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| Status |
Public on Dec 08, 2015 |
| Title |
Control ID FG150 |
| Sample type |
SRA |
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| Source name |
Saline Control
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
age: adult
gender: male
sample group: Saline Control
tissue: whole blood
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| Treatment protocol |
Whole blood was obtained via cardiac puncture at 4:30 to 5:30 pm, and immediately frozen, from adult 85 to 90 day old male Sprague-Dawley rats at 3 hr after four sequential injections of saline, saline in a cool environmental, saline in a hot envrionment (39°C), amphetamine or amphetamine in a cool environment
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| Growth protocol |
Animals used in these experiments were Charles River male Sprague-Dawley. They were given access to water and food ad lib and kept on a 12 hour light cycle 6:00am to 6:00pm until testing
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Tri Reagent (Molecular Research Center Inc., Cincinnati, OH) (Chomczynski and Mackey, 1995) with modifications similar to those previously described (Bowyer et al., 2007).
Alpha and Beta Globin mRNA were substantially depleted from total RNA samples using the GlobinClear-Mouse/Rat Kit (Life Technologies # AM1981) as described by the vendor at EA/Quintiles; 4324 S. Alton Ave. Durham, N.C. Analysis.
Globin mRNA-depleted RNA samples were converted into cDNA libraries using the TruSeq Stranded mRNA Sample Prep Kit (Illumina, #RS-122-2103). Starting with 300 ng of Globin mRNA-depleted RNA, polyadenylated RNA (primarily mRNA) was selected and purified using oligo-dT conjugated magnetic beads. Performed at EA/ Quintiles.
Final cDNA libraries were analyzed for size distribution and using an Agilent 2200 TapeStation, quantitated by qPCR (KAPA Library Quant Kit, KAPA Biosystems # KK4824) and normalized to 2 nM for sequencing. Performed at EA/Quintiles.
Clusters were generated on an Illumina cBOT using an Illumina TruSeq Paired-End Cluster Kit on an Illumina Paired End Flow Cell. The Flowcell was sequencing through 51 bases, paired end, (8 base index cycle) on an Illumina HiSeq 2000 (HiSeq Control Software v 1.5.15.1). Performed at EA/Quintiles.
Quality control files contained read length and depth results (before and after clipping), presence of artifact/duplicate sequences, distribution of base quality and base frequency by sample. Also, flow cell total yield, PF reads, barcode quality, alignment summaries and # of genes detected were determined. FASTQ files for each RNA aliquot were generated.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Saline Control #15
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| Data processing |
Basecall files were converted to fastq files using CASAVA 1.8.2
Fastq files were clipped using fastq-mcf (parameters: “--max-ns 4 --qual-mean 25 -H -p 5 -q 7 -l 25”)
Fastq files were aligned to rat Ensembl release 70 transcriptome (rn5) using bowtie 0.12.9 (params: “-e 500 –m 100 –chunkmbs 256”)
Alignments were quantified using RSEM v 1.2.0 (no special parameters)
Genome_build: Genome build: rn5
Supplementary_files_format_and_content: Separate count per gene files for each sample. A tab is between the gene and the count. One count per gene on each line.
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| Submission date |
Oct 15, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
John Francis Bowyer |
| E-mail(s) |
john.bowyer@fda.hhs.gov
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| Phone |
870-543-7194
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| Organization name |
National Center for Toxicological Research FDA
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| Department |
Neurotoxicology
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| Lab |
Neurobiology
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| Street address |
3900 NCTR Drive
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| City |
Jefferson |
| State/province |
AR |
| ZIP/Postal code |
72079-9502 |
| Country |
USA |
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| Platform ID |
GPL14844 |
| Series (1) |
| GSE62368 |
Transcript expression in circulating whole blood after saline injections |
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| Relations |
| BioSample |
SAMN03112756 |
| SRA |
SRX733707 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1525863_H30621_FG150_L1.D712.txt.gz |
176.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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