Porcine Transcriptome and Methylome Map

Experiment ID:ERP009821
Technology:RNA-Seq
Description:This study is part of the FAANG project, promoting rapid prepublication of data to support the research community. These data are released under Fort Lauderdale principles, as confirmed in the Toronto Statement (Toronto International Data Release Workshop. Birney et al. 2009. Pre-publication data sharing. Nature 461:168-170). Any use of this dataset must abide by the FAANG data sharing principles. Data producers reserve the right to make the first publication of a global analysis of this data. If you are unsure if you are allowed to publish on this dataset, please contact faang@iastate.edu to enquire. The full guidelines can be found at http://www.faang.org/data-share-principle. Pigs (Sus scrofa) provide relevant biomedical models to dissect complex diseases due to their anatomical, genetic, and physiological similarities with humans. Aberrant DNA methylation has been linked to many of these diseases and is associated with gene expression; however, the functional similarities and differences between porcine and human DNA methylation patterns are largely unknown. DNA and RNA was isolated from eight tissue samples (fat, heart, kidney, liver, lung, lymph node, muscle, and spleen) from the adult female Duroc utilized for the pig genome sequencing project. Reduced representation bisulfite sequencing (RRBS) and RNA-seq were performed on an Illumina HiSeq2000. RRBS reads were aligned using BSseeker2, and only sites with a minimum depth of 10 reads were used for methylation analysis. RNA-seq reads were aligned using Tophat, and expression analysis was performed using Cufflinks. In addition, SNP calling was performed using GATK for targeted control and whole genome sequencing reads for CpG site validation and allelic expression analysis, respectively. These results provide transcriptional and DNA methylation datasets for the biomedical community that are directly relatable to current genomic resources. In addition, the correlation between TSS CpG density and expression suggests increased mutation rates at CpG sites play a significant role in adaptive evolution by reducing CpG density at TSS over time, resulting in higher methylation levels in these regions and more permanent changes to lower gene expression. This is proposed to occur predominantly through deamination of 5-methylcytosine to thymidine, resulting in the replacement of CpG with TpG sites in these regions, as indicated by the increased TSS TpG density observed in non-expressed genes, resulting in a negative correlation between expression and TSS TpG density. This study provides baseline methylation and gene transcription profiles for a healthy adult pig, reports similar patterns to those observed in humans, and supports future porcine studies related to human disease and development. Additionally, the observed reduced CpG and increased TpG density at TSS of lowly expressed genes suggests DNA methylation plays a significant role in adaptive evolution through more permanent changes to lower gene expression.
Source:ERP009821 SRA
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Bulk RNA-Seq processed expression values in Sus scrofa

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Showing 1 to 20 of 27 entries

