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Pineal gland (RP), retina (RR) and mixed tissue (RX); 24-hr time series (Rat)

Specimens

Pools (>10 animals) of mixed sexes rat pineal glands or retinas were prepared from tissue obtained at six time points during a 24-hour period. Animals were housed in a 14:10 light:dark lighting cycle. Samples were collected at mid-day (ZT7) and mid-night (ZT19), and at one hour before and one hour after the light-to-dark transition (ZT13 and ZT15) and the dark-to-light transition (ZT23 and ZT1). In addition, a mixed tissue sample was prepared from material collected from three rats at ZT7 and at ZT19. The tissues were: cortex, cerebellum, midbrain, hypothalamus, hindbrain, spinal cord, retina, pituitary, heart, liver, lung, kidney, skeletal muscle, small intestine, adrenal gland.

RNA Preparation

Samples of tissue from the three animals were mixed. Total RNA was extracted using an RNeasy Kit with on-column DNase treatment. To prepare the mixed tissue sample, equal amounts of RNA from each of the 15 tissues were combined.

RNA-Seq libary preparation and sequencing

Total RNA (10 ug) was polyA-selected, fragmented and barcoded. Samples were run six per sequencing lane on an Illumina HiSeq2000 machine, generating paired-end 101-mer reads.

Note: In some cases, the mixed tissue values for selected genes are exceptionally high because that gene is very highly expressed in only one tissue, e.g., Rho and GH are strongly expressed only in the retina and pituitary gland, respectively.

Bioinformatics methods

See bioinformatics methods for details.

Samples

The following table describes the sample metadata for this experiment. Accessions in GEO, BioProject, and SRA link to their resepective entries. Raw data were downloaded as FASTQ format using fastq-dump for each of the SRR run accessions.

Note: scroll to the right to see the full extent of the table.

