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Metadata and Annotations
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| Meta data for RNA-Seq samples and individual assignments. |
SheepGTEx_v0.MetaData.xlsx |
3.05 MB |
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| The relationship between sample ID, QTL mapping ID, and tissue name. |
SheepGTEx_v0.sample_qtl_tis.tsv |
373.33 KB |
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| The sheep reference genome (GCF_016772045.1, ARS-UI_Ramb_v2.0). |
sheep.fna.gz |
818.99 MB |
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| Gene annotation of ARS-UI_Ramb_v2.0 (NCBI Ovis aries Annotation Release 104). |
sheep.gtf.gz |
20.89 MB |
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Bulk tissue expression
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| Gene raw read counts matrix. The original sample ID can be transformed into QTL mapping ID based on the relationship (SheepGTEx_v0.sample_qtl_tis.tsv). |
SheepGTEx_v0.Gene.count.txt.gz |
268.73 MB |
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| Gene expression (TPM) matrix. The original sample ID can be transformed into QTL mapping ID based on the relationship (SheepGTEx_v0.sample_qtl_tis.tsv). |
SheepGTEx_v0.Gene.TPM.txt.gz |
566.53 MB |
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| Gene raw read counts matrix across 60 tissues for (imputed) eQTL mapping. |
SheepGTEx_v0.Gene.count.qtl.txt.gz |
259 MB |
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| Gene expression (TPM) matrix across 60 tissues for (imputed) eQTL mapping. |
SheepGTEx_v0.Gene.TPM.qtl.txt.gz |
567 MB |
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| Gene expression (inverse normal transformed TMM) matrix across 51 tissues for eQTL mapping. |
SheepGTEx_v0.Gene.TMM.tar.gz |
439.16 MB |
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| Imputed gene expression (inverse normal transformed TMM) matrix across 57 tissues for imputed eQTL mapping. |
SheepGTEx_v0.Gene.imputed_TMM.tar.gz |
5.43 GB |
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| Exon raw read counts matrix. The original sample ID can be transformed into QTL mapping ID based on the relationship (SheepGTEx_v0.sample_qtl_tis.tsv). |
SheepGTEx_v0.Exon.count.txt.gz |
421.53 MB |
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| Exon expression (TPM) matrix. The original sample ID can be transformed into QTL mapping ID based on the relationship (SheepGTEx_v0.sample_qtl_tis.tsv). |
SheepGTEx_v0.Exon.TPM.txt.gz |
1.28 GB |
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| Exon raw read counts matrix across 51 tissues for eeQTL mapping. |
SheepGTEx_v0.Exon.count.qtl.txt.gz |
421 MB |
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| Exon expression (TPM) matrix across 51 tissues for eeQTL mapping. |
SheepGTEx_v0.Exon.TPM.qtl.txt.gz |
1.3 GB |
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| Exon expression (inverse normal transformed TMM) matrix across 51 tissues for eeQTL mapping, with the information of grouped features by genes. |
SheepGTEx_v0.Exon.TMM.tar.gz |
862.89 MB |
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| Isoform raw read counts matrix. The original sample ID can be transformed into QTL mapping ID based on the relationship (SheepGTEx_v0.sample_qtl_tis.tsv). |
SheepGTEx_v0.Isoform.count.txt.gz |
760.96 MB |
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| Isoform expression (TPM) matrix. The original sample ID can be transformed into QTL mapping ID based on the relationship (SheepGTEx_v0.sample_qtl_tis.tsv). |
SheepGTEx_v0.Isoform.TPM.txt.gz |
952.70 MB |
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| Isoform raw read counts matrix across 51 tissues for isoQTL mapping. |
SheepGTEx_v0.Isoform.count.qtl.txt.gz |
761 MB |
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| Isoform expression (TPM) matrix across 51 tissues for isoQTL mapping. |
SheepGTEx_v0.Isoform.TPM.qtl.txt.gz |
953 MB |
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| Isoform expression (inverse normal transformed TMM) matrix across 51 tissues for isoQTL mapping, with the information of grouped features by genes. |
SheepGTEx_v0.Isoform.TMM.tar.gz |
727.86 MB |
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| Enhancer raw read counts matrix. The original sample ID can be transformed into QTL mapping ID based on the relationship (SheepGTEx_v0.sample_qtl_tis.tsv). |
SheepGTEx_v0.Enhancer.count.txt.gz |
92.75 MB |