Library ID
Identifier of the RNA-Seq library
Anat. entity ID
ID of the anatomical localization of the sample
Anat. entity name
Name of the anatomical localization of the sample
Anat. entity author annotation
Free text annotation of anatomical localization of the sample as provided by authors
Stage ID
ID of the developmental and life stage of the sample
Stage name
Name of the developmental and life stage of the sample
Stage author annotation
Free text annotation of the developmental and life stage of the sample as provided by authors
Sex
Annotation of the sex of the sample
Strain
Annotation of the strain of the sample
Time
Free text annotation of the time of sampling as provided by authors
Time unit
Unit for the time of sampling as provided by authors
Species
Physiological status
Physiological status of the organism at time of sampling
Technology
Sequencing platform
Sequenced transcript part
Possible values are: full length, all parts of the transcript are sequenced; 3': only the 3' end of the transcript is sequenced; 5': only the 5' end of the transcript is sequenced.
Fragmentation
Size of the RNA fragmentation
Run sequencing type
Paired-end or single-read run
Total read count
Total number of reads for the library.
Mapped read count
Number of reads that could be mapped to the transcriptome.
Total UMI count
Total number of individual RNA molecules (UMI) for the annotated sample. Only applicable for libraries producing UMIs.
Mapped UMI count
Number of UMIs that could be mapped to the transcriptome. Only applicable for libraries producing UMIs.
Distinct rank count
When performing a fractional ranking of the genes in the annotated sample, based on their expression level, number of distinct ranks observed, to have a value of the power for distinguishing expression levels. Used as a weight to compute a weighted mean rank accross samples for each gene and compute expression scores in Bgee.
Max rank
When performing a fractional ranking of the genes in the annotated sample, based on their expression level, maximum rank attained in the sample. Used to normalize ranks accross samples and compute expression scores in Bgee.
Link to processed expression values
See the processed expression value results for this assay
ERX1049364UBERON:0002106 spleenSpleenUBERON:0018241 prime adult stage3 yearsmaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2000FULL_LENGTH100paired3052869625987400001926221926Browse results
ERX1049365UBERON:0002107 liverLiverUBERON:0018241 prime adult stage3 yearsmaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2000FULL_LENGTH100paired3837984835009682001812221153.5Browse results
ERX1049366UBERON:0002385 muscle tissueMuscleUBERON:0018241 prime adult stage3 yearsmaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2000FULL_LENGTH100paired3660566233520350001723220607Browse results
ERX779590UBERON:0001013 adipose tissueFatSscrDv:0000067 3-year-old stage (pig)3 years 4 monthsfemaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2000FULL_LENGTH100paired3827477932086494001775821203Browse results
ERX779591UBERON:0000948 heartHeartSscrDv:0000067 3-year-old stage (pig)3 years 4 monthsfemaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2000FULL_LENGTH100paired4075027935342180001673720645.5Browse results
ERX779592UBERON:0000082 adult mammalian kidneyKidneySscrDv:0000067 3-year-old stage (pig)3 years 4 monthsfemaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2000FULL_LENGTH100paired3954080632539833001786721268Browse results
ERX779593UBERON:0002107 liverLiverUBERON:0018241 prime adult stage3 years 4 monthsfemaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2000FULL_LENGTH100paired4421219526650690001545219367Browse results
ERX779594UBERON:0002048 lungLungSscrDv:0000067 3-year-old stage (pig)3 years 4 monthsfemaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2000FULL_LENGTH100paired3392837026793361001791821256.5Browse results
ERX779595UBERON:0000029 lymph nodeLymph NodeUBERON:0018241 prime adult stage3 years 4 monthsfemaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2000FULL_LENGTH100paired3708019020863088001560519480Browse results
ERX779596UBERON:0002385 muscle tissueMuscleUBERON:0018241 prime adult stage3 years 4 monthsfemaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2000FULL_LENGTH100paired4034235126102522001496219108.5Browse results
ERX779597UBERON:0002106 spleenSpleenUBERON:0018241 prime adult stage3 years 4 monthsfemaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2000FULL_LENGTH100paired3240753618031814001609319789Browse results
ERX779598UBERON:0001013 adipose tissueFatUBERON:0018241 prime adult stage3 years 4 monthsfemaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2000FULL_LENGTH100paired2271431019466308001724320642.5Browse results
ERX779599UBERON:0000948 heartHeartUBERON:0018241 prime adult stage3 years 4 monthsfemaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2000FULL_LENGTH100paired1675227914164106001632020096Browse results
ERX779600UBERON:0000082 adult mammalian kidneyKidneyUBERON:0018241 prime adult stage3 years 4 monthsfemaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2000FULL_LENGTH100paired2384101920116394001737120680.5Browse results
ERX779601UBERON:0002107 liverLiverSscrDv:0000067 3-year-old stage (pig)3 years 4 monthsfemaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2000FULL_LENGTH98paired2034643517497865001632720248.5Browse results
ERX779602UBERON:0002048 lungLungUBERON:0018241 prime adult stage3 years 4 monthsfemaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2000FULL_LENGTH100paired2049370816990062001740920669Browse results
ERX779603UBERON:0000029 lymph nodeLymph NodeUBERON:0018241 prime adult stage3 years 4 monthsfemaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2000FULL_LENGTH100paired1249793510649018001633720053Browse results
ERX779604UBERON:0002385 muscle tissueMuscleUBERON:0018241 prime adult stage3 years 4 monthsfemaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2000FULL_LENGTH100paired1963367617314533001565719656Browse results
ERX779605UBERON:0002106 spleenSpleenUBERON:0018241 prime adult stage3 years 4 monthsfemaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2000FULL_LENGTH100paired1445748312073208001697620479.5Browse results
ERX779606UBERON:0001013 adipose tissueFatUBERON:0018241 prime adult stage3 years 4 monthsfemaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2000FULL_LENGTH100paired4722370138626826001993922303Browse results

Showing 1 to 20 of 27 entries

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