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| Status |
Public on Oct 24, 2014 |
| Title |
Whole transcriptome profiling of the rat pineal gland during development from embryonic day 21 to adult |
| Organism |
Rattus norvegicus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The transcriptome of the rat pineal gland is highly dynamic, with many hundreds of genes changing more than two-fold on a 24-hr daily rhythm, as revealed earlier using Affymetrix GeneChip analysis. Several key transcription factors and enzymes are known to change dramatically during development of the pineal gland. Studies on a small number of genes indicate that the onset of rhythmic expression generally occurs later in development. This study characterizes 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.
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| Overall design |
The rat pineal transcriptome was sequenced in samples from four ages, from embryonic day 21 through adult. At each age, samples were taken at mid-day and mid-night. Data were collected to describe the changes in the developing pineal transcriptome and to identify transcripts that exhibit day/night differences in expression at each age.
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| Contributor(s) |
Coon SL, Fu C, Clokie SJ, Munson PJ, Cherukuri PF, Sugden D, Mullikin JC, Klein DC |
| Citation(s) |
24647753 |
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| Submission date |
Apr 16, 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 (8)
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| GSM1124036 |
Rat pineal gland, embryonic day 21 (E21), mid-day (ZT7) |
| GSM1124037 |
Rat pineal gland, embryonic day 21 (E21), mid-night (ZT19) |
| GSM1124038 |
Rat pineal gland, post-natal day 5 (P5), mid-day (ZT7) |
| GSM1124039 |
Rat pineal gland, post-natal day 5 (P5), mid-night (ZT19) |
| GSM1124040 |
Rat pineal gland, post-natal day 20 (P20), mid-day (ZT7) |
| GSM1124041 |
Rat pineal gland, post-natal day 20 (P20), mid-night (ZT19) |
| GSM1124042 |
Rat pineal gland, post-natal day 40 (P40), mid-day (ZT7) |
| GSM1124043 |
Rat pineal gland, post-natal day 40 (P40), mid-night (ZT19) |
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| Relations |
| BioProject |
PRJNA197305 |
| SRA |
SRP021119 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE46127_FPKM_dev_all.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
| GSE46127_RAW.tar |
6.4 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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