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)