|
| Status |
Public on Oct 16, 2019 |
| Title |
ESC230 |
| Sample type |
SRA |
| |
|
| Source name |
skin
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6
genotype/variation: JunB dep
age: 6-7 months
tissue: Skin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Isolation of poly A+ RNA from total RNA.
Samples of 1µg of total RNA were used as provided by the user. Average sample RNA Integrity Number was 7.75 (range 7-9.2) when assayed on an Agilent 2100 Bioanalyzer. PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" kit (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by PCR with Illumina PE primers. The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument by following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Genotype2_0
processed data file: Experiment1_genes.fpkm_table.xls
|
| Data processing |
RNA-seq processing:
RNA-seq data was analysed with the nextpresso pipeline (http://bioinfo.cnio.es/nextpresso/) as follows:
Reads are quality-checked with FastQC, and aligned to the mouse genome (mm9) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing 2 mismatches and 20 multihits.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Experiment1_genes.fpkm_table.xls: FPKM values calculated with Cufflinks.
|
| |
|
| Submission date |
Aug 29, 2019 |
| Last update date |
Oct 16, 2019 |
| Contact name |
Kevin Troulé |
| Organization name |
SPANISH NATIONAL CANCER CENTER
|
| Street address |
Melchor Fernandez Almagro, 3
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE136657 |
RNAseq analysis of total skin from control or JunBdep mice |
|
| Relations |
| BioSample |
SAMN12659987 |
| SRA |
SRX6772479 |
