|
| Status |
Public on Dec 28, 2020 |
| Title |
Control 24h rep4 [MC_24_4] |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic forelimb
|
| Organism |
Mus musculus |
| Characteristics |
strain: CD1
gestation day: GD 13
tissue: limb bud
treatment: DMSO
time point: 24 hours
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cultured limb buds were preserved in RNAlater (Qiagen) and RNA was extracted using the Qiagen RNeasy Plus Mini Kit
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.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
MC_24_4_1
|
| 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
|
| |
|
| Submission date |
Sep 15, 2020 |
| Last update date |
Dec 28, 2020 |
| Contact name |
Barbara F. Hales |
| E-mail(s) |
barbara.hales@mcgill.ca
|
| Phone |
514-398-3610
|
| Organization name |
McGill University
|
| Department |
Pharmacology and Therapeutics
|
| Street address |
3655 Prom. Sir William Osler, room 110
|
| City |
Montreal |
| State/province |
QC |
| ZIP/Postal code |
H3G 1Y6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE157940 |
Effects of an environmentally relevant mixture of organophosphate esters derived from house dust on endochondral ossification in murine limb bud cultures |
|
| Relations |
| BioSample |
SAMN16132785 |
| SRA |
SRX9123783 |
