, Untreated Control, T cells

description: Sequencing outsourced to GeneWiz

value: Untreated


title: M0489

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

data_processing:
Counts and TPM values were obtained using kallisto v0.46 against the Ensembl mouse transcriptome (v97)
Assembly: mm10
Supplementary files format and content: tab-delimited files contain counts and TPM values

organism: Mus musculus

source_name: liver

extract_protocol:
Total RNA from a 20 mg piece of the large lobe of the liver was purified from one mouse per strain of the HMDP, and from 3 mice per diet group in the C57BL6J Control study, using the Qiagen miRNeasy Mini kit (Qiagen cat#217004) per the manufacturer’s instructions. RNA preparation was as previously described (Ma, Fuqua et al. 2019) except that samples were homogenized in QIAzol using a TissueLyzer (Qiagen). All samples had RINe values greater than 8.
RNA sequencing libraries were prepared as described previously (Ma, Fuqua et al. 2019) using the KAPA Stranded mRNA-Seq Kit (cat #KK8421, KAPA Biosystems, Wilmington, MA).

value: liver

tag: Sex

value: male

tag: strain

tag: diet

value: 2% carbonyl iron (20,000 ppm)


title: M0495


title: NIP-RNA_seq-3


title: WD49420


title: GP5d, H3K27ac HiChIP

data_processing:
Raw read were processed with HiC-Pro v3.1.0 with default parameters and hg38 MboI restriction sites .bed file as input.
allValidPairs output from HiC-Pro was converted to a .hic file with the hicpro2juicebox.sh script from HiC-Pro, with juicer tools v1.22.
Assembly: hg38
Supplementary files format and content: juicer .hic file

growth_protocol: GP5d cells were grown in DMEM supplemented with 10% FBS, 2 mM L-glutamine and 1% penicillin-streptocmycin. Cells were checked for mycoplasma contamination and were passaged at 80% confluency.

extract_protocol:
GP5d cells were formaldehyde cross-linked, washed with ice-cold PBS and lysed to isolate the nuclei. H2K27ac HiChIP was performed by using HiChIP protocol as described earlier (Mumbach et al. Nat Methods. 2016).
HiChIP libraries were constructed as described earlier (Mumbach et al. Nat Methods. 2016).
OTHER: Hi-ChIP-seq

value: Colon adenocarcinoma

tag: chip antibody


title: M0483


title: NIP-RNA_seq-2


title: WD49124


title: GP5d, ATAC-seq

data_processing:
FastQC v.0.11.9 was used for quality control and determination of read lengths of raw data.
Raw reads were mapped with bowtie2 v.2.4.1 (bowtie2 --very-sensitive) to the reference genome.
Reads mapped to the mitochondrial genome were removed with removeChrom.py script (https://github.com/jsh58/harvard/blob/master/removeChrom.py).
Picard v.2.23.4 was used to remove duplicates (MarkDuplicates -REMOVE_DUPLICATES false -ASSUME_SORT_ORDER coordinate) and analyzing insert sizes with CollectInsertSizeMetrics.
Samtools v.1.7 was used to filter reads with MAPQ smaller than 10 and remove marked duplicates (samtools view -F 1024 -b -q 10).
Peaks were called with MACS2 v.2.2.7.1 (macs2 callpeak -f BAMPE -g hs --keep-dup all).
Peaks overlapping with ENCODE blacklisted regions were removed from the narrowPeak and summit files with bedtools v.2.29.2 (bedtools subtract -A).
A RPKM normalized bigwig file was created with deepTools v.3.5.0 (bamCoverage --binSize 50 --normalizeUsing RPKM --effectiveGenomeSize 2913022398).
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
The cells were extracted and processed as per ATAC-seq protocol (Buenrostro et al. Curr Protoc Mol Biol 2015)
The ATAC-seq library was prepared as described earlier (Buenrostro et al. Curr Protoc Mol Biol 2015).


title: NIP-RNA_seq-1


title: WD49123


title: HCoEpiC, rep2

data_processing:
Trim Galore v.0.6.7 was used to remove adaptor/overepresented sequences, discarding reads left with < 20 bp. FastQC v.0.11.9 was used for quality control.
Reads were also aligned with STAR v.2.5.3a (Dobin et al. 2013) by using the SQuIRE pipeline v. 0.9.9.92 (Yang et al. 2019).
Read counts were calculated with featureCounts 2.0.1 (Liao et al. 2014)
Diffential expression analysis was performed with DESeq2 v.1.32.0 (Love et al. 2014).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized counts for each sample, featureCounts table contains unnormalized counts

source_name: HCoEpiC

growth_protocol: GP5d cells were grown in DMEM supplemented with 10% FBS, 2 mM L-glutamine and 1% penicillin-streptocmycin.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using KAPA stranded mRNA-seq kit for Illumina (Roche) as per manufacturer’s instruction

treatment_protocol:
GP5d cells were seeded in 6 well plates and treated with 500 nM/L 5-aza-2'-deoxycytidine  or DMSO. 5-aza-2'-deoxycytidine containing media were replaced each day for three days. SB939 was added at a concentration of 500 nmol/L  and cell were harvested after 18 hours.
Generation of p53-null GP5d cell line is described in Sahu et al., Nat. Gen. (2022)

value: HCoEpiC

value: Colon epithelial cell


title: WD49105


title: M0450


title: 3975 WT+H.felis 3

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Stomach

growth_protocol: Wild type mice were maintained in a specific-pathogen free facility. One group of mice was infected with H. felis for 6 months while the other group served as uninfected controls. Single cells were then dissocaited from the stomach using EDTA followed by LIberase.

extract_protocol: Library was performed according to the manufacter’s instructions (single cell Immune Profiling v2 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropiate sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: The stomachs were treated with EDTA followed by Liberase to dissociate single cells.

value: Stomach

value: Total stomach cells

value: 6 month H. felis-infected mice


title: M0464


title: HCoEpiC, rep3


title: 3975 WT+H.felis 2

description: 10x Genomics


title: WD49103


title: 3975 WT 1

description: 10x Genomics


title: GP5d, C2, rep3

value: CRISPR-Cas9 targeting


title: M0448

value: I/LnJ


title: WD49104

value: Skin


title: WD48922

value: melanocyte


title: 3672 WT+H.felis 3

description: 10x Genomics

value: WT


title: M0431


title: WD48920

value: darkly pigmented

value: growth medium


title: HCoEpiC, rep1


title: 3672 WT 1

description: 10x Genomics

value: Untreated


title: 3672 WT+H.felis 2

description: 10x Genomics


title: M0417

value: liver


title: GP5d, C2, rep2


title: GP5d, WT, rep3


title: M0476

value: male


title: WD48919


title: M0408

value: 2% carbonyl iron (20,000 ppm)


title: ND1W1

value: Lightly pigmented


title: GP5d, WT, rep2

value: Colon adenocarcinoma


title: M0400


title: Kidney, Control-4

city: Chongqing

first: Qihuan

last: Fu

state: Chongqing

address: 181 Hanyu Road, Shapingba District

department: Chongqing University Cancer Hospital

institute: Chongqing University

description:
mRNA_Expression_Summary.txt
FPKMs-all-samples.txt

data_processing:
Illumina bcl2fastq 2.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2
Transcript abundance values were obtained from gene-level count matrices were generated by StringTie
Gene counts were normalized using geometric mean (GEO) in DESeq2 package and log2 transformed. Removal of unwanted variation (RUV) was used to remove batch effects and genes with no counts in over 50% of the samples were removed.
Differential gene expression by limma voom was performed on normalized gene counts, using batch effects and the first two PCAs of aligning and sequencing as covariates.
Assembly: Genome_build: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text files include raw FPKM values for each sample

source_name: kidney

growth_protocol: The mice were housed at 25°C and fed standard rodent chow and tap water.

extract_protocol:
Total RNA was extracted from each tissue sample using the Trizol method.
After incubation of RNA with a biotin-modified probe, the probe was captured by a streptavidin magnetic bead to eliminate rRNA. The obtained samples were purified by AMPure XP magnetic beads, and then buffer composed of elution, fragmented, and random primers was added and the samples were incubated at 94°C. Thermal fracture led to fragments distributed between 100 and 300 bp. Using first-strand synthesis buffer and Invitrogen SuperScript IV reverse transcriptase, this fragmented RNA was used as a template to synthesize the first-strand cDNA. Actinomycin D was added to the first-strand synthesis buffer to prevent the reverse transcription of DNA templates and to ensure the reverse transcription specificity of RNA templates. After that, the double-stranded synthesis premix system was added to the synthesized first-strand cDNA, and the product was purified by Agencourt AMpure XP magnetic beads. From this reaction we obtained purified double-stranded cDNA and then added a 3' end plus "A" buffer reaction system to this system. Finally, ligation buffer and a double-stranded sequencing linker was added to the library; we used T4 DNA ligase to attach the Illumina sequencing linker to the DNA library. The library was purified using the Agencourt SPRI select Nucleic Acid Fragment Screening kit.

treatment_protocol: In the cisplatin group, mice were intraperitoneally injected with cisplatin (Cat No. 232120, Sigma-Aldrich, USA) through a single injection. In the LPS group, mice were intraperitoneally injected with lipopolysaccharide (LPS) from Escherichia coli O111:B4 (Cat No. L2630, Sigma-Aldrich, USA) through a single injection. In the control group, mice were injected with the same volume of saline. 48 h after the injection, all mice were sacrificed. The blood and kidney tissues of the mice were collected.

value: kidney

value: wild type

value: HBSS (control)


title: Kidney, Control-3


title: M0440

value: KK/HlJ


title: GP5d, WT, rep1


title: M0396


title: HepG2, CpG-methylated, rep1

data_processing:
FastQC v.0.11.9 was used for quality control and determination of read lengths of raw data.
Two technical replicates were combined before alignment.
Raw reads were mapped with bowtie2 v.2.4.1 (bowtie2 --maxins 1000) to the reference genome.
Picard v.2.23.4 was used to remove duplicates (MarkDuplicates -REMOVE_DUPLICATES false -ASSUME_SORTED true)
Samtools v.1.7 was used to filter non-concordant reads and reads with a MAPQ of smaller than 20 (samtools view -F 1024 -b -q 20).
Peaks were called with MACS2 v.2.2.7.1 with the STARR input library as control (macs2 callpeak -f BAMPE -g hs).
Peaks overlapping with ENCODE blacklisted regions were removed from the narrowPeak and summit files with bedtools v.2.29.2 (bedtools subtract -A).
Genome read coverage was calculated with bedtools v.2.29.2 (bedtools coverage –pc -bg) and bedGraphToBigWig v377 was used to create a bigwig file.
A RPKM normalized bigwig file was created with deepTools v.3.5.0 (bamCoverage --binSize 50 --normalizeUsing RPKM --effectiveGenomeSize 2913022398).
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
Extraction was performed as described in (Sahu et al., Nat. Gen. 2022).
Library was prepared as described in (Sahu et al., Nat. Gen. 2022).
OTHER: STARR-seq

treatment_protocol: As described in (Sahu et al., Nat. Gen. 2022).

