Key resources table

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological samples
Tissues from 4 individuals from ENCODE project	This paper	https://www.encodeproject.org/entex-matrix/?type=Experiment&status=released&internaltags=ENTEx
HG002	Human Pangenome Reference Consortium	ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG002_NA24385_son
Critical commercial assays
Express Kit V2	PacBio	N/A
SQK-LSK110 Kit	Oxford Nanopore	N/A
TruSeq DNA PCR-Free Library Preparation Kit	Illunmina	N/A
Deposited data
Spectra, results, and supporting files, including the personal proteome database	This paper	PRIDE: PXD022787
imprinted_genes_in_ENTEx_ASE.tsv	This paper	http://entex.encodeproject.org/data/imprinted_genes_in_ENTEx_ASE.tsv
phased_block.tar.gz	This paper	http://entex.encodeproject.org/data/phased_block.tar.gz
fithic2_out.tar.gz	This paper	http://entex.encodeproject.org/data/fithic2_out.tar.gz
TopDomTADcalls.tar.gz	This paper	http://entex.encodeproject.org/data/TopDomTADcalls.tar.gz
Supp_data_proteomics.xlsx	This paper	http://entex.encodeproject.org/data/Supp_data_proteomics.xlsx
table.DE.genes.tsv	This paper	http://entex.encodeproject.org/data/table.DE.genes.tsv
table.DE.genes.techReps.liver.tsv	This paper	http://entex.encodeproject.org/data/table.DE.genes.techReps.liver.tsv
table.DE.genes.GM12878.tsv	This paper	http://entex.encodeproject.org/data/table.DE.genes.GM12878.tsv
differentially_marked_H3K27ac_cCREs.txt	This paper	http://entex.encodeproject.org/data/differentially_marked_H3K27ac_cCREs.txt
Similarity_of_functional_genomic_activities_of_cCREs.xlsx	This paper	http://entex.encodeproject.org/data/Similarity_of_functional_genomic_activities_of_cCREs.xlsx
normalized_proteomics_RNA-seq.dat	This paper	http://entex.encodeproject.org/data/normalized_proteomics_RNA-seq.dat
sample_signal_track.tar.gz	This paper	http://entex.encodeproject.org/data/sample_signal_track.tar.gz
AlleleSeq2_workflow_examples.tar.gz	This paper	http://entex.encodeproject.org/data/AlleleSeq2_workflow_examples.tar.gz
hetSNVs_default_AS.tsv	This paper	http://entex.encodeproject.org/data/hetSNVs_default_AS.tsv
hetSNVs_default_AS_DNase.tsv	This paper	http://entex.gersteinlab.org/data/hetSNVs_default_AS_DNase.tsv
ENTEx.TissueStacked.phased.final.txt	This paper	http://entex.encodeproject.org/data/ENTEx.TissueStacked.phased.final.txt
hic_files.tar.gz	This paper	http://entex.encodeproject.org/data/hic_files.tar.gz
genes_default_AS.tsv	This paper	http://entex.encodeproject.org/data/genes_default_AS.tsv
cCREs_default_AS.tsv	This paper	http://entex.encodeproject.org/data/cCREs_default_AS.tsv
Associated_AS_Disease_Genes.xlsx	This paper	http://entex.encodeproject.org/data/Associated_AS_Disease_Genes.xlsx
hetSNVs_pooled_AS.tsv	This paper	http://entex.encodeproject.org/data/hetSNVs_pooled_AS.tsv
hetSNVs_pooled_AS_DNase.tsv	This paper	http://entex.gersteinlab.org/data/hetSNVs_pooled_AS_DNase.tsv
ENTEx.TissueAggregated.final.txt	This paper	http://entex.encodeproject.org/data/ENTEx.TissueAggregated.final.txt
pgenome_NA12878.tar.gz	This paper	http://entex.encodeproject.org/data/pgenome_NA12878.tar.gz
pgenome_STL-002.tar.gz	This paper	http://entex.encodeproject.org/data/pgenome_STL-002.tar.gz
pgenome_STL-003.tar.gz	This paper	http://entex.encodeproject.org/data/pgenome_STL-003.tar.gz
