Pineal gland and retina, retina and mixed tissue; day and night; Eya2 KO (Mouse)

Specimens

The data were generated from Eya2 knockout (KO) mice and from 129sv wild-type control mice. The Eya2 knockout mice were generated in the 129sv strain and propagated on a C57bl6 background (Dr. Pin-Xian Xu, personal communication). Pools of 10 mouse pineal glands and 10 retinas were collected at mid-day (ZT6) and mid-night (ZT18) from animals housed in a 12:12 light:dark lighting cycle. In addition, mixed tissue samples were prepared from material collected from 3 mice at ZT6 and ZT18, respectively. The tissues were: cortex, cerebellum, midbrain, hypothalamus, hindbrain, spinal cord, retina, pituitary, heart, liver, lung, kidney, skeletal muscle, small intestine, adrenal gland. Samples of tissue from the three animals were mixed.

RNA Preparation

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 library preparation and sequencing

Total RNA (1-6 ug) from the pineal gland and retina pools, and mixed tissue samples were polyA-selected, fragmented and sequenced on an Illumina GAIIx machine, yielding paired-end 76-mer reads.

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	Library_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	Sample_Name
Pineal_KO_day_G1	Pineal_KO_day_G1	SAMN00630304	SRX079427	SRR290895	SRS212561	MJO1 Pineal Eya2 KO ZT7	SRP007294	PRJNA68307	2014-05-30	927	567	RNA-Seq	NICHD	public	sra	ncbi	Illumina Genome Analyzer IIx	PAIRED	other	TRANSCRIPTOMIC	Mus musculus	ILLUMINA	2012-06-23	152	375	Mouse pineal gland, Eya2 KO, ZT7
Pineal_KO_night_C1	Pineal_KO_night_C1	SAMN00630305	SRX079428	SRR290896	SRS212562	MJO2 Pineal Eya2 KO ZT19	SRP007294	PRJNA68307	2014-05-30	697	422	RNA-Seq	NICHD	public	sra	ncbi	Illumina Genome Analyzer IIx	PAIRED	other	TRANSCRIPTOMIC	Mus musculus	ILLUMINA	2012-06-23	152	375	Mouse pineal gland, Eya2 KO, ZT19
Pineal_control_day_A1	Pineal_control_day_A1	SAMN00630306	SRX079429	SRR290897	SRS212563	MJO3 Pineal control ZT7	SRP007294	PRJNA68307	2014-05-30	979	600	RNA-Seq	NICHD	public	sra	ncbi	Illumina Genome Analyzer IIx	PAIRED	other	TRANSCRIPTOMIC	Mus musculus	ILLUMINA	2012-06-23	152	375	Mouse pineal gland, control, ZT7
Pineal_control_night_T1	Pineal_control_night_T1	SAMN00630307	SRX079430	SRR290898	SRS212564	MJO4 Pineal control ZT19	SRP007294	PRJNA68307	2014-05-30	1272	747	RNA-Seq	NICHD	public	sra	ncbi	Illumina Genome Analyzer IIx	PAIRED	other	TRANSCRIPTOMIC	Mus musculus	ILLUMINA	2012-06-23	152	375	Mouse pineal gland, control, ZT19
Retina_KO_day_G3	Retina_KO_day_G3	SAMN00630308	SRX079431	SRR290899	SRS212565	MJO5 Retina Eya2 KO ZT7	SRP007294	PRJNA68307	2014-05-30	1194	717	RNA-Seq	NICHD	public	sra	ncbi	Illumina Genome Analyzer IIx	PAIRED	other	TRANSCRIPTOMIC	Mus musculus	ILLUMINA	2012-06-23	152	375	Mouse retina, Eya2 KO, ZT7
Retina_KO_night_C3	Retina_KO_night_C3	SAMN00630309	SRX079433	SRR290900	SRS212566	MJO6 Retina Eya2 KO ZT19	SRP007294	PRJNA68307	2014-05-30	1046	619	RNA-Seq	NICHD	public	sra	ncbi	Illumina Genome Analyzer IIx	PAIRED	other	TRANSCRIPTOMIC	Mus musculus	ILLUMINA	2012-06-23	152	375	Mouse retina, Eya2 KO, ZT19
Retina_control_day_A3	Retina_control_day_A3	SAMN00630310	SRX079434	SRR290901	SRS212567	MJO7 Retina control ZT7	SRP007294	PRJNA68307	2014-05-30	1240	741	RNA-Seq	NICHD	public	sra	ncbi	Illumina Genome Analyzer IIx	PAIRED	other	TRANSCRIPTOMIC	Mus musculus	ILLUMINA	2012-06-23	152	375	Mouse retina, control, ZT7
Retina_control_night_T3	Retina_control_night_T3	SAMN00630311	SRX079435	SRR290902	SRS212568	MJO8 Retina control ZT19	SRP007294	PRJNA68307	2014-05-30	1257	745	RNA-Seq	NICHD	public	sra	ncbi	Illumina Genome Analyzer IIx	PAIRED	other	TRANSCRIPTOMIC	Mus musculus	ILLUMINA	2012-06-23	152	375	Mouse retina, control, ZT19
Mixed_day_G2	Mixed_day_G2	SAMN00630312	SRX079436	SRR290903	SRS212569	MJO9 Mixed control ZT7	SRP007294	PRJNA68307	2014-05-30	2475	1483	RNA-Seq	NICHD	public	sra	ncbi	Illumina Genome Analyzer IIx	PAIRED	other	TRANSCRIPTOMIC	Mus musculus	ILLUMINA	2012-06-23	152	375	Mouse non-pineal mixed tissue, ZT7
Mixed_night_C2	Mixed_night_C2	SAMN00630313	SRX079437	SRR290904	SRS212570	MJO10 Mixed control ZT19	SRP007294	PRJNA68307	2014-05-30	2412	1427	RNA-Seq	NICHD	public	sra	ncbi	Illumina Genome Analyzer IIx	PAIRED	other	TRANSCRIPTOMIC	Mus musculus	ILLUMINA	2012-06-23	152	375	Mouse non-pineal mixed tissue, ZT19