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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 06, 2018 |
| Title |
Transgenic rep 3 |
| Sample type |
SRA |
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| Source name |
Skin tissue
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| Organism |
Mus musculus |
| Characteristics |
strain: P33 YAP2-5SA-deltaC mice
Sex: female
condition: YAP2-5SA-DC transgenic mouse
tissue: skin
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from the dissected mouse tissues using TRI-reagent (Sigma), following the manufacturer’s instructions, which included a chloroform phase separation and ethanol precipitation. RNA was resuspended in 70 μL of RNase-free water. RNA samples were assessed for quantity and quality using a NanoDrop UV spectrophotometer (Thermo Fisher Scientific Inc), conventional RNA electrophoresis and using a Bioanalyser (Agilent Technology Inc). All RNA integrity numbers (RIN) for the analysed samples ranged from 9 to 9.5
mRNA libraries were prepared at the Ramaciotti Centre for Genomics (UNSW University of New South Wales, Australia). The Illumina TruSeq Stranded Total RNA Prep Kit was used .The six RNA-Seq libraries in Experiments 2 were sequenced using the Illumina NextSeq 500. R1.fastq and R2.fastq files were produced for each sample.
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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 |
The reads for Experiment 2 were mapped to the Ensembl Mus musculus genome (GRCm38). Mapping was performed with Tophat2 (v 2.0.12) [14] calling Bowtie2 (v 2.1.0). 50 bp used in Tophat mapping.
HTSeq-count (Python package HTSeq, python v 2.7.3) (47) was used to generate counts of reads uniquely mapped to annotated genes using the GRCm38 annotation gtf file.
The table of read counts was used as input to assess differential expression using the Bioconductor packages, edgeR and limma (voom).
Genome_build: Ensembl Mus musculus genome (GRCm38)
Supplementary_files_format_and_content: Tab-delimited text file with read count for each sample.
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| Submission date |
Oct 12, 2018 |
| Last update date |
Nov 06, 2018 |
| Contact name |
Susan Corley |
| E-mail(s) |
[email protected]
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| Phone |
+61 02 9385 8853
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| Organization name |
UNSW
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| Department |
Biotechnology & Biomolecular Sciences
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| Lab |
Systems Biology Initiative
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| Street address |
D26, Kensignton Campus
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| City |
Sydney |
| State/province |
NSW |
| ZIP/Postal code |
2052 |
| Country |
Australia |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE121194 |
Downstream effects of YAP examined by RNA-Seq analysis of skin in YAP2-5SA-∆C transgenic mice |
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| Relations |
| BioSample |
SAMN10236718 |
| SRA |
SRX4877805 |
| 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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