Rat pineal gland, RNA-Seq, P5, ZT7 - SRA

SRX082005: Rat pineal gland, RNA-Seq, P5, ZT7
1 ILLUMINA (Illumina HiSeq 2000) run: 27M spots, 5.5G bases, 3.1Gb downloads

Design: For the mRNA-Seq sample preparation, the NEB Master Mix Set was used according to the manufacturer's protocol. Briefly, 10 *g of each total RNA sample was used for polyA mRNA selection using streptavidin-coated magnetic beads, followed by Covaris mRNA fragmentation. The fragmented mRNA was used to synthesize cDNA using reverse transcriptase (SuperScript II) and random primers. The cDNA was further converted into double stranded cDNA and, after an end repair process (Klenow fragment, T4 polynucleotide kinase and T4 polymerase), was finally ligated to Illumina multiplex paired-end (PE) adaptors.Size selection was performed using a 1.5% cassette on a Pippin Prep (Sage Science). Finally, the libraries were enriched and barcodes incorporated using 14-16 cycles of PCR and purified Ampure XP bead (Agilent). The enriched libraries were diluted with Elution Buffer to a final concentration of 10 nM. Libraries were barcoded and four were run together in one lane at a concentration of 15 pM on an Illumina HiSeq 2000 using paired-end 101 base-pair sequencing, including a 7 cycle index read. Image analysis and base calling was done by Illumina Genome Analyzer Pipeline software (GAPipeline) with default parameters. All eight samples were analyzed in this manner.

Submitted by: (NICHD)

Study: Development of daily rhythmicity in the rat pineal transcriptome interrogated using RNA-Seq

PRJNA68829 • SRP007413 • All experiments • All runs

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Rats were sacrificed at various development stages at both mid-day and mid-night. Pineal glands were removed and the transcriptomes were interrogated using RNA-Seq to determine developmental changes in gene expression with special emphasis on the acquisition of day-night differences in gene expression levels. It is known from previous studies that in the rat pineal gland several hundred genes exhibit at least a two-fold greater expression at night than during the day; and more than a hundred have a more than two-fold higher expression during the day.

Sample: Rat pineal gland, P5, ZT7

SAMN00632252 • SRS214094 • All experiments • All runs

Organism: Rattus norvegicus

Library:

Name: P5 Day

Instrument: Illumina HiSeq 2000

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: other

Layout: PAIRED

Spot descriptor:

1 forward102 reverse

Runs: 1 run, 27M spots, 5.5G bases, 3.1Gb

Run	# of Spots	# of Bases	Size	Published
SRR306878	26,989,035	5.5G	3.1Gb	2012-07-07

ID:: 92736

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