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| Status |
Public on Feb 22, 2018 |
| Title |
PNW20_X31R |
| Sample type |
SRA |
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| Source name |
liver
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| Organism |
Mus musculus |
| Characteristics |
tissue: liver
Sex: male
exposure: Vehicle
time point: postnatal week 20
strain: CD-1
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| Treatment protocol |
The dams were assigned to one of two treatment groups (n=5 per group) based on weight match, and were exposed to tocopherol-stripped corn oil (MP Biomedicals, Solon, OH) or 0.2 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 1 µl/gram BW from the tip of a pipette, resulting in exposure of 0.2 mg/kg BW/day. One male pup per litter were euthanized on PND21 and 1 male pup per litter was euthanized on PNW20.
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| Growth protocol |
Eight-week old male (30–35 g) and female (27–30 g) CD-1 mice were obtained from Charles River Laboratories (Kingston, NY, USA) 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. After 3 days of acclimation, the animals were bred and the day of vaginal plug detection was considered pregnancy day 1.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated from liver tissue using TRIzol reagent (Invitrogen).
The NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490, New England BioLabs Inc., Ipswich, MA) was then used to isolate intact poly(A)+ RNA from 3 µg of total RNA. Libraries were constructed using NEBNext mRNA Library Prep Reagent Set for Illumina with multiplexing indexes from NEBNext Multiplex Oligos for Illumina (E6100 and E7335 respectively, New England BioLabs Inc., Ipswich, MA).
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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 mouse genome (MM10) using TopHat 2 aligner.
Aligned reads were used for assembly of novel transcriptsand differential expression of novel and reference transcripts with Cuffdiff 2.1.1.
Genome_build: MM10
Supplementary_files_format_and_content: XLSX files showing Log2(FPKM) for control and exposed condition and Log2 of their FPKM ratio for each tanscript, as well as transcript coordinates and gene names.
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| Submission date |
Aug 04, 2016 |
| Last update date |
May 15, 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 |
GPL19057 |
| Series (1) |
| GSE85221 |
Developmental Exposure to 2,2’,4, 4’ –Tetrabromodiphenyl Ether Induces Long-Lasting Changes in Liver Metabolism in Male Mice |
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| Relations |
| BioSample |
SAMN05513394 |
| SRA |
SRX2001175 |
| 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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