value: CpG methylation

value: Hepatocellular carcinoma


title: M0392


title: HepG2, CpG-methylated, rep2


title: GP5d, DNMT-HDAC 3

value: DNMT HDAC inhibition

tag: time

value: 96 hours


title: Kidney, Control-2


title: GP5d, DNMT-HDAC 2

value: WT


title: M0391


title: Kidney, Control-1


title: GP5d, C2, rep1

value: CRISPR-Cas9 targeting


title: Kidney, LPS-5

value: LPS


title: GP5d, DMSO control 3


title: A549_dORF6_biolrep3

city: New York

first: Thomas

last: Kehrer

state: New York

address: 1 Gustave L. Levy Place

department: Microbiology

institute: Icahn School of Medicine at Mount Sinai

description: sample, mapped_reads, gRNA_count, orf, sgRNA_count, coverage, sgRPTL, sgRPHT

data_processing:
Raw BCL files were convered to fastq files using bcl2fastq/2.20.0 (Illumina, Inc)
For quantification of SARS-CoV-2 sgRNA and gRNA expression, the periscope/0.1.2 package was used with the technology argument set to “illumina"
sgRNA reads per total mapped reads were calculated and plotted using PRISM (VERSION 9)
Assembly: SARS-CoV-2/USA-WA1/2020 (MN985325.1)
Supplementary files format and content: Periscope output in .csv format

source_name: Cell Culture

growth_protocol: A549-ACE2 (described previously in doi.org/10.1101/2022.02.08.479634) were maintained in Dulbecco’s modified Eagle’s medium (Corning) supplemented with 10% fetal bovine serum (Peak Serum) and penicillin/streptomycin (Corning) at 37 °C and 5% CO2

extract_protocol:
Samples for bulk RNA sequencing were lysed in Trizol Reagent and total RNA was extracted using the miRNeasy mini kit (Qiagen) per the manufacturer’s instructions. DNAse treatment was performed on isolated RNA using the RNA Clean and Concentrator Kit (Zymo). Total RNA was examined for quantity and quality using the TapeStation (Agilent) and Quant-It RNA (ThermoFisher) systems.
RNA samples with sufficient material (10 pg–10 ng) were passed to whole-transcriptome library preparation using the SMART-Seq v4 PLUS Kit (Takara Bio) following the manufacturer’s instructions. Briefly, total RNA inputs were normalized to 10ng in 10.5 µl going into preparation. 3’ ends of cDNA were then adenylated prior to ligation with adapters utilizing unique dual indices (96 UDIs) to barcode samples to allow for efficient pooling and high throughput sequencing. Libraries were enriched with PCR, with all samples undergoing 14 cycles of amplification prior to purification and pooling for sequencing.

treatment_protocol: Cells were either mock-infected or infected with recombinant SARS-CoV-2 viruses at an MOI of 0.5 for 24 h before harvest. Infections were performed in Dulbecco’s modified Eagle’s medium (Corning) supplemented with 2% fetal bovine serum (Peak Serum), 1% non-essential amino acids (Gibco), 1% HEPES (Gibco) and 1% penicillin/streptomycin (Corning) at 37 °C and 5% CO2. Recombiant viruses were generated based on the WA/01 strain and had either wildtype sequence (rSARS-CoV-2 WT) or a deletion of the coding sequence of ORF6 (deleted positions: 27192-27385 : rSARS-CoV-2 ∆ORF6).

value: Cell Culture

value: Lung Epithelial Carcinoma

value: ACE2 expressing

value: SARS-CoV-2 Viral Infection


title: A549_dORF6_biolrep2


title: A549_dORF6_biolrep1


title: M0387

value: liver

value: male

value: 2% carbonyl iron (20,000 ppm)


title: Kidney, Control-5

value: kidney

value: wild type


title: Kidney, LPS-4


title: M0384


title: A549_WT_biolrep3


title: Kidney, LPS-3


title: M0378


title: A549_WT_biolrep2


title: GP5d, DMSO control 1

value: Colon adenocarcinoma


title: Kidney, LPS-2


title: M0375


title: GP5d, DNMT-HDAC 1


title: A549_Mock_biolrep3


title: 18576X12 Molm-14_EV3

city: Salt Lake City

first: Ryan

last: O'Connell

state: UT

address: Emma Eccles Jones, Medical Research Building, 15 North Medical Drive East

department: Pathology, Microbiology & Immunology

institute: University of Utah

data_processing:
The human GRCh38 genome and gene annotation files were downloaded from Ensembl release 102 and a reference database was created using STAR version 2.7.6a.
Optical duplicates were removed from the paired end FASTQ files using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16.
The trimmed reads were aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3.
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.30.1.
Assembly: GRCh38
Supplementary files format and content: featureCount output files combined into a single tab-delimited raw count matrix.

extract_protocol:
mRNA was isolated by following manufacturer protocols using the Qiagen miRNeasy Mini kit (Cat.: 217084). The cell extracts were treated with Qiagen RNase free DNase by following manufacturer protocol (Cat.: 79254).
Illumina Stranded Total RNA Library Prep w Ribo-Zero Plus.

value: AML cell line

value: EV


title: GP5d, DMSO control 2


title: A549_WT_biolrep1


title: M0372


title: 18576X11 Molm-14_EV2


title: 18576X10 Molm-14_EV1


title: M0358


title: Kidney, Cisplatin-5

value: Cisplatin


title: M0364


title: A549_Mock_biolrep2


title: Kidney, Cisplatin-4


title: 18576X8 Molm-14_OE2

value: OE


title: Kidney, Cisplatin-3


title: M0350


title: P10_38F_Smith_R

city: Perth

last: Lister

state: WA

address: 35 Stirling Highway

country: Australia

institute: The University of Western Australia

data_processing:
Sequencing adapters were trimmed with BBduk with the options mink = 3, qtrim = r, trimq = 10 minlength = 20 before alignment to hg19 with Bowtie and BSseeker2 with the option -n 1. PCR duplicates were removed using Sambamba and DNA methylation levels at base resolution calculated using CGmap tools. The non–conversion rate was calculated using the DNA methylation levels for the spiked–in lambda phage genome. When DNA methylation levels were calculated for regions such as promoters, enhancers, DMRs or ICRs, the methylation level was calculated as a coverage–weighted average by summing the number of methylated C calls (mCG) and dividing that by the total number of reads with either a C or T call (CG). This is represented in the figures and text as mCG/CG. To calculate methylation in CH contexts (where H = A, T or C), the level of methylation was calculated as above (mCH/CH) with the non–conversion rate subtracted from this value. When CH methylation was calculated for individual contexts, for example CA methylation, the non–conversion rate for that context was subtracted from the calculated methylation levels. For CA methylation browser tracks, mCA/CA was calculated for 5kb sliding windows (1kb slide), with the CA methylation non–conversion rate for that library subtracted from each window. To calculate per-read methylation, reads classified as methylated had methylation calls at every CG position in the read; unmethylated reads had zero methylation calls at CG positions; partially methylated reads had at least one CG methylation call  and one non-methylated CG call.
Genome_build: hg19
Supplementary_files_format_and_content: CGmap file generated with CGmap tools. File has 8 columns: [1]chromosome [2] nucleotide on Watson (+) strand [3] position [4] context (CG/CHG/CHH) [5] dinucleotide-context (CA/CC/CG/CT) [6] methylation-level = #_of_C / (#_of_C + #_of_T) [7] #_of_C (methylated C, the count of reads showing C here) [8] = #_of_C + #_of_T (all Cytosines, the count of reads showing C or T here).

source_name: Human pluripotent stem cells

growth_protocol: To generate human primed and naïve iPSCs used for this study, somatic cell reprogramming with the Cytotune 2.0 kit, experiments were performed according to the manufacturer’s instructions (Invitrogen). Briefly, human dermal fibroblast (adult) were seeded at ~5x104 cells per well of a 6-well plate in fibroblast medium containing DMEM (Gibco), 10% FBS (Hyclone), 1% nonessential amino acids (Gibco), 1mM GlutaMAX (Gibco), Pen-strep (Gibco), 0.1mM 2-mercaptoethanol (Gibco) and 1mM sodium pyruvate (Gibco) . After 2 days, cells were transduced with Sendai viruses in fibroblast medium with multiplicity of infections (MOIs) as follows, KOS MOI=5, c-MYC MOI=15, KLF4 MOI=6. After 24 hours, the medium was replaced with fresh fibroblast medium and media were changed every other day thereafter. On day 7, cells were trypsinized and seeded onto a layer of iMEF feeders at ~0.5x105~1x105 per flask in fibroblast medium. The next day, the cells were switched to primed or naive media. 21-24 days after transduction, cells were passaged and expanded. Reprogramming intermediates were collected at the indicated time and isolated by FACS.

extract_protocol:
Genomic DNA was isolated with the Qiagen Blood and Tissue Kit according to manufacturer's instructions. 0.5% (w/w) of unmethylated lambda phage DNA (Promega) was added to the sample genomic DNA for the purpose of an unmethylated control to measure the bisulfite non-conversion frequency in each sample.
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to methylated Illumina TruSeq adapters, and subjected to PCR amplification with KAPA HiFi Uracil+ DNA polymerase (KAPA Biosystems). Single-end sequencing was performed on a HiSeq1500, NextSeq500 or NovaSeq.

treatment_protocol: On day 8, the cells were switched to primed, naive, naive-to-primed (NtP) or transient-naive-treatment (TNT) reprogramming protocols. For primed: Cells were transient primed essential8 (E8) culture media after the initial 7 days culturing in fibroblast media. For Naive: Naive hiPSCs colonies were established through extended naive culturing. For TNT: cells were transient naive culture for 5 days after the initial 7 days culturing in fibroblast media, followed by culturing in primed E8 media. For NtP: Naive hiPSCs colonies were established through extended naive culturing and then transitioned the cells to a primed pluripotent state in E8 media to give rise to naive-to-primed hiPSCs.