hetSNVs_high-confidence_AS.tsv	This paper	http://entex.encodeproject.org/data/hetSNVs_high-confidence_AS.tsv
hetSNVs_high-power_AS.tsv	This paper	http://entex.encodeproject.org/data/hetSNVs_high-power_AS.tsv
Supp_Data_SVs_associated_with_eQTL.xlsx	This paper	http://entex.encodeproject.org/data/Supp_Data_SVs_associated_with_eQTL.xlsx
cCRE_histoneSignals_q norm.tar.gz	This paper	http://entex.encodeproject.org/data/cCRE_histoneSignals_qnorm.tar.gz
cCRE_decoration.matrix	This paper	http://entex.encodeproject.org/data/cCREdecoration.matrix
active.combined_set.txt.zip	This paper	http://entex.encodeproject.org/data/active.combined_set.txt.zip
bivalent.combined_set.txt.zip	This paper	http://entex.encodeproject.org/data/bivalent.combined_set.txt.zip
repressed.combined_set.txt.zip	This paper	http://entex.encodeproject.org/data/repressed.combined_set.txt.zip
Repressive_cCRE_DNAmethy_repressiveHM.zip	This paper	http://entex.encodeproject.org/data/Repressive_cCRE_DNAmethy_repressiveHM.zip
Repressive_cCRE_DNAmethy_repressiveHM_summary.csv	This paper	http://entex.encodeproject.org/data/Repressive_cCRE_DNAmethy_repressiveHM_summary.csv
cCRE_DNAme_subset.tsv.zip	This paper	http://entex.encodeproject.org/data/cCRE_DNAme_subset.tsv.zip
stringent.regions.MF.hg38.bed	This paper	http://entex.encodeproject.org/data/stringent.regions.MF.hg38.bed
ENTEx_fully_repressed_regions_independent_of_cCREs.bed	This paper	http://entex.encodeproject.org/data/ENTEx_fully_repressed_regions_independent_of_cCREs.bed
Tissue_Specificity.zip	This paper	http://entex.encodeproject.org/data/Tissue_Specificity.zip
QTL_enrichment.zip	This paper	http://entex.encodeproject.org/data/QTL_enrichment.zip
GWAS_enrichment.zip	This paper	http://entex.encodeproject.org/data/GWAS_enrichment.zip
Supp_Data_Compatibility.xlsx	This paper	http://entex.encodeproject.org/data/Supp_Data_Compatibility.xlsx
AS_ratios_and_eQTL_effect.tsv	This paper	http://entex.encodeproject.org/data/AS_ratios_and_eQTL_effect.tsv
R6_RData.objects	This paper	http://entex.encodeproject.org/data/R6_RData.objects.html
R6_RData.4hm.objects	This paper	http://entex.encodeproject.org/data/R6_RData.4hm.objects.html
perTissue.likely.eQTLs.tsv	This paper	http://entex.encodeproject.org/data/perTissue.likely.eQTLs.tsv
predictions.blood.eQTLs.tar.gz	This paper	http://entex.encodeproject.org/data/predictions.blood.eQTLs.tar.gz
motif_ranking.tsv	This paper	http://entex.encodeproject.org/data/motif_ranking.tsv
SNPs_motif_cCRE.txt.gz	This paper	http://entex.encodeproject.org/data/SNPs_motif_cCRE.txt.gz
ASB-predictions-on-GTEx-cohort.tsv	This paper	http://entex.encodeproject.org/data/ASB-predictions-on-GTEx-cohort.tsv
ENTEx.Explorer.cCRE.Combined.zip	This paper	http://entex.encodeproject.org/data/ENTEx.Explorer.cCRE.Combined.zip
ENTEx.Explorer.Expression.Combined.zip	This paper	http://entex.encodeproject.org/data/ENTEx.Explorer.Expression.Combined.zip
ENTEx.Proteomics.cCRE.Combined.zip	This paper	http://entex.encodeproject.org/data/ENTEx.Proteomics.cCRE.Combined.zip
Software and algorithms
AlleleSeq2	This paper	https://github.com/gersteinlab/AlleleSeq2
transferQTL	This paper	https://github.com/gersteinlab/transferQTL
Chromosome Painter	This paper	https://github.com/gersteinlab/ChromosomePaintingTool
