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Pineal gland development; day and night (Rat)

Specimens

Pools of rat pineal glands (3-10 animals) were collected at mid-day (ZT7) and mid-night (ZT19) at four of developmental ages: Embryonic day 21 (E21; 1-2 days before birth); Post-natal day 5 (P5); P20 and P40. Animals were housed in a 14:10 light:dark lighting cycle. Total RNA was extracted using an RNeasy Kit with on-column DNase treatment.

RNA Preparation

Total RNA (10 ug) was polyA-selected, fragmented and sequenced on an Illumina HiSeq2000 machine, yielding paired-end 101-mer reads.

Bioinformatics methods

See bioinformatics methods for details.

References

Yamazaki F, Møller M, Fu C, Clokie SJ, Zykovich A, Coon SL, Klein DC, Rath MF. The Lhx9 homeobox gene controls pineal gland development and prevents postnatal hydrocephalus Brain Struct Funct. 2015;220(3):1497-509. doi:10.1007/s00429-014-0740-x. Epub 2014 Mar 20. PMID:24647753

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 ReleaseDate MBases MBytes Assay_Type Center_Name Consent DATASTORE_filetype DATASTORE_provider Instrument LibraryLayout LibrarySelection LibrarySource Organism Platform LoadDate AvgSpotLen InsertSize source_name strain tissue age animals_in_pool time_of_day
E21_day_ad Embryonic day-21 SAMN02046794 SRX266516 SRR828671 SRS413528 GSM1124036 SRP021119 PRJNA197305 2014-10-24 4175 2637 RNA-Seq GEO public sra ncbi Illumina HiSeq 2000 PAIRED cDNA TRANSCRIPTOMIC Rattus norvegicus ILLUMINA 2013-04-16 202 0 Pineal gland Sprague-Dawley Pineal gland embryonic day 21 (E21) 13 mid-day (ZT7)
E21_night_ad Embryonic night-21 SAMN02046795 SRX266517 SRR828672 SRS413529 GSM1124037 SRP021119 PRJNA197305 2014-10-24 4891 3103 RNA-Seq GEO public sra ncbi Illumina HiSeq 2000 PAIRED cDNA TRANSCRIPTOMIC Rattus norvegicus ILLUMINA 2013-04-16 202 0 Pineal gland Sprague-Dawley Pineal gland embryonic day 21 (E21) 15 mid-night (ZT19)
P5_day_ad Postnatal day-5 SAMN02046796 SRX266518 SRR828673 SRS413530 GSM1124038 SRP021119 PRJNA197305 2014-10-24 6861 4235 RNA-Seq GEO public sra ncbi Illumina HiSeq 2000 PAIRED cDNA TRANSCRIPTOMIC Rattus norvegicus ILLUMINA 2013-04-17 202 0 Pineal gland Sprague-Dawley Pineal gland post-natal day 5 (P5) 17 mid-day (ZT7)
P5_night_ad Postnatal night-5 SAMN02046797 SRX266519 SRR828674 SRS413531 GSM1124039 SRP021119 PRJNA197305 2014-10-24 4141 2615 RNA-Seq GEO public sra ncbi Illumina HiSeq 2000 PAIRED cDNA TRANSCRIPTOMIC Rattus norvegicus ILLUMINA 2013-04-17 202 0 Pineal gland Sprague-Dawley Pineal gland post-natal day 5 (P5) 19 mid-night (ZT19)
P20_day_ad Postnatal day-20 SAMN02046798 SRX266520 SRR828675 SRS413532 GSM1124040 SRP021119 PRJNA197305 2014-10-24 2852 1792 RNA-Seq GEO public sra ncbi Illumina HiSeq 2000 PAIRED cDNA TRANSCRIPTOMIC Rattus norvegicus ILLUMINA 2013-04-17 202 0 Pineal gland Sprague-Dawley Pineal gland post-natal day 20 (P20) 13 mid-day (ZT7)
P20_night_ad Postnatal night-20 SAMN02046799 SRX266521 SRR828676 SRS413533 GSM1124041 SRP021119 PRJNA197305 2014-10-24 3991 2440 RNA-Seq GEO public sra ncbi Illumina HiSeq 2000 PAIRED cDNA TRANSCRIPTOMIC Rattus norvegicus ILLUMINA 2013-04-17 202 0 Pineal gland Sprague-Dawley Pineal gland post-natal day 20 (P20) 10 mid-night (ZT19)
P40_day_ad Postnatal day-40 SAMN02046800 SRX266522 SRR828677 SRS413534 GSM1124042 SRP021119 PRJNA197305 2014-10-24 5471 3392 RNA-Seq GEO public sra ncbi Illumina HiSeq 2000 PAIRED cDNA TRANSCRIPTOMIC Rattus norvegicus ILLUMINA 2013-04-17 202 0 Pineal gland Sprague-Dawley Pineal gland post-natal day 40 (P40) 3 mid-day (ZT7)
P40_night_ad Postnatal night-40 SAMN02046801 SRX266523 SRR828678 SRS413535 GSM1124043 SRP021119 PRJNA197305 2014-10-24 6910 4286 RNA-Seq GEO public sra ncbi Illumina HiSeq 2000 PAIRED cDNA TRANSCRIPTOMIC Rattus norvegicus ILLUMINA 2013-04-17 202 0 Pineal gland Sprague-Dawley Pineal gland post-natal day 40 (P40) 3 mid-night (ZT19)