Pineal gland; day and night (Human)

Specimens

Pineal glands were obtained from NDRI (National Disease Research Interchange; Pennsylvania Medical Center, Philadelphia, PA). Two glands were from individuals who died at mid-day (11:00-13:00) and four from deaths occurring at mid-night (23:00-01:00). Samples were stored at -80C until use.

RNA Preparation

RNA was extracted from individual glands with Trizol (Invitrogen, Carlsbad, CA) and subsequently cleaned up using an RNeasy Micro Kit with on-column DNase treatment (Qiagen, Valencia, CA). The amount and quality of RNA were determined using a NanoDrop spectrophotometer (NanoDrop, Wilmington, DE) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA), respectively. RIN values ranged from 7.3-8.7.

RNA-Seq library preparation and sequencing

Ribosomal-depleted RNA was used to construct stranded libraries from 1 µg aliquots of total RNA using a TruSeq Stranded Total RNA Sample Prep Kit (Illumina cat. no. RS-122-2301) according to the manufacturer's instructions. The library insert sizes were approximately 170 bp. Unique barcode adapters were appended to each library. The pooled libraries were sequenced on a HiSeq 2500 (Illumina, San Diego, CA) using version 4 chemistry. This yielded an average of 81 million 126-bp read-pairs for each sample.

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	source_name	tissue
Pineal_Gland-Day-1	human_pineal_gland_day-1	SAMN07278521	SRX2956606	SRR5756462	SRS2313809	GSM2684714	SRP110509	PRJNA391921	2017-07-13	20826	10834	RNA-Seq	GEO	public	sra	ncbi	Illumina HiSeq 2500	PAIRED	cDNA	TRANSCRIPTOMIC	Homo sapiens	ILLUMINA	2018-02-01	252	died at mid-day (11:00-13:00)	Pineal Gland
Pineal_Gland_Day-2	human_pineal_gland_day-2	SAMN07278520	SRX2956607	SRR5756463	SRS2313810	GSM2684715	SRP110509	PRJNA391921	2017-07-15	19427	10164	RNA-Seq	GEO	public	sra	ncbi	Illumina HiSeq 2500	PAIRED	cDNA	TRANSCRIPTOMIC	Homo sapiens	ILLUMINA	2018-02-01	252	died at mid-day (11:00-13:00)	Pineal Gland
Pineal_Gland_Night-1	human_pineal_gland_night-1	SAMN07278518	SRX2956609	SRR5756465	SRS2313811	GSM2684717	SRP110509	PRJNA391921	2017-07-14	20764	11094	RNA-Seq	GEO	public	sra	ncbi	Illumina HiSeq 2500	PAIRED	cDNA	TRANSCRIPTOMIC	Homo sapiens	ILLUMINA	2018-02-01	252	died at mid-night (23:00-01:00)	Pineal Gland
Pineal_Gland_Night-2	human_pineal_gland_night-2	SAMN07278519	SRX2956608	SRR5756464	SRS2313812	GSM2684716	SRP110509	PRJNA391921	2017-07-15	20701	10847	RNA-Seq	GEO	public	sra	ncbi	Illumina HiSeq 2500	PAIRED	cDNA	TRANSCRIPTOMIC	Homo sapiens	ILLUMINA	2018-02-01	252	died at mid-night (23:00-01:00)	Pineal Gland
Pineal_Gland_Night-3	human_pineal_gland_night-3	SAMN07278517	SRX2956610	SRR5756466	SRS2313813	GSM2684718	SRP110509	PRJNA391921	2017-07-14	19381	10032	RNA-Seq	GEO	public	sra	ncbi	Illumina HiSeq 2500	PAIRED	cDNA	TRANSCRIPTOMIC	Homo sapiens	ILLUMINA	2018-02-01	252	died at mid-night (23:00-01:00)	Pineal Gland
Pineal_Gland_Night-4	human_pineal_gland_night-4	SAMN07278516	SRX2956611	SRR5756467	SRS2313814	GSM2684719	SRP110509	PRJNA391921	2017-07-15	19698	10283	RNA-Seq	GEO	public	sra	ncbi	Illumina HiSeq 2500	PAIRED	cDNA	TRANSCRIPTOMIC	Homo sapiens	ILLUMINA	2018-02-01	252	died at mid-night (23:00-01:00)	Pineal Gland