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Sample GSM2266534

Query DataSets for GSM2266534

Status

Public on Aug 10, 2019

Title

BFR2_C5-2

Sample type

SRA

Source name

testis

Organism

Rattus norvegicus

Characteristics

treatment: 0.2 mg/kg BDE-47
strain: Wistar
tissue: testis
age: postnatal day 120

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.

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.

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).

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NextSeq 500

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.

Submission date

Aug 10, 2016

Last update date

Aug 10, 2019

Contact name

Alexander Suvorov

E-mail(s)

asuvorov@schoolph.umass.edu

Organization name

University of Massachusetts

Department

Environmental Health Sciences