RNA-seq data from Blackmore et al. 2017
GSE96870.RdDataset from The effect of upper-respiratory infection on transcriptomic changes in the CNS by Blackmore et al. (2017) (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5544260/) used as data for the Bioconductor intro and RNA-seq lessons and WSBIM1207 courses. The two variables are of class SummarizedExperiment.
Details
For details on how the data was prepared, see https://github.com/Bioconductor/bioconductor-teaching/tree/master/data/GSE96870.
Examples
data("GSE96870_intro")
GSE96870_intro
#> Loading required package: SummarizedExperiment
#> Loading required package: MatrixGenerics
#> Loading required package: matrixStats
#>
#> Attaching package: ‘MatrixGenerics’
#> The following objects are masked from ‘package:matrixStats’:
#>
#> colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
#> colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
#> colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
#> colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
#> colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
#> colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
#> colWeightedMeans, colWeightedMedians, colWeightedSds,
#> colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
#> rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
#> rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
#> rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
#> rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
#> rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
#> rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
#> rowWeightedSds, rowWeightedVars
#> Loading required package: GenomicRanges
#> Loading required package: stats4
#> Loading required package: BiocGenerics
#>
#> Attaching package: ‘BiocGenerics’
#> The following objects are masked from ‘package:stats’:
#>
#> IQR, mad, sd, var, xtabs
#> The following objects are masked from ‘package:base’:
#>
#> Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
#> as.data.frame, basename, cbind, colnames, dirname, do.call,
#> duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
#> lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
#> pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
#> union, unique, unsplit, which.max, which.min
#> Loading required package: S4Vectors
#>
#> Attaching package: ‘S4Vectors’
#> The following object is masked from ‘package:utils’:
#>
#> findMatches
#> The following objects are masked from ‘package:base’:
#>
#> I, expand.grid, unname
#> Loading required package: IRanges
#> Loading required package: GenomeInfoDb
#> Loading required package: Biobase
#> Welcome to Bioconductor
#>
#> Vignettes contain introductory material; view with
#> 'browseVignettes()'. To cite Bioconductor, see
#> 'citation("Biobase")', and for packages 'citation("pkgname")'.
#>
#> Attaching package: ‘Biobase’
#> The following object is masked from ‘package:MatrixGenerics’:
#>
#> rowMedians
#> The following objects are masked from ‘package:matrixStats’:
#>
#> anyMissing, rowMedians
#> class: RangedSummarizedExperiment
#> dim: 1474 22
#> metadata(0):
#> assays(1): counts
#> rownames(1474): Asl Apod ... Pbx1 Rgs4
#> rowData names(11): gene ENTREZID ... phenotype_description
#> hsapiens_homolog_associated_gene_name
#> colnames(22): GSM2545336 GSM2545337 ... GSM2545363 GSM2545380
#> colData names(10): title geo_accession ... tissue mouse
rowData(GSE96870_intro)
#> DataFrame with 1474 rows and 11 columns
#> gene ENTREZID product gbkey
#> <character> <character> <character> <character>
#> Asl Asl 109900 argininosuccinate ly.. mRNA
#> Apod Apod 11815 apolipoprotein D, tr.. mRNA
#> Cyp2d22 Cyp2d22 56448 cytochrome P450, fam.. mRNA
#> Klk6 Klk6 19144 kallikrein related-p.. mRNA
#> Fcrls Fcrls 80891 Fc receptor-like S, .. mRNA
#> ... ... ... ... ...
#> Lrrc52 Lrrc52 240899 leucine rich repeat .. mRNA
#> Rxrg Rxrg 20183 retinoid X receptor .. mRNA
#> Lmx1a Lmx1a 110648 LIM homeobox transcr.. mRNA
#> Pbx1 Pbx1 18514 pre B cell leukemia .. mRNA
#> Rgs4 Rgs4 19736 regulator of G-prote.. mRNA
#> external_gene_name ensembl_gene_id external_synonym chromosome_name
#> <character> <character> <character> <character>
#> Asl Asl ENSMUSG00000025533 2510006M18Rik 5
#> Apod Apod ENSMUSG00000022548 NA 16
#> Cyp2d22 Cyp2d22 ENSMUSG00000061740 2D22 15
#> Klk6 Klk6 ENSMUSG00000050063 Bssp 7
#> Fcrls Fcrls ENSMUSG00000015852 2810439C17Rik 3
#> ... ... ... ... ...
#> Lrrc52 Lrrc52 ENSMUSG00000040485 4930413P14Rik 1
#> Rxrg Rxrg ENSMUSG00000015843 Nr2b3 1
#> Lmx1a Lmx1a ENSMUSG00000026686 Lmx1.1 1
#> Pbx1 Pbx1 ENSMUSG00000052534 2310056B04Rik 1
#> Rgs4 Rgs4 ENSMUSG00000038530 ESTM48 1
#> gene_biotype phenotype_description
#> <character> <character>
#> Asl protein_coding abnormal circulating..
#> Apod protein_coding abnormal lipid homeo..
