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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