tag: background


title: M0345


title: Kidney, Cisplatin-2


title: RL703: Primed_hiPSC_P20_38F

value: Human pluripotent stem cells


title: M0338


title: A549_Mock_biolrep1


title: Kidney, Cisplatin-1


title: 18576X7 Molm-14_OE1


title: 18576X6 MV4-11_EV3


title: RL702: Day_0_38F

source_name: Cultured human fibroblasts

value: Cultured human fibroblasts

value: Fibroblast


title: Kidney, LPS-1

value: LPS


title: M0334


title: 18576X5 MV4-11_EV2


title: H2030-OE-1 rep1

city: DaeJeon

first: Mi Young

last: Kim

address: Biological science

country: South Korea

institute: KAIST

data_processing:
Base calling was performed by Illumina Genome Studio(V2010.1).
Reference genome sequence data from Homo sapiens were obtained from the National Center for Biotechnology Information (NCBI) Genome database (assembly ID: GRCh38).
Raw reads were mapped to the reference human (hg19) genome assembly with Tophat, and rpkm values were calculated with Cufflink.
Genome_build: GRCh38
Supplementary_files_format_and_content: log2_CPMs

source_name: Lung cancer cells

growth_protocol: H2030 cells were cultured in RPMI (Welgene, Republic of Korea) supplemented with 10% fetal bovine serum (FBS; Welgene, Republic of Korea) for 2 days.

extract_protocol:
Total RNAs were isolated using RNeasy mini kits (Qiagen, Valencia, CA).
The Libraries were prepared using the TruSeq stranded mRNA sample preparation kit (Illumina).

value: Lung cancer cell line H2030

tag: passage

value: GALNT3 overexpression


title: H2030-OE-2 rep2


title: M0331

value: BUB/BnJ


title: 18576X9 Molm-14_OE3


title: 18576X4 MV4-11_EV1


title: M0327

value: liver


title: WT-WD-20W-8

city: TIANJIN

first: Yin

last: Wen

state: TIANJIN

address: Address:No.6 North Huanrui Rd, Beichen District, Tianjin, P.R China

department: NHC Key Laboratory of Hormones and Development

institute: Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

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

value: male

value: WT

value: WD-20 WEEKS


title: H2030-vec-2 rep2

value: control vector overexpression


title: 18576X3 MV4-11_OE3


title: M0326

value: 2% carbonyl iron (20,000 ppm)


title: WT-WD-20W-9


title: Prdx1C52S-WD-20w-4


title: H2030-vec-1 rep1


title: M0322


title: Prdx1C52S-WD-20w-2


title: 18576X1 MV4-11_OE1

value: AML cell line


title: Prdx1C52S-WD-20w-1


title: M0317

value: AKR/J


title: K562, 3xFLAG-TopoIIa, amrubicin 10 µM, 4h, anti-Flag M2, ChIP, biol rep 1

city: Leiden

first: Minkang

last: Tan

address: Einthovenweg 20

department: Department of Cell and Chemical Biology

country: Netherlands

institute: Leiden University Medical Center

description:
TOP2A_Amr.merged.sorted.bigwig
TOP2A_Amr.overlap_conservative_peak.bed

data_processing:
ChIP-seq data were processed identically using the ENCODE Data Coordination Center (DCC) ChIP-seq pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2) (v1.9.0)
ChIP-seq reads were aligned to the human reference genome (GRCh37/hg19) using Bowtie2. Duplicate reads were removed using Picard MarkDuplicates.
TopoIIα ChIP-seq signal files were generated using "bedtools genomecov -scale" to convert the merged bam file from two replicates to bedgraph file. The bedgraph files were further converted to bigwig files using bedGraphToBigWig. The bigwig data was normalized by read counts per million (RPM).
ChIP-seq peaks of each sample were called against the whole-cell lysates (WCL) replicates using SPP48 with the parameters ‘-npeak 300000 -speak 155 -fdr 0.01’,  then followed by blacklisted regions filtering described by ENCODE. Reproducible peaks were intersected from two biological replicates using bedtools intersect command.
hg19
bigwig, bed

growth_protocol: Endogenous tagged 3×Flag-TopoIIα K562 cells (for ChIP-seq) were cultured in RPMI-1640 medium supplemented with 8% fetal calf serum.

extract_protocol:
ChIP samples were processed as described in PMID 19275939 and 25961671.
ChIP samples were processed as described in PMID 19275939 and 25961671.

treatment_protocol: Cells were treated with 10 µM of indicated drug for 4 hours.

value: lymphoblast cells

value: amrubicin 10 microM

value: anti-Flag M2 (F3165, Sigma)


title: M0316

value: LG/J


title: Ishikawa_siTCF19_3

city: Ji’nan

first: Xinyue

last: Ma

state: Shandong

address: 107 West Wenhua Road

institute: Qilu Hospital of Shandong University

data_processing:
Sequenced reads were generated by base calling using the Illumina standard pipeline
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data.
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.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: hg38
Supplementary files format and content: File format: Tab-delimited text file. Content: raw counts and FPKM values for each sample

source_name: Ishikawa

growth_protocol: Ishikawa cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was harvested using Trizol reagent.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Ishikawa cells were transfected with siRNAs (si-NC or si-TCF19) using lipo2000 reagent according to the manufacturer's protocol. After that, cells were maintained in DMEM supplemented with 10% FBS for 48 hours before RNA extraction.

value: Ishikawa

value: Endometrial cancer cell line

value: TCF19 knockdown


title: K562, 3xFLAG-TopoIIa, aclarubicin 10 µM, 4h, anti-Flag M2, ChIP, biol rep 2

description:
TOP2A_Acla.merged.sorted.bigwig
TOP2A_Acla.overlap_conservative_peak.bed

value: aclarubicin 10 microM


title: M0312


title: WT-WD-20-6


title: K562, 3xFLAG-TopoIIa, aclarubicin 10 µM, 4h, anti-Flag M2, ChIP, biol rep 1


title: M0256

value: LP/J


title: Ishikawa_siTCF19_1


title: 20764X15 Tet2KO_Th1_Secondary_Day7_biol_rep_1

first: Jeffrey

middle: Scott

last: Hale

state: Utah

address: 15 North Medical Drive

department: Pathology

data_processing:
Sequencing data quality was assessed using FastQC v0.11.4. Adapters were trimmed from the sequencing reads using Trim Galore!v0.4.4. Alignment to the mm10 reference genome was performed using Bismark v0.19.0. Deduplication was performed with deduplicate_bismark. Library quality was considered sufficient if greater than 50% of reads uniquely aligned to the genome. Bisulfite conversion efficiency was assessed by evaluating the percent of methylation observed in the CHH genome context and considered sufficient when this value was less than 3%. Library genome coverage was considered sufficient if 80% of the genome had a depth of at least 10 reads. CpG positions in the reference genome were quantified using the Bismark Methylation Extractor v0.19.0. This analysis pipeline was developed and executed in the Seven Bridges cloud platform, and included use of the Bismark Analysis public workflow. Differentially methylated regions (DMR) were detected using Bsmooth, Bsmooth.tst and dmrFinder in the bsseq R package
Assembly: mm10
Supplementary files format and content: Tab-delimited Bismark coverage file
Library strategy: Whole Genome Enzymatic Methyl-seq

source_name: Spleen

extract_protocol:
DNA was harvested from FACS sorted cells using the Quick-DNA MicroPrep Kit (Zymo Research)
10-200ng were fragmented by sonication (Covaris).Unmethylated cytosines were converted to uracils and sequencing libraries were created using the NEBNext Enzymatic Methyl Seq kit (New England Biolabs) according the manufacturer’s instructions. DNA libraries were sequenced using an Illumina NovaSeq 6000 system following the manufacturer’s protocols.

value: female

value: Spleen

value: SMARTA CD4 T Cells

tag: cell subset

value: Tet2 Knockout

tag: infection

value: LCMV Armstrong

value: day 7 recall response


title: Ishikawa_siNC_3

value: negative control


title: 20764X16 Tet2KO_Th1_Secondary_Day7_biol_rep_2


title: 20764X13 Tet2KO_Tfh_Secondary_Day7_biol_rep_2

value: Tfh


title: K562, 3xFLAG-TopoIIa, amrubicin 10 µM, 4h, anti-Flag M2, ChIP, biol rep 2

value: lymphoblast cells


title: M0251

value: liver

value: male

value: 2% carbonyl iron (20,000 ppm)


title: 18576X2 MV4-11_OE2

value: AML cell line

value: OE


title: K562, 3xFLAG-TopoIIa, idarubicin 10 µM, 4h, anti-Flag M2, ChIP, biol rep 2

description:
TOP2A_Ida.merged.sorted.bigwig
TOP2A_Ida.overlap_conservative_peak.bed

value: idarubicin 10 microM

value: anti-Flag M2 (F3165, Sigma)


title: 20764X11 Tet2KO_Tfh_Secondary_Day7_biol_rep_1


title: M0248

value: NZW/LacJ


title: Ishikawa_siNC_2

value: Ishikawa

value: Endometrial cancer cell line


title: Ishikawa_siNC_1


title: K562, 3xFLAG-TopoIIa, idarubicin 10 µM, 4h, anti-Flag M2, ChIP, biol rep 1


title: K562, 3xFLAG-TopoIIa, daunorubicin 10 µM, 4h, anti-Flag M2, ChIP, biol rep 1

description:
TOP2A_Daun.merged.sorted.bigwig
TOP2A_Daun.overlap_conservative_peak.bed

value: daunorubicin 10 microM


title: 20764X9 WT_Th1_Secondary_Day7_biol_rep_2

value: female

value: Spleen

value: SMARTA CD4 T Cells

value: wild type


title: Ishikawa_TCF19_OE

data_processing:
Sequenced reads were generated by base calling using the Illumina standard pipeline.
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 BWA v0.7.12 and clean reads were aligned to the reference genome using BWA mem v 0.7.12.
After mapping reads to the reference genome, MACS2 version 2.1.0 (model-based analysis of ChIP-seq) peak finding algorithm was used to indentify regions of IP enrichment over background. A q value threshold of enrichment of 0.05 was used for all data sets.
PeakAnnotator was used to identify the nearest TSS of every peak and the distance distribution between peaks and TSS was shown. Besides, the distribution of peak summits on different function regions, such as 5’ UTR, CDS, 3’UTR, was performed.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor automatic sonicator (Diagenode, Denville, NJ).
Antibody immunoprecipitation DNA was quantified with QubitTM (Thermo Fisher Scientifc,USA) and Agilent 2200 TapeStation (Agilent Technologies, USA). The DNA library building kit from NEB corporation was used to construct the sequencing library.

treatment_protocol: Ishikawa cells were infected with TCF19 over-expressing or control lentivirus at 50% confluency, then incubated with lentivirus for 24 hours. After that, cells were selected with puromycin.