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| Enhancer expression (TPM) matrix. The original sample ID can be transformed into QTL mapping ID based on the relationship (SheepGTEx_v0.sample_qtl_tis.tsv). |
SheepGTEx_v0.Enhancer.TPM.txt.gz |
302.33 MB |
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| Enhancer raw read counts matrix across 51 tissues for enQTL mapping. |
SheepGTEx_v0.Enhancer.count.qtl.txt.gz |
93 MB |
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| Enhancer expression (TPM) matrix across 51 tissues for enQTL mapping. |
SheepGTEx_v0.Enhancer.TPM.qtl.txt.gz |
303 MB |
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| Enhancer expression (inverse normal transformed TMM) matrix across 51 tissues for enQTL mapping, with the information of grouped features by genes. |
SheepGTEx_v0.Enhancer.TMM.tar.gz |
93.28 MB |
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| Alternative splicing of intron excision level. The original sample ID can be transformed into QTL mapping ID based on the relationship (SheepGTEx_v0.sample_qtl_tis.tsv). |
SheepGTEx_v0.Splicing.excision.gz |
4.25 GB |
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| The cluster name and the corresponding gene name of alternative splicing. |
SheepGTEx_v0.Splicing.clusters_to_genes.txt |
18.39 MB |
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| Normalized alternative splicing values (Percent Spliced In, PSI) across 51 tissues for sQTL mapping, with the information of grouped features by genes. |
SheepGTEx_v0.Splicing.PSI.tar.gz |
7.03 GB |
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| Ratio of read counts between constitutive exons and all introns, quantified as RNA stability. The original sample ID can be transformed into QTL mapping ID based on the relationship (SheepGTEx_v0.sample_qtl_tis.tsv). |
SheepGTEx_v0.RNA_stability.ratio.bed.gz |
293.88 MB |
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| Normalized constitutive exon/intron ratios of RNA stability across 51 tissues for stQTL mapping. |
SheepGTEx_v0.RNA_stability.norm_ratio.tar.gz |
214.83 MB |
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| PDUI values of 3'TUR alternative polyadenylations. The original sample ID can be transformed into QTL mapping ID based on the relationship (SheepGTEx_v0.sample_qtl_tis.tsv). |
SheepGTEx_v0.3UTRAPA.PDUI.txt.gz |
97.46 MB |
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| Normalized PDUI values of 3'TUR alternative polyadenylations across 50 tissues for 3'aQTL mapping. |
SheepGTEx_v0.3UTRAPA.norm_PDUI.tar.gz |
250.85 MB |
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| Gene expression (inverse normal transformed TMM) matrix stratified by ancestries across 14 tissues. |
SheepGTEx_v0.Gene.ancestry.TMM.tar.gz |
196.09 MB |
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| Gene expression (inverse normal transformed TMM) matrix of different sex across 19 tissues. |
SheepGTEx_v0.Gene.sex.TMM.tar.gz |
256.61 MB |
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| Gene expression (inverse normal transformed TMM) matrix of different developmental stage across 26 tissues. |
SheepGTEx_v0.Gene.developmental_stage.TMM.tar.gz |
284.27 MB |
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Genotype
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| Raw genotype files of all samples (PLINK v1.9 binary format). The original sample ID can be transformed into QTL mapping ID based on the relationship (SheepGTEx_v0.sample_qtl_tis.tsv). |
SheepGTEx_v0.Genotype.all_samples.tar.gz |
2.01 GB |
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| Information of the variants in dbSNP database. |
snpid2rsid.txt.gz |
916.55 MB |
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| Genotype files used for molQTL mapping across 51 tissues (PLINK v1.9 binary format). |
SheepGTEx_v0.Genotype.molQTL.tar.gz |
2.63 GB |
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| Genotype files used for eQTL mapping based on the imputed gene expression across 57 tissues (PLINK v1.9 binary format). |
SheepGTEx_v0.Genotype.imputed_eQTL.tar.gz |
20.48 GB |
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| Genotype files used for context-stratified (i.e., ancestries, sexes and developmental stages) eQTL mapping (PLINK v1.9 binary format). |
SheepGTEx_v0.Genotype.stratified_eQTL.tar.gz |
5.35 GB |
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Covariates
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| Covariates used in molQTL analysis based on all samples, including phenotype and genotype principal components, and sex and age. |
SheepGTEx_v0.Covariates.molQTL.tar.gz |
9.48 MB |
