Whole transcriptome profiling of the rat pineal gland

Experiment ID:SRP006893
Technology:RNA-Seq
Description:The rat pineal gland is a highly dynamic tissue with many hundreds of genes changing more than two-fold in a 24-hr daily rhythm as measured by Affymetrix GeneChip analysis. We sought to more completely understand this dynamic transcriptome using RNA-Seq in order to capture information regarding alternative splicing, novel exons, unannotated mRNAs, non-coding RNAs, etc. We also wished to identify transcripts that were selectively expressed in the pineal glands relative to other tissues. Toward this end we performed RNA-Seq on three types of samples; 1) a pool of pineal glands sampled at mid-day (ZT7); 2) a pool of pineal glands sampled at mid-night (ZT19); and a pool of 15 different non-pineal tissues collected from 3 animals at mid-day (ZT7). Animals were housed in a 14:10 light:dark lighting cycle. PolyA-selected RNA was fragmented and sequenced on an Illumina GAii machine, yielding paired-end 51-mer reads.
DOI:10.1073/pnas.1207748109
Source:SRP006893 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
SRX066204UBERON:0001905 pineal bodypineal glandUBERON:0000113 post-juvenile2 to 3 months oldNASprague-DawleyNANARattus norvegicusNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH102paired145139549211123001839822290Browse results
SRX069234UBERON:0001905 pineal bodypineal glandUBERON:0000113 post-juvenile2 to 3 months oldNASprague-DawleyNANARattus norvegicusNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH102paired113819537239800001779521818.5Browse results
SRX069235UBERON:0000468 multicellular organismmixed organsUBERON:0000113 post-juvenile2 to 3 months oldNASprague-DawleyNANARattus norvegicusNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH102paired1479353310537127002009123228Browse results
SRX076903UBERON:0001905 pineal bodypineal glandUBERON:0000113 post-juvenile2 to 3 months oldNASprague-DawleyNANARattus norvegicusNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH102paired3295242116803905001913126333Browse results
SRX076913UBERON:0001905 pineal bodypineal glandUBERON:0000113 post-juvenile2 to 3 months oldNASprague-DawleyNANARattus norvegicusNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH102paired2048429712197935001794525615Browse results
SRX076921UBERON:0000468 multicellular organismmixed organsUBERON:0000113 post-juvenile2 to 3 months oldNASprague-DawleyNANARattus norvegicusNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH102paired2750870217972198002015526836.5Browse results

Showing 1 to 6 of 6 entries

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