value: TCF19 (Santa Cruz, #sc-101169)

value: TCF19 over-expression


title: M0244

value: liver

value: MRL/MpJ


title: M0230

value: male

value: 2% carbonyl iron (20,000 ppm)


title: K562, 3xFLAG-TopoIIa, epirubicin 10 µM, 4h, anti-Flag M2, ChIP, biol rep 2

description:
TOP2A_Epi.merged.sorted.bigwig
TOP2A_Epi.overlap_conservative_peak.bed

value: lymphoblast cells

value: epirubicin 10 microM


title: Ishikawa_NC

value: negative control


title: M0220

value: CBA/J


title: 20764X8 WT_Th1_Secondary_Day7_biol_rep_1

value: LCMV Armstrong

value: day 7 recall response


title: Ishikawa_siTCF19_2

value: Ishikawa

value: Endometrial cancer cell line

value: TCF19 knockdown


title: 20764X7 WT_Tfh_Secondary_Day7_biol_rep_3

value: female

value: Spleen

value: SMARTA CD4 T Cells

value: Tfh


title: M0217

value: liver

value: FVB/NJ


title: K562, 3xFLAG-TopoIIa, epirubicin 10 µM, 4h, anti-Flag M2, ChIP, biol rep 1

value: anti-Flag M2 (F3165, Sigma)


title: K562, 3xFLAG-TopoIIa, doxorubicin 10 µM, 4h, anti-Flag M2, ChIP, biol rep 2

description:
TOP2A_Doxo.merged.sorted.bigwig
TOP2A_Doxo.overlap_conservative_peak.bed

value: doxorubicin 10 microM


title: HepG2_Input_bio-rep1

city: Stuttgart

first: Albert

last: Jeltsch

address: Allmandring 31

department: Institute of Biochemistry and Technical Biochemistry

institute: University Stuttgart

data_processing:
Adapters were clipped and low-quality reads removed with Trimmomatic (v0.38) in default settings, and quality controlled with FastQC (v0.72).
The high-quality, clean reads were mapped to hg38 using HISAT2 (v2.2.1).
Using bamcoverage (v3.3.2), the mapped reads were quantified in 10 bp bins using RPKM, omitting blacklisted regions (hg38-blacklist.v2). Biological replicates were pooled using bigwigcompare (v3.3.2) and mean RPKM signal.
Broad peaks for UHRF1-TTD were called with MACS2 (v2.1.1) using cuttoff 30, cutoff-link 13, d 150, t 89. Blacklisted regions were subtracted and the peaks were manually curated for artefacts/large, false positives.
Assembly: hg38
Supplementary files format and content: .bigwig files contain the RPKM quantified reads from the UHRF1-TTD CIDOP, the α-H3K9me2 ChIP or the input (control) chromatin.
Supplementary files format and content: .bed file contains the regions of statistically significant enrichment from two biological replicates of UHRF1-TTD CIDOP experiments

growth_protocol: HepG2 cells were acquired from DSMZ - German Collection of Microorganisms and Cell Cultures (No: ACC 180) and grown in RPMI 1640 medium (Gibco) supplemented with 10% FBS, 100 U/ml penicillin and 100 mg/ml streptomycin, at 37 °C, under humidified air with 5% CO2 atmosphere. Cells pellets were washed with PBS, flash-frozen and stored at -80 °C.

extract_protocol:
The UHRF1-TTD CIDOP-seq and α-H3K9me2 ChIP-seq experiments were performed in biological duplicates. Mononucleosome generation and histone precipitation were performed with a modular protocol, all parameters optimized for each enrichment reagent. Briefly, the cells were resuspended in lysis buffer and digested with MNase in one tube, centrifuged, and the supernatant containing mononucleosomes collected, flash-frozen and stored in -80 °C. UHRF1-TTD or α-H3K9me2 (ab1220) were first incubated with appropriate magnetic beads (GST-Pierce magnetic or DynabeadsG 10004D) for 2 h, and then with precleared chromatin for overnight binding. Beads were washed three times with PB200 (Tris-HCl pH 8.0 50 mM, NaCl 200 mM,  DTT 2mM, Igepal CA-360 0.5%), followed by two rinse steps (Tris-HCl pH 8.0 10 mM or Tris-HCl pH 8.0 10 mM, LiCl 150 mM). Then they were eluted (Tris-HCl pH 8.0 50 mM, NaCl 50 mM, EDTA 5mM, SDS 1%), digested with Proteinase K, and purified with ChIP DNA Purification Kit (Active Motif).
NGS libraries were prepared with 10 ng DNA using the NEBNext® Ultra™ II DNA Library Prep Kit according to the manufacturer’s instructions

treatment_protocol: No treatment

value: Hepatoblastoma

tag: cidop reagent_-_chip_antibody


title: HepG2_Input_bio-rep2


title: 20764X6 WT_Tfh_Secondary_Day7_biol_rep_2

value: wild type


title: M0207

data_processing:
Counts and TPM values were obtained using kallisto v0.46 against the Ensembl mouse transcriptome (v97)
Assembly: mm10
Supplementary files format and content: tab-delimited files contain counts and TPM values

extract_protocol:
Total RNA from a 20 mg piece of the large lobe of the liver was purified from one mouse per strain of the HMDP, and from 3 mice per diet group in the C57BL6J Control study, using the Qiagen miRNeasy Mini kit (Qiagen cat#217004) per the manufacturer’s instructions. RNA preparation was as previously described (Ma, Fuqua et al. 2019) except that samples were homogenized in QIAzol using a TissueLyzer (Qiagen). All samples had RINe values greater than 8.
RNA sequencing libraries were prepared as described previously (Ma, Fuqua et al. 2019) using the KAPA Stranded mRNA-Seq Kit (cat #KK8421, KAPA Biosystems, Wilmington, MA).

value: male

value: 2% carbonyl iron (20,000 ppm)


title: M0196


title: K562, 3xFLAG-TopoIIa, daunorubicin 10 µM, 4h, anti-Flag M2, ChIP, biol rep 2

value: lymphoblast cells

value: daunorubicin 10 microM


title: K562, 3xFLAG-TopoIIa, doxorubicin 10 µM, 4h, anti-Flag M2, ChIP, biol rep 1


title: K562, 3xFLAG-TopoIIa, anti-Flag M2, ChIP, biol rep 2

description:
TOP2A_Ctr.merged.sorted.bigwig
TOP2A_Ctr.overlap_conservative_peak.bed

value: untreated


title: 20764X10 WT_Th1_Secondary_Day7_biol_rep_3

value: LCMV Armstrong

value: day 7 recall response


title: K562, 3xFLAG-TopoIIa, anti-Flag M2, ChIP, biol rep 1


title: M0202


title: M0193


title: HepG2_UHRF1-TTD_CIDOP_bio-rep2

value: GST-UHRF1-TTD (Uniprot Q96T88, residues 126-280)


title: P28_aCM_2

city: Boston

first: William

middle: T.

last: Pu

state: Ma

address: 300 Longwood Ave

department: Cardiology

institute: Boston Children's Hospital

description:
Bulk RNA seq
DEseq2_P28_aCMvVcm.xlsx
Normalized_counts_P28vP0_aCMs.csv
Normalized_counts_P28_aCM_vs_vCM.csv

data_processing:
After trimming, FASTQ files were aligned to mm10
Star mapping was performed
.count files were produced with htseq-count (htseq-count -f bam -s no -t exon -i gene_id -m intersection-nonempty ./${sample}.sort.bam $gtf_path >$count/${sample}.count)
DEG analysis was performed by loading count files and running DeSeq2.
data for vCMs (GSM5856166, GSM5856167, GSM5856168) was processed identically and compared with P28 aCMs with DEseq2
Assembly: mm10
Supplementary files format and content: DEseq2 files for each experiment
Supplementary files format and content: Normalized count matricies for each experiment

molecule: polyA RNA

source_name: Isolated P28 aCM

growth_protocol: Mice were harvested at the indicated stage

extract_protocol:
RNA was extracted using Direct-zol RNA miniprep plus kit with on-column DNA digest
Takara SMART-Seq v4 Ultra low Input RNA kit

treatment_protocol: aCMs were harvested at the indicated stage from atria

value: Isolated P28 aCM

value: atrial cardiomyocyte

value: WT


title: P28_aCM_4


title: P28_aCM_3


title: HepG2_UHRF1-TTD_CIDOP_bio-rep1

value: liver


title: P28_aCM_1


title: K562, 3xFLAG-TopoIIa, Input, biol rep 1


title: M0186


title: CWR22-RH Tasquinimod-treated PDX Tumor 2

city: Seattle

first: Ilsa

last: Coleman

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

data_processing:
Sequencing reads were mapped to the hg38 human genome and mm10 mouse genomes using STAR.v2.7.3a. Sequences aligning to the mouse genome deriving from potential contamination with mouse tissue were removed from the analysis using XenofilteR (v1.6).
Gene level abundance was quantitated using the GenomicAlignments summarizeOverlaps function using mode=IntersectionStrict, restricting to primary aligned reads, and counting reads mapping to the exonic regions of genes.
Assembly: hg38
Supplementary files format and content: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

source_name: CWR22-RH PDX tumor

growth_protocol: Triple immune‐deficient NSG (i.e. NOD.Cg‐PrkdcScidIl2rgtm1Wji/Szj), adult (>8 week old) male mice obtained from the Sidney Kimmel Comprehensive Cancer Center (SKCCC) Animal Core Facility were used for xenografting. For each line tested, 100 μl of sterile saline containing 2 x 10^6 cancer cells was mixed at 4˚C with 100 μl of Matrigel obtained from BD Biosciences and then the mixture inoculated subcutaneously in the flank of castrated adult male NSG mice.

extract_protocol:
Total RNA was isolated from flash frozen xenograft tissue with RNeasy Mini Kit (Qiagen) utilizing the manufacturer’s recommended DNase digestion (Qiagen).
RNA-seq libraries were constructed from 1 ug total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol.