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| Covariates used in molQTL analysis based on imputed gene expression. |
SheepGTEx_v0.Covariates.imputed_eQTL.tar.gz |
23.07 MB |
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| Covariates used in eQTL analysis based on stratified contexts (i.e., ancestries, sexes and developmental stages). |
SheepGTEx_v0.Covariates.stratified_eQTL.tar.gz |
2.24 MB |
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molQTL
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| Columns interpretation. |
README.md |
2.65KB |
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| Significance level of all genes and their lead variant for cis-eQTL. |
SheepGTEx_v0.permutations_eQTL.txt.gz |
72.84 MB |
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| Significance level of all genes and their lead variant for cis-eQTL based on the imputed gene expression matrix. |
SheepGTEx_v0.permutations_imputed_eQTL.txt.gz |
59.64 MB |
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| Significance level of all genes and their lead variant for cis-eeQTL. |
SheepGTEx_v0.permutations_eeQTL.txt.gz |
53.22 MB |
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| Significance level of all genes and their lead variant for cis-isoQTL. |
SheepGTEx_v0.permutations_isoQTL.txt.gz |
42.92 MB |
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| Significance level of all genes and their lead variant for cis-enQTL. |
SheepGTEx_v0.permutations_enQTL.txt.gz |
11.56 MB |
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| Significance level of all genes and their lead variant for cis-sQTL. |
SheepGTEx_v0.permutations_sQTL.txt.gz |
51.40 MB |
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| Significance level of all genes and their lead variant for cis-stQTL. |
SheepGTEx_v0.permutations_stQTL.txt.gz |
43.74 MB |
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| Significance level of all genes and their lead variant for cis-3aQTL. |
SheepGTEx_v0.permutations_3aQTL.txt.gz |
42.38 MB |
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| Summary statistics of significant variant-gene expression associations using linear regression model (LM). |
SheepGTEx_v0.significant_eQTL.txt.gz |
533.91 MB |
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| Summary statistics of significant variant-gene expression associations using linear mixed model (LMM). |
SheepGTEx_v0.significant_eQTL.LMM.txt.gz |
303.17 MB |
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| Summary statistics of significant variant-gene expression associations based on the imputed gene expression matrix. |
SheepGTEx_v0.significant_imputed_eQTL.txt.gz |
670.52 MB |
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| Summary statistics of significant variant-exon expression associations. |
SheepGTEx_v0.significant_eeQTL.txt.gz |
385.74 MB |
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| Summary statistics of significant variant-isoform expression associations. |
SheepGTEx_v0.significant_isoQTL.txt.gz |
402.56 MB |
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| Summary statistics of significant variant-enhancer expression associations. |
SheepGTEx_v0.significant_enQTL.txt.gz |
75.86 MB |
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| Summary statistics of significant variant-splicing associations. |
SheepGTEx_v0.significant_sQTL.txt.gz |
450.14 MB |
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| Summary statistics of significant variant-RNA stability associations. |
SheepGTEx_v0.significant_stQTL.txt.gz |
263.86 MB |
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| Summary statistics of significant variant-3'UTR APA associations. |
SheepGTEx_v0.significant_3aQTL.txt.gz |
67.68 MB |
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| Independent cis-eQTL for each eGene. |
SheepGTEx_v0.independent_eQTL.txt.gz |
12.71 MB |
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| Independent cis-eQTL for each eGene based on the imputed gene expression matrix. |
SheepGTEx_v0.independent_imputed_eQTL.txt.gz |
26.82 MB |
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| Independent cis-eeQTL for each eeGene. |
SheepGTEx_v0.independent_eeQTL.txt.gz |
8.95 MB |
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| Independent cis-isoQTL for each isoGene. |
SheepGTEx_v0.independent_isoQTL.txt.gz |
8.66 MB |
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| Independent cis-enQTL for each enGene. |
SheepGTEx_v0.independent_enQTL.txt.gz |
1.84 MB |
