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| Status |
Public on Feb 05, 2014 |
| Title |
Whole transcriptome profiling of rat pineal glands and retinas collected throughout a 24-hour cycle |
| Organism |
Rattus norvegicus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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. The retina is evolutionally related to the pineal gland so these two tissues share many gene expression patterns. This study more completely characterizes the temporally dynamic transcriptomes of these tissues 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. We also identified transcripts that were selectively expressed in the pineal gland relative to other tissues by comparing pineal samples to a sample of pooled non-pineal tissues.
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| Overall design |
The transcriptomes of the rat pineal gland and retina were sequenced using samples collected at 6 time points throughout a 24-hour cycle to identify rhythmically expressed transcripts. The transcriptomes of pools of mixed tissues collected at mid-day (ZT7) and mid-night (ZT19) were also sequenced for comparison to aid in determining pineal-enriched transcripts.
Contributor: NISC, Comparative Sequencing Program
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| Contributor(s) |
Coon SL, Fu C, Clokie SJ, Munson PJ, Cherukuri PF, Sugden D, Mullikin JC, Klein DC |
| Citation(s) |
24351931 |
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| Submission date |
Apr 15, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Steven Coon |
| E-mail(s) |
coons@mail.nih.gov
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| Phone |
3014516622
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| Organization name |
NIH
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| Department |
NICHD/PDEGEN
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| Lab |
Section on Neuroendocrinology
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| Street address |
49 Convent Drive Room 6A83
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892-4510 |
| Country |
USA |
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| Platforms (1) |
| GPL14844 |
Illumina HiSeq 2000 (Rattus norvegicus) |
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| Samples (14)
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| GSM1122813 |
Rat pineal gland, Time series, ZT1 (1 hr after lights on) |
| GSM1122814 |
Rat pineal gland, Time series, ZT7 (mid-day) |
| GSM1122815 |
Rat pineal gland, Time series, ZT13 (1 hr before lights off) |
| GSM1122816 |
Rat pineal gland, Time series, ZT15 (1 hr after lights off) |
| GSM1122817 |
Rat pineal gland, Time series, ZT19 (mid-night) |
| GSM1122818 |
Rat pineal gland, Time series, ZT23 (1 hr before lights on) |
| GSM1122819 |
Rat retina, Time series, ZT1 (1 hr after lights on) |
| GSM1122820 |
Rat retina, Time series, ZT7 (mid-day) |
| GSM1122821 |
Rat retina, Time series, ZT13 (1 hr before lights off) |
| GSM1122822 |
Rat retina, Time series, ZT15 (1 hr after lights off) |
| GSM1122823 |
Rat retina, Time series, ZT19 (mid-night) |
| GSM1122824 |
Rat retina, Time series, ZT23 (1 hr before lights on) |
| GSM1122825 |
Rat non-pineal mixed tissue, ZT7 (mid-day) |
| GSM1122826 |
Rat non-pineal mixed tissue, ZT19 (mid-night) |
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| Relations |
| BioProject |
PRJNA197149 |
| SRA |
SRP021090 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE46069_FPKM_time_all.txt.gz |
1.5 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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