tag: gender

value: prostate cancer

value: CWR22-RH PDXs in castrate hosts treated orally with TasQ (10 mg/kg/d)


title: P0_aCM_4

description:
Bulk RNA seq
DEseq2_P28aCM_v_P0aCM.xlsx
Normalized_counts_P28vP0_aCMs.csv

source_name: Isolated P0 aCM

tag: tissue

value: Isolated P0 aCM


title: 20764X5 WT_Tfh_Secondary_Day7_biol_rep_1

value: female

value: Spleen

value: SMARTA CD4 T Cells

value: Tfh

tag: genotype


title: HepG2_H3K9me2_ChIP_bio-rep1

tag: cell line

value: Hepatoblastoma


title: EC_woIAA

first: Satoshi

last: Kimura

state: Massachusetts

address: 181 Longwood Avenue

institute: Brigham and Women's Hospital

library_source: other

data_processing:
Analysis: 3’ linker sequences and two nucleotides at the 5’ end were trimmed using cutadapt and fastx-trimmer. Bowtie v1.2.2 was used with default settings to map reads to reference Mtb tRNA sequences retrieved from Mycobrowser[40]. Mpileup files were generated using samtools (samtools mpileup -I -A --ff 4 -x -B -q 0 -d 10000000). For analysis of termination frequencies, 5’ end termini of mapped reads were piled up using bedtools genomecov (option, -d -5 -ibam). The number of 5’ termini at each tRNA position was divided by the total number of mapped termini at that position plus all upstream (5’) positions.
Assembly: EC-tRNA.fa, Mtb-tRNA.fa
Supplementary files format and content: Misincporation and Termination frequencies are shown in the csv file format

molecule: other

organism: Escherichia coli

source_name: bacteria

extract_protocol:
Extraction of total RNA: Strains were grown to mid-log phase with the appropriate antibiotics and inducing agents described above. RNA was collected at the same OD600 for each strain (between 0.4-0.6). Cells were left on ice for 20 minutes, then pelleted by centrifuging at 4,000 rpm for 10 minutes at 4 °C. Pellets were resuspended in 0.5-1 mL of TriZol (Life Technologies) and lysed using a BeadBug microtube homogenizer (Millipore Sigma). 200 uL of chloroform was added to each tube, after which samples obtained from Mtb strains were removed from biosafety level 3 precautions. Samples were centrifuged at 15,000 rpm for 15 minutes at 4 °C and the aqueous layer was collected into a fresh tube. To the original tube, 250 uL of sodium acetate buffer (300 mM sodium acetate pH 5.2 and 10 mM EDTA pH 8.0) was added, and samples were vortexed at 4 °C for 5 minutes then centrifuged at 15,000 g for 15 minutes at 4 °C. The aqueous layer was added to the fresh sample-containing tubes. 400 uL chloroform was added, and tubes were briefly vortexed and then centrifuged at 15,000 rpm for 1 minute at 4 °C. The aqueous phase was collected into a fresh tube and RNA recovered by ethanol precipitation. RNA pellets were resuspended in 10 mM sodium acetate pH 5.2 and stored at -80 °C until processed for sequencing. Total RNA samples were alkali-treated prior to tRNA extraction to deacylate all tRNAs (1 hour at 37 °C in 100 mM Tris-HCl pH 9.0).  Isolation of tRNA fraction: 1-2 ug of total RNA was run on a 10% TBE-UREA gel (ThermoFisher Scientific) at 250 V for 1 hour. Gels were stained with SYBR Gold (ThermoFisher Scientific), and tRNA was excised. Excised gels containing tRNA fractions were mashed in RNAse-free tubes, and 300 uL elution buffer (300 mM NaOAc pH 5.5, 1 mM EDTA pH 8.0, 0.10% SDS) was added to each tube. Samples were shaken on a thermoshaker (Eppendorf) for 1-4 hours at 37 °C and supernatant was collected using an Ultrafree filter column (Millipore Sigma). tRNA was recovered by isopropanol precipitation.
tRNA dephosphorylation: tRNA was dephosphorylated using QuickCIP (New England BioLabs) according to manufacturer instructions, and tRNA was collected by phenol-chloroform extraction followed by isopropanol precipitation.   Iodoacetamide (IAA) treatment: IAA treatment was performed as described. Briefly, 500 ng of total RNA is combined with 10 mM of iodoacetamide, 50 mM NaPO4 pH 8.0, and 50% DMSO in a final volume of 50 uL. Reactions were incubated at 50 °C for 15 minutes and quenched with DTT.  CMC treatment: CMC treatment was carried out as described in ref. Briefly, 2.5 ug tRNA fraction in 0.5 ul was mixed with 15 ul CMC-BEU buffer with or without CMC (0.34 M or 0 M CMC, 7 M urea, 4 mM EDTA, and 50 mM bicine pH 7.9) and incubated at 37 °C for 20 min. Adding 100 ul CMC stop solution (0.3 M NaOAc pH 5.2 and 100 mM EDTA) quenched the reaction. RNA was desalted with PD-10 desalting column (Cytiva) and recovered by ethanol precipitation. RNA was dissolved in 40 ul of 50 mM sodium carbonate buffer (pH 10.4) and incubated at 37 °C for 4 hours, followed by ethanol precipitation.  Adapter ligation: 0.5 uL RNase inhibitor was added to 3.5uL dephosphorylated tRNA (200-250 ng tRNA) and samples were boiled at 80 °C for 2 minutes. Boiled tRNA was mixed with 12 uL PEG buffer mix (10 uL 50% PEG8000, 2 uL 10 x buffer B0216S; New England Biolabs). 3 uL of 5’ adenylated linkers (Supplementary Table 4) were added (33 pmol/uL) along with 1 uL T4 RNA ligase 2 truncated (New England BioLabs) and incubated at 25 uC for 2.5 hours. Samples were recovered by isopropanol precipitation and run on a 10% TBE-Urea PAGE gel for 40 minutes at 250 V. Ligated products were recovered by gel excision as described above.  Reverse transcription: Identical quantities of samples with different adapter sequences were pooled for reverse transcription for a total of 200250 ng tRNA. Reverse transcription was performed by combining 2.1 uL dephosphorylated tRNA with 100 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 1.25 uM RT primer, 450 mM NaCl, 5 mM MgCl2, 5 mM DTT, 500 nM TGIRT (InGex), and 15% PEG8000 in a final volume of 9 uL. Samples were incubated at 25 °C for 30 minutes, after which 1 uL 10 mM dNTPs (New England BioLabs) were added and reactions incubated at 60 °C for 1 hour. 1.15 uL NaOH was added, and samples were boiled for 15 minutes and run on a 10% TBE Urea PAGE gel at 250V for 1 hour. Reverse transcription products were excised from gels and cDNA recovered by isopropanol precipitation. Linear single-stranded cDNA was circularized using CircLigase II (Lucigen) in accordance with manufacturer instructions.  PCR of tRNA libraries: PCR reactions were set up using HF Phusion according to the manufacturer’s instructions using a universal reverse primer and a different index primer for each pool of samples. PCR reactions were aliquoted into 4 tubes and collected after 6, 8, 10, and 12 cycles. Samples were run on a Native TBE PAGE gel (ThermoFisher Scientific) at 180 V for 50 minutes, and amplified products were cut from the same cycle for each sequencing run. Samples were recovered by gel excision and isopropanol precipitation.

tag: cell type

value: bacteria


title: M0156

value: male

value: BALB/cByJ

value: 2% carbonyl iron (20,000 ppm)


title: CWR22-RH Tasquinimod-treated PDX Tumor 1

tag: treatment


title: M0173


title: EC_woCMC


title: CWR22-RH Vehicle-treated PDX Tumor 1

value: CWR22-RH PDXs in castrate hosts treated orally with vehicle


title: EC_CMC

value: CMC


title: M0142


title: P0_aCM_2

value: atrial cardiomyocyte


title: P0_aCM_1

value: WT


title: HepG2_H3K9me2_ChIP_bio-rep2

value: liver


title: CWR22-RH Vehicle-treated PDX Tumor 3

value: prostate cancer


title: K562, 3xFLAG-TopoIIa, Input, biol rep 2

value: lymphoblast cells


title: M0150

value: NZB/BlNJ


title: OVCAR8, Input

city: Shanghai

first: Jianfeng

last: Chen

state: Shanghai

address: 270 Dong'an Road

institute: Fudan University Shanghai Cancer Center

data_processing:
Raw reads were filtered and cleaned by fastp software.
Aliments were performed followed by bowtie2 and STAR instruction
MACS2 were used for the binding profile
IGV and R were used for visualization
Supplementary files format and content: hg19
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: Human high grade serous ovarian cancer

growth_protocol: OVCAR8 cellls were cultured in RPMI1640 medium supplemented with 10% FBS and 1% P/S.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared according to NEB ChIP-Seq Library Prep Kit (E6240).

value: Human high grade serous ovarian cancer

tag: antibody

value: no antibody


title: M0141

tag: Sex


title: WT_TRF_12_30

city: El Cajon

first: Daniel

last: Carlin

address: 1250 Mountain View Rd.

institute: UC-San Diego

data_processing:
Sequence alignment of the resulting high-quality reads to the mouse reference genome (build GRCm38) was done using HISAT2 and quantification of gene-level expression was performed using featureCounts. DESEQ2 was used to generate normalized read counts and to determine differentially expressed genes. Genes with an averageexpression of more than 2 counts per minute (CPM) across all samples were considered as expressed.
Assembly: GRCm38
Supplementary files format and content: tab delimited deseq2 normalized counts

source_name: Hippocampus

growth_protocol: APP23 transgenic (TG) mice (B6.Cg-Tg(Thy1-APP)3Somm/J; JAX Stock No: 030504) and non-transgenic (NTG) littermates control mice were housed in light-tight enclosures at the University of California, Los Angeles in the Laboratory of Circadian and Sleep Medicine. APP-SAA KI (B6.Cg-Apptm1.1Dnli/J; JAX Stock No: 034711) were obtained from Jackson Laboratory as heterozygotes and bred to develop heterozygote APP-SAA KI mice (APP-KI) and non-transgenic (NTG) littermates. APP-KI were housed in light-tight enclosures at the University of California, San Diego. The mice were given ad libitum food (Teklad rodent diet 8604; Envigo, Indianapolis, IN) and water access until they were placed in the time-restricted feeding (TRF) or ad libitum feeding (ALF) cohorts. The work presented in this study followed all guidelines and regulations of the UCSD and UCLA Division of Animal Medicine that are consistent with the Animal Welfare Policy Statements and the recommendations of the Panel on Euthanasia of the American Veterinary Medical Association.

extract_protocol:
Mice were euthanized with isoflurane, either in the dark ( ZT12 and ZT18) or in the light (ZT0 and ZT6). Brain hemispheres were collected and placed in either RNAlater Stabilization Solution (Thermo Fisher Scientific, Waltham, MA) or 4% paraformaldehyde. Serum was collected from blood incubated on ice for 30 min, centrifuged at 2000 g for 10 min at 4°C, and then stored until used at -80°C.
Total RNA was isolated from hippocampus tissue dissected from one hemibrain per animal using RNeasy Lipid Tissue Mini kit (Qiagen, Hilden, Germany) as indicated by the manufacturer. Quality of the extracted RNA was assessed using TapeStation (Agilent Technologies, Inc., Santa Clara, CA). All samples showed RIN 8. RNA-Seq library preparation was performed with poly-A enrichment using poly-T oligo-attached magnetic beads employing the PE150 sequencing strategy performed on a NovaSeq 6000 (Illumina, Inc., San Diego, CA) by Novogene Inc. (Sacramento, CA). Raw reads (>20M per sample) were imported to Galaxy platform for analysis 83. Reads were first cleaned by removing adapter sequences, trimming low-quality ends, and filtering reads with low quality using Trimmomatic.