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| Independent cis-sQTL for each sGene. |
SheepGTEx_v0.independent_sQTL.txt.gz |
6.88 MB |
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| Independent cis-stQTL for each stGene. |
SheepGTEx_v0.independent_stQTL.txt.gz |
6.35 MB |
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| Independent cis-3aQTL for each 3aGene. |
SheepGTEx_v0.independent_3aQTL.txt.gz |
1.90 MB |
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| Fine-mapped credible sets from SuSiE for each eGene. |
SheepGTEx_v0.finemapped_eQTL.txt.gz |
60.52 MB |
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| Fine-mapped credible sets from SuSiE for each eGene based on the imputed gene expression matrix. |
SheepGTEx_v0.finemapped_imputed_eQTL.txt.gz |
78.61 MB |
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| Fine-mapped credible sets from SuSiE for each eeGene. |
SheepGTEx_v0.finemapped_eeQTL.txt.gz |
61.28 MB |
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| Fine-mapped credible sets from SuSiE for each isoGene. |
SheepGTEx_v0.finemapped_isoQTL.txt.gz |
61.96 MB |
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| Fine-mapped credible sets from SuSiE for each enGene. |
SheepGTEx_v0.finemapped_enQTL.txt.gz |
10.82 MB |
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| Fine-mapped credible sets from SuSiE for each sGene. |
SheepGTEx_v0.finemapped_sQTL.txt.gz |
90.13 MB |
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| Fine-mapped credible sets from SuSiE for each stGene. |
SheepGTEx_v0.finemapped_stQTL.txt.gz |
34.39 MB |
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| Fine-mapped credible sets from SuSiE for each 3aGene. |
SheepGTEx_v0.finemapped_3aQTL.txt.gz |
11.88 MB |
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| Summary statistics of trans-eGenes and their lead eVariants. |
SheepGTEx_v0.trans_eGene.txt.gz |
140.27 KB |
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| Summary statistics of significant trans-eQTL using linear mixed model (LMM). |
SheepGTEx_v0.significant_trans_eQTL.txt.gz |
5.56 MB |
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| Summary statistics of context-dependent eQTL, including ancestry specific eQTL (anc-eQTL), sex-biased eQTL (sb-eQTL) and developmental stage-biased eQTL (db-eQTL) |
SheepGTEx_v0.context_eQTL.tar.gz |
1.16 MB |
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Integration Analysis Data
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| TWAS ElasticNet prediction model database and covariance matrices for cis-eQTL per tissue. |
SheepGTEx_v0.twas.predictDB_elasticNet.eQTL.tar.gz |
2.18 GB |
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| TWAS ElasticNet prediction model database and covariance matrices for cis-eeQTL per tissue. |
SheepGTEx_v0.twas.predictDB_elasticNet.eeQTL.tar.gz |
2.69 GB |
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| TWAS ElasticNet prediction model database and covariance matrices for cis-isoQTL per tissue. |
SheepGTEx_v0.twas.predictDB_elasticNet.isoQTL.tar.gz |
2.40 GB |
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| TWAS ElasticNet prediction model database and covariance matrices for cis-enQTL per tissue. |
SheepGTEx_v0.twas.predictDB_elasticNet.enQTL.tar.gz |
365.64 MB |
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| TWAS ElasticNet prediction model database and covariance matrices for cis-sQTL per tissue. |
SheepGTEx_v0.twas.predictDB_elasticNet.sQTL.tar.gz |
4.53 GB |
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| TWAS ElasticNet prediction model database and covariance matrices for cis-stQTL per tissue. |
SheepGTEx_v0.twas.predictDB_elasticNet.stQTL.tar.gz |
1.04 GB |
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| TWAS ElasticNet prediction model database and covariance matrices for cis-3aQTL per tissue. |
SheepGTEx_v0.twas.predictDB_elasticNet.3aQTL.tar.gz |
583.97 MB |
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| Single-tissue TWAS results of of 34 complex traits. |
SheepGTEx_v0.twas.SPrediXcan.tar.gz |
2.61 GB |
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| Multi-tissue TWAS results of of 34 complex traits. |
SheepGTEx_v0.twas.SMulTiXcan.tar.gz |
642.92 MB |
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| Results of colocalization between GWAS and molQTL. |
SheepGTEx_v0.GWAS_coloc.tar.gz |
163.61 MB |
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| Detailed information of GWAS summary statistics of 34 sheep complex traits. |
GWAS_summary.xlsx |
10.40KB |
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