samplename Label BioSample Experiment SRRrun SRA_Sample Sample_Name SRA_Study BioProject LoadDate MBases MBytes Assay_Type Center_Name Consent DATASTORE_filetype DATASTORE_provider Instrument LibraryLayout LibrarySelection LibrarySource Organism Platform ReleaseDate AvgSpotLen InsertSize animals_in_pool source_name time_of_day tissue age strain
RP1_ad RP1 SAMN02045887 SRX265395 SRR827498 SRS413245 GSM1122813 SRP021090 PRJNA197149 2013-04-15 5808 4199 RNA-Seq GEO public sra ncbi Illumina HiSeq 2000 PAIRED cDNA TRANSCRIPTOMIC Rattus norvegicus ILLUMINA 2014-02-06 202 0 10 Rat pineal gland, ZT1 (1 hr after lights on) ZT1 (1 hr after lights on) Pineal gland 6-8 weeks Sprague-Dawley
RP7_ad RP7 SAMN02045888 SRX265396 SRR827499 SRS413244 GSM1122814 SRP021090 PRJNA197149 2013-04-15 6042 4359 RNA-Seq GEO public sra ncbi Illumina HiSeq 2000 PAIRED cDNA TRANSCRIPTOMIC Rattus norvegicus ILLUMINA 2014-02-06 202 0 10 Rat pineal gland, ZT7 (mid-day) ZT7 (mid-day) Pineal gland 6-8 weeks Sprague-Dawley
RP13_ad RP13 SAMN02045889 SRX265397 SRR827500 SRS413246 GSM1122815 SRP021090 PRJNA197149 2013-04-15 6017 4345 RNA-Seq GEO public sra ncbi Illumina HiSeq 2000 PAIRED cDNA TRANSCRIPTOMIC Rattus norvegicus ILLUMINA 2014-02-06 202 0 10 Rat pineal gland, ZT13 (1 hr before lights off) ZT13 (1 hr before lights off) Pineal gland 6-8 weeks Sprague-Dawley
RP15_ad RP15 SAMN02045890 SRX265398 SRR827501 SRS413248 GSM1122816 SRP021090 PRJNA197149 2013-04-15 6152 4430 RNA-Seq GEO public sra ncbi Illumina HiSeq 2000 PAIRED cDNA TRANSCRIPTOMIC Rattus norvegicus ILLUMINA 2014-02-06 202 0 10 Rat pineal gland, ZT15 (1 hr after lights off) ZT15 (1 hr after lights off) Pineal gland 6-8 weeks Sprague-Dawley
RP19_ad RP19 SAMN02045891 SRX265399 SRR827502 SRS413247 GSM1122817 SRP021090 PRJNA197149 2013-04-15 3869 2804 RNA-Seq GEO public sra ncbi Illumina HiSeq 2000 PAIRED cDNA TRANSCRIPTOMIC Rattus norvegicus ILLUMINA 2014-02-06 202 0 10 Rat pineal gland, ZT19 (mid-night) ZT19 (mid-night) Pineal gland 6-8 weeks Sprague-Dawley
RP23_ad RP23 SAMN02045892 SRX265400 SRR827503 SRS413250 GSM1122818 SRP021090 PRJNA197149 2013-04-15 4336 3160 RNA-Seq GEO public sra ncbi Illumina HiSeq 2000 PAIRED cDNA TRANSCRIPTOMIC Rattus norvegicus ILLUMINA 2014-02-06 202 0 10 Rat pineal gland, ZT23 (1 hr before lights on) ZT23 (1 hr before lights on) Pineal gland 6-8 weeks Sprague-Dawley
RR1_ad RR1 SAMN02045893 SRX265401 SRR827504 SRS413249 GSM1122819 SRP021090 PRJNA197149 2013-04-15 4349 3157 RNA-Seq GEO public sra ncbi Illumina HiSeq 2000 PAIRED cDNA TRANSCRIPTOMIC Rattus norvegicus ILLUMINA 2014-02-06 202 0 10 Rat retina, ZT1 (1 hr after lights on) ZT1 (1 hr after lights on) Retina 6-8 weeks Sprague-Dawley
RR7_ad RR7 SAMN02045894 SRX265402 SRR827505 SRS413251 GSM1122820 SRP021090 PRJNA197149 2013-04-15 7645 5535 RNA-Seq GEO public sra ncbi Illumina HiSeq 2000 PAIRED cDNA TRANSCRIPTOMIC Rattus norvegicus ILLUMINA 2014-02-06 202 0 10 Rat retina, ZT7 (mid-day) ZT7 (mid-day) Retina 6-8 weeks Sprague-Dawley
RR13_ad RR13 SAMN02045895 SRX265403 SRR827506 SRS413252 GSM1122821 SRP021090 PRJNA197149 2013-04-15 5585 4061 RNA-Seq GEO public sra ncbi Illumina HiSeq 2000 PAIRED cDNA TRANSCRIPTOMIC Rattus norvegicus ILLUMINA 2014-02-06 202 0 10 Rat retina, ZT13 (1 hr before lights off) ZT13 (1 hr before lights off) Retina 6-8 weeks Sprague-Dawley
RR15_ad RR15 SAMN02045896 SRX265404 SRR827507 SRS413253 GSM1122822 SRP021090 PRJNA197149 2013-04-15 5797 4204 RNA-Seq GEO public sra ncbi Illumina HiSeq 2000 PAIRED cDNA TRANSCRIPTOMIC Rattus norvegicus ILLUMINA 2014-02-06 202 0 10 Rat retina, ZT15 (1 hr after lights off) ZT15 (1 hr after lights off) Retina 6-8 weeks Sprague-Dawley
RR19_ad RR19 SAMN02045897 SRX265405 SRR827508 SRS413254 GSM1122823 SRP021090 PRJNA197149 2013-04-15 7059 5152 RNA-Seq GEO public sra ncbi Illumina HiSeq 2000 PAIRED cDNA TRANSCRIPTOMIC Rattus norvegicus ILLUMINA 2014-02-06 202 0 10 Rat retina, ZT19 (mid-night) ZT19 (mid-night) Retina 6-8 weeks Sprague-Dawley
RR23_ad RR23 SAMN02045898 SRX265406 SRR827509 SRS413255 GSM1122824 SRP021090 PRJNA197149 2013-04-15 9421 6842 RNA-Seq GEO public sra ncbi Illumina HiSeq 2000 PAIRED cDNA TRANSCRIPTOMIC Rattus norvegicus ILLUMINA 2014-02-06 202 0 10 Rat retina, ZT23 (1 hr before lights on) ZT23 (1 hr before lights on) Retina 6-8 weeks Sprague-Dawley
RX7_ad RX7 SAMN02045899 SRX265407 SRR827510 SRS413256 GSM1122825 SRP021090 PRJNA197149 2013-04-15 5385 3845 RNA-Seq GEO public sra ncbi Illumina HiSeq 2000 PAIRED cDNA TRANSCRIPTOMIC Rattus norvegicus ILLUMINA 2014-02-06 202 0 3 Rat non-pineal mixed tissue, ZT7 (mid-day) ZT7 (mid-day) Non-pineal mixed tissue 6-8 weeks Sprague-Dawley
RX19_ad RX19 SAMN02045875 SRX265408 SRR827511 SRS413257 GSM1122826 SRP021090 PRJNA197149 2013-04-15 7281 5243 RNA-Seq GEO public sra ncbi Illumina HiSeq 2000 PAIRED cDNA TRANSCRIPTOMIC Rattus norvegicus ILLUMINA 2014-02-06 202 0 3 Rat non-pineal mixed tissue, ZT19 (mid-night) ZT19 (mid-night) Non-pineal mixed tissue 6-8 weeks Sprague-Dawley