treatment_protocol: Prior to any measurements or beginning any experiments, mice were habituated to a 12:12 light-dark (LD 12:12) cycle and single housing conditions in custom light-tight cabinets. We then measured diurnal rhythms in activity and sleep behavior from the mice. To assess circadian impairments in the mice, some animals were placed in constant darkness (DD), followed by light masking and 6 h phase advance protocols. Feeding manipulations were then performed on mice habituated to LD 12:12. Animals within each sex and genotype were randomly divided into two groups with one group continuing ALF and the other placed on TRF, with food available during 6 h in the middle of the mouse active phase, during zeitgeber time (ZT) 15 to ZT21. By definition, ZT0 is the time when lights go on and ZT12 is the time when the lights go off when the mice are in a 12:12 LD cycle. After habituating to the feeding protocol, metabolites were measured in the mice to ensure the treatment was inducing the expected metabolic effects. The mice remained on TRF or ALF food access until sacrificed for tissue collection. After all tests were completed and the mice had re-entrained to the LD cycle, mice within each genotype and treatment group were randomly assigned for sacrifice at one of four time points: ZT0, ZT6, ZT12, or ZT18. ZT0 and ZT6 tissues were collected in the light; ZT12 and ZT18 were collected in the dark. Brain tissue and blood serum were collected for analysis. This study used a total of 110 mice almost equally distributed across sex/ genotype/treatment throughout the study, and further grouped by ZT collection times. Treated mice started TRF at 6 to 9 months of age and were maintained on TRF until tissue collection, which occurred at 10 to 13 months of age. Experimental mice were housed in standard cages with either normal ad libitum food or with a custom-made programmable food hopper that could temporally control access to food and prevent food consumption during restricted times. Feeders were open for 6 h in the middle of the mouse active phase (ZT15 to ZT21). Food consumption was initially measured twice per week to ensure that all mice acclimated to the new feeding regimen. Mice are coprophagic and were moved to new cages twice per week, as determined empirically, to diminish coprophagic behavior during the fasting period.

value: Hippocampus

value: NTG

value: TRF


title: WT_TRF_18_313


title: M0188

last: Pan

address: 675 Charles Young Dr South

tag: strain


title: NB-119

city: Jerusalem

first: Miriam

last: Adam

state: Israel

address: Givat Ram

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Demultiplexing and Fastq files genration was done using Illumina's bcl2fastq  v2.19.1.403
Aligmnet to human genome (hg38) was done with STAR v2.7.3a
Transcriptome alignment and gene counts were generated with HTseq  v0.13.5
csv file with normalized gene counts. Variance stabilizing transformation was used to normalize the counts.
Assembly: hg38
Supplementary files format and content: csv file with normalized gene counts

source_name: meningioma tumor

extract_protocol:
RNA was extracted with NucleoSpin RNA kit (MACHEREY-NAGEL)
Libraries were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina according to manufacturers protocol

value: meningioma tumor

tag: grade

value: Grade 1 meningioma


title: WT_TRF_6_312


title: NB-160


title: EC_IAA

value: bacteria

value: IAA


title: M0114

first: Calvin

institute: UCLA

source_name: liver

value: male

tag: diet

value: 2% carbonyl iron (20,000 ppm)


title: OVCAR8, H3K27me3


title: M0112


title: WT_TRF_12_233


title: NB-113


title: NB-123-B


title: OVCAR8, EZH2


title: WT_TRF_12_232R


title: NB-149


title: M0096


title: WT_TRF_12_232


title: M0095


title: SCARB2ko3

city: Bei Jing

first: Yang

last: Gao

address: Tiantan Xili 2

department: Institute of Medicinal Biotechnology

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

description: liver

data_processing:
Trimmomatic software were used to remove adapter and low quality reads.
Quality distribution plot and base content distribution were generated by FASTQC.
Mapping of pair-end reads. Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences. The clean reads were then aligned to reference genome sequences using the bwa program.
We calculate the fragment sizes for read pairs given a BAM file from paired-end sequencing.
Using macs2 software for callpeak with cutoff qvalue < 0.05.
Assembly: Homo_sapiens.GRCh38.89.chr
Supplementary files format and content: bigWig files
Library strategy: CUT&Tag

source_name: HepG2 cells

extract_protocol:
Cells were harvested, counted and were washed with Wash Buffer. Concanavalin A Beads were prepared with Binding buffer and 10 µL of activated beads were added per sample, invert to mix and incubate at room temperature.
The primary antibody incubation was performed on a rotating platform overnight at 4 °C. Beads were washed and incubated with secondary antibody. After incubation, the beads were washed and incubated with hyperactive pA/G-transposon (pA/G-Tnp) at RT. Next, cells were re-suspended in Trueprep Tagment Buffer L and the DNA fragments were extracted with DNA Extract Beads. Beads were washed twice with Buffer WA and Buffer WB. After drying ~ 5 min, 20 µL ddH2O was added. To amplify libraries, 15 µL DNA was mixed with 25 µL 2×CUT&Tag amplification mix, 5 µL N5, and 5 µL N7 primer, using a different barcode for each sample. The sample was placed in a Thermocycler with a heated lid using the following cycling conditions: 72 °C for 3 min; 95 °C for 30 min; 14 cycles of 98 °C for 10 s and 60 °C for 5 s; final extension at 72 °C for 1 min and hold at 4 °C. Post-PCR clean-up was performed by adding 100 µL VAHTS DNA Clean Beads (Vazyme, #N411), and libraries were incubated with beads for 5 min at RT, washed twice gently in 80% ethanol, and eluted in 20 µL ddH2O.

value: hepatocyte

value: c-Myc antibody (CST, #9402)


title: OVCAR8, SUZ12


title: NB-126


title: CWR22-RH Vehicle-treated PDX Tumor 2

value: CWR22-RH PDXs in castrate hosts treated orally with vehicle


title: SCARB2ko2

description: liver


title: M0092

city: Los Angeles

value: liver


title: NB-110


title: WT_TRF_0_32


title: M0084

value: NOD/ShiLtJ


title: SCARB2ko1

description: liver


title: WT_TRF_0_116


title: P0_aCM_3

value: Isolated P0 aCM

value: atrial cardiomyocyte

value: WT


title: M0079


title: WT_TRF_6_309

value: Hippocampus


title: CTRL3

description: liver


title: NB-124


title: NB-098


title: M0104


title: IgG

description: liver

value: Normal IgG antibody (CST, #2729)


title: CTRL2

description: liver


title: NB-132


title: CTRL1

description: liver


title: WT_TRF_18_326

value: NTG

value: TRF


title: M0061


title: M0058

value: BTBR T<+> tf/J


title: WT_TRF_12_144


title: PMB-3

description: liver

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data).
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other style.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Million Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
DEGseq was used for differential gene expression analysis.
The GO (Gene Ontology, http://geneontology.org/) enrichment of DEGs was implemented by the hypergeometric test, in which p-value is calculated and adjusted as q-value, and data background is genes in the whole genome.
KEGG (Kyoto Encyclopedia of Genes and Genomes, http://www.kegg.jp/) is a database resource containing a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks.
Assembly: Homo_sapiens.GRCh38.89.chr
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample.

extract_protocol:
Cells were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. A total amount of 2 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® (#E7530L, NEB, USA).

value: PMB for 24 hours


title: M0055


title: M0048


title: WT_TRF_12_142


title: PMB-2

description: liver


title: WT_TRF_0_118


title: NB-109

value: meningioma tumor

value: Grade 1 meningioma


title: WT_TRF_12_10


title: NB-111


title: M0045

value: male

value: 2% carbonyl iron (20,000 ppm)


title: NB-147

value: Grade 2 meningioma


title: PMB-1

description: liver

value: hepatocyte


title: NB-123


title: M0041

value: liver


title: CON-3

description: liver

value: untreated


title: CON-2

description: liver


title: WT_TRF_0_8


title: M0039


title: NB-127


title: WT_TRF_0_204


title: WT_TRF_0_202


title: NB-118


title: CON-1

description: liver


title: NB-114


title: NB-103


title: WT_ALF_18_328

value: ALF


title: WT_ALF_6_301


title: M0036


title: M0025

value: SJL/J


title: WT_ALF_12_322


title: M0018


title: M0015


title: M0030


title: WT_ALF_12_26


title: WT_ALF_12_106


title: biventricular heart, CEK, ZT03, bio rep 4

city: Birmingham

first: Lamario

middle: J

last: Williams

state: AL

address: 1825 University Boulevard, Room 121

department: Medicine

institute: University of Alabama at Birmingham

data_processing:
Basecalls were performed using Illumina's bcl2fastq version 2.18.0.12
Raw sequence reads were aligned with STAR (version 2.6.1d) using parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated from the STAR alignment BAM files using HTSeq-count (version 0.11.1) using parameters -m union -r pos -t exon -i gene_id -a 10 -s no -f bam
Assembly: Gencode GRCm38 p4 Release M11
Supplementary files format and content: tab-delimited text file containing Esnembl ID# and raw counts for each gene in each sample

source_name: biventricular heart

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

value: biventricular heart

value: CEK

tag: time


title: biventricular heart, CEK, ZT09, bio rep 3


title: biventricular heart, CON, ZT03, bio rep 4

value: CON


title: M0008

value: NOR/LtJ


title: K562, amrubicin 10 µM, 4h, ATAC-seq, biol rep 2

description:
ATAC_Amr.merged.sorted.bigwig
ATAC_Amr.overlap_conservative_narrowPeak.bed

data_processing:
ATAC-seq samples were processed identically using the ENCODE Data Coordination Center (DCC) ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline) (v1.10.0).
ATAC-seq reads were aligned to the human reference genome (GRCh37/hg19) using Bowtie2. Duplicate reads were removed using Picard MarkDuplicates.
ATAC-seq signal files were generated using "bedtools genomecov -scale" to convert the merged bam file from two replicates to bedgraph file. The bedgraph files were further converted to bigwig files using bedGraphToBigWig. The bigwig data was normalized by read counts per million (RPM).
ATAC-seq peaks were called using MACS253 with the setting of ‘-p 0.01 --shift -75 --extsize 150 --nomodel -B --SPMR --keep-dup all’, then followed by blacklisted regions filtering described by ENCODE. Reproducible peaks were intersected from two biological replicates using bedtools intersect command.
hg19
bigwig, bed

growth_protocol: wildtype K562 cells (for ATAC-seq) were cultured in RPMI-1640 medium supplemented with 8% fetal calf serum.

extract_protocol:
ATAC samples were processed as described in PMID 24097267 and 28846090.
ATAC samples were processed as described in PMID 24097267 and 28846090.