EN-TEx Data Explorer	This paper	https://github.com/gersteinlab/shiny-dim-reduction
Transformer model	This paper	https://github.com/gersteinlab/entexBERT
CrossStitch	https://github.com/schatzlab/crossstitch	https://github.com/schatzlab/crossstitch
Long Ranger (ver. 2.1.2)	10X Genomics	https://support.10xgenomics.com/genomeexome/software/pipelines/latest/what-is-long-rang
HapCUT2 (ver. 1.1)	Edge et al., 2017	https://github.com/vibansal/HapCUT2
Sniffles (ver. 1.0.11)	Sedlazeck et al., 2018	https://github.com/fritzsedlazeck/Sniffles
pbsv (ver. 2.2.1)	PacBio	https://github.com/PacificBiosciences/pbsv
SURVIVOR (ver. 1.0.6)	Jeffares et al., 2017	https://github.com/fritzsedlazeck/SURVIVOR
Iris (ver. 1.0)	Kirsche et al., 2021	https://github.com/mkirsche/Iris
NanoSV	Cretu Stancu et al., 2017	https://github.com/mroosmalen/nanosv
vcf2diploid	Rozowsky et al., 2011	https://github.com/abyzovlab/vcf2diploid
ngmlr	Sedlazeck et al., 2018	https://github.com/philres/ngmlr
Genomestudio (v2011.1)	Illumina	https://support.illumina.com/downloads/genomestudio_software_20111.html
Juicer	Durand et al., 2016	https://github.com/aidenlab/juicer
BWA-MEM	Li and Durbin, 2010	https://github.com/lh3/bwa
FitHiC2 (ver. 2.0.7)	Kaul et al., 2020	https://github.com/ay-lab/fithic
Knight-Ruiz matrix-balancing algorithm	Knight and Ruiz, 2012	https://doi.org/10.1093/imanum/drs019
TopDom (ver. 0.9.0)	Shin et al., 2016	https://github.com/jasminezhoulab/TopDom
GFFRead	Pertea and Pertea, 2020	https://github.com/gpertea/gffread
DecoyPYrat	Wright et al., 2016	https://github.com/wtsi-proteomics/DecoyPYrat
ProteomeDiscoverer (ver. 2.4)	Thermo Fisher Scientific	https://www.thermofisher.com/us/en/home/industrial/mass-spectrometry/liquid-chromatography-mass-spectrometry-lc-ms/lc-ms-software/multi-omics-data-analysis/proteome-discoverer-software.html
Mascot (ver. 2.4)	Matrix Science	http://www.matrixscience.com/mascot_support_v2_4.html
Percolator	Spivak et al., 2009	https://github.com/percolator/percolator
OpenMS	Weisser et al., 2016	https://www.openms.de
STAR (ver. 2.7)	Dobin et al., 2013	https://github.com/alexdobin/STAR
DESeq2	Love et al., 2014	https://bioconductor.org/packages/release/bioc/html/DESeq2.html
Metascape	Zhou et al., 2019	https://metascape.org
Joint and Individual Variance Explained (JIVE)	Hellton and Thoresen, 2016	https://cran.r-project.org/web/packages/r.jive/index.html
Cutadapt	Martin, 2011	https://cutadapt.readthedocs.io/en/stable
Picard	http://broadinstitute.github.io/picard/	http://broadinstitute.github.io/picard
SAMtools	Danecek et al., 2021	https://github.com/samtools/samtools
BEDTools	Quinlan and Hall, 2010	https://bedtools.readthedocs.io/en/latest
Integrative Genomics Viewer (IGV)	Robinson et al., 2011	https://software.broadinstitute.org/software/igv
DAVID	Huang da et al., 2009a; 2009b	https://david.ncifcrf.gov
ANNOVAR	Wang et al., 2010	https://annovar.openbioinformatics.org/en/latest
RepeatMasker (ver. 4.0.7)	http://www.repeatmasker.org	https://www.repeatmasker.org
Umap and Bismap mappability	Karimzadeh et al., 2018	https://bismap.hoffmanlab.org
BERT	Devlin et al., 2019	https://huggingface.co/docs/transformers/model_doc/bert
DNABERT	Ji et al., 2021	https://github.com/jerryji1993/DNABERT
dna2vec	Ng, 2017	https://github.com/pnpnpn/dna2vec