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Status |
Public on Aug 10, 2019 |
Title |
BFR2_X8b2 |
Sample type |
SRA |
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Source name |
testis
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Organism |
Rattus norvegicus |
Characteristics |
treatment: Vehicle strain: Wistar tissue: testis age: postnatal day 120
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Treatment protocol |
The dams were assigned to one of two treatment groups (n=7 per group) based on weight match, and were exposed to tocopherol stripped corn oil (MP Biomedicals, Solon, OH) or 1 mg/ml solution of BDE-47 (AccuStandard, Inc., New Haven, CT; 100% purity) in tocopherol stripped corn oil daily from pregnancy day 8 through postpartum day 21; the females were fed 0.2 µl/gram body weight from the tip of a pipette, resulting in exposure of 0.2 mg/kg body weight/day.
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Growth protocol |
Seven-week old timed-pregnant female (150-200 g) Wistar rats were obtained from Charles River Laboratories (Kingston, NY, USA) on 6th day after vaginal plaque detection and housed in a temperature (23±2◦C), and humidity (40±10%) controlled environment, with a 12-h light/dark cycle, and food and water available ad libitum.
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Extracted molecule |
polyA RNA |
Extraction protocol |
Total RNA was isolated from liver tissue using TRIzol reagent (Invitrogen). Samples of RNA isolated from testis samples with integrity values > 9 were used for library preparation. RS-122-2101-TruSeq® Stranded mRNA LT – SetA kit (Illumina, San-Diego, CA) was used to isolate intact poly(A)+ RNA from 4 µg of total RNA and construct strand-specific libraries with multiplexing indexes. The quality and purity of the libraries was assessed by The Agilent 2200 TapeStation system, and the concentration of the libraries was measured by real time PCR with primers for P5 and P7 flow cell oligo sequences using KAPA Library Quantification Kit (KR0405, Kapa Biosystems, Boston, MA) in a 384-well plate on a CFX384 Touch Real-Time PCR Detection System (Bio-Rad, Hercules, CA).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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Data processing |
Reads were mapped to the reference rat genome (rn5) using TopHat 2 aligner. Aligned reads were used for assembly of novel transcripts and differential expression of novel and reference transcripts with Cuffdiff 2.1.1. Genome_build: rn5 Supplementary_files_format_and_content: XLSX file showing Log2(FPKM) for control and exposed condition and Log2 of their FPKM ratio for each transcript, as well as transcript coordinates and gene names.
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Submission date |
Aug 10, 2016 |
Last update date |
Aug 10, 2019 |
Contact name |
Alexander Suvorov |
E-mail(s) |
asuvorov@schoolph.umass.edu
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Organization name |
University of Massachusetts
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Department |
Environmental Health Sciences
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Street address |
149A Goessman, 686 N.Pleasant Str
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City |
Amherst |
State/province |
MA |
ZIP/Postal code |
01003-9303 |
Country |
USA |
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Platform ID |
GPL20084 |
Series (1) |
GSE85420 |
Perinatal Exposure to 2,2’,4’4’ –Tetrabromodiphenyl Ether Impairs Male Reproductive Health in Adult Rats |
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Relations |
BioSample |
SAMN05557880 |
SRA |
SRX2011248 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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