value: lymphoblast cells

value: WT

value: amrubicin 10 microM

tag: chip antibody


title: biventricular heart, CEK, ZT21, bio rep 4


title: WT_ALF_0_107

value: Hippocampus

value: NTG


title: K562, amrubicin 10 µM, 4h, ATAC-seq, biol rep 1


title: biventricular heart, CEK, ZT15, bio rep 4

value: male


title: K562, aclarubicin 10 µM, 4h, ATAC-seq, biol rep 2

description:
ATAC_Acla.merged.sorted.bigwig
ATAC_Acla.overlap_conservative_narrowPeak.bed

value: aclarubicin 10 microM


title: biventricular heart, CON, ZT21, bio rep 4


title: WT_ALF_0_101


title: biventricular heart, CON, ZT15, bio rep 4


title: K562, aclarubicin 10 µM, 4h, ATAC-seq, biol rep 1


title: biventricular heart, CEK, ZT09, bio rep 4


title: WT_ALF_12_22


title: WT_ALF_18_325


title: K562, idarubicin 10 µM, 4h, ATAC-seq, biol rep 2

description:
ATAC_Ida.merged.sorted.bigwig
ATAC_Ida.overlap_conservative_narrowPeak.bed

value: idarubicin 10 microM


title: biventricular heart, CON, ZT12, bio rep 4


title: biventricular heart, CON, ZT06, bio rep 4


title: WT_ALF_12_122


title: biventricular heart, CEK, ZT09, bio rep 1


title: K562, idarubicin 10 µM, 4h, ATAC-seq, biol rep 1


title: WT_ALF_12_135


title: biventricular heart, CEK, ZT12, bio rep 4


title: K562, epirubicin 10 µM, 4h, ATAC-seq, biol rep 1

description:
ATAC_Epi.merged.sorted.bigwig
ATAC_Epi.overlap_conservative_narrowPeak.bed

value: epirubicin 10 microM


title: biventricular heart, CEK, ZT00, bio rep 3


title: WT_ALF_0_3


title: K562, daunorubicin 10 µM, 4h, ATAC-seq, biol rep 1

description:
ATAC_Daun.merged.sorted.bigwig
ATAC_Daun.overlap_conservative_narrowPeak.bed

value: daunorubicin 10 microM


title: biventricular heart, CEK, ZT06, bio rep 3


title: K562, epirubicin 10 µM, 4h, ATAC-seq, biol rep 2


title: WT_ALF_0_136


title: WT_ALF_0_134


title: biventricular heart, CEK, ZT00, bio rep 4


title: K562, daunorubicin 10 µM, 4h, ATAC-seq, biol rep 2


title: K562, doxorubicin 10 µM, 4h, ATAC-seq, biol rep 1

description:
ATAC_Doxo.merged.sorted.bigwig
ATAC_Doxo.overlap_conservative_narrowPeak.bed

value: doxorubicin 10 microM


title: biventricular heart, CON, ZT00, bio rep 4


title: K562, doxorubicin 10 µM, 4h, ATAC-seq, biol rep 2


title: WT_ALF_0_120

value: ALF


title: TG_TRF_6_307

value: TG

value: TRF


title: TG_TRF_6_315


title: biventricular heart, CON, ZT12, bio rep 3

value: biventricular heart


title: TG_TRF_18_305


title: K562, ATAC-seq, biol rep 2

description:
ATAC_Ctr.merged.sorted.bigwig
ATAC_Ctr.overlap_conservative_narrowPeak.bed

value: untreated


title: K562, ATAC-seq, biol rep 1


title: biventricular heart, CEK, ZT12, bio rep 3

value: CEK


title: TG_TRF_18_302


title: WT_ALF_0_1


title: biventricular heart, CON, ZT09, bio rep 3

value: CON


title: HPK-DT+6p#3

city: Singapore

first: Franklin

last: ZHONG

state: Singapore

address: 11 Mandalay Road

country: Singapore

institute: NTU LKC School of Medicine

data_processing:
Trimmed reads are mapped to reference genome with HISAT2
After the read mapping, Stringtie was used for transcript assembly. Expression profile was calculated for each sample and transcript/gene as read count, FPKM (Fragment per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Kilobase Million).
DEG (Differentially Expressed Genes) analysis was performed on 5 comparisons pairs as requested using DESeq2. The results showed 4,643 genes which satisfied |fc|>=2 & nbinomWaldTest raw p-value<0.05 conditions in at least one of comparison pairs.
Assembly: GRCh38
Supplementary files format and content: FKPM and TPM in txt

source_name: Skin

growth_protocol: HPK culture

extract_protocol:
Total RNA by Trizol
TruSeq Stranded mRNA LT Sample Prep Kit

treatment_protocol: DT (150ng/mL), 4hours with/without Compound 6p (1uM)

value: Skin

value: HPK

value: Keratinocytes

value: Wild type


title: biventricular heart, CON, ZT06, bio rep 2

value: male


title: HPK-6p#3


title: biventricular heart, CON, ZT00, bio rep 3


title: biventricular heart, CON, ZT18, bio rep 4


title: biventricular heart, CEK, ZT18, bio rep 4


title: HPK-6p#1


title: biventricular heart, CEK, ZT06, bio rep 2


title: HPK-DT#3

value: DT


title: HPK-DT+6p#1


title: biventricular heart, CEK, ZT18, bio rep 3


title: HPK-DT+6p#2


title: HPK-DT#1


title: biventricular heart, CON, ZT15, bio rep 3


title: biventricular heart, CON, ZT00, bio rep 2


title: TG_TRF_12_104

value: Hippocampus


title: TG_TRF_18_330


title: TG_TRF_0_102


title: TG_TRF_0_321


title: HPK-6p#2


title: biventricular heart, CEK, ZT15, bio rep 3


title: TG_TRF_0_7


title: HPK-DT#2


title: TG_TRF_6_308


title: TG_TRF_6_331


title: TG_TRF_12_126


title: HPK-Untreated #3

value: Untreated


title: biventricular heart, CON, ZT15, bio rep 2


title: M. Vastus Lateralis , Obese, RES36 (RRBS)

city: Orlando

first: Lauren

last: Sparks

state: Florida

address: 301 E Princeton St, 301

institute: AdventHealth

data_processing:
Initially, Trim Galore, a wrapper tool around Cutadapt and FastQC, was applies to FastQ files for QC and adapter trimming. Once trimmed, Bismark was performed for read mapping and methylation calling (Krueger & Andrews, 2011). The former aligns reads to a reference genome and the later reveals the methylation status of cytosines. Cytosines in the reference sequenced as thymines are labeled unmethylated, and those that remained as cytosines are labeled methylated. The results of the Bismark-run is a methylation matrix, reporting the percentage of cytosine methylations.
Genome_build: hg38
Supplementary_files_format_and_content: TXT of methylation matrix reporting percentage of cytosine methylations for each participant . Files are the output of bismark methylation extractor in the bsmark package that are formatted for  the methyKit program for subsequent analysis

source_name: M. Vastus Lateralis

extract_protocol:
Skeletal muscle biopsies were performed in the m. vastus lateralis using Bergström needle technique and snap frozen. Total DNA was isolated from 10-20 mg of skeletal muscle tissue using DNeasy blood and tissue extraction kit (QIAGEN Inc, Valencia, CA).
RRBS library was generated from  ≥ 1.5 μg genomic DNA at Novogene. Libraries were sequenced  as Paired-end 150bp on Novaseq 6000 sequencer at an  average out per sample ≥ 10 Gb .

value: Skeletal Muscle Tissue

tag: phenotype

value: Obese


title: TG_TRF_12_24


title: HPK-Untreated #2


title: M. Vastus Lateralis , T2D, RES34 (RRBS)


title: TG_TRF_12_121


title: HPK-Untreated #1


title: M. Vastus Lateralis , Obese, RES26 (RRBS)


title: TG_TRF_0_323


title: biventricular heart, CON, ZT09, bio rep 2


title: TG_TRF_0_211


title: M. Vastus Lateralis , T2D, RES20 (RRBS)


title: WD56039

city: Stanford

first: Tomek

last: Swigut

address: 265 Campus Dr

institute: Stanford University

data_processing:
salmon quant
Assembly: GRCm39 and gencode_M31 gene models
Supplementary files format and content: salmon quant.genes.sf with pseudocounts and TPM

growth_protocol: melanocytes were isolated from foreskin human tissue and cultured in the presence of serum-free medium 254 supplemented with 1x human melanocyte growth supplement

extract_protocol:
Total RNA was isolated from melanocytes using an RNA isolation kit (Zymo Research) following manufacturer’s instructions
RNA Sequencing libraries were prepared using Ovation Ultralow System (Nugen/Tecan) following manufacturer’s instructions

tag: group

value: darkly pigmented

value: melanocyte

value: WT

value: growth medium


title: TG_TRF_12_220

value: TG

value: TRF


title: biventricular heart, CON, ZT03, bio rep 2

value: biventricular heart

value: CON


title: biventricular heart, CON, ZT12, bio rep 2


title: WD56237

value: Skin


title: M. Vastus Lateralis , Active, RES13 (RRBS)

value: Active


title: biventricular heart, CON, ZT09, bio rep 1


title: TG_ALF_6_304

value: ALF


title: WD55939


title: biventricular heart, CEK, ZT21, bio rep 3

value: male

value: CEK


title: M. Vastus Lateralis , Active, RES09 (RRBS)


title: M. Vastus Lateralis , Active, RES05 (RRBS)


title: WD55938


title: biventricular heart, CON, ZT21, bio rep 3


title: TG_ALF_18_314

value: Hippocampus


title: M. Vastus Lateralis , T2D, RES03 (RRBS)


title: WD55937


title: M. Vastus Lateralis , Obese, RES24 (RRBS)


title: TG_ALF_18_303


title: biventricular heart, CON, ZT18, bio rep 3


title: M. Vastus Lateralis , Obese, RES36 (RNA-seq)

description: SkeletalMuscle_Active_T2D_Obese_RNA_Seq.csv

data_processing:
Adaptor was trimmed with Cutadapt and low quality reads(Q30) were filtered out before aligning with STAR to the reference genome hg38. Raw counts were calculated with featureCounts. Cufflinks was used to generate normalized read counts per gene and isoform in terms of FPKM values.
Genome_build: hg38
Supplementary_files_format_and_content: CSV file of FPKM values for each Sample

extract_protocol:
Skeletal muscle biopsies were performed in the m. vastus lateralis using Bergström needle technique and snap frozen. RNA was extracted from 30-50mg of skeletal muscle tissue using RNeasy Fibrous Tissue Kit (Qiagen, Valencia, CA).
Following polyA selection and library preparation and Quality Control (QC), sample libraries were underwent mRNA sequencing, with the average depth of 20 million paired-end reads per sample using the Illumina Novaseq 6000.


