|
| Status |
Public on May 25, 2016 |
| Title |
TG for Nanog rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
papilloma was obtained from a DMBA/TPA treated Nanog-overexpressing C57Bl/6 background mice
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6
tissue: skin
mouse id number: 91
genotype: Transgenic mice contain the trasactivator under the control of the K5 promoter (K5-rtTA) and the tetO-Nanog transgene
|
| Treatment protocol |
Doxycycline treatment in their drinking water (2 mg/ml) throughout the entire DMBA/TPA protocol
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted combining the Trizol reagent (Life Technologies) with the RNeasy Mini kit (Qiagen).
1 µg of total RNA samples was used as provided by the user. RNA Integrity Numbers were in the range 7.2 to 8.9 when assayed on an Agilent 2100 Bioanalyzer. PolyA+ fractions were 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" (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 8 cycles of PCR with Illumina PE primers. The resulting purified cDNA library of template molecules of known strand origin was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Genome Analyzer IIx with SBS TruSeq v5 reagents by following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Isolation of poly A+ RNA from total RNA
|
| Data processing |
Read files were quality-checked with FastQC.
Reads were aligned with the mouse genome (GRCm38/mm10) with TopHat-2.0.4 (using Bowtie 0.12.7 and Samtools 0.1.16), allowing 2 mismatches and 5 multihits.
Transcripts quantification and differential expression calculated with Cufflinks 1.3.0
Transcripts annotations used were Mus musculus GRCm38/mm10 from the UCSC Genome Browser
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tables were generated with Cufflinks 1.3.0 and contain transcripts abundance measured in FPKM values
|
| |
|
| Submission date |
Apr 07, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Manuel Serrano |
| E-mail(s) |
manuel.serrano@irbbarcelona.org
|
| Organization name |
IRB
|
| Department |
Molecular Medicine
|
| Lab |
Cellular Plasticity and Disease
|
| Street address |
Parc Científic de Barcelona, C/ Baldiri Reixac 10
|
| City |
Barcelona |
| State/province |
Barcelona |
| ZIP/Postal code |
08028 |
| Country |
Spain |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE56566 |
Transcriptional profiles by deep sequencing (RNA-seq) of papillomas generated using the DMBA/TPA protocol from control and transgenic Nanog overexpressing mice |
|
| Relations |
| BioSample |
SAMN02720957 |
| SRA |
SRX512330 |