#> Cyp2d22 protein_coding abnormal skin morpho..
#> Klk6 protein_coding abnormal cytokine le..
#> Fcrls protein_coding decreased CD8-positi..
#> ... ... ...
#> Lrrc52 protein_coding abnormal sperm physi..
#> Rxrg protein_coding abnormal bone minera..
#> Lmx1a protein_coding abnormal bony labyri..
#> Pbx1 protein_coding abnormal adrenal gla..
#> Rgs4 protein_coding abnormal touch/ noci..
#> hsapiens_homolog_associated_gene_name
#> <character>
#> Asl ASL
#> Apod APOD
#> Cyp2d22 CYP2D6
#> Klk6 KLK6
#> Fcrls FCRL4
#> ... ...
#> Lrrc52 LRRC52
#> Rxrg RXRG
#> Lmx1a LMX1A
#> Pbx1 PBX1
#> Rgs4 RGS4
data("GSE96870_intro_ranges")
GSE96870_intro_ranges
#> class: RangedSummarizedExperiment
#> dim: 1474 22
#> metadata(0):
#> assays(1): counts
#> rownames(1474): Asl Apod ... Pbx1 Rgs4
#> rowData names(11): gene ENTREZID ... phenotype_description
#> hsapiens_homolog_associated_gene_name
#> colnames(22): GSM2545336 GSM2545337 ... GSM2545363 GSM2545380
#> colData names(10): title geo_accession ... tissue mouse
rowRanges(GSE96870_intro_ranges)
#> GRanges object with 1474 ranges and 11 metadata columns:
#> seqnames ranges strand | gene ENTREZID
#> <Rle> <IRanges> <Rle> | <character> <character>
#> Asl 5 130024208-130024330 - | Asl 109900
#> Apod 16 31314552-31314808 - | Apod 11815
#> Cyp2d22 15 82380078-82380260 - | Cyp2d22 56448
#> Klk6 7 43824544-43824595 + | Klk6 19144
#> Fcrls 3 87263678-87263765 - | Fcrls 80891
#> ... ... ... ... . ... ...
#> Lrrc52 1 167466093-167466780 - | Lrrc52 240899
#> Rxrg 1 167598362-167598800 + | Rxrg 20183
#> Lmx1a 1 167688300-167688991 + | Lmx1a 110648
#> Pbx1 1 168431314-168432169 - | Pbx1 18514
#> Rgs4 1 169747480-169747642 - | Rgs4 19736
#> product gbkey external_gene_name
#> <character> <character> <character>
#> Asl argininosuccinate ly.. mRNA Asl
#> Apod apolipoprotein D, tr.. mRNA Apod
#> Cyp2d22 cytochrome P450, fam.. mRNA Cyp2d22
#> Klk6 kallikrein related-p.. mRNA Klk6
#> Fcrls Fc receptor-like S, .. mRNA Fcrls
#> ... ... ... ...
#> Lrrc52 leucine rich repeat .. mRNA Lrrc52
#> Rxrg retinoid X receptor .. mRNA Rxrg
#> Lmx1a LIM homeobox transcr.. mRNA Lmx1a
#> Pbx1 pre B cell leukemia .. mRNA Pbx1
#> Rgs4 regulator of G-prote.. mRNA Rgs4
#> ensembl_gene_id external_synonym chromosome_name gene_biotype
#> <character> <character> <character> <character>
#> Asl ENSMUSG00000025533 2510006M18Rik 5 protein_coding
#> Apod ENSMUSG00000022548 <NA> 16 protein_coding
#> Cyp2d22 ENSMUSG00000061740 2D22 15 protein_coding
#> Klk6 ENSMUSG00000050063 Bssp 7 protein_coding
#> Fcrls ENSMUSG00000015852 2810439C17Rik 3 protein_coding
#> ... ... ... ... ...
#> Lrrc52 ENSMUSG00000040485 4930413P14Rik 1 protein_coding
#> Rxrg ENSMUSG00000015843 Nr2b3 1 protein_coding
#> Lmx1a ENSMUSG00000026686 Lmx1.1 1 protein_coding
#> Pbx1 ENSMUSG00000052534 2310056B04Rik 1 protein_coding
#> Rgs4 ENSMUSG00000038530 ESTM48 1 protein_coding
#> phenotype_description hsapiens_homolog_associated_gene_name
#> <character> <character>
#> Asl abnormal circulating.. ASL
#> Apod abnormal lipid homeo.. APOD
#> Cyp2d22 abnormal skin morpho.. CYP2D6
#> Klk6 abnormal cytokine le.. KLK6
#> Fcrls decreased CD8-positi.. FCRL4
#> ... ... ...
#> Lrrc52 abnormal sperm physi.. LRRC52
#> Rxrg abnormal bone minera.. RXRG
#> Lmx1a abnormal bony labyri.. LMX1A
#> Pbx1 abnormal adrenal gla.. PBX1
#> Rgs4 abnormal touch/ noci.. RGS4
#> -------
#> seqinfo: 182 sequences from an unspecified genome; no seqlengths