title: WD55781


title: M. Vastus Lateralis , T2D, RES34 (RNA-seq)


title: WD56038


title: WD55611


title: TG_ALF_12_109


title: TG_ALF_12_117


title: M. Vastus Lateralis , Obese, RES32 (RNA-seq)


title: TG_ALF_12_115


title: TG_ALF_6_332


title: M. Vastus Lateralis , T2D, RES30 (RNA-seq)


title: biventricular heart, CEK, ZT21, bio rep 2


title: biventricular heart, CEK, ZT03, bio rep 3


title: WD55215

value: Lightly pigmented


title: TG_ALF_0_5


title: biventricular heart, CON, ZT21, bio rep 2


title: M. Vastus Lateralis , Obese, RES28 (RNA-seq)

value: Skeletal Muscle Tissue


title: WD55015


title: TG_ALF_0_234


title: M. Vastus Lateralis , Obese, RES26 (RNA-seq)

value: Obese


title: biventricular heart, CEK, ZT21, bio rep 1


title: WD54977

value: darkly pigmented


title: biventricular heart, CON, ZT18, bio rep 2


title: TG_ALF_0_16


title: biventricular heart, CON, ZT21, bio rep 1


title: M. Vastus Lateralis , Obese, RES24 (RNA-seq)


title: WD54976

value: melanocyte


title: WD55309

value: WT


title: biventricular heart, CEK, ZT18, bio rep 2


title: TG_TRF_0_129


title: M. Vastus Lateralis , Obese, RES22 (RNA-seq)


title: WD54975

value: growth medium


title: TG_ALF_6_310

value: TG


title: TG_ALF_6_319


title: M. Vastus Lateralis , T2D, RES20 (RNA-seq)


title: biventricular heart, CEK, ZT15, bio rep 2


title: biventricular heart, CON, ZT18, bio rep 1


title: biventricular heart, CEK, ZT18, bio rep 1


title: M. Vastus Lateralis , Active, RES18 (RNA-seq)


title: TG_ALF_12_23


title: WD54878


title: WD54879


title: biventricular heart, CEK, ZT15, bio rep 1


title: WD54781


title: M. Vastus Lateralis , Active, RES15 (RNA-seq)


title: biventricular heart, CEK, ZT12, bio rep 2


title: TG_ALF_12_19


title: M. Vastus Lateralis , Active, RES13 (RNA-seq)


title: WD54779


title: biventricular heart, CEK, ZT06, bio rep 1


title: M. Vastus Lateralis , Active, RES11 (RNA-seq)


title: Biological rep#1, Cells transfected with HDR-CRISPR, T cells

city: Freiburg

first: Claudio

last: Mussolino

address: Breisacherstr. 115

institute: Institute for Transfusion Medicine and Gene Therapy

description: Sequencing outsourced to GeneWiz

data_processing:
Mate paired reads were merged using BBmerge from BBmap (v38.76) software. BBmap  was also used for filtering and trimming as follow: merged reads containing the designer nuclease target site were filtered-in, whereas PCR mispriming products reads were filtered-out. Linker sequences, Illumina adapter sequences, targeted elongation sequence and bad quality reads were trimmed.
Selected reads were aligned to the human genome GRCh38 (hg38) using Bowtie2 (v2.3.4.2) and the very-sensitive preset parameters. Aligned reads with good mapping quality (MAPQ >15) were selected. The aligned BAM file was converted into bed file using bedtools (v2.27.1).
Translocated sites were identified using the CAST-Seq pipeline with default parameters, as described on https://github.com/AG-Boerries/CAST-Seq
Assembly: hg38
Supplementary files format and content: matrix table of translocation sites detected with T-CAST pipeline. It includes the genomic coordinates of translocated sites, read coverage.
Library strategy: CAST-seq

source_name: T cells

growth_protocol: Human peripheral blood mononuclear cells (PBMCs) were isolated from leukocyte reduction system chambers by density gradient centrifugation (Ficoll-Paque). PBMCs were kept in RPMI 1640 medium (Life Technologies) supplemented with 10% FCS (Thermo Fisher Scientific) and 1% Penicillin/Streptomycin (Merck) for 4 hours before activation. PBMCs/ T cells were cultured at 37°C with 5% CO2.

extract_protocol:
Cells were harvested 2 days post electroporation and their genomic DNA was extracted using the NucleoSpin® Tissue gDNA extraction kit (Machery Nagel) following the manufacture’s procedure and resuspended in 40 uL of Nuclease-free water.
Library construction was essentially performed as described by Turchiano et. al (Cell Stem Cell, 2021). Briefly, gDNA was fragmented by enzymatic digestion using the NEBNext® Ultra™ II FS DNA Library Prep (NEB) to obtain average fragment lengths of 200-350 bp. The DNA was end repaired and a protruding 3’-A nucleotide was added according to the manufacturer’s instructions  in order to enable the ligation of a linker sequence with a protruding 3’-T. After linker ligation, fragments were purified using the QIAquick PCR Purification Kit (NEB). The region of interes (on-target site) was amplified in two rounds of PCR using Q5® Hot Start High-Fidelity DNA Polymerase (NEB). PCR conditions were: 20 cycles at 95°C for 15 s, 63°C (first reaction) or 68°C (second reaction) for 20 s, 72°C for 20 s. The first reaction was performed with primers complementary to the linker sequence and to a sequence in close proximity to the on-target site (bait primer). Two decoy primers were introduced to reduce full-length amplification of the fragments which contain the on-target sequence without a chromosomal aberration event. The second PCR utilized nested primers to reduce the amount of mis-amplified fragments and to introduce a binding platform for barcoding primers. DNA fragments from the second PCR with a size of 200-500bp were subsequently isolated using the QIAquick® Gel Extraction Kit (Qiagen) and barcoded.
Third PCR introduced the barcoded Illumina adapter for sequencing (NEBNext® Multiplex Oligos for Illumina; Index Primers Sets 1-4). Sequencing was outsourced to service NGS provider Genewiz (part of Azenta Life Sciences) on where it was performed on Illumina HiSeq or NovaSeq devices collecting 2x150 bp paired-end reads.

value: T cells

value: Electroporated with HDR-CRISPR expressing IVT mRNA + sgRNA


title: biventricular heart, CON, ZT06, bio rep 1

value: biventricular heart

value: CON


title: TG_ALF_0_13


title: Biological rep#1, Cells transfected with Cas9, T cells

description: Sequencing outsourced to GeneWiz

value: Electroporated with Cas9 expressing IVT mRNA + sgRNA


title: TG_ALF_0_127

value: ALF


title: biventricular heart, CON, ZT03, bio rep 1

value: male


title: TG_ALF_18_329


title: Biological rep#1, Untreated Control, T cells

description: Sequencing outsourced to GeneWiz

value: Untreated


title: biventricular heart, CEK, ZT03, bio rep 1

value: CEK


title: TG_ALF_0_124

value: Hippocampus


title: M. Vastus Lateralis , Active, RES05 (RNA-seq)

value: Skeletal Muscle Tissue

value: Active


title: biventricular heart, CEK, ZT00, bio rep 2


title: M. Vastus Lateralis , T2D, RES03 (RNA-seq)


title: Uterus, DES 12-month-old, sample B

city: RTP

first: Wendy

last: Jefferson

state: NC

address: 111 Alexander Drive

institute: NIH

data_processing:
base calling by bcl2fastq v2.20.0.422
Visium processed by Space Ranger v 1.2.2
Assembly: mm10
Supplementary files format and content: *count.csv.gz Raw count matrix provided by 10X pipeline.
Supplementary files format and content: *meta.csv.gz CSV of relevant metadata for all cells in count matrix.

source_name: Uterus

extract_protocol:
Extraction was performed using Visium Spatial Gene Expression Slide kit (10X Genomics)
Library prep was performed using Visium Spatial Gene Expression Slide kit (10X Genomics)

value: Uterus

value: Neonatal DES (1mg/kg/day)


title: 124_AYNO

city: Godollo

first: Eva

last: Varallyay

address: 4 Szent-Györgyi Albert Street

department: Institute of Plant Protection

country: Hungary

institute: Hungarian University of Agriculture and Life Sciences

description: small RNA

data_processing:
The quality check of the sequenced small RNA libraries was done by FastQC Program and CLC Genomic Workbench 11
Trimming of raw reads was performed using the CLC Genomic Workbench 11
Removing redundant reads using the CLC Genomic Workbench 11
Supplementary files format and content: trimmed redundant list, each read with its number of repeats

organism: Catharanthus roseus

source_name: leaf

extract_protocol:
Phenol chloroform extraction method (White & Kaper, 1989) DOI: 10.1016/0166-0934(89)90122-5
modified Illumina Trueseq small RNA kit protocol: https://doi.org/10.1007/978-1-4939-7683-6_9

value: leaf

tag: symptoms

value: no symptoms

tag: ay phytoplasma presence

value: no

tag: year of sampling

tag: place of collection

value: glasshouse, with insectproof net


title: Uterus, Control, 12-month-old, sample B

tag: tissue

value: Control (corn oil)


title: 125_AYNO

description: small RNA


title: M. Vastus Lateralis , T2D, RES01 (RNA-seq)


title: biventricular heart, CON, ZT15, bio rep 1

value: biventricular heart

tag: genotype


title: 123_AYNO

description: small RNA


title: T2KO-old-LSK-MicroC

city: Houston

first: Jia

last: Li

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

data_processing:
Micro-C pipeline (https://micro-c.readthedocs.io/en/latest/) was used to analysis the Micro-C data. Specifically, we used bwa (0.17.17) to align raw reads on mm10 genome and the proper mapped read pairs were retained to downstream analysis. For each sample, mapped.pairs file was used as input for juicer_tools_1.22.01 to generate contact maps (hic format file). hicPCA function from HiCExplorer (3.7.2) with H3K4me3 ChIPseq tracks of young (4 month old) mice HSCs as correction for PCA values was applied to determine A/B compartment regions.
Assembly: mm10
Supplementary files format and content: hic format include contact matrix

source_name: Bone marrow

growth_protocol: 6-8 weeks WT mice were used as WT-young; 12-24 months WT mice were used as WT-old;  6-8 weeks Tet2KO mice were used as Tet2KO-young; 12-24 months Tet2KO mice were used as Tet2KO-old;

extract_protocol:
0.5 million LSK (Lin-cKit+Sca1+) cells were harvested from WT-young, WT-old, T2KO-young and T2KO-old mice
micro-C data were generated using Dovetail® Micro-C Kit. In briefly, the cells were crosslinked with FA in the presence of DSG, followed by in situ MNase Nuclease digestion and cell lysis. Then chromatins were captured by chromatin bind beads for future end polishing, bridge ligation, intra-aggregate ligation and reverse crosslinking. The purified DNA were proceeded with library generation.

value: Bone marrow

tag: cell type

value: Tet2 knockout


title: 122_AYWB

description: small RNA

value: witches broom

value: yes


title: T2KO-Young-LSK-MicroC


title: biventricular heart, CON, ZT12, bio rep 1

value: male

value: CON


title: M. Vastus Lateralis , Active, RES09 (RNA-seq)


title: M. Vastus Lateralis , T2D, RES07 (RNA-seq)


title: biventricular heart, CON, ZT09, bio rep 4