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| Status |
Public on Jun 16, 2016 |
| Title |
mRNA-seq WT1 |
| Sample type |
SRA |
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| Source name |
mouse skin squamous tumours
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| Organism |
Mus musculus |
| Characteristics |
tumour stage: skin papilloma
strain: C57BL/6
age: 1 month
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| Extracted molecule |
total RNA |
| Extraction protocol |
1 cm2 pieces of skin papilloma were snap-frozen in liquid N2 and then transferred to lysis buffer.
RNAs were prepared for Ribo-seq as in Ingolia, N. T., Brar, G. A., Rouskin, S., McGeachy, A. M. & Weissman, J. S. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc 7, 1534-1550, doi:10.1038/nprot.2012.086 (2012). For mRNA-seq standard Illumina library preparation protocols were used.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
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| Data processing |
For Ribo-seq analysis, Adapters were removed, and Ribo-seq reads were initially aligned to a collection of rRNA sequences to filter rRNA reads in the libraries; and non-rRNA reads with at least 23 nt length were kept. To obtain only high-confidence assignments of ribosome footprints to transcripts, the reads were aligned to the mouse reference genome (GRCm38/UCSC mm10) with Tophat2 (version: 2.1; options: ‘--read-mismatch 1 --max-multihits 1 –GTF’) guided by ENSEMBL gene models to account for splice sites, allowing one mismatch per read and unique alignments only.
For RNA-seq analysis, the reads were aligned to the mouse reference genome (GRCm38/UCSC mm10) with Tophat2 (version: 2.1; options: ‘--read-mismatch 1 --max-multihits 1 –GTF’) guided by ENSEMBL gene models allowing one mismatch per read and unique alignments only.
Genome_build: GRCm38/UCSC mm10
Supplementary_files_format_and_content: Processed data files were generated with bedtools genomeCoveragBed showing counts per genomic position.
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| Submission date |
Aug 14, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Sabine Dietmann |
| Organization name |
Washington University School of Medicine
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| Street address |
4565 McKinley Avenue
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| City |
St Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
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| Platform ID |
GPL9250 |
| Series (2) |
| GSE72066 |
Ribosome Profiling of mouse skin squamous tumours |
| GSE72067 |
Stem cell function and sensitivity to genotoxic stress is controlled by protein translation rates |
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| Relations |
| BioSample |
SAMN03992963 |
| SRA |
SRX1149709 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1854037_in.vivo.tumour.wt.1.bedGraph.gz |
8.8 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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