A rat RNA-Seq transcriptomic Bodymap across eleven organs and four developmental stages

Experiment ID:SRP037986
Technology:RNA-Seq
Description:The rat has been used extensively as a model for evaluating chemical toxicities and for understanding drug mechanisms. However, its transcriptome across multiple organs, or developmental stages, has not yet been reported. Here we show, as part of the SEQC consortium efforts, a comprehensive rat transcriptomic BodyMap created by performing RNASeq on 320 samples from 11 organs of both sexes of juvenile, adolescent, adult and aged Fischer 344 rats. We catalogue the expression profiles of 40,064 genes, 65,167 transcripts, 31,909 alternatively spliced transcript variants and 2,367 non-coding genes/non-coding RNAs (ncRNAs) annotated in AceView. We find that organ-enriched, differentially expressed genes reflect the known organ-specific biological activities. A large number of transcripts show organ-specific, age-dependent or sex-specific differential expression patterns. We create a web-based, open-access rat BodyMap database of expression profiles with crosslinks to other widely used databases, anticipating that it will serve as a primary resource for biomedical research using the rat model. Overall design: We constructed a comprehensive RNA-Seq data set for studying the dynamics of the rat transcriptome using 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old). Four biological replicates were used for each of the 80 sample groups.
Source:SRP037986  SRA
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Bulk RNA-Seq processed expression values in Rattus norvegicus

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Showing 1 to 20 of 320 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
SRX471368UBERON:0002369 adrenal glandAdrenalUBERON:0007221 neonate stagedevelopmental stage (week): 2femaleFischer 344NANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH50single3289391214395546001835821519.5Browse results
SRX471369UBERON:0002369 adrenal glandAdrenalUBERON:0007221 neonate stagedevelopmental stage (week): 2femaleFischer 344NANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH50single3421625914713326001849221603Browse results
SRX471370UBERON:0002369 adrenal glandAdrenalUBERON:0007221 neonate stagedevelopmental stage (week): 2femaleFischer 344NANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH50single4035307017212317001873021708.5Browse results
SRX471371UBERON:0002369 adrenal glandAdrenalUBERON:0007221 neonate stagedevelopmental stage (week): 2femaleFischer 344NANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH50single3814233016027474001865921678Browse results
SRX471372UBERON:0002369 adrenal glandAdrenalUBERON:0034919 juvenile stagedevelopmental stage (week): 6femaleFischer 344NANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH50single4216939720945130001875021734.5Browse results
SRX471373UBERON:0002369 adrenal glandAdrenalUBERON:0034919 juvenile stagedevelopmental stage (week): 6femaleFischer 344NANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH50single4103142919724353001861621657.5Browse results
SRX471374UBERON:0002369 adrenal glandAdrenalUBERON:0034919 juvenile stagedevelopmental stage (week): 6femaleFischer 344NANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH50single4253705319754991001915021939Browse results
SRX471375UBERON:0002369 adrenal glandAdrenalUBERON:0034919 juvenile stagedevelopmental stage (week): 6femaleFischer 344NANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH50single4072352819002133001863921680Browse results
SRX471376UBERON:0002369 adrenal glandAdrenalRnorDv:0000020 4-month-old stage (rat)developmental stage (week): 21femaleFischer 344NANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH50single5664023528832577001872721705Browse results
SRX471377UBERON:0002369 adrenal glandAdrenalRnorDv:0000020 4-month-old stage (rat)developmental stage (week): 21femaleFischer 344NANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH50single6316773932563227001890421831.5Browse results
SRX471378UBERON:0002369 adrenal glandAdrenalRnorDv:0000020 4-month-old stage (rat)developmental stage (week): 21femaleFischer 344NANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH50single3333640217907438001827821496Browse results
SRX471379UBERON:0002369 adrenal glandAdrenalRnorDv:0000020 4-month-old stage (rat)developmental stage (week): 21femaleFischer 344NANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH50single4997338525741116001852821632Browse results
SRX471380UBERON:0002369 adrenal glandAdrenalRnorDv:0000039 23-month-old stage (rat)developmental stage (week): 104femaleFischer 344NANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH50single5095928623192725001891621819.5Browse results
SRX471381UBERON:0002369 adrenal glandAdrenalRnorDv:0000039 23-month-old stage (rat)developmental stage (week): 104femaleFischer 344NANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH50single3949984419023312001873421737Browse results
SRX471382UBERON:0002369 adrenal glandAdrenalRnorDv:0000039 23-month-old stage (rat)developmental stage (week): 104femaleFischer 344NANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH50single3040632614471834001834321529Browse results
SRX471383UBERON:0002369 adrenal glandAdrenalRnorDv:0000039 23-month-old stage (rat)developmental stage (week): 104femaleFischer 344NANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH50single4451217220918123001862021687.5Browse results
SRX471384UBERON:0002369 adrenal glandAdrenalUBERON:0007221 neonate stagedevelopmental stage (week): 2maleFischer 344NANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH50single4321720518232806001856721625.5Browse results
SRX471385UBERON:0002369 adrenal glandAdrenalUBERON:0007221 neonate stagedevelopmental stage (week): 2maleFischer 344NANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH50single3408609914757100001837421522Browse results
SRX471386UBERON:0002369 adrenal glandAdrenalUBERON:0007221 neonate stagedevelopmental stage (week): 2maleFischer 344NANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH50single5462369424450623001922021955Browse results
SRX471387UBERON:0002369 adrenal glandAdrenalUBERON:0007221 neonate stagedevelopmental stage (week): 2maleFischer 344NANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH50single5838241124432082001907821905.5Browse results

Showing 1 to 20 of 320 entries