Origins and functional evolution of Y chromosome gene repertoires across the class Mammalia

Experiment ID:SRP029760
Technology:RNA-Seq
Description:We collected (Illumina) RNA-seq data (polyadenylated RNA fraction) for a number of tissue samples from common marmoset and elephant. We developed a subtraction approach based on male/female RNA-seq data, Illumina genomic data and available genomes to identify and assemble Y transcripts. For marmoset samples, we added Y coding genes and noncoding sequences to the reference genomes in order to assess their expression levels. We then mapped all RNA-seq reads with TopHat 1.4.0 and used Cufflinks 2.0.0 (all mapped reads, embedded multi-read and fragment bias correction) to calculate the FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values for all genes in the genomes with our refined annotations.
Source:SRP029760  GEO
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Bulk RNA-Seq processed expression values in Rattus norvegicusBulk RNA-Seq processed expression values in Callithrix jacchus

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Showing 1 to 20 of 26 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
SRX347653UBERON:0001870 frontal cortexfrontal cortexUBERON:0000113 post-juvenileadultfemaleNANANACallithrix jacchusNAIlluminaIllumina HiSeq 2000FULL_LENGTH101single3654497915620486001937920713.5Browse results
SRX347654UBERON:0001870 frontal cortexfrontal cortexUBERON:0000113 post-juvenileadultmaleNANANACallithrix jacchusNAIlluminaIllumina HiSeq 2000FULL_LENGTH101single260934039976412001921120697Browse results
SRX347655UBERON:0002037 cerebellumcerebellumUBERON:0000113 post-juvenileadultfemaleNANANACallithrix jacchusNAIlluminaIllumina HiSeq 2000FULL_LENGTH101single3843755115555716001918520573.5Browse results
SRX347656UBERON:0002037 cerebellumcerebellumUBERON:0000113 post-juvenileadultmaleNANANACallithrix jacchusNAIlluminaIllumina HiSeq 2000FULL_LENGTH101single2947491612161115001939420699.5Browse results
SRX347657UBERON:0000948 heartheartUBERON:0000113 post-juvenileadultfemaleNANANACallithrix jacchusNAIlluminaIllumina HiSeq 2000FULL_LENGTH101single248592316269154001737019533.5Browse results
SRX347658UBERON:0000948 heartheartUBERON:0000113 post-juvenileadultmaleNANANACallithrix jacchusNAIlluminaIllumina HiSeq 2000FULL_LENGTH101single3021155612809743001834820127Browse results
SRX347659UBERON:0002113 kidneykidneyUBERON:0000113 post-juvenileadultfemaleNANANACallithrix jacchusNAIlluminaIllumina HiSeq 2000FULL_LENGTH101single2455332910932394001929920767Browse results
SRX347660UBERON:0002113 kidneykidneyUBERON:0000113 post-juvenileadultmaleNANANACallithrix jacchusNAIlluminaIllumina HiSeq 2000FULL_LENGTH101single2401779010694465001924220728Browse results
SRX347661UBERON:0002107 liverliverUBERON:0000113 post-juvenileadultfemaleNANANACallithrix jacchusNAIlluminaIllumina HiSeq 2000FULL_LENGTH101single3219277417828591001828020139Browse results
SRX347662UBERON:0002107 liverliverUBERON:0000113 post-juvenileadultmaleNANANACallithrix jacchusNAIlluminaIllumina HiSeq 2000FULL_LENGTH101single4750411029904238001870120413.5Browse results
SRX347663UBERON:0000992 ovaryovaryUBERON:0000113 post-juvenileadultfemaleNANANACallithrix jacchusNAIlluminaIllumina HiSeq 2000FULL_LENGTH101single220344699692359001956620905.5Browse results
SRX347664UBERON:0000473 testistestisUBERON:0000113 post-juvenileadultmaleNANANACallithrix jacchusNAIlluminaIllumina HiSeq 2000FULL_LENGTH101single3020550813309499002043021378.5Browse results
SRX347665UBERON:0000473 testistestisUBERON:0000113 post-juvenileadultmaleNANANACallithrix jacchusNAIlluminaIllumina Genome Analyzer IIxFULL_LENGTH79single4020084420730099001988520883.5Browse results
SRX347666UBERON:0000473 testistestisUBERON:0000113 post-juvenileadultmaleNANANACallithrix jacchusNAIlluminaIllumina Genome Analyzer IIxFULL_LENGTH79single4016263220737454001988720857.5Browse results
SRX386100UBERON:0001870 frontal cortexfrontal cortexRnorDv:0000017 11-week-old stage (rat)11 weeksfemaleBrown NorwayNANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH101single2889718219910734001864920962Browse results
SRX386101UBERON:0001870 frontal cortexfrontal cortexRnorDv:0000018 3-month-old stage (rat)13 weeksmaleBrown NorwayNANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH101single3343774124061664001895221043.5Browse results
SRX386102UBERON:0002037 cerebellumcerebellumRnorDv:0000017 11-week-old stage (rat)11 weeksfemaleBrown NorwayNANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH101single1834207813318055001842220729.5Browse results
SRX386103UBERON:0002037 cerebellumcerebellumRnorDv:0000018 3-month-old stage (rat)13 weeksmaleBrown NorwayNANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH101single2496732616540027001819420610.5Browse results
SRX386104UBERON:0000948 heartheartRnorDv:0000017 11-week-old stage (rat)11 weeksfemaleBrown NorwayNANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH101single2630235421463088001729720131Browse results
SRX386105UBERON:0000948 heartheartRnorDv:0000018 3-month-old stage (rat)13 weeksmaleBrown NorwayNANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH101single3505869428851677001725620109Browse results

Showing 1 to 20 of 26 entries