Whole transcriptome profiling of the rat pineal gland using mid-day and mid-night samples (Experiment 4)

Experiment ID:SRP013378
Technology:RNA-Seq
Description:The rat pineal transcriptome is highly dynamic, with many hundreds of transcripts changing more than two-fold on a 24-hr basis, as revealed earlier using Affymetrix GeneChip analysis. We sought to more completely characterize this temporally dynamic transcriptome using RNA-Seq to capture information regarding alternative splicing, novel exons, unannotated mRNAs, non-coding RNAs, and coding transcripts not represented on the Affymetrix chips. Toward this end we performed RNA-Seq on pools of pineal glands at mid-day (ZT7) and at mid-night (ZT19) from animals that were housed in a 14:10 light:dark lighting cycle. We also wished to identify transcripts that were selectively expressed in the pineal glands relative to other tissues; to do this, RNA was sequenced from a pool of 15 different tissues collected from 3 animals at mid-day (ZT7). PolyA-selected RNA was fragmented and sequenced on an Illumina HiSeq 2000 machine, yielding paired-end, 101-mer reads. This is Experiment 4 of several similar RNA-Seq experiments investigating the rat pineal transcriptome at ZT7 compared to ZT19. Experiments 1 through 4 are included in Coon et al., 2012 and have been archived as separate SRA entries: Experiment 1, SRP006893; Experiment 2, SRP013114; Experiment 3, SRP013116. SRP013378(SRA053154)is actually 'Experiment 4', not 'Experiment 3'
DOI:10.1073/pnas.1207748109
Source:SRP013378 SRA
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Bulk RNA-Seq processed expression values in Rattus norvegicus

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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
SRX149623UBERON:0001905 pineal bodypineal glandUBERON:0000113 post-juvenile2 to 3 months oldNASprague-DawleyNANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH202paired19627773895015884002078623687Browse results
SRX149624UBERON:0001905 pineal bodypineal glandUBERON:0000113 post-juvenile2 to 3 months oldNASprague-DawleyNANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH202paired17708238387721342002031323418Browse results
SRX149625UBERON:0000468 multicellular organismmixed organsUBERON:0000113 post-juvenile2 to 3 months oldNASprague-DawleyNANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH202paired15345601779888640002076623517Browse results

Showing 1 to 3 of 3 entries

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