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| Status |
Public on Jul 31, 2023 |
| Title |
10 μM BPA 3h_rep 1 |
| Sample type |
SRA |
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| Source name |
Embryonic forelimb
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| Organism |
Mus musculus |
| Characteristics |
strain: CD1
gestation day: GD 13
tissue: limb bud
treatment: 10 uM BPA
treatment length: 3 hours
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| Treatment protocol |
Culture bottles were gassed for two minutes with 5% CO2, 50% O2 balanced with N2. Each bottle subsequently received one of two treatments: dimethyl sulfoxide (DMSO, vehicle control) or bisphenol A (BPA 10 or 50 μM). Limbs were then cultured at 37° for 3 hours.
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| Growth protocol |
Forelimbs of each gestational day 13 embryo were excised, pooled, and placed in glass bottles containing 6 mL of a culture medium consisting of 75% BGJb medium (Gibco, ThermoFisher Scientific), 25% salt solution, supplemented with ascorbic acid (0.16 mg/mL) and gentamycin (50 mg/mL, Wisent Bioproducts, QC, Canada). Limbs from male and female embryos were cultured together.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Rneasy Mini kit (Qiagen). The concentration and purity of extracted RNA was assessed using NanoDrop 2000 spectrophotometer (Thermofisher).
mRNA was purified from 1ug of total RNA using poly-T oligo-attached magnetic beads and fragmented randomly in a fragmentation buffer. First-strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-); second-strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. Double-stranded cDNA was purified using AMPure XP beads. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of the 3' ends of DNA fragments, NEBNext Adaptor was ligated to prepare for hybridization. The library fragments were purified with AMPure XP system. The final library was obtained by PCR amplification and purification of PCR products using AMPure XP beads.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
A10_3vsAC_3.txt
A10031
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| Data processing |
Base calling was performed using Illumina CASAVA (v1.8)
Sequences were filtered for reads containing adapter or of low quality, then mapped to mm10 using STAR (v2.5, mismatch=2)
Quantification was performed using HTSeq (v0.6.1, -m union)
Differential analysis was performed using DESeq2 (v2_1.6.3, q-value < 0.05)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table containing raw count, FPKM value, and normalized abundance output (from DESeq2) of each gene for each sample and each treatment group
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| Submission date |
Aug 13, 2021 |
| Last update date |
Jul 31, 2023 |
| Contact name |
Barbara Hales |
| E-mail(s) |
barbara.hales@mcgill.ca
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| Organization name |
McGill University
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| Department |
Pharmacology and Therapeutics
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| Street address |
3655 Promenade Sir-William-Osler
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| City |
MONTRÉAL |
| State/province |
QC |
| ZIP/Postal code |
H3G 1Y6 |
| Country |
Canada |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE182039 |
Effects of BPA, BPAF, and BPS on Endochondral Ossification and on the Transcriptome of Ex Vivo Murine Limb Bud Cultures I |
| GSE182523 |
Effects of BPA, BPAF, and BPS on Endochondral Ossification and on the Transcriptome of Ex Vivo Murine Limb Bud Cultures |
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| Relations |
| BioSample |
SAMN20752525 |
| SRA |
SRX11740963 |
| 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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