Transcriptional landscape of porcine circulating immune cells

Experiment ID:ERP127795
Technology:scRNA-Seq
Description:Bulk RNA-seq from immune sorted cells and single cell RNA sequencing data from porcine PBMCs were generated to determine the gene expression pattern of porcine immune cells. 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 the FAANG Data Coordination Centre and FAANG consortium (email faang-dcc@ebi.ac.uk and cc faang@iastate.edu) to enquire. The full guidelines can be found at http://www.faang.org/data-share-principle."
DOI:10.3389/fgene.2021.689406
Source:ERP127795 SRA
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Bulk RNA-Seq processed expression values in Sus scrofascRNA-Seq droplet-based processed expression values per cell population in Sus scrofascRNA-Seq droplet-based H5AD data per cell in Sus scrofa

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Library ID
Identifier of the RNA-Seq library
Cell type ID
ID of the cell type of the sample
Cell type name
Name of the cell type of the sample
Cell type author annotation
Free text annotation of cell type as provided by authors
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.
Fractionation
Possible values are: cell, transcripts are extracted from the cell; nuclei, transcripts are extracted from the nucleus.
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
ERX5304229NACL:0000798 gamma-delta T cellA1_SWC6gdTSscrDv:0000059 6-month-old stage (pig)6 monthsmaleLarge white X LandraceNANASus scrofaNAIlluminaNextSeq 500FULL_LENGTHCELL75paired4546639137787944001959125884.5Browse results
ERX5304230NACL:0000084 T cellA1_CD8TSscrDv:0000059 6-month-old stage (pig)6 monthsmaleLarge white X LandraceNANASus scrofaNAIlluminaNextSeq 500FULL_LENGTHCELL75paired5529503646563950001881225491Browse results
ERX5304231NACL:0000084 T cellA1_CD4TSscrDv:0000059 6-month-old stage (pig)6 monthsmaleLarge white X LandraceNANASus scrofaNAIlluminaNextSeq 500FULL_LENGTHCELL75paired5095125942384909001921925682.5Browse results
ERX5304232NACL:0000084 T cellA1_CD4CD8TSscrDv:0000059 6-month-old stage (pig)6 monthsmaleLarge white X LandraceNANASus scrofaNAIlluminaNextSeq 500FULL_LENGTHCELL75paired3843345432268479001905025623.5Browse results
ERX5304233NACL:0000763 myeloid cellA1_MyeloidSscrDv:0000059 6-month-old stage (pig)6 monthsmaleLarge white X LandraceNANASus scrofaNAIlluminaNextSeq 500FULL_LENGTHCELL75paired3804410333555199001838425278.5Browse results
ERX5304234NACL:0000623 natural killer cellA1_NKSscrDv:0000059 6-month-old stage (pig)6 monthsmaleLarge white X LandraceNANASus scrofaNAIlluminaNextSeq 500FULL_LENGTHCELL75paired4336403836851636001861725359.5Browse results
ERX5304235NACL:0000236 B cellA1_CD21pBSscrDv:0000059 6-month-old stage (pig)6 monthsmaleLarge white X LandraceNANASus scrofaNAIlluminaNextSeq 500FULL_LENGTHCELL75paired4134009932531868001952525835Browse results
ERX5304236NACL:0000236 B cellA1_CD21nBSscrDv:0000059 6-month-old stage (pig)6 monthsmaleLarge white X LandraceNANASus scrofaNAIlluminaNextSeq 500FULL_LENGTHCELL75paired4110162834019717002132526767.5Browse results
ERX5304237NACL:0000798 gamma-delta T cellA2_SWC6gdTSscrDv:0000059 6-month-old stage (pig)6 monthsmaleLarge white X LandraceNANASus scrofaNAIlluminaNextSeq 500FULL_LENGTHCELL75paired5189650238582775001998026067.5Browse results
ERX5304238NACL:0000084 T cellA2_CD8TSscrDv:0000059 6-month-old stage (pig)6 monthsmaleLarge white X LandraceNANASus scrofaNAIlluminaNextSeq 500FULL_LENGTHCELL75paired5902212750873028001673524410.5Browse results
ERX5304239NACL:0000084 T cellA2_CD4TSscrDv:0000059 6-month-old stage (pig)6 monthsmaleLarge white X LandraceNANASus scrofaNAIlluminaNextSeq 500FULL_LENGTHCELL75paired4200937131045830001930025713Browse results
ERX5304240NACL:0000084 T cellA2_CD4CD8TSscrDv:0000059 6-month-old stage (pig)6 monthsmaleLarge white X LandraceNANASus scrofaNAIlluminaNextSeq 500FULL_LENGTHCELL74paired4441627735352828001839025240Browse results
ERX5304241NACL:0000763 myeloid cellA2_MyeloidSscrDv:0000059 6-month-old stage (pig)6 monthsmaleLarge white X LandraceNANASus scrofaNAIlluminaNextSeq 500FULL_LENGTHCELL75paired5976388448112450001900025596.5Browse results
ERX5304242NACL:0000236 B cellA2_CD21pBSscrDv:0000059 6-month-old stage (pig)6 monthsmaleLarge white X LandraceNANASus scrofaNAIlluminaNextSeq 500FULL_LENGTHCELL75paired4804262440644306001693424523Browse results
ERX5304243NACL:0000236 B cellA2_CD21nBSscrDv:0000059 6-month-old stage (pig)6 monthsmaleLarge white X LandraceNANASus scrofaNAIlluminaNextSeq 500FULL_LENGTHCELL75paired4490981038089807001599324004Browse results
ERX5304244CL:0000576 monocyteMonocytesUBERON:0000178 bloodbloodSscrDv:0000065 1-year-old stage (pig)12 monthsmaleLarge white X LandraceNANASus scrofaNA10X Genomics V2Illumina HiSeq 3000THREE_PRIMECELL0paired1508980698590743405530808299618692.5Browse results
ERX5304244CL:0000946 antibody secreting cellASCUBERON:0000178 bloodbloodSscrDv:0000065 1-year-old stage (pig)12 monthsmaleLarge white X LandraceNANASus scrofaNA10X Genomics V2Illumina HiSeq 3000THREE_PRIMECELL0paired1508980698590743409171544314722Browse results
ERX5304244CL:0000232 erythrocyteErythrocytesUBERON:0000178 bloodbloodSscrDv:0000065 1-year-old stage (pig)12 monthsmaleLarge white X LandraceNANASus scrofaNA10X Genomics V2Illumina HiSeq 3000THREE_PRIMECELL0paired150898069859074340968512512810.5Browse results
ERX5304244CL:0000990 conventional dendritic cellcDCsUBERON:0000178 bloodbloodSscrDv:0000065 1-year-old stage (pig)12 monthsmaleLarge white X LandraceNANASus scrofaNA10X Genomics V2Illumina HiSeq 3000THREE_PRIMECELL0paired15089806985907434047827293916859.5Browse results
ERX5304244CL:0000625 CD8-positive, alpha-beta T cellCD8ab+ ab T cellsUBERON:0000178 bloodbloodSscrDv:0000065 1-year-old stage (pig)12 monthsmaleLarge white X LandraceNANASus scrofaNA10X Genomics V2Illumina HiSeq 3000THREE_PRIMECELL0paired150898069859074340605808113317241.5Browse results

Showing 1 to 20 